Patent Grant
11584785
This application includes a sequence listing submitted electronically, in a file entitled “AbSci-005PCTCON1_ST25.txt”, created on 30 Apr. 2020 and having a size of 63 kilobytes (KB), which is incorporated by reference herein.
The present invention is in the general technical fields of molecular biology and biotechnological manufacturing. More particularly, the present invention is in the technical field of recombinant protein production.
Efficient expression of recombinant proteins or other gene products requires the use of a system, the various aspects of which—expression construct(s), host cell strain, growth conditions, and purification methods—all work together to make the desired product in sufficient quantities, while minimizing the expenditure of materials and time.
Many expression systems that are currently used for industrial production of recombinant products rely on expensive mammalian cell culture, or utilize the secretion of proteins into the periplasm of bacterial cells, which is more limited in the quantity of product per cell and is more time-consuming than expression of gene products in bacterial cytoplasm. In many expression systems developed by others, in which bacterial cytoplasm is used as the preferred cellular compartment for recombinant expression, it is common for the desired proteins to be produced as insoluble inclusion bodies (see for example Chung et al., “Recombinant production of biologically active giant grouper (Epinephelus lanceolatus) growth hormone from inclusion bodies of Escherichia coli by fed-batch culture”, Protein Expr Purif 2015 June; 110: 79-88; doi: 10.1016/j.pep.2015.02.012; Epub 2015 Feb. 19). To recover some soluble and correctly folded protein from inclusion bodies, it has been necessary to perform additional refolding steps (Yamaguchi and Miyazaki, “Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies”, Biomolecules 2014 Feb. 20; 4(1): 235-251; doi: 10.3390/biom4010235; Review). For proteins containing disulfide bonds, these refolding steps typically include the use of reducing agents to convert to thiol groups any inappropriately formed disulfide bonds, particularly inter-molecular disulfide bonds that could be contributing to the aggregation of protein into insoluble inclusion bodies.
Improved expression systems and methods of using them to more efficiently produce gene products such as recombinant proteins in a properly folded and soluble form, and in a manner that is capable of scaling up to commercial production levels, are clearly needed.
The present invention provides methods of purifying proteins and other gene products, expressed in the form of solubilizable complexes that yield properly folded and active gene product when solubilized, without requiring the use of a reducing agent. An advantage of the invention is the ability to collect the solubilizable complexes of gene product in the form of a solubilizable pellet, allowing undesirable components of host cell lysate to be discarded in the supernatant. When the solubilizable complexes of gene product are present in a host cell lysate, for example, this mixture can be considered a suspension in that the solubilizable complexes can be sedimented into a pellet by centrifugation or other means, and separated from a predominantly liquid fraction of the host cell lysate. As used herein, the term “solution” encompasses mixtures that can exhibit the properties of a suspension. Further aspects of the invention relate to polypeptide prosequences that can be used in the expression and purification of proteins.
An aspect of the invention is a method for producing one or more gene products comprising: providing a first solution comprising at least one gene product that was expressed in a host cell, wherein at least some of said at least one gene product in the first solution can be sedimented by centrifugation (in salt conditions of 200 mM NaCl at pH 7.4 and 4 degrees C.) at a force of: 900×g, or at between 900×g and 7,000×g, or at 7,000×g, to form a solubilizable pellet; and placing at least some of said at least one gene product in a solubilization solution. The above method of the invention can be utilized according to any aspect of the method of the invention as expressed in the following paragraphs, in any combination thereof:
A further aspect of the invention is a polypeptide comprising an amino acid sequence selected from the group consisting of: (a) any of SEQ ID NOs 12-14 and 27-36; and (b) an amino acid sequence that shares at least 70% (or at least 80%, or at least 90%) amino acid sequence identity across at least 50% (or at least 60%, or at least 70%, or at least 80%, or at least 90%) of the length of any of the amino acid sequences of (a).
Treating the solubilized CPBpro_lispro proinsulin with the reducing agent DTT caused the solubilized CPBpro_lispro proinsulin to migrate at a slightly slower rate on the gel, indicating that the DTT treatment reduced disulfide bonds present in the non-reduced solubilized CPBpro_lispro proinsulin.
The problem of producing gene products such as recombinant proteins at commercial scale and in active form is addressed by providing the methods for protein expression and purification described herein. We have found that gene products such as polypeptides, when expressed in host cells to sufficient gene product density and in a manner that permits the gene product to be properly folded when expressed, and to have any disulfide bonds properly formed, will form solubilizable complexes that are easily purified away from other cell components and then solubilized to produce properly folded and presumably active gene product. These methods of the invention, directed to the production of gene product in the form of such solubilizable complexes, and the subsequent purification of properly folded gene product, has the advantage of not requiring a procedure involving contacting the gene product with a reducing agent.
As another aspect of the invention, methods are provided for the direct solubilization of polypeptides produced by host cells in the form of solubilizable complexes, without an initial centrifugation step to separate the insoluble and soluble fractions following cell lysis, and allowing for the purification of properly folded and/or active polypeptides that form disulfide bonds without the need for contacting such polypeptides with a reducing agent.
The proper folding of a gene product, such as a gene product comprising one or more polypeptides, is consistent with any disulfide bonds in that gene product being formed in the proper location within that gene product. Therefore, determining whether a gene product is properly folded can involve characterization of any disulfide bonds present in the gene product, as described further in Examples 2C and 8, to assess whether those disulfide bonds are properly formed. A properly formed disulfide bond is one that, when assayed, is a covalent bond joining two sulfur atoms, and that when present within a polypeptide or between two polypeptides, is a covalent bond that links (or connects) the sulfur atoms of two sulfur-containing amino acid residues (such as cysteine or Cys residues) that are linked by a disulfide bond in the desired form of the gene product comprising the polypeptide(s). For example, for glargine proinsulin as shown in
Active gene products include any gene products with measurable activity of the type associated with the desired form of the gene product. For example, an active insulin gene product can have measurable insulin receptor binding activity, or measurable anti-insulin antibody binding activity, or any other type of activity associated with the desired form of the insulin gene product.
Recovery of properly folded and/or active forms of proteins from inclusion bodies typically includes treatment with at least one reducing agent. The term ‘reducing agent’, as used herein, includes chemical substances (not proteins) with reducing potentials that are more negative than −0.26 V at pH 7.0 and 25 degrees C., such as DTE (dithioerythritol), DTT (dithiothreitol), and TCEP (tris(2-carboxyethyl)-phosphine); the term ‘reducing agent’ therefore does not include L-cysteine (‘L-cys’) or glutathione. Unlike recovery of gene product from inclusion bodies, the solubilization methods disclosed herein—which do not involve the use of reducing agents—result in substantially greater recovery of gene product, for example recovery of at least 50%, 60%, 70%, or 80% of the total gene product material present in the host cell lysate, as calculated by the methods described in Example 7. Given the high yields of gene product (5-20 g/L) achieved in the cell lysate, the solubilization methods described herein (as in Examples 1-3), can result in yields of 4-16 g/L of gene product.
In order for the host cell to produce gene product(s) in the form of solubilizable complexes, it is most advantageous to utilize a suitable combination of the following aspects I-IV of gene product expression, as described in detail herein:
I. The gene product(s) to be produced, including any transporters, cofactors, chaperones, and/or tags or propeptides to be used in expression of the desired gene product(s).
II. The expression construct(s) to be used for expression of the gene product(s).
III. The host cells to be used to express the expression construct(s) encoding the gene product(s).
IV. The conditions for host cell growth and the induction of expression.
Section V. describes solubilization and purification methods of the invention.
The following patent publications and application(s), all of which are expressly incorporated by reference herein, provide additional examples of gene products, expression constructs, host cells, and growth and induction conditions that can be employed in the production of solubilizable complexes suitable for the purification methods of the invention: U.S. Pat. No. 9,617,335B2, “Inducible Coexpression System”; WO2016205570A1, “Vectors for Use in an Inducible Coexpression System”; and International Application PCT/US2016/067064, “Cytoplasmic Expression System”.
I. Products Made by the Methods of the Invention
There is broad versatility in utilizing the gene expression and gene product purification methods of the present invention in numerous expression applications, and in the properties of the products.
Gene products produced by the methods of the invention can comprise any, or more than one, of the following: 1-antitrypsin; 2C4; activin; addressins; alkaline phosphatase; anti-CD11a; anti-CD18; anti-CD20; anti-clotting factors such as Protein C; anti-HER-2 antibody; anti-IgE; anti-IgG; anti-VEGF; antibodies and antibody fragments; antibodies to ErbB2 domain(s) such as 2C4 (WO 01/00245 hybridoma ATCC HB-12697), which binds to a region in the extracellular domain of ErbB2 (e.g., any one or more residues in the region from about residue 22 to about residue 584 of ErbB2, inclusive); Apo2 ligand (Apo2L); atrial naturietic factor; BDNF; beta-lactamase; bombesin; bone morphogenetic protein (BMP); botulinum toxin; brain IGF-I; calcitonin; cardiotrophins (cardiac hypertrophy factor) such as cardiotrophin-1 (CT-1); CD proteins such as CD-3, CD-4, CD-8, and CD-19; clotting factors such as factor VIIIC, factor IX, tissue factor, and von Willebrands factor; colony stimulating factors (CSFs), e.g., M-CSF, GM-CSF, and G-CSF; cytokines; decay-accelerating factor; des(1-3)-IGF-I (brain IGF-I); DNase; enkephalinase; epidermal growth factor (EGF); erythropoietin; fibroblast growth factor such as aFGF and bFGF; follicle-stimulating hormone; glucagon; gp120; ghrelin; growth hormone, including human growth hormone or bovine growth hormone; growth-hormone releasing factor; hemopoietic growth factor; homing receptors; HSA; IGF-I; IGF-II; immunotoxins; inhibin; insulin chains (insulin A-chain, insulin B-chain) or proinsulin; insulin-like growth factor binding proteins; insulin-like growth factor-I and -II (IGF-I and IGF-II); integrin; interferon such as interferon-alpha, -beta, and -gamma; interleukins (ILs), e.g., IL-1 to IL-10; leptin; lipoproteins; lung surfactant; luteinizing hormone; metreleptin; mouse gonadotropin-associated peptide; mullerian-inhibiting substance; nerve growth factor (NGF); neurotrophic factor such as brain-derived neurotrophic factor (BDNF), neurotrophin-3, -4, -5, or -6 (NT-3, NT-4, NT-5, or NT-6); osteoinductive factors; parathyroid hormone; plasminogen activator, such as urokinase or human urine or tissue-type plasminogen activator (t-PA); platelet-derived growth factor (PDGF); prorelaxin; protein A or D; receptors for hormones or growth factors; regulatory proteins; relaxin A-chain; relaxin B-chain; rennin; rheumatoid factors; serum albumin, such as human serum albumin (HSA) or bovine serum albumin (BSA); superoxide dismutase; surface-membrane proteins; T-cell receptors; TGF-beta; thrombin; thrombopoietin; thyroid-stimulating hormone; transforming growth factor (TGF) such as TGF-alpha and TGF-beta, including TGF-1, TGF-2, TGF-3, TGF-4, or TGF-5; transport proteins; tumor necrosis factor-alpha and -beta; urokinase; vascular endothelial growth factor (VEGF); viral antigens such as, for example, a portion of the AIDS envelope; fragments of any of the above; and any of the above or a fragment thereof covalently bound to one or more of the proteins above or fragments thereof or functional domains such as: an antibody Fc domain, an antibody single-chain variable fragment (scFv), a domain with enzymatic activity (such as a glycoside hydrolase domain or a kinase domain), an EVH1 (Ena/Vasp homology, or WH1) domain, a PAS (Per-Arnt-Sim) domain, a PDZ domain, a POU (Pit-1, Oct, Unc-86) domain, an SPR (Spread, Sprouty) domain, a VWFC (Von Willebrand factor, type C or VWC) domain, or a zinc-finger domain (for example, a RING-finger domain).
Gene products produced by the methods of the invention can include any, or more than one, of the following insulin polypeptides. An insulin polypeptide produced by the methods of the invention comprises in some embodiments the amino acid sequence of a mature A chain or of a mature B chain of insulin, and in other embodiments comprises both a mature A chain and a mature B chain. A proinsulin polypeptide comprises a mature A chain of insulin and a mature B chain of insulin. Insulin polypeptide chains in certain embodiments comprise one or more of any of the naturally occurring amino acid sequences of insulins, or fragments thereof, and in other embodiments comprise one or more insulin analogue amino acid sequences, or fragments thereof, and in further embodiments comprise combinations of naturally occurring insulin amino acid sequences and/or insulin analogue amino acid sequences. Examples of naturally occurring insulin amino acid sequences and insulin analogue amino acid sequences are shown in Table 1.
Table 1. Insulin Chain Amino Acid Sequences
A: mature A chain; B: mature B chain;
Underlining: differences from native human insulin; *: modified residue
Preproinsulin polypeptides can comprise the following components, preferably in the following N-terminal to C-terminal order: a prepeptide, which can be a signal peptide that is cleaved off during protein expression by the host cell signal peptidase; a propeptide; the B-chain; a C-peptide (or ‘connecting peptide’); and the A-chain. Preproinsulin polypeptides can also comprise the A- and B-chains in a different N-terminal to C-terminal order, for example: a prepeptide; a propeptide; the A-chain; a C-peptide; and the B-chain. For proinsulin polypeptides that are to be expressed in the cytoplasm of host cells, a prepeptide comprising a signal sequence is not present. A diagram of a proinsulin glargine polypeptide is shown in
Gene products produced by the methods of the invention can include leptin and/or metreleptin polypeptides. An example of a leptin polypeptide, also called metreleptin, is shown in SEQ ID NO:15, and corresponds to mature human leptin with a methionine residue at its N-terminus. Other examples of leptin polypeptides comprise an amino acid sequence lacking the N-terminal methionine residue, such as amino acids 2 through 147 of SEQ ID NO:15. A common isoform of leptin has a methionine residue at position 74 of SEQ ID NO:15 instead of a valine residue. A leptin polypeptide produced by the methods of the invention comprises in some embodiments the amino acid sequence of a leptin polypeptide with a methionine residue at its N-terminus (metreleptin), and in other embodiments with a tag, linker, or other propeptide amino acid sequence (as described further below) added to the N-terminus of the leptin polypeptide, in some embodiments with, and in other embodiments without, inclusion of the methionine at the N-terminus of the metreleptin amino acid sequence.
Signal Peptides.
Polypeptide gene products produced by the methods of the invention can have or lack signal peptides. In certain embodiments of the invention, polypeptide gene products lack signal peptides because it is advantageous for such gene products to be retained in the oxidizing cytoplasm of the host cell. Signal peptides (also termed signal sequences, leader sequences, or leader peptides) are characterized structurally by a stretch of hydrophobic amino acids, approximately five to twenty amino acids long and often around ten to fifteen amino acids in length, that has a tendency to form a single alpha-helix. This hydrophobic stretch is often immediately preceded by a shorter stretch enriched in positively charged amino acids (particularly lysine). Signal peptides that are to be cleaved from the mature polypeptide typically end in a stretch of amino acids that is recognized and cleaved by signal peptidase. Signal peptides that direct insertion of the polypeptide gene product into membranes, sometimes referred to as signal anchor sequences, can lack the amino acid sequence that is cleaved by signal peptidase and in that case are retained in the polypeptide gene product. Signal peptides can often be characterized functionally by the ability to direct transport of a polypeptide, either co-translationally or post-translationally, out of the cytoplasm and, for example, through the plasma membrane of prokaryotes (or the inner membrane of grain negative bacteria like E. coli), or into the endoplasmic reticulum of eukaryotic cells. The degree to which a signal peptide enables a polypeptide to be transported into the periplasmic space of a host cell like E. coli, for example, can be determined by separating periplasmic proteins from proteins retained in the cytoplasm, using a method such as that provided in Example 9 below.
Tags and Other Polypeptide Sequences that can be Used with Gene Products.
Tags.
Gene products to be expressed by the methods of the invention can be designed to include molecular moieties that aid in the purification and/or detection of the gene products. Many such moieties are known in the art; as one example, a polypeptide gene product can be designed to include a polyhistidine ‘tag’ sequence—a run of six or more histidines, preferably six to ten histidine residues, and most preferably six histidines (‘6×His’)—at its N- or C-terminus. The presence of a polyhistidine sequence on the end of a polypeptide allows it to be bound by cobalt- or nickel-based affinity media, and separated from other polypeptides. The polyhistidine tag sequence can be removed by exopeptidases.
Additional tags, expressed at the N-terminal end of the amino acid sequence of a polypeptide gene product produced by the methods of the invention, comprise in certain embodiments: (1) the self-cleaving N-terminal portions (Npro) of polyproteins from pestiviruses such as Hog cholera virus (strain Alfort) (SEQ ID NO:16), also called classical swine fever virus (CSFV), and from border disease virus (BDV) and bovine viral diarrhea virus (BVDV), and fragments thereof; and/or (2) small ubiquitin-related modifier (SUMO) (SEQ ID NO:17, SwissProt P55853.1) Any N-terminal tag may itself be further tagged at its N-terminus with a polyhistidine tag such as 6×His, allowing for initial purification of the tagged polypeptide on a nickel column, followed by self-cleavage of tags such as Npro, or enzymatic cleavage of the SUMO N-terminal tag by SUMO protease, respectively, and elution of the freed polypeptide from the column. In one embodiment of this method, the SUMO protease polypeptides are also fusion proteins comprising 6×His tags, allowing for a two-step purification: in the first step, the expressed 6×His-SUMO-tagged polypeptide is purified by binding to a nickel column, followed by elution from the column. In the second step, the SUMO tags on the purified polypeptides are cleaved by the 6×His-tagged SUMO protease, and the SUMO protease—polypeptide reaction mixture is run through a second nickel column, which retains the SUMO protease but allows the now untagged polypeptide to flow through.
As another example, fluorescent protein sequences can be expressed as part of a polypeptide gene product, with the amino acid sequence for the fluorescent protein preferably added at the N- or C-terminal end of the amino acid sequence of the polypeptide gene product. The resulting fusion protein fluoresces when exposed to light of certain wavelengths, allowing the presence of the fusion protein to be detected visually. A well-known fluorescent protein is the green fluorescent protein of Aequorea victoria, and many other fluorescent proteins are commercially available, along with nucleotide sequences encoding them.
Linkers.
Linkers are polypeptides that are used to connect two other polypeptides. Examples of linker polypeptides that form alpha-helices are provided as SEQ ID NO:18 and SEQ ID NO:19 (Amet et al., “Insertion of the designed helical linker led to increased expression of Tf-based fusion proteins”, Pharm Res 2009 March; 26(3): 523-528; doi: 10.1007/s11095-008-9767-0; Epub 2008 Nov. 11).
Cleavage Sequences.
Cleavage sequences are discrete amino acid sequences that can be acted upon by chemical reagents or enzymes to effect cleavage of the polypeptide containing the cleavage sequence. One or more of these sequences can be introduced between a tag or propeptide sequence and the amino acid sequence of a polypeptide gene product, to allow the tag or propeptide to be cleaved off during the process of purification of the gene product. Examples of cleavage sequences include the amino sequences DP and GGDPGGG (SEQ ID NO:20, which can be cleaved by treatment with formic acid at the bond between D (Asp) and P (Pro). Certain acid-cleavable sequences are present within particular propeptides described below (SEQ ID NOs 33-35). Additional examples are amino acid sequences cleavable by proteases such as TEV (tobacco etch virus) protease (cleavage sequence ENLYFQGG (SEQ ID NO:21)), enterokinase (cleavage sequence DDDDKG (SEQ ID NO:22)), and thrombin (cleavage sequence LVPRGS (SEQ ID NO:23)).
Propeptides.
The propeptides described herein can be attached to polypeptide gene products, either N-terminal or C-terminal to the amino acid sequence of a polypeptide gene product, or both, and attached either directly to the amino acid sequence of a polypeptide gene product, or with other polypeptide sequences such as linkers or tags placed between the propeptide and the polypeptide gene product. Examples of polypeptides that can be used as propeptides include mammalian carboxypeptidase B precursor proteins (described further below) and maltose binding protein or ‘MBP’ (UniProtKB/Swiss-Prot: POAEX9.1, SEQ ID NO:24), which has a signal sequence; amino acids 2-26 of SEQ ID NO:24 can be removed to generate a propeptide that will remain localized in the cell cytoplasm. Another polypeptide that has been used as a propeptide is the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10a or ‘CBM9’ (SEQ ID NO:25, amino acids 700-868 of UniProtKB/Swiss-Prot: Q60037, Notenboom et al., “Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms”, Biochemistry 2001 May 29; 40(21): 6248-6256).
Carboxypeptidase B Propeptide (CPBpro).
The typical mammalian carboxypeptidase B precursor protein has a signal peptide at its N-terminus, followed by a propeptide of 95 amino acids having an arginine residue at its C-terminus; this propeptide which is also termed the carboxypeptidase B activation domain is cleaved from the remainder of the carboxypeptidase B enzyme (EC 3.4.17.2) by tryptic hydrolysis, activating the enzyme (Coll et al., “Three-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity”, EMBO J 1991 January; 10(1): 1-9). The amino acid sequence of human carboxypeptidase B precursor protein or CPBpro is provided as SEQ ID NO:26.
The terms ‘CPBpro’ and ‘CPBpro propeptides’ are used herein to refer to carboxypeptidase B propeptides, including the novel variants disclosed herein. CPBpro propeptides can be used in the production of recombinant polypeptides, fused for example at the C-terminal arginine residue of the CPBpro propeptide to the desired N-terminal residue of the polypeptide of interest: following expression of the CPBpro polypeptide, the CPBpro propeptide can be cleaved from the polypeptide of interest by trypsin to generate the desired N-terminus. Examples of variant CPBpro propeptides include SEQ ID NOs 27-36, and a further propeptide is provided having the amino acid sequence of SEQ ID NO:37.
Formation of Solubilizable Gene Products.
In certain instances, expression of gene products using the expression methods described herein results in the formation of solubilizable gene product complexes without the need for the addition of tags or other polypeptides to the gene product. For example, in small-volume experiments, the coexpression of metreleptin (SEQ ID NO:15) with the Erv1p sulfhydryl oxidase (SEQ ID NO:38, described below) according to expression methods described herein resulted in most (about 70%) of the expressed metreleptin forming solubilizable complexes; similar coexpression of Erv1p with a gene product (SEQ ID NO:39) formed by addition of a CPBpro variant propeptide (SEQ ID NO:27) to metreleptin (SEQ ID NO:15) resulted in a larger portion of the gene product (about 84%) forming solubilizable complexes. For optimization of expression of gene product(s) in solubilizable complexes, the gene product(s) can first be expressed without modification, and the amount of solubilizable complexes produced can be determined. The effect of the addition of various polypeptide sequences (tags, propeptides, optionally in combination, and optionally in further combination with linker and/or cleavage sequences) to polypeptide gene product(s) can then be assessed, preferably in small-volume expression experiments, to determine whether a larger portion of the desired gene product(s) is then expressed as solubilizable complexes.
Disulfide Bonds.
Gene products produced by the methods of the invention are in some instances polypeptides that form disulfide bonds. The numbers and locations of disulfide bonds formed by a polypeptide can be determined by methods such as that of Example 8 below. The number of disulfide bonds for a gene product such as a polypeptide is the total number of intramolecular and intermolecular bonds formed by that gene product when it is present in a functional product. For example, a light chain of a human IgG antibody typically has three disulfide bonds (two intramolecular bonds and one intermolecular bond), and a heavy chain of a human IgG antibody typically has seven disulfide bonds (four intramolecular bonds and three intermolecular bonds). In certain embodiments of the invention, a gene product produced by methods of the invention is a polypeptide that forms at least one and fewer than twenty disulfide bonds, or at least two and fewer than seventeen disulfide bonds, or at least seventeen and fewer than fifty disulfide bonds, or at least three and fewer than ten disulfide bonds, or at least three and fewer than eight disulfide bonds, or is a polypeptide that forms a number of disulfide bonds selected from the group consisting of one, two, three, four, five, six, seven, eight, and nine disulfide bonds.
Glycosylation.
Gene products produced by the methods of the invention may be glycosylated or unglycosylated. In one embodiment of the invention, the gene products are polypeptides. Glycosylated polypeptides are polypeptides that comprise a covalently attached glycosyl group, and include polypeptides comprising all the glycosyl groups normally attached to particular residues of that polypeptide (fully glycosylated polypeptides), partially glycosylated polypeptides, polypeptides with glycosylation at one or more residues where glycosylation does not normally occur (altered glycosylation), and polypeptides glycosylated with at least one glycosyl group that differs in structure from the glycosyl group normally attached to one or more specified residues (modified glycosylation). An example of modified glycosylation is the production of “defucosylated” or “fucose-deficient” polypeptides, polypeptides lacking fucosyl moieties in the glycosyl groups attached to them, by expression of polypeptides in host cells lacking the ability to fucosylate polypeptides. Unglycosylated polypeptides are polypeptides that do not comprise a covalently bound glycosyl group. An unglycosylated polypeptide can be the result of deglycosylation of a polypeptide, or of production of an aglycosylated polypeptide. Deglycosylated polypeptides can be obtained by enzymatically deglycosylating glycosylated polypeptides, whereas aglycosylated polypeptides can be produced by expressing polypeptides in host cells that do not have the capability to glycosylate polypeptides, such as prokaryotic cells or cells in which the function of at least one glycosylation enzyme has been eliminated or reduced. In a particular embodiment, the expressed polypeptides are aglycosylated, and in a more specific embodiment, the aglycosylated polypeptides are expressed in prokaryotic cells such as E. coli.
Other Modifications of Gene Products.
Gene products produced by the methods of the invention may be covalently linked to other types of molecules. Examples of molecules that may be covalently linked to gene products, without limiting the scope of the invention, include polypeptides (such as those present in receptors, ligands, cytokines, growth factors, polypeptide hormones, DNA-binding domains, protein interaction domains such as PDZ domains, kinase domains, antibodies, and fragments of any such polypeptides); water-soluble polymers (such as polyethylene glycol (PEG), carboxymethylcellulose, dextran, polyvinyl alcohol, polyoxyethylated polyols (such as glycerol), polyethylene glycol propionaldehyde, and similar compounds, derivatives, or mixtures thereof); and cytotoxic agents (such as chemotherapeutic agents, growth-inhibitory agents, toxins (such as enzymatically active toxins of bacterial, fungal, plant, or animal origin, or fragments thereof), and radioactive isotopes).
Chaperones.
In some embodiments, desired gene products are coexpressed with other gene products, such as chaperones, that are beneficial to the production of the desired gene product. Chaperones are proteins that assist the non-covalent folding or unfolding, and/or the assembly or disassembly, of other gene products, but do not occur in the resulting monomeric or multimeric gene product structures when the structures are performing their normal biological functions (having completed the processes of folding and/or assembly). Chaperones can be expressed from an inducible promoter or a constitutive promoter within an expression construct, or can be expressed from the host cell chromosome; preferably, expression of chaperone protein(s) in the host cell is at a sufficiently high level to produce coexpressed gene products that are properly folded and/or assembled into the desired product. Examples of chaperones present in E. coli host cells are the folding factors DnaK/DnaJ/GrpE, DsbC/DsbG, GroEL/GroES, IbpA/IbpB, Skp, Tig (trigger factor), and FkpA, which have been used to prevent protein aggregation of cytoplasmic or periplasmic proteins. DnaK/DnaJ/GrpE, GroEL/GroES, and ClpB can function synergistically in assisting protein folding and therefore expression of these chaperones in combinations has been shown to be beneficial for protein expression (Makino et al., “Strain engineering for improved expression of recombinant proteins in bacteria”, Microb Cell Fact 2011 May 14; 10: 32). When expressing eukaryotic proteins in prokaryotic host cells, a eukaryotic chaperone protein, such as protein disulfide isomerase (PDI) from the same or a related eukaryotic species, is in certain embodiments of the invention coexpressed or inducibly coexpressed with the desired gene product.
One chaperone that can be expressed in host cells is a protein disulfide isomerase from Humicola insolens, a soil hyphomycete (soft-rot fungus). An amino acid sequence of Humicola insolens PDI is shown as SEQ ID NO:40; it lacks the signal peptide of the native protein so that it remains in the host cell cytoplasm. The nucleotide sequence encoding PDI was optimized for expression in E. coli; the expression construct for PDI is shown as SEQ ID NO:41. SEQ ID NO:41 contains a GCTAGC NheI restriction site at its 5′ end, an AGGAGG ribosome binding site at nucleotides 7 through 12, the PDI coding sequence at nucleotides 21 through 1478, and a GTCGAC SalI restriction site at its 3′ end. The nucleotide sequence of SEQ ID NO:41 was designed to be inserted immediately downstream of a promoter, such as an inducible promoter. The NheI and SalI restriction sites in SEQ ID NO:41 can be used to insert it into a vector multiple cloning site, such as that of the pSOL expression vector (SEQ ID NO:42), described in published US patent application US2015353940A1, which is incorporated by reference in its entirety herein. Other PDI polypeptides can also be expressed in host cells, including PDI polypeptides from a variety of species (Saccharomyces cerevisiae (UniProtKB P17967), Homo sapiens (UniProtKB P07237), Mus musculus (UniProtKB P09103), Caenorhabditis elegans (UniProtKB Q17770 and Q17967), Arabdopsis thaliana (UniProtKB O48773, Q9XI01, Q9SRG3, Q9LJU2, Q9MAU6, Q94F09, and Q9T042), Aspergillus niger (UniProtKB Q12730) and also modified forms of such PDI polypeptides. In certain embodiments of the invention, a PDI polypeptide expressed in host cells of the invention shares at least 70%, or 80%, or 90%, or 95% amino acid sequence identity across at least 50% (or at least 60%, or at least 70%, or at least 80%, or at least 90%) of the length of SEQ ID NO:40, where amino acid sequence identity is determined according to Example 11.
Cellular Transport of Cofactors.
When using the expression systems of the invention to produce gene products that require cofactors for function, it is helpful to use a host cell capable of synthesizing the cofactor from available precursors, or taking it up from the environment. Common cofactors include ATP, coenzyme A, flavin adenine dinucleotide (FAD), NAD+/NADH, and heme. Polynucleotides encoding cofactor transport polypeptides and/or cofactor synthesizing polypeptides can be introduced into host cells, and such polypeptides can be constitutively expressed, or inducibly coexpressed with the gene products to be produced by methods of the invention.
II. Expression Constructs.
Expression constructs are polynucleotides designed for the expression of one or more gene products of interest. Certain gene products of interest are ‘heterologous’ gene products, that are derived from species that are different from that of the host cell in which they are expressed, and/or are heterologous gene products that are not natively expressed from the promoter(s) utilized within the expression construct, and/or are modified gene products that have been designed to include differences from naturally occurring forms of such gene products. Expression constructs comprising polynucleotides encoding heterologous and/or modified gene products, or comprising a combination of polynucleotides that were derived from organisms of different species, or comprising polynucleotides that have been modified to differ from naturally occurring polynucleotides, are not naturally occurring molecules. Expression constructs can be integrated into a host cell chromosome, or maintained within the host cell as polynucleotide molecules replicating independently of the host cell chromosome, such as plasmids or artificial chromosomes. An example of an expression construct is a polynucleotide resulting from the insertion of one or more polynucleotide sequences into a host cell chromosome, where the inserted polynucleotide sequences alter the expression of chromosomal coding sequences. An expression vector is a plasmid expression construct specifically used for the expression of one or more gene products. One or more expression constructs can be integrated into a host cell chromosome or be maintained on an extrachromosomal polynucleotide such as a plasmid or artificial chromosome. In certain embodiments of the invention, the expression construct is the pSOL expression vector (SEQ ID NO:42).
Expression constructs can comprise certain polynucleotide elements, such as origins of replication, selectable markers, promoters such as constitutive or inducible promoters (described further below), ribosome binding sites, and multiple cloning sites. Examples of these polynucleotide elements are well known in the art, and further descriptions of them can be found in the following patent publications and application(s), all of which are expressly incorporated by reference herein: U.S. Pat. No. 9,617,335B2 and WO2014025663A1, “Inducible Coexpression System”; WO2016205570A1, “Vectors for Use in an Inducible Coexpression System”; and International Application PCT/US2016/067064, “Cytoplasmic Expression System”.
Inducible Promoter.
As described further below, there are several different inducible promoters that can be included in expression constructs as part of the expression systems of the invention. Preferred inducible promoters share at least 80% polynucleotide sequence identity (more preferably, at least 90% identity, and most preferably, at least 95% identity) to at least 30 (more preferably, at least 40, and most preferably, at least 50) contiguous bases of a promoter polynucleotide sequence as defined in Table 1 of WO2014025663A1, where percent polynucleotide sequence identity is determined using the methods of Example 11. Under ‘standard’ inducing conditions (see Example 10), preferred inducible promoters have at least 75% (more preferably, at least 100%, and most preferably, at least 110%) of the strength of the corresponding ‘wild-type’ inducible promoter of E. coli K-12 substrain MG1655, as determined using the quantitative PCR method of De Mey et al. “Promoter knock-in: a novel rational method for the fine tuning of genes”, BMC Biotechnol 2010 Mar. 24; 10: 26 (see WO2014025663A1, Example 8A). Within the expression construct, an inducible promoter is placed 5′ to (or ‘upstream of’) the coding sequence for the gene product that is to be inducibly expressed, so that the presence of the inducible promoter will direct transcription of the gene product coding sequence in a 5′ to 3′ direction relative to the coding strand of the polynucleotide encoding the gene product. The gene products expressed from the inducible promoters within expression constructs are not the gene products natively expressed from these inducible promoters; rather, they are heterologous gene products, with the result that the expression constructs comprising heterologous gene products expressed from inducible promoters are necessarily artificial constructs not found in nature.
Inducible Promoters.
The following is a description of inducible promoters that can be used in expression constructs for expression of gene products, along with some of the genetic modifications that can be made to host cells that contain such expression constructs. Examples of these inducible promoters and related genes are, unless otherwise specified, those derived from Escherichia coli (E. coli) strain MG1655 (American Type Culture Collection deposit ATCC 700926), which is a substrain of E. coli K-12 (American Type Culture Collection deposit ATCC 10798). Table 1 of International Application PCT/US13/53562 (published as WO2014025663A1) lists the genomic locations, in E. coli MG1655, of the nucleotide sequences for these examples of inducible promoters and related genes; the WO2014025663A1 publication is incorporated by reference in its entirety herein. Nucleotide and other genetic sequences, referenced by genomic location as in Table 1 of WO2014025663A1, are expressly incorporated by reference herein. Additional information about E. coli promoters, genes, and strains described herein can be found in many public sources, including the online EcoliWiki resource, located at ecoliwiki.net.
Arabinose Promoter.
(As used herein, ‘arabinose’ means L-arabinose.) Several E. coli operons involved in arabinose utilization are inducible by arabinose—araBAD, araC, araE, and araFGH—but the terms ‘arabinose promoter’ and ‘ara promoter’ are typically used to designate the araBAD promoter. Several additional terms have been used to indicate the E. coli araBAD promoter, such as Para, ParaB, ParaBAD, and PBAD. The use herein of ‘ara promoter’ or any of the alternative terms given above, means the E. coli araBAD promoter. As can be seen from the use of another term, ‘araC-araBAD promoter’, the araBAD promoter is considered to be part of a bidirectional promoter, with the araBAD promoter controlling expression of the araBAD operon in one direction, and the araC promoter, in close proximity to and on the opposite strand from the araBAD promoter, controlling expression of the araC coding sequence in the other direction. The AraC protein is both a positive and a negative transcriptional regulator of the araBAD promoter. In the absence of arabinose, the AraC protein represses transcription from PBAD, but in the presence of arabinose, the AraC protein, which alters its conformation upon binding arabinose, becomes a positive regulatory element that allows transcription from PBAD. The araBAD operon encodes proteins that metabolize L-arabinose by converting it, through the intermediates L-ribulose and L-ribulose-phosphate, to D-xylulose-5-phosphate. For the purpose of maximizing induction of expression from an arabinose-inducible promoter, it is useful to eliminate or reduce the function of AraA, which catalyzes the conversion of L-arabinose to L-ribulose, and optionally to eliminate or reduce the function of at least one of AraB and AraD, as well. Eliminating or reducing the ability of host cells to decrease the effective concentration of arabinose in the cell, by eliminating or reducing the cell's ability to convert arabinose to other sugars, allows more arabinose to be available for induction of the arabinose-inducible promoter. The genes encoding the transporters which move arabinose into the host cell are araE, which encodes the low-affinity L-arabinose proton symporter, and the araFGH operon, which encodes the subunits of an ABC superfamily high-affinity L-arabinose transporter. Other proteins which can transport L-arabinose into the cell are certain mutants of the LacY lactose permease: the LacY(A177C) and the LacY(A177V) proteins, having a cysteine or a valine amino acid instead of alanine at position 177, respectively (Morgan-Kiss et al., “Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity”, Proc Natl Acad Sci USA 2002 May 28; 99(11): 7373-7377). In order to achieve homogenous induction of an arabinose-inducible promoter, it is useful to make transport of arabinose into the cell independent of regulation by arabinose. This can be accomplished by eliminating or reducing the activity of the AraFGH transporter proteins and altering the expression of araE so that it is only transcribed from a constitutive promoter. Constitutive expression of araE can be accomplished by eliminating or reducing the function of the native araE gene, and introducing into the cell an expression construct which includes a coding sequence for the AraE protein expressed from a constitutive promoter. Alternatively, in a cell lacking AraFGH function, the promoter controlling expression of the host cell's chromosomal araE gene can be changed from an arabinose-inducible promoter to a constitutive promoter. In similar manner, as additional alternatives for homogenous induction of an arabinose-inducible promoter, a host cell that lacks AraR function can have any functional AraFGH coding sequence present in the cell expressed from a constitutive promoter. As another alternative, it is possible to express both the araE gene and the araFGH operon from constitutive promoters, by replacing the native araE and araFGH promoters with constitutive promoters in the host chromosome. It is also possible to eliminate or reduce the activity of both the AraE and the AraFGH arabinose transporters, and in that situation to use a mutation in the LacY lactose permease that allows this protein to transport arabinose. Since expression of the lacY gene is not normally regulated by arabinose, use of a LacY mutant such as LacY(A177C) or LacY(A177V), will not lead to the ‘all or none’ induction phenomenon when the arabinose-inducible promoter is induced by the presence of arabinose. Because the LacY(A177C) protein appears to be more effective in transporting arabinose into the cell, use of polynucleotides encoding the LacY(A177C) protein is preferred to the use of polynucleotides encoding the LacY(A177V) protein.
Propionate Promoter.
The ‘propionate promoter’ or ‘prp promoter’ is the promoter for the E. coli prpBCDE operon, and is also called PprpB. Like the ara promoter, the prp promoter is part of a bidirectional promoter, controlling expression of the prpBCDE operon in one direction, and with the prpR promoter controlling expression of the prpR coding sequence in the other direction. The PrpR protein is the transcriptional regulator of the prp promoter, and activates transcription from the prp promoter when the PrpR protein binds 2-methylcitrate (‘2-MC’). Propionate (also called propanoate) is the ion, CH3CH2COO−, of propionic acid (or ‘propanoic acid’), and is the smallest of the ‘fatty’ acids having the general formula H(CH2)nCOOH that shares certain properties of this class of molecules: producing an oily layer when salted out of water and having a soapy potassium salt. Commercially available propionate is generally sold as a monovalent cation salt of propionic acid, such as sodium propionate (CH3CH2COONa), or as a divalent cation salt, such as calcium propionate (Ca(CH3CH2COO)2). Propionate is membrane-permeable and is metabolized to 2-MC by conversion of propionate to propionyl-CoA by PrpE (propionyl-CoA synthetase), and then conversion of propionyl-CoA to 2-MC by PrpC (2-methylcitrate synthase). The other proteins encoded by the prpBCDE operon, PrpD (2-methylcitrate dehydratase) and PrpB (2-methylisocitrate lyase), are involved in further catabolism of 2-MC into smaller products such as pyruvate and succinate. In order to maximize induction of a propionate-inducible promoter by propionate added to the cell growth medium, it is therefore desirable to have a host cell with PrpC and PrpE activity, to convert propionate into 2-MC, but also having eliminated or reduced PrpD activity, and optionally eliminated or reduced PrpB activity as well, to prevent 2-MC from being metabolized. Another operon encoding proteins involved in 2-MC biosynthesis is the scpA-argK-scpBC operon, also called the sbm-ygfDGH operon. These genes encode proteins required for the conversion of succinate to propionyl-CoA, which can then be converted to 2-MC by PrpC. Elimination or reduction of the function of these proteins would remove a parallel pathway for the production of the 2-MC inducer, and thus might reduce background levels of expression of a propionate-inducible promoter, and increase sensitivity of the propionate-inducible promoter to exogenously supplied propionate. It has been found that a deletion of sbm-ygfD-ygfG-ygfH-ygfI, introduced into E. coli BL21(DE3) to create strain JSB (Lee and Keasling, “A propionate-inducible expression system for enteric bacteria”, Appl Environ Microbiol 2005 November; 71(11): 6856-6862), was helpful in reducing background expression in the absence of exogenously supplied inducer, but this deletion also reduced overall expression from the prp promoter in strain JSB. It should be noted, however, that the deletion sbm-ygfD-ygfG-ygfH-ygfI also apparently affects ygfI, which encodes a putative LysR-family transcriptional regulator of unknown function. The genes sbm-ygfDGH are transcribed as one operon, and ygfI is transcribed from the opposite strand. The 3′ ends of the ygfH and ygfI coding sequences overlap by a few base pairs, so a deletion that takes out all of the sbm-ygfDGH operon apparently takes out ygfI coding function as well. Eliminating or reducing the function of a subset of the sbm-ygfDGH gene products, such as YgfG (also called ScpB, methylmalonyl-CoA decarboxylase), or deleting the majority of the sbm-ygfDGH (or scpA-argK-scpBC) operon while leaving enough of the 3′ end of the ygfH (or scpC) gene so that the expression of ygfI is not affected, could be sufficient to reduce background expression from a propionate-inducible promoter without reducing the maximal level of induced expression.
Rhamnose Promoter.
(As used herein, ‘rhamnose’ means L-rhamnose.) The ‘rhamnose promoter’ or ‘rha promoter’, or PrhaSR, is the promoter for the E. coli rhaSR operon. Like the ara and pip promoters, the rha promoter is part of a bidirectional promoter, controlling expression of the rhaSR operon in one direction, and with the rhaBAD promoter controlling expression of the rhaBAD operon in the other direction. The rha promoter, however, has two transcriptional regulators involved in modulating expression: RhaR and RhaS. The RhaR protein activates expression of the rhaSR operon in the presence of rhamnose, while RhaS protein activates expression of the L-rhamnose catabolic and transport operons, rhaBAD and rhaT, respectively (Wickstrum et al., “The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation”, J Bacteriol 2010 January; 192(1): 225-232). Although the RhaS protein can also activate expression of the rhaSR operon, in effect RhaS negatively autoregulates this expression by interfering with the ability of the cyclic AMP receptor protein (CRP) to coactivate expression with RhaR to a much greater level. The rhaBAD operon encodes the rhamnose catabolic proteins RhaA (L-rhamnose isomerase), which converts L-rhamnose to L-rhamnulose; RhaB (rhamnulokinase), which phosphorylates L-rhamnulose to form L-rhamnulose-1-P; and RhaD (rhamnulose-1-phosphate aldolase), which converts L-rhamnulose-1-P to L-lactaldehyde and DHAP (dihydroxyacetone phosphate). To maximize the amount of rhamnose in the cell available for induction of expression from a rhamnose-inducible promoter, it is desirable to reduce the amount of rhamnose that is broken down by catalysis, by eliminating or reducing the function of RhaA, or optionally of RhaA and at least one of RhaB and RhaD. E. coli cells can also synthesize L-rhamnose from alpha-D-glucose-1-P through the activities of the proteins RmlA, RmlB, RmlC, and RmlD (also called RfbA, RfbB, RfbC, and RfbD, respectively) encoded by the rmlBDACX (or rfbBDACX) operon. To reduce background expression from a rhamnose-inducible promoter, and to enhance the sensitivity of induction of the rhamnose-inducible promoter by exogenously supplied rhamnose, it could be useful to eliminate or reduce the function of one or more of the RmlA, RmlB, RmlC, and RmlD proteins. L-rhamnose is transported into the cell by RhaT, the rhamnose permease or L-rhamnose:proton symporter. As noted above, the expression of RhaT is activated by the transcriptional regulator RhaS. To make expression of RhaT independent of induction by rhamnose (which induces expression of RhaS), the host cell can be altered so that all functional RhaT coding sequences in the cell are expressed from constitutive promoters. Additionally, the coding sequences for RhaS can be deleted or inactivated, so that no functional RhaS is produced. By eliminating or reducing the function of RhaS in the cell, the level of expression from the rhaSR promoter is increased due to the absence of negative autoregulation by RhaS, and the level of expression of the rhamnose catalytic operon rhaBAD is decreased, further increasing the ability of rhamnose to induce expression from the rha promoter.
Xylose Promoter.
(As used herein, ‘xylose’ means D-xylose.) The xylose promoter, or ‘xyl promoter’, or PxylA, means the promoter for the E. coli xylAB operon. The xylose promoter region is similar in organization to other inducible promoters in that the xylAB operon and the xylFGHR operon are both expressed from adjacent xylose-inducible promoters in opposite directions on the E. coli chromosome (Song and Park, “Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator”, J Bacteriol. 1997 November; 179(22): 7025-7032). The transcriptional regulator of both the PxylA and PxylF promoters is XylR, which activates expression of these promoters in the presence of xylose. The xylR gene is expressed either as part of the xylFGHR operon or from its own weak promoter, which is not inducible by xylose, located between the xylH and xylR protein-coding sequences. D-xylose is catabolized by XylA (D-xylose isomerase), which converts D-xylose to D-xylulose, which is then phosphorylated by XylB (xylulokinase) to form D-xylulose-5-P. To maximize the amount of xylose in the cell available for induction of expression from a xylose-inducible promoter, it is desirable to reduce the amount of xylose that is broken down by catalysis, by eliminating or reducing the function of at least XylA, or optionally of both XylA and XylB. The xylFGHR operon encodes XylF, XylG, and XylH, the subunits of an ABC superfamily high-affinity D-xylose transporter. The xylE gene, which encodes the E. coli low-affinity xylose-proton symporter, represents a separate operon, the expression of which is also inducible by xylose. To make expression of a xylose transporter independent of induction by xylose, the host cell can be altered so that all functional xylose transporters are expressed from constitutive promoters. For example, the xylFGHR operon could be altered so that the xylFGH coding sequences are deleted, leaving XylR as the only active protein expressed from the xylose-inducible PxylF promoter, and with the xylE coding sequence expressed from a constitutive promoter rather than its native promoter. As another example, the xylR coding sequence is expressed from the PxylA or the PxylF promoter in an expression construct, while either the xylFGHR operon is deleted and xylE is constitutively expressed, or alternatively an xylFGH operon (lacking the xylR coding sequence since that is present in an expression construct) is expressed from a constitutive promoter and the xylE coding sequence is deleted or altered so that it does not produce an active protein.
Lactose Promoter.
The term ‘lactose promoter’ refers to the lactose-inducible promoter for the lacZYA operon, a promoter which is also called lacZp1; this lactose promoter is located at ca. 365603-365568 (minus strand, with the RNA polymerase binding (‘−35’) site at ca. 365603-365598, the Pribnow box (‘−10’) at 365579-365573, and a transcription initiation site at 365567) in the genomic sequence of the E. coli K-12 substrain MG1655 (NCBI Reference Sequence NC_000913.2, 11 Jan. 2012). In some embodiments, expression systems of the invention can comprise a lactose-inducible promoter such as the lacZYA promoter. In other embodiments, the expression systems of the invention comprise one or more inducible promoters that are not lactose-inducible promoters.
Alkaline Phosphatase Promoter.
The terms ‘alkaline phosphatase promoter’ and ‘phoA promoter’ refer to the promoter for the phoApsiF operon, a promoter which is induced under conditions of phosphate starvation. The phoA promoter region is located at ca. 401647-401746 (plus strand, with the Pribnow box (‘−10’) at 401695-401701 (Kikuchi et al., “The nucleotide sequence of the promoter and the amino-terminal region of alkaline phosphatase structural gene (phoA) of Escherichia coli”, Nucleic Acids Res 1981 Nov. 11; 9(21): 5671-5678)) in the genomic sequence of the E. coli K-12 substrain MG1655 (NCBI Reference Sequence NC_000913.3, 16 Dec. 2014). The transcriptional activator for the phoA promoter is PhoB, a transcriptional regulator that, along with the sensor protein PhoR, forms a two-component signal transduction system in E. coli. PhoB and PhoR are transcribed from the phoBR operon, located at ca. 417050-419300 (plus strand, with the PhoB coding sequence at 417,142-417,831 and the PhoR coding sequence at 417,889-419,184) in the genomic sequence of the E. coli K-12 substrain MG1655 (NCBI Reference Sequence NC_000913.3, 16 Dec. 2014). The phoA promoter differs from the inducible promoters described above in that it is induced by the lack of a substance—intracellular phosphate—rather than by the addition of an inducer. For this reason the phoA promoter is generally used to direct transcription of gene products that are to be produced at a stage when the host cells are depleted for phosphate, such as the later stages of fermentation. In some embodiments, expression systems of the invention can comprise a phoA promoter. In other embodiments, the expression systems of the invention comprise one or more inducible promoters that are not phoA promoters.
III. Host Cells.
Expression constructs encoding gene products of interest are expressed in host cells to produce the gene products of interest. Host cells can be any cell capable of comprising such expression constructs and expressing them. Particularly suitable host cells are capable of growth at high cell density in fermentation culture, and can produce gene products in oxidizing host cell cytoplasm through highly controlled inducible gene expression. Host cells with these qualities are produced by combining some or all of the following characteristics. (1) The host cells are genetically modified to have an oxidizing cytoplasm, through increasing the expression or function of oxidizing polypeptides in the cytoplasm, and/or by decreasing the expression or function of reducing polypeptides in the cytoplasm. Specific examples of such genetic alterations are provided herein. Optionally, host cells can also be genetically modified to express chaperones and/or cofactors that assist in the production of the desired gene product(s), and/or to glycosylate polypeptide gene products. (2) The host cells comprise one or more expression constructs designed for the expression of one or more gene products of interest; in certain embodiments, at least one expression construct comprises an inducible promoter and a polynucleotide encoding a gene product to be expressed from the inducible promoter. (3) The host cells contain additional genetic modifications designed to improve certain aspects of gene product expression from the expression construct(s). In particular embodiments, the host cells (A) have an alteration of gene function of at least one gene encoding a transporter protein for an inducer of at least one inducible promoter, and as another example, wherein the gene encoding the transporter protein is selected from the group consisting of araE, araF, araG, araH, rhaT, xylF, xylG, and xylH, or particularly is araE, or wherein the alteration of gene function more particularly is expression of araE from a constitutive promoter; and/or (B) have a reduced level of gene function of at least one gene encoding a protein that metabolizes an inducer of at least one inducible promoter, and as further examples, wherein the gene encoding a protein that metabolizes an inducer of at least one said inducible promoter is selected from the group consisting of araA, araB, araD, prpB, prpD, rhaA, rhaB, rhaD, xylA, and xylB; and/or (C) have a reduced level of gene function of at least one gene encoding a protein involved in biosynthesis of an inducer of at least one inducible promoter, which gene in further embodiments is selected from the group consisting of scpA/sbm, argK/ygfD, scpB/ygfG, scpC/ygfH, rmlA, rmlB, rmlC, and rmlD.
Examples of host cells are provided that allow for the efficient and cost-effective production of gene products, including multimeric products. Host cells can include, in addition to isolated cells in culture, cells that are part of a multicellular organism, or cells grown within a different organism or system of organisms. In certain embodiments of the invention, the host cells are microbial cells such as yeasts (Saccharomyces, Schizosaccharomyces, etc.) or bacterial cells, or are gram-positive bacteria or grain-negative bacteria, or are E. coli, or are an E. coli B strain, or are E. coli (B strain) EB0001 cells (also called E. coli ASE(DGH) cells), or are E. coli (B strain) EB0002 cells. In growth experiments with E. coli host cells having oxidizing cytoplasm, specifically the E. coli B strains SHuffle® Express (NEB Catalog No. C3028H) and SHuffle® T7 Express (NEB Catalog No. C3029H) and the E. coli K strain SHuffle® T7 (NEB Catalog No. C3026H), we have determined that these E. coli B strains with oxidizing cytoplasm are able to grow to much higher cell densities than the most closely corresponding E. coli K strain.
Prokaryotic Host Cells.
In some embodiments of the invention, expression constructs designed for expression of gene products are provided in host cells, such as prokaryotic host cells. Prokaryotic host cells can include archaea (such as Haloferax volcanii, Sulfolobus solfataricus), Gram-positive bacteria (such as Bacillus subtilis, Bacillus licheniformis, Brevibacillus choshinensis, Lactobacillus brevis, Lactobacillus buchneri, Lactococcus lactis, and Streptomyces lividans), or Gram-negative bacteria, including Alphaproteobacteria (Agrobacterium tumefaciens, Caulobacter crescentus, Rhodobacter sphaeroides, and Sinorhizobium meliloti), Betaproteobacteria (Alcaligenes eutrophus), and Gammaproteobacteria (Acinetobacter calcoaceticus, Azotobacter vinelandii, Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida). Preferred host cells include Gammaproteobacteria of the family Enterobacteriaceae, such as Enterobacter, Erwinia, Escherichia (including E. coli), Klebsiella, Proteus, Salmonella (including Salmonella typhimurium), Serratia (including Serratia marcescans), and Shigella.
Eukaryotic Host Cells.
Many additional types of host cells can be used for the expression systems of the invention, including eukaryotic cells such as yeast (Candida shehatae, Kluyveromyces lactis, Kluyveromyces fragilis, other Kluyveromyces species, Pichia pastoris, Saccharomyces cerevisiae, Saccharomyces pastorianus also known as Saccharomyces carlsbergensis, Schizosaccharomyces pombe, Dekkera/Brettanomyces species, and Yarrowia lipolytica); other fungi (Aspergillus nidulans, Aspergillus niger, Neurospora crassa, Penicillium, Tolypocladium, Trichoderma reesia); insect cell lines (Drosophila melanogaster Schneider 2 cells and Spodoptera frugiperda Sf9 cells); and mammalian cell lines including immortalized cell lines (Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human embryonic kidney (HEK, 293, or HEK-293) cells, and human hepatocellular carcinoma cells (Hep G2)). The above host cells are available from the American Type Culture Collection.
Alterations to Host Cell Gene Functions.
Certain alterations can be made to the gene functions of host cells comprising inducible expression constructs, to promote efficient and homogeneous induction of the host cell population by an inducer. Preferably, the combination of expression constructs, host cell genotype, and induction conditions results in at least 75% (more preferably at least 85%, and most preferably, at least 95%) of the cells in the culture expressing gene product from each induced promoter, as measured by the method of Khlebnikov et al. “Regulatable arabinose-inducible gene expression system with consistent control in all cells of a culture”, J Bacteriol 2000 December; 182(24): 7029-7034, as described in WO2014025663A1, Example 8B. For host cells other than E. coli, these alterations can involve the function of genes that are structurally similar to an E. coli gene, or genes that carry out a function within the host cell similar to that of the E. coli gene. Alterations to host cell gene functions include eliminating or reducing gene function by deleting the gene protein-coding sequence in its entirety, or deleting a large enough portion of the gene, inserting sequence into the gene, or otherwise altering the gene sequence so that a reduced level of functional gene product is made from that gene. Alterations to host cell gene functions also include increasing gene function by, for example, altering the native promoter to create a stronger promoter that directs a higher level of transcription of the gene, or introducing a missense mutation into the protein-coding sequence that results in a more highly active gene product. Alterations to host cell gene functions include altering gene function in any way, including for example, altering a native inducible promoter to create a promoter that is constitutively activated. In addition to alterations in gene functions for the transport and metabolism of inducers, as described herein with relation to inducible promoters, and/or an altered expression of chaperone proteins, it is also possible to alter the reduction-oxidation environment of the host cell.
Host Cell Reduction-Oxidation Environment.
In bacterial cells such as E. coli, proteins that need disulfide bonds are typically exported into the periplasm where disulfide bond formation and isomerization is catalyzed by the Dsb system, comprising DsbABCD and DsbG. Increased expression of the cysteine oxidase DsbA, the disulfide isomerase DsbC, or combinations of the Dsb proteins, which are all normally transported into the periplasm, has been utilized in the expression of heterologous proteins that require disulfide bonds (Makino et al., “Strain engineering for improved expression of recombinant proteins in bacteria”, Microb Cell Fact 2011 May 14; 10: 32). It is also possible to express cytoplasmic forms of these Dsb proteins, such as a cytoplasmic version of DsbA and/or of DsbC (‘cDsbA’ or ‘cDsbC’), that lacks a signal peptide and therefore is not transported into the periplasm. Cytoplasmic Dsb proteins such as cDsbA and/or cDsbC are useful for making the cytoplasm of the host cell more oxidizing and thus more conducive to the formation of disulfide bonds in heterologous proteins produced in the cytoplasm. The host cell cytoplasm can also be made less reducing and thus more oxidizing by altering the thioredoxin and the glutaredoxin/glutathione enzyme systems directly: mutant strains defective in glutathione reductase (gor) or glutathione synthetase (gshB), together with thioredoxin reductase (trxB), render the cytoplasm oxidizing. These strains are unable to reduce ribonucleotides and therefore cannot grow in the absence of exogenous reductant, such as dithiothreitol (DTT). Suppressor mutations (such as ahpC* and ahpC4, Lobstein et al., “SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm”, Microb Cell Fact 2012 May 8; 11: 56; doi: 10.1186/1475-2859-11-56) in the gene ahpC, which encodes the peroxiredoxin AhpC, convert it to a disulfide reductase that generates reduced glutathione, allowing the channeling of electrons onto the enzyme ribonucleotide reductase and enabling the cells defective in gor and trxB, or defective in gshB and trxB, to grow in the absence of DTT. A different class of mutated forms of AhpC can allow strains, defective in the activity of gamma-glutamylcysteine synthetase (gshA) and defective in trxB, to grow in the absence of DTT; these include AhpC V164G, AhpC S71F, AhpC E173/S71F, AhpC E171Ter, and AhpC dup162-169 (Faulkner et al., “Functional plasticity of a peroxidase allows evolution of diverse disulfide-reducing pathways”, Proc Natl Acad Sci USA 2008 May 6; 105(18): 6735-6740, Epub 2008 May 2). In such strains with oxidizing cytoplasm, exposed protein cysteines become readily oxidized in a process that is catalyzed by thioredoxins, in a reversal of their physiological function, resulting in the formation of disulfide bonds. Other proteins that may be helpful to reduce the oxidative stress effects in host cells of an oxidizing cytoplasm are HPI (hydroperoxidase I) catalase-peroxidase encoded by E. coli katG and HPII (hydroperoxidase II) catalase-peroxidase encoded by E. coli katE, which disproportionate peroxide into water and O2 (Farr and Kogoma, “Oxidative stress responses in Escherichia coli and Salmonella typhimurium”, Microbiol Rev. 1991 December; 55(4): 561-585; Review). Increasing levels of KatG and/or KatE protein in host cells through induced coexpression or through elevated levels of constitutive expression is an aspect of some embodiments of the invention.
Another alteration that can be made to host cells is to express the sulfhydryl oxidase Erv1p from the inner membrane space of yeast mitochondria in the host cell cytoplasm, which has been shown to increase the production of a variety of complex, disulfide-bonded proteins of eukaryotic origin in the cytoplasm of E. coli, even in the absence of mutations in gor or trxB (Nguyen et al., “Pre-expression of a sulfhydryl oxidase significantly increases the yields of eukaryotic disulfide bond containing proteins expressed in the cytoplasm of E. coli” Microb Cell Fact 2011 Jan. 7; 10: 1).
Host cells comprising expression constructs preferably also express cDsbA and/or cDsbC and/or Erv1p; are deficient in trxB gene function; are also deficient in the gene function of gor, gshB, and/or gshA; optionally have increased levels of katG and/or katE gene function; and optionally express an appropriate mutant form of AhpC so that the host cells can be grown in the absence of DTT.
Glycosylation of Polypeptide Gene Products.
Host cells can have alterations in their ability to glycosylate polypeptides. For example, eukaryotic host cells can have eliminated or reduced gene function in glycosyltransferase and/or oligosaccharyltransferase genes, impairing the normal eukaryotic glycosylation of polypeptides to form glycoproteins. Prokaryotic host cells such as E. coli, which do not normally glycosylate polypeptides, can be altered to express a set of eukaryotic or prokaryotic genes that provide a glycosylation function (DeLisa et al., “Glycosylated protein expression in prokaryotes”, WO2009089154A2, 2009 Jul. 16).
Available Host Cell Strains with Altered Gene Functions.
To create preferred strains of host cells to be used in the expression systems and methods of the invention, it is useful to start with a strain that already comprises desired genetic alterations, examples of which are provided in Table 2.
E. coli
E. coli
Methods of Altering Host Cell Gene Functions.
There are many methods known in the art for making alterations to host cell genes in order to eliminate, reduce, or change gene function. Methods of making targeted disruptions of genes in host cells such as E. coli and other prokaryotes have been described (Muyrers et al., “Rapid modification of bacterial artificial chromosomes by ET-recombination”, Nucleic Acids Res 1999 Mar. 15; 27(6): 1555-1557; Datsenko and Wanner, “One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products”, Proc Natl Acad Sci USA 2000 Jun. 6; 97(12): 6640-6645), and kits for using similar Red/ET recombination methods are commercially available (for example, the Quick & Easy E. coli Gene Deletion Kit from Gene Bridges GmbH, Heidelberg, Germany). In one embodiment of the invention, the function of one or more genes of host cells is eliminated or reduced by identifying a nucleotide sequence within the coding sequence of the gene to be disrupted, such as one of the E. coli K-12 substrain MG1655 coding sequences incorporated herein by reference to the genomic location of the sequence, and more specifically by selecting two adjacent stretches of 50 nucleotides each within that coding sequence. The Quick & Easy E. coli Gene Deletion Kit is then used according to the manufacturer's instructions to insert a polynucleotide construct containing a selectable marker between the selected adjacent stretches of coding sequence, eliminating or reducing the normal function of the gene. Red/ET recombination methods can also be used to replace a promoter sequence with that of a different promoter, such as a constitutive promoter, or an artificial promoter that is predicted to promote a certain level of transcription (De Mey et al., “Promoter knock-in: a novel rational method for the fine tuning of genes”, BMC Biotechnol 2010 Mar. 24; 10: 26). The function of host cell genes can also be eliminated or reduced by RNA silencing methods (Man et al., “Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria”, Nucleic Acids Res 2011 April; 39(8): e50, Epub 2011 Feb. 3). Further, known mutations that alter host cell gene function can be introduced into host cells through traditional genetic methods.
IV. Methods for Growing Host Cells
Small-Volume Growth.
Host cells used to carry out the methods of the invention can be grown in small volumes for the purpose of testing growth or induction conditions, or for the production of multiple different gene products, etc. The nature of the experiments to be performed will determine the volume that the host cells are to be grown in, such as one mL up to one liter, or between 5 mL and 500 mL, or any convenient volume. In certain embodiments, the vessel in which the host cells are grown is moved repeatedly in order to agitate the growth medium and thus provide oxygen to the host cells. Host cells are grown in a medium containing suitable nutrients and any antibiotics required to select for the retention by the host cells of expression constructs that provide antibiotic resistance. Examples of the small-volume growth of host cells are provided in Example 1. To determine the appropriate amount of inducer to be used to induce expression of inducible expression constructs present in cells, experiments such as those described in Example 10 can advantageously be performed with host cells grown in small volumes such as in multiwell plates.
Fermentation.
The fermentation processes involved in the production of recombinant proteins will use a mode of operation which falls within one of the following categories: (1) discontinuous (batch process) operation, (2) continuous operation, and (3) semi-continuous (fed-batch) operation. A batch process is characterized by inoculation of the sterile culture medium (batch medium) with microorganisms at the start of the process, cultivated for a specific reaction period. During cultivation, cell concentrations, substrate concentrations (carbon source, nutrient salts, vitamins, etc.) and product concentrations change. Good mixing ensures that there are no significant local differences in composition or temperature of the reaction mixture. The reaction is non-stationary and cells are grown until the growth-limiting substrate (generally the carbon source) has been consumed.
Continuous operation is characterized in that fresh culture medium (feed medium) is added continuously to the fermentor and spent media and cells are drawn continuously from the fermentor at the same rate. In a continuous operation, growth rate is determined by the rate of medium addition, and the growth yield is determined by the concentration of the growth limiting substrate (i.e. carbon source). All reaction variables and control parameters remain constant in time and therefore a time-constant state is established in the fermentor followed by constant productivity and output.
Semi-continuous operation can be regarded as a combination of batch and continuous operation. The fermentation is started off as a batch process and when the growth-limiting substrate has been consumed, a continuous feed medium containing glucose and minerals is added in a specified manner (fed-batch). In other words, this operation employs both a batch medium and a feed medium to achieve cell growth and efficient production of the desired protein. No cells are added or taken away during the cultivation period and therefore the fermentor operates batchwise as far as the microorganisms are concerned. While the present invention can be utilized in a variety of processes, including those mentioned above, a particular utilization is in conjunction with a fed-batch process.
In each of the above processes, cell growth and product accumulation can be monitored indirectly by taking advantage of a correlation between metabolite formation and some other variable, such as medium pH, optical density, color, and titrable acidity. For example, optical density provides an indication of the accumulation of insoluble cell particles and can be monitored on-stream using a micro-OD unit coupled to a display device or a recorder, or off-line by sampling. Optical density readings at 600 nanometers (OD600) are used as a means of determining dry cell weight.
High-cell-density fermentations are generally described as those processes which result in a yield of >30 g cell dry weight/liter (OD600>60) at a minimum, and in certain embodiments result in a yield of >40 g cell dry weight/liter (OD600>80). All high-cell-density fermentation processes employ a concentrated nutrient media that is gradually metered into the fermentor in a “fed-batch” process. A concentrated nutrient feed media is required for high-cell-density processes in order to minimize the dilution of the fermentor contents during feeding. A fed-batch process is required because it allows the operator to control the carbon source feeding, which is important because if the cells are exposed to concentrations of the carbon source high enough to generate high cell densities, the cells will produce so much of the inhibitory biproduct, acetate, that growth will stop (Majewski and Domach, “Simple constrained-optimization view of acetate overflow in E. coli”, Biotechnol Bioeng 1990 Mar. 25; 35(7): 732-738).
Acetic acid and its deprotonated ion, acetate, together represent one of the main inhibitory byproducts of bacterial growth and recombinant protein production in bioreactors. At pH 7, acetate is the most prevalent form of acetic acid. Any excess carbon energy source may be converted to acetic acid when the amount of the carbon energy source greatly exceeds the processing ability of the bacterium. Research has shown that saturation of the tricarboxylic acid cycle and/or the electron transport chain is the most likely cause of the acetic acid accumulation. The choice of growth medium may affect the level of acetic acid inhibition; cells grown in defined media may be affected by acetic acid more than those grown in complex media. Replacement of glucose with glycerol may also greatly decrease the amount of acetic acid produced. It is believed that glycerol produces less acetic acid than glucose because its rate of transport into a cell is much slower than that of glucose. However, glycerol is more expensive than glucose, and may cause the bacteria to grow more slowly. The use of reduced growth temperatures can also decrease the speed of carbon source uptake and growth rate thus decreasing the production of acetic acid. Bacteria produce acetic acid not only in the presence of an excess carbon energy source or during fast growth, but also under anaerobic conditions. When bacteria such as E. coli are allowed to grow too fast, they may exceed the oxygen delivery ability of the bioreactor system which may lead to anaerobic growth conditions. To prevent this from happening, a slower constant growth rate may be maintained through nutrient limitation. Other methods for reducing acetic acid accumulation include genetic modification to prevent acetic acid production, addition of acetic acid utilization genes, and selection of strains with reduced acetic acid. E. coli BL21(DE3) is one of the strains that has been shown to produce lower levels of acetic acid because of its ability to use acetic acid in its glyoxylate shunt pathway.
Various larger-scale fed-batch fermentors are available for production of recombinant proteins. Larger fermentors have at least 1000 liters of capacity, preferably about 1000 to 100,000 liters of capacity (i.e. working volume), leaving adequate room for headspace. These fermentors use agitator impellers or other suitable means to distribute oxygen and nutrients, especially glucose (the preferred carbon/energy source). Small-scale fermentation refers generally to fermentation in a fermentor that is no more than approximately 100 liters in volumetric capacity, and in some specific embodiments no more than approximately 10 liters.
Standard reaction conditions for the fermentation processes used to produce recombinant proteins generally involve maintenance of pH at about 5.0 to 8.0 and cultivation temperatures ranging from 20 to 50 degrees C. for microbial host cells such as E. coli. In one embodiment of the present invention which utilizes E. coli as the host system, fermentation is performed at an optimal pH of about 7.0 and an optimal cultivation temperature of about 30 degrees C.
The standard nutrient media components in these fermentation processes generally include a source of energy, carbon, nitrogen, phosphorus, magnesium, and trace amounts of iron and calcium. In addition, the media may contain growth factors (such as vitamins and amino acids), inorganic salts, and any other precursors essential to product formation. The media may contain a transportable organophosphate such as a glycerophosphate, for example an alpha-glycerophosphate and/or a beta-glycerophosphate, and as a more specific example, glycerol-2-phosphate and/or glycerol-3-phosphate. The elemental composition of the host cell being cultivated can be used to calculate the proportion of each component required to support cell growth. The component concentrations will vary depending upon whether the process is a low-cell-density or a high-cell-density process. For example, the glucose concentrations in low-cell-density batch fermentation processes range from 1 to 5 g/L, while high-cell-density batch processes use glucose concentrations ranging from 45 g/L to 75 g/L. In addition, growth media may contain modest concentrations (for example, in the range of 0.1-5 mM, or 0.25 mM, 0.5 mM, 1 mM, 1.5 mM, or 2 mM) of protective osmolytes such as betaine, dimethylsulfoniopropionate, and/or choline.
One or more inducers can be introduced into the growth medium to induce expression of the gene product(s) of interest. Induction can be initiated during the exponential growth phase, for example, such as toward the end of the exponential growth phase but before the culture reaches maximum cell density, or at earlier or later times during fermentation. When expressing the gene product(s) of interest from one or more promoters inducible by depletion of nutrients such as phosphate, induction will occur when that nutrient has been sufficiently depleted from the growth medium, without the addition of an exogenous inducer.
During exponential growth of host cells, the metabolic rate is directly proportional to availability of oxygen and a carbon/energy source; thus, reducing the levels of available oxygen or carbon/energy sources, or both, will reduce metabolic rate. Manipulation of fermentor operating parameters, such as agitation rate or back pressure, or reducing O2 pressure, modulates available oxygen levels and can reduce host cell metabolic rate. Reducing concentration or delivery rate, or both, of the carbon/energy source(s) has a similar effect. Furthermore, depending on the nature of the expression system, induction of expression can lead to a decrease in host cell metabolic rate. Finally, upon reaching maximum cell density, the growth rate stops or decreases dramatically. Reduction in host cell metabolic rate can result in more controlled expression of the gene product(s) of interest, including the processes of protein folding and assembly. Host cell metabolic rate can be assessed by measuring cell growth rates, either specific growth rates or instantaneous growth rates (by measuring optical density (OD) such as OD600 and or optionally by converting OD to biomass). The approximate biomass (cell dry weight) at each assayed point is calculated: approximate biomass (g)=(OD600÷2)×volume (L). Desirable growth rates are, in certain embodiments of the invention, in the range of 0.01 to 0.7, or are in the range of 0.05 to 0.3, or are in the range of 0.1 to 0.2, or are approximately 0.15 (0.15 plus-or-minus 10%), or are 0.15.
Fermentation Equipment.
The following are examples of equipment that can be used to grow host cells; many other configurations of fermentation systems are commercially available. Host cells can be grown in a New Brunswick BioFlo/CelliGen 115 water jacketed fermentor (Eppendorf North America, Hauppauge, N.Y.), 1 L vessel size with a 2× Rushton impeller and a BioFlo/CelliGen 115 Fermentor/Bioreactor controller; temperature, pH, and dissolved oxygen (DO) are monitored. It is also possible to grow host cells in a four-fold configurable DASGIP system (Eppendorf North America, Hauppauge, N.Y.) comprising four 60- to 250-ml DASbox fermentation vessels, each with a 2× Rushton impeller, a DASbox exhaust condenser, and a DASbox feeding and monitoring module (which includes a temperature sensor, a pH/redox sensor, and a dissolved oxygen sensor). Suitable fermentation equipment also includes NLF 22 30L lab fermentors (Bioengineering, Inc., Somerville, Mass.), with 30-L capacity and 20-L maximum working volume in a stainless steel vessel; two Rushton impellers, sparged with air only; and a control system running BioSCADA software that allows for tracking and control of all relevant parameters including pH, DO, exhaust O2, exhaust CO2, temperature, and pressure.
V. Solubilization and Purification Methods.
The gene products expressed by the methods described herein can be purified using any of a variety of purification methods. When gene products are expressed in such a way as to produce solubilizable complexes, as described herein and as in particular embodiments described in Examples 1 and 2, a highly advantageous purification method can be used to efficiently produce properly folded and active gene product, without the need for additional refolding steps. Example 3 describes a further ‘direct solubilization’ method for purifying gene products expressed as solubilizable complexes, including gene products that form disulfide bonds, without the need for centrifugation following lysis to separate the soluble and insoluble fractions, and without the use of reducing agents. Methods for purifying solubilizable gene product complexes in these ways are outlined schematically in
Collecting Host Cells by Centrifugation.
Host cells comprising expression constructs are grown and the expression of the gene product of interest is induced as described further herein, resulting in the production of solubilizable complexes of the gene product of interest within the host cell. After the growth and induction periods are complete, the host cells are collected by centrifugation at 4,000×g at 4 degrees C. for 10 minutes, for example. The host cells can be frozen at this point and stored for later purification.
Lysis of Host Cells.
The resulting pellet of intact host cells is then lysed using one of several alternative methods. The pellet of host cells is resuspended in a nondenaturing lysis buffer, such as phosphate-buffered saline (PBS) or Tris-buffered saline (TBS) supplemented with from 0 mM to 300 mM NaCl or with 2.5 mM L-cysteine, pH 9.5. After resuspension in lysis buffer, the host cells can be lysed by methods including enzymatic or chemical lysis, mechanical lysis, and/or a freeze-thaw method. For enzymatic lysis, the lysis can be accomplished by adding recombinant lysozyme, benzonase, and octyl glucoside to the lysis buffer. For mechanical lysis, the resuspended host cells are passed one or more times through a microfluidizer, such as a Microfluidics model LV1 microfluidizer for volumes up to 60 ml, or a Microfluidics model M-110Y microfluidizer for volumes greater than 60 mL (Microfluidics International Corp., Westwood, Mass.), or a PandaPLUS 2000 table-top homogenizer or a GEA Niro (GEA North America, Columbia, Md.). For the freeze-thaw method, the cell suspension is frozen at −80 degrees C. and then thawed at a temperature between 25 and 37 degrees C.
Following Lysis, the Lysed Cell Mixture is Optionally Centrifuged to Pellet the Solubilizable Gene Product Complexes.
The speed and time of this centrifugation step can vary from 3,300 to 20,000×g and from 30 to 60 minutes. Using a higher speed can result in a pellet of the solubilizable gene product complex that is more difficult to resuspend. The lower the speed that is used in this centrifugation step, the longer the duration of centrifugation that is needed to complete the separation of the solubilizable gene product complex from the supernatant. It is possible to vary the salt concentration and/or the pH of the cell lysate to alter the centrifugation or other conditions needed to separate the solubilizable gene product complexes from other components in the cell lysate.
One significant advantage to collecting the gene product of interest in this way is that the majority of potentially contaminating host cell proteins and other molecules will remain in the supernatant and be removed from the pelleted solubilizable gene product complex, which is then a preparation highly enriched for the gene product of interest. Alternatively, if the supernatant remaining after pelleting of the solubillizable complexes retains sufficient gene product, the gene product in this supernatant can be solubilized as described for the direct solubilization method, and/or further purified. If analysis of the pelleted material indicates that a significant number of cells survive lysis and are being spun down with the solubilizable gene product complexes, it is possible to use a dense and/or viscous solution, such as high-concentration sucrose solution, as a “cushion” in the centrifugation procedure to separate out the intact cells from the solubilizable gene product complexes. When mechanical lysis is used, the lysed cell mixture can be passed through the microfluidizer multiple times (for example, four or five times). When the above centrifugation procedure is omitted in a direct solubilization method, the cell lysate is mixed with reagents to create the conditions for solubilization of the solubilizable gene product complexes, as described below.
The Gene Product is Released from the Solubilizable Complexes by Placement in a Solubilization Solution, Resulting in Solubilized Gene Product.
The gene product, either in a pellet resulting from centrifugation, or in the cell lysate, is solubilized as follows. Solubilization solutions preferably contain one or more chaotropic agent, such as n-butanol, ethanol, guanidinium chloride, guanidine hydrochloride, lithium perchlorate, lithium acetate, magnesium chloride, phenol, 2-propanol, sodium dodecyl sulfate, thiourea, or urea. Exemplary solubilization solutions can contain 7M to 8M urea in PBS or TRIS at pH 9.5, optionally with 2.5 mM L-cysteine, or alternatively 6M guanidine hydrochloride in PBS at pH 7.5; effective solubilization experiments have used solubilization buffers at pH values ranging from 6.5 to 11.0. Experiments for determining alternative buffer compositions to be used for solubilization are described in Example 5. The pellet may optionally be washed prior to resuspension. After addition of solubilization buffer to the pellet, it is more effective to mechanically agitate the tube containing the pellet, for example by the use of a plate vortexer for at least 10 minutes, than to resuspend the pellet by hand using a pipette tip. Reversible chemical modification of the gene product, for example citraconylation of the free lysine residues and primary amino groups, can alter the solubility of the gene product.
Optional Clarification of Solubilized Gene Product by Centrifugation.
As shown in
Placing the Solubilized Gene Product into a Solution that is Less Concentrated than the Solubilization Solution.
For samples of protein gene products that are to be analyzed by peptide mapping, the solubilized gene product is typically placed in a solution having a two- to ten-fold reduced concentration of denaturant, using methods such as dialysis, dilution, or diafiltration, as the presence of 7M to 8M urea or 6M guanidine hydrochloride inhibits the cleavage efficiency of a number of proteases. For example, following solubilization in 7M to 8M urea in PBS or TRIS, pH 6.5 to 9.5, optionally with 2.5 mM L-cysteine, the samples containing gene product can be placed in 2M to 4M urea in PBS or TRIS, pH 6.5 to 9.5, optionally with 2.5 mM L-cysteine, and incubated for a period of 10 to 120 hours, for example at 16 degrees C. with shaking.
Optional Formation of Solution with a Higher Concentration of Gene Product.
For purposes such as storage, further purification, or characterization, the solution of solubilized gene product can be reconcentrated to result in a solution with a higher concentration of gene product. This can be accomplished by running the solution over a chromatography column and eluting into the desired buffer, as described below, or by spin desalting or diafiltration as described below, or by other known methods. Another alternative is the use of a precipitation method such as ammonium sulfate precipitation to precipitate the gene product; the gene product can optionally be washed before resuspension of the pellet in the desired buffer at the desired concentration.
Gene Products with Cleavage Sequences can Optionally be Cleaved by Chemical or Enzymatic Treatment.
Gene products that comprise, for example, sequences that are cleaved by enzymes such as trypsin, and/or sequences such as the ‘DP’ (Asp-Pro) chemical cleavage sequence described above and in Example 2, can be cleaved by the appropriate enzymatic or chemical treatment prior to use or further purification.
The Solubilized Gene Product can Optionally be Additionally Purified.
For example, gene products that include a 6×His tag can be purified by immobilized metal affinity chromatography (IMAC), such as the use of a nickel-nitrilotriacetic acid (Ni-NTA) column to specifically retain the 6×His-tagged gene product of interest while other molecules flow through. IMAC exploits interactions between histidine residues and divalent metal ions, most commonly Ni2+; other metal ions including Cu2+, Co2+, Fe2+, and Zn2+ have also been shown to have affinity for His residues. The metal ions are typically immobilized on the matrix via various metal-chelator systems, including iminodiacetic acid (IDA) and the more commonly used nitrilotriacetic acid (NTA). A wide variety of matrices are commercially available such as nickel-nitrilotriacetic acid (Ni-NTA), Ni Sepharose, and copper-carboxylmethylaspartate (CO-CMA). The column can be equilibrated with a buffer such as 50 mM Tris, 3 M urea, 0.5 M NaCl, 25 mM imidazole, pH 8.0. After binding of the 6×HIs-tagged gene product, a wash step with a buffer containing a low concentration of imidazole (0 mM, or 10 to 50 mM), or a buffer with a pH higher or lower than that of the binding buffer, can be included to remove nonspecific proteins that are weakly bound to the column during sample loading. For example, a wash buffer of 50 mM Tris, 100 mM NaCl, pH 10 can be used. The 6×His-tagged gene product can be eluted from the matrix using a buffer containing imidazole at a concentration of at least 100 mM imidazole, or 250 to 500 mM imidazole, or 500 mM imidazole. It is also possible to elute the gene products of interest by lowering the buffer pH, and/or by including chelating agents such as EDTA (at a concentration of 50 to 200 mM, or 100 mM) in the elution buffer. For example, an elution buffer of 50 mM Tris, 100 mM NaCl, 100 mM imidazole, pH 10 can be used. Purification methods for gene products that include a polyhistidine tag are further described in Bornhorst and Falke, “Purification of proteins using polyhistidine affinity tags”, Methods Enzymol 2000; 326: 245-254, which is incorporated by reference herein. In the purification by IMAC of 6×His-tagged CPBpro proinsulin proteins from solubilizable complexes, using either Ni-NTA Superflow (QIAgen, Germantown, Md.) or HisTrap HP Ni Sepharose columns (GE Healthcare, Pittsburgh, Pa.), this method allowed for purification of the proinsulin gene product to greater than 90% purity.
For samples lacking a 6×His tag, or for procedures where use of such a tag is not necessary, cation or anion exchange chromatography, such as the use of DEAE resins, and/or reversed-phase or high-performance liquid chromatography (RPLC or HPLC), can be employed to further separate the gene product of interest from other contaminants or from the unwanted product(s) of chemical or enzymatic treatment.
Chemical or enzymatic procedures can optionally be performed on gene products that are retained by a solid substrate such as a column: for example, trypsin cleavage of proinsulin gene products for preparative or analytical purposes, also called transversion of proinsulin to mature insulin, as described below in Example 3C.
Chromatography procedures such as IMAC can also be used to elute the solubilized complexes into buffers other than those used to solubilize the complexes, for example, into 250 mM up to 500 mM imidazole in PBS pH 7.5, optionally followed by spin desalting to exchange the elution buffer for a more preferred buffer, as described in Example 2D. Methods for removing undesirable buffer components such as salts include dialysis, diafiltration (using, for example, centrifugal concentrators or tangential flow filtration), and gel filtration using, for example, polyacrylamide beads (Bio-Rad, Hercules, Calif.), Sephadex resin (GE Healthcare, Pittsburgh, Pa.), and/or other chromatography resins such as size-exclusion resins (Zeba™ Spin Desalting Columns, ThermoFisher Scientific Inc., Waltham, Mass.).
The Solubilized Gene Product can be Chemically and/or Structurally Characterized.
For protein gene products containing disulfide bonds, the proper folding of the protein produced by the methods of the invention can be inferred from the presence of correctly formed disulfide bonds. The identification and characterization of disulfide bonds can be achieved using peptide mapping methods in which chemical or enzymatic treatment of the protein is used to produce peptide fragments. Separation and identification of these fragments is accomplished by liquid chromatography-mass spectrometry (LC-MS) analysis; peptide mapping and LC-MS methods are described further in Example 8 below. Peptide mapping and LC-MS analysis can also identify differences in protein primary structure such as point mutations and post-translational modifications (PTMs).
The number and presence of oxidized disulfide bonds can be verified for intact protein samples. Protein gene products can be treated with a reducing agent, such as dithiothreitol (DTT), and/or a sulfhydryl-reactive reagent, such as iodoacetamide (IAA). LC-MS analysis of reduced and/or alkylated samples will result in a mass increase of 2 Da per disulfide bond reduction and a mass increase of 57 Da per alkylation of each free thiol. The protein gene product can be characterized not only on the formation of the correct number of disulfides, but also on the correct bridging arrangement or “disulfide structure.” This procedure consists of proteolytic cleavage, separation of the resulting peptides by high-performance liquid chromatography (HPLC), and mass spectrometry (MS) analysis of the peptides represented by HPLC peaks. To generate proteolytic peptide products, the protein gene product can be fragmented via chemical agents, such as cyanogen bromide, and/or enzymatic agents, such as trypsin, pepsin, lysyl endopeptidase (Lys-C), glutamyl endopeptidase (Glu-C), and peptidyl-Asp metallo-endopeptidase (Asp-N). For the protein gene product proinsulin, a sequential proteolytic cleavage reaction can be performed using Glu-C and trypsin, where the order of protease addition can be interchanged (i.e. Glu-C then trypsin, or trypsin then Glu-C). The protease digestion reaction can be carried out at a temperature range of 25 to 37 degrees C. for 4 to 16 hours, with a substrate to enzyme ratio ranging from 12 to 200 micrograms of proinsulin per microgram of protease. Proteolytic cleavage efficiency and specificity can be improved through the addition of commercially available surfactants, such as ProteaseMax™ (Promega, Madison, Wis.) and RapiGest SF (Waters, Milford, Mass.), and/or low concentrations of organic solvents, such as 10-20% acetonitrile.
As described further in Example 2C and as shown in
Use of CPBpro Variant Propeptides in the Production of Lispro Proinsulin
A. Preparation of Expression Constructs for CPBpro_lispro Proinsulin
In these experiments, certain CPBpro variants were used as propeptides in the small-scale expression of lispro proinsulin polypeptides. Expression constructs comprising polynucleotides encoding the CPBpro proinsulin polypeptides shown in Table 3 and optimized for expression in E. coli were synthesized by ATUM (Newark, Calif.). The first column of Table 3 provides the protein number (PN) and SEQ ID NO for each complete CPBpro proinsulin polypeptide amino acid sequence. The polynucleotides encoding each of the CPBpro proinsulin polypeptides, presented from the RBS sequence through the termination codon, have SEQ ID NOs 44, 46, 48, 50, 52, and 54, respectively. The second through fifth columns of Table 3 indicate the amino acid sequences of each portion of each CPBpro proinsulin polypeptide: the N-terminal CPBpro propeptide sequence, and then following in N-to-C order, the lispro insulin B chain (as shown in Table 1), the C-peptide, and the lispro insulin A chain (as shown in Table 1).
The polynucleotides encoding each of the CPBpro proinsulin polypeptides were located downstream of the araBAD promoter in the pSOL expression vector (SEQ ID NO:42). These expression constructs each also contained the coding sequence for protein disulfide isomerase (PDI, SEQ ID NO:41) downstream of the prpBCDE promoter within the pSOL expression vector.
B. Transformation of Host Cells and Expression of CPBpro_lispro Proinsulin
The pSOL:CPBpro-lispro/PDI expression constructs were transformed into EB0001 cells as follows; the genotype of EB0001 cells is shown in Table 2. Chemically competent (CaCl-treated) EB0001 cells were thawed on ice for 10 minutes. DNA (1 microliter from each expression construct DNA stock) was added to a cold, sterile eppendorf tube. EB0001 cells (100 microliters) were added to each tube of DNA and the mixture was incubated on ice for 30 minutes. The tubes were heat-shocked at 42 degrees C. for 20 seconds and allowed to rest on ice for 5 minutes. The transformed cells recovered in 900 microliters SOC outgrowth medium (New England Biolabs catalog number B9020S) at 37 degrees C. for one hour with 275 RPM shaking. After the recovery period, the cells were pelleted at 3.8 k×g for 2 minutes and resuspended in about a 100-microliter volume of recovery medium remaining from the supernatant, then plated onto agar plates containing 50 micrograms/mL kanamycin. The transformed plated cells were grown for 18 hours at 37 degrees C. For each transformation, three colonies were picked from the plate and cultured in LB medium with 50 micrograms/mL kanamycin at 30 degrees C., with shaking at 275 RPM overnight until reaching stationary phase (OD600>2.0). Glycerol stocks were made by adding 750 microliters of the overnight culture to 750 microliters 40% glycerol. Glycerol stocks were stored at −80 degrees C.
Host cell cultures for expression of CPBpro_lispro proinsulin were started by stabbing glycerol stocks and inoculating 0.1 L of LB medium containing 50 micrograms/mL kanamycin in 0.5-L non-baffled flasks. The cells were grown overnight at 30 degrees C. with shaking at 275 RPM until the OD600 reached 2. The host cell cultures were diluted to an OD600 of 0.2 in LB medium containing 50 micrograms/mL kanamycin, and grown in a total volume of 0.1 L in 0.5-L baffled flasks at 30 degrees C. with shaking at 275 RPM until the OD600 reached 0.6-0.8. At this time, the appropriate volume was pelleted (3800×g, 10 minutes) so that resuspension in M9 minimal medium containing 50 micrograms/mL kanamycin gave an OD600 of 0.7-0.75.
M9 Minimal Medium.
In a volume of 1.2 L, autoclave:
Adjust pH to 7.2 with KOH, autoclave at 121 degrees C. for 45 minutes, and allow to cool to room temperature; this creates an incomplete M9 minimal medium. To complete the medium: for each 10 mL incomplete medium, add the following volumes of filter-sterilized salts: 20 microliters 1M MgSO4; 1 microliter 1M CaCl2; 1 microliter 5 mg/mL FeSO4.
Cultures were transferred into 24-well deep-well plates. A 3-mL sample of host cell culture was added to each well, for each of the following induction conditions: 6 wells for each expression construct with 15 micromolar arabinose, and 6 wells for each construct with 45 micromolar arabinose. The host cells were induced at 27 or 30 degrees C.
for 6 hours with
275 RPM shaking. The optical density of the host cells was measured after the induction period; the OD600 was between 1.0 and 1.2 in all the wells. Replicate samples (3×1 mL, 2×5 mL pellets) for each induction condition for each expression construct were collected by centrifugation at 3800×g for 7 minutes at room temperature.
The success of induction of the PN2.5, PN2.7, and PN2.9 expression constructs was confirmed using SDS-PAGE with coomassie blue staining. A 5-mL pellet for each induction condition for each expression construct was thawed on ice for 10 minutes. The host cells were lysed at a 6-fold concentration over culture concentration at harvest in GLB-OG lysis buffer, pH 7.4 (50 mM Tris pH 7.4, 200 mM NaCl, with 1% octylglucoside,
1× protease inhibitors;
2 U benzonase (EMD #70746) per mL culture, and 2.25 kU rLysozyme (EMD #71110) per mL culture). Lysis proceeded by incubating on ice for 10 minutes. After lysis, samples were split into two pools, one of which received total lysate prep, the other received soluble lysate prep. For the total lysate prep, after lysis 8M urea in 50 mM Tris pH 7.4, 200 mM NaCl was added to each sample at a 1:1 ratio and incubated at room temperature for 20 minutes prior to preparing to run the samples on a gel. For the soluble lysate prep, the samples were centrifuged at 20 k×g for 30 minutes at 4 degrees C., the supernatant (soluble fraction) was removed and added to 8M urea in 50 mM Tris pH 7.4, 200 mM NaCl at a 1:1 ratio and incubated at room temperature for 20 minutes prior to preparing to run the samples on a gel. Polyacrylamide gel electrophoresis (PAGE) was performed on the samples on a reducing 12% Bis-Tris gel in SDS-MES buffer, and the gel was stained with a coomassie blue stain. In the lanes with the total lysate prep, substantial bands of the expected size were seen for the PN2.5 (SEQ ID NO:43), PN2.7 (SEQ ID NO:47), and PN2.9 (SEQ ID NO:51) samples only: the CPBpro polypeptides in these samples all have a 6×His sequence immediately following the N-terminal methionine residue. However, no bands for PN2.5, PN2.7, and PN2.9 were observed in the soluble lysate prep, indicating that the substantial amounts of protein produced from the corresponding expression constructs was produced in an insoluble (and solubilizable) form. No expression was observed in any preparation for the PN2.6, PN2.8, and PN2.10 expression constructs, nor was there expression detected from the PN2.6 expression construct in follow-up experiments. While the cause of the absence of expression from the expression constructs encoding PN2.6, PN2.8, and PN2.10 has not been determined, these expression constructs share a common nucleotide sequence around the translation initiation site that differs from that in the expression constructs encoding PN2.5, PN2.7, and PN2.9, and it is possible that the message transcribed from the PN2.6, PN2.8, and PN2.10 expression constructs is not translated efficiently.
C. Solubilization and Characterization of CPBpro_lispro Proinsulin
Solubilization by 2M-6M Urea.
To determine conditions for solubilization of PN2.5 CPBpro_lispro proinsulin (SEQ ID NO:43), a 5-mL pellet of the host cells containing PN2.5 CPBpro_lispro proinsulin, produced in Example 1.B, was thawed on ice for 10 minutes. The host cells were lysed, at a 2-fold concentration over culture concentration at harvest, in GLB-OG lysis buffer pH 7.4 on ice for 10 minutes. The lysate was then divided into 12 samples and treated as follows; all of the following samples except the total lysate sample were centrifuged at 20 k×g at 4 degrees C. for 30 minutes:
The amount of PN2.5 CPBpro_lispro proinsulin present in each sample was determined by automated capillary electrophoresis “Western blot” using the WES instrument (ProteinSimple, San Jose, Calif.), following the manufacturer's protocol and as generally described in Example 6. In preparation for analysis under reducing conditions, the total lysate, no treatment, and solubilized samples shown above were diluted 1:300 into 0.1×WES buffer (ProteinSimple) with DTT added (48 mM), bringing the samples to a final concentration of 0.0033×. The PN2.5 CPBpro_lispro proinsulin was detected by capillary electrophoresis on the WES instrument, using a mouse anti-lispro primary antibody and a HRP-conjugated goat anti-mouse secondary antibody, with exposures at 5, 15, 30, 60, 120, 240, and 480 seconds (only the 5-second exposure is used for quantitation). The Triton-X-only solubilization treatments were generally not successful in this experiment, solubilizing only around 10% or less of the total PN2.5 CPBpro_lispro proinsulin present in the samples, as indicated by the amount of PN2.5 CPBpro_lispro proinsulin detected in the total lysate. Solubilization with urea at a concentration of at least 2M was more successful: the amount of solubilized PN2.5 CPBpro_lispro proinsulin increased with increasing urea concentration, with 6M urea solubilizing about 70% of the PN2.5 CPBpro_lispro proinsulin present in the sample.
Characterization of the Size of Solubilizable CPBpro_Lispro Proinsulin Complexes.
Host cells containing solubilizable PN2.5 CPBpro_lispro proinsulin complexes were lysed as follows. To create a control “guanidine lysis” sample representing the total amount of protein generated by host cell lysis, a 1-mL pellet of the host cells containing PN2.5 CPBpro_lispro proinsulin, produced in Example 1.B, was thawed on ice for 10 minutes and resuspended in 500 microliters 6M guanidine HCl buffer, pH 8 (6M guanidine HCl, 100 mM NaPO4,
10 mM Tris Base,
10 mM imidazole,
adjusted to pH 8 with 5M NaOH). The host cells were lysed by freezing at −80 degrees C. for one hour, and then thawing at room temperature for 30 minutes or until fully thawed. Host cells were also lysed in GLB-OG lysis buffer as described above and the lysate was centrifuged at 900×g at 4 degrees C. for 15 minutes to create a pellet fraction (‘P1’) and a supernatant (‘S1’) fraction. A portion of the S1 supernatant fraction was retained, and the remainder was centrifuged at 7000×g at 4 degrees C. for 30 minutes to create a pellet fraction (‘P2’) and a supernatant (‘S2’) fraction. A portion of the S2 supernatant fraction was retained, and the remainder was centrifuged at 20K×g at 4 degrees C. for 30 minutes to create a pellet fraction (‘P3’) and a supernatant (‘S3’) fraction. The P1 pellet was solubilized in 6M guanidine HCl buffer, pH 8. The guanidine lysis, solubilized P1, S1, S2, and S3 samples were analyzed by capillary electrophoresis on the WES instrument, under reducing conditions as described above. After the 900×g spin, the amount of PN2.5 CPBpro_lispro proinsulin detected in the S1 soluble fraction was about 42% of the “total lysis” amount detected in the guanidine lysis sample. The amount of PN2.5 CPBpro_lispro proinsulin detected from the solubilized P1 pellet was about 35% of the “total lysis” amount in the guanidine lysis sample, rather than the expected 58%, suggesting that loss of potentially recoverable PN2.5 CPBpro_lispro proinsulin occurred in some phase of the GLB-OG lysis, centrifugation, and solubilization procedure. Following the higher speed 7000×g and 20K×g spins, only a small amount (about 7%) of the PN2.5 CPBpro_lispro proinsulin was detected in the S2 and S3 soluble fractions, with the majority of the protein presumably ending up in the P2 and P3 pellets.
These results are consistent with a significant portion of the PN2.5 CPBpro_lispro proinsulin, perhaps about half of what was in the host cells, being present in complexes large enough to be spun down at 900×g, a relatively low centrifugation speed at which cell debris from lysed cells can be pelleted, but not soluble proteins (see Cube Biotech, “Screening detergents for optimal solubilization and purification of membrane proteins”, 2013, retrieved from www.cube-biotech.com/files/protocols/Screening_Detergents.pdf on 2017 Mar. 29). Of the PN2.5 CPBpro_lispro proinsulin present in host cells that remained soluble during the 900×g spin, the vast majority of it was pelleted at an intermediate centrifugation speed of 7000×g, consistent with the remaining CPBpro_lispro proinsulin also being present in the host cells in the form of large solubilizable complexes.
Solubilization in 8M Urea and in 3.5M Urea/5% Triton-X.
To further evaluate solubilization conditions for preparation of PN2.5 CPBpro_lispro proinsulin (SEQ ID NO:43), EB0001 host cells comprising PN2.5 pSOL:CPBpro-lispro/PDI expression constructs were grown and induced with 15 micromolar arabinose as described in Example 1B. Following induction, 1-mL samples of the host cell culture were harvested by centrifugation at 3800×g at 4 degrees C. for 10 minutes. For lysis, host cell pellets were resuspended in GLB-OG lysis buffer pH 7.4 and lysis proceeded on ice for 15 minutes. Host cell lysate was centrifuged at 20K×g at 4 degrees C. for 15 minutes, and the resulting pellets were resuspended in either 8M urea in 1×Tris-buffered saline (TBS) pH 8.0, or 3.5M urea/5% triton-X in 1×TBS pH 8.0. Samples of the solubilized protein were prepared for PAGE by removing triton-X from the 3.5M urea/5% triton-X samples using a Pierce™ SDS PAGE Prep Kit (Thermo Fisher Scientific, Waltham, Mass.), and by preparing both a non-reduced (in LDS sample buffer, Thermo Fisher Scientific) and a reduced sample (in LDS sample buffer plus 100 mM DTT) to be analyzed by PAGE for each solubilization condition. The amount of solubilized PN2.5 CPBpro_lispro proinsulin in each sample was assessed by PAGE on a 12% Bis-Tris gel in SDS-MES buffer, and the gels were stained with a coomassie blue stain. Bands migrating as expected for the molecular weight of PN2.5 CPBpro_lispro proinsulin (12.25 kD) were clearly seen, with the samples solubilized in 8M urea producing significantly denser bands than those solubilized in 3.5M urea/5% triton-X buffer. This result indicates that under these conditions 8M urea is more effective than 3.5M urea/5% triton-X in solubilizing the proinsulin complexes.
CPBpro_lispro Proinsulin from Solubilizable Complexes has Disulfide Bonds and is Significantly Purified.
In order to determine whether the PN2.5 CPBpro_lispro proinsulin from solubilizable complexes has disulfide bonds or free thiol residues, the samples solubilized in 8M urea and prepared as described above were analyzed by PAGE on a 12% Bis-Tris gel in SDS-MES buffer, with the non-reduced and reduced pairs of samples run in adjacent lanes. The gel was stained with coomassie blue and is shown in
Solubilizable CPBpro_lispro Proinsulin Complexes Form Throughout Induction.
To further characterize the formation of the solubilizable CPBpro_lispro proinsulin complexes, an induction time course was performed with EB0001 host cells comprising the PN2.5 pSOL:CPBpro-lispro/PDI expression construct, which were grown and induced generally as described in Example 1B. In this experiment, induction was performed on host cell cultures in three volumes of 200 mL each in 1-L baffled flasks, with 15 micromolar arabinose as inducer, and with 1-mL samples taken at the 0-, 2-, 4-, and 6-hour timepoints after the initiation of induction. Host cells were harvested, lysis performed, and solubilizable pellets were resuspended in 8M urea in 1×Tris-buffered saline (TBS) pH 8.0 as described above, and analyzed by PAGE. Solubilizable CPBpro_lispro proinsulin complexes were present in host cells at each of the 2-, 4-, and 6-hour time points, as indicated by a band in each lane at the expected position. This result indicates that the solubilizable complexes are being formed in the host cells throughout the induction period, with sufficient CPBpro_lispro proinsulin present within the host cells to form solubilizable complexes after only two hours of induction.
Use of CPBpro Variant Propeptides in the Production of Glargine Proinsulin
A. Host Cells for Expression of CPBpro_glargine Proinsulin
In these experiments, the CPBpro propeptide having the amino acid sequence of SEQ ID NO:27 (‘His-CPB1’) was used in the fermentation-scale expression of glargine proinsulin polypeptides. A polynucleotide encoding the His-CPB1 propeptide and optimized for expression in E. coli had previously been synthesized (see Example 1A). The sequence encoding His-CPB1 propeptide was cloned into an existing expression construct comprising a polynucleotide sequence encoding glargine proinsulin, similarly optimized for expression in E. coli, that had also been synthesized by ATUM (Newark, Calif.). The PN3.13 CPBpro_glargine proinsulin polypeptide (SEQ ID NO:55) has the His-CPB1 propeptide (SEQ ID NO:27) at its N-terminus, followed by the glargine insulin B chain (SEQ ID NO:7); a C-peptide corresponding to RRYPGDVKR (SEQ ID NO:11), except that the initial arginines (RR) of the C-peptide are indicated in this case as being at the end of the B-chain sequence of SEQ ID NO:7; and the glargine insulin A chain (SEQ ID NO:6). The structure of the PN3.13 CPBpro_glargine proinsulin polypeptide is shown schematically in
B. Host Cell Growth and Induction of Expression of CPBpro_glargine Proinsulin
The EB0001(pSOL:PN3.13-CPBpro-glargine/Erv1p) host cells were grown in a DASGIP fermentation system (Eppendorf North America, Hauppauge, N.Y.) in one 250-ml DASbox fermentation vessel, bioreactor 1 (‘BR1’) (see ‘Fermentation Equipment’, above). The bioreactor was calibrated as follows: pH offset 0.80 pH; pH slope 104.15%; DO offset 0.01 nA; DO slope 66.72 nA.
Fermentation Media.
The 100-mL total volume of fermentation media, and the growth and induction feeds, were prepared as follows.
Fermentation medium; pre-sterilization components, concentration in g/L per 90 mL volume added to each bioreactor:
Modified Korz trace metals (100× stock); combine components below, where final concentration is shown in g/L, and filter sterilize:
Fermentation medium; post-sterilization components (sterile stock concentration), amount in mL added to reach total volume of ca. 100 mL in the bioreactor:
Growth feed; components (sterile stock concentration), amount in mL that can be prepared for one bioreactor:
Induction feed; components (sterile stock concentration), amount in mL that can be prepared for one bioreactor:
10× Tremendous Broth (‘10×TB’):
Add the following to 90 mL distilled H2O: 12 g soytone, 24 g yeast extract. Adjust to 100 mL with distilled H2O. Sterilize by autoclaving. Allow to cool to room temperature.
Fermentation Procedure.
A feeder culture of EB0001(pSOL:PN3.13-CPBpro-glargine/Erv1p) host cells was grown generally according to the methods described in Example 1B, but with overnight growth until the OD600 reached ca. 3, and with a larger second day inoculum into LB medium with 1% glucose in order to reach a final cell density of OD600 2.40 after 5.5 hours of growth. This feeder culture was used to inoculate the fermentation medium in the bioreactor: a 4.2-mL aliquot was added to the ca. 100 mL of medium so that the initial optical density reading (OD600) would be ca. 0.1.
The cells were grown under the growth stage conditions (30.0 degrees C., DO 30%, pH 7.0, growth feed containing 70% glucose at an initial feed rate of 0.6 mL/hr, for a set growth rate of 0.15/hr with a maximum feed rate of 3.2 mLs per hour) for 29 hours Immediately prior to the start of induction, 5 mL of 10× Tremendous Broth was added to the bioreactor. Induction was initiated; the fermentation conditions were set to the induction stage conditions: 30.0 degrees C., DO 30%, pH 7.0, and induction feed containing 70% glycerol at an induction feed coefficient of 2.1 mL per hour. The induction feed also contained the inducer L-arabinose, at a concentration calculated as follows from the total volume of components added to create the induction feed:
[L-arabinose] in induction feed: (0.97 mL×500 g/L)/89.25 mL=5.4 g/L
The host cells in the bioreactor were sampled at several time points during fermentation and induction; the optical densities of the growth culture at these time points, expressed in terms of elapsed fermentation time (EFT (hrs)) and elapsed induction time (EIT (hrs)) are shown below.
The host cells in the 2-mL samples taken for optical density measurements at 9 hours or more after induction, and 125 microliters of 1:20-diluted host cells in PBS buffer, were harvested by centrifugation at 4300 RPM at 4 degrees C. for seven minutes and stored as dry frozen pellets at −80 degrees C.
C. Solubilization and Characterization of CPBpro_glargine Proinsulin
To investigate whether the disulfide bonds present in solubilizable CPBpro_glargine proinsulin complexes are formed between the correct residues, solubilized CPBpro_glargine proinsulin complexes were analyzed by liquid chromatography-mass spectrometry (LC-MS). Pellets of host cells which were grown, induced, and harvested from 1 mL of culture as described in Example 2B, were resuspended in 15 mL GLB-OG lysis buffer pH 7.4 and lysis proceeded on ice for 15 minutes. Host cell lysate was centrifuged at 20K×g at 4 degrees C. for 30 minutes, and the resulting pellets were resuspended in 5 mL 8M urea in 1× phosphate-buffered saline (PBS) pH 7.5.
The following procedures were performed in the enzymatic digestion and non-reduced disulfide mapping of CPBpro_glargine proinsulin, and are schematically shown in
The Nano-LC MS/MS analysis was conducted on a recently calibrated Orbitrap Fusion™ Tribrid™ mass spectrometer and Dionex UltiMate™ 3000 RSLCnano System (Thermo Fisher Scientific) with a 60-minute method. An Acclaim™ Pepmap™ 100 C18 75 micrometer×25 cm×2 micrometer analytical column was used with an Acclaim™ Pepmap™ 100 C18 100 micrometer×2 cm×5 micrometer trapping column (Thermo Fisher Scientific). Buffer A consisted of 0.1% formic acid in LC-MS grade water, and buffer B consisted of 0.1% formic acid in LC-MS grade acetonitrile. A 200-ng amount of sample was injected onto the trap. A gradient was run as follows: 0-5 minutes 2% buffer B; 5-5.1 minutes 2-7.5% buffer B; 5.1-35 minutes 7.5-30% buffer B; 36-41 minutes 30-98% buffer B; and 42-60 minutes 2% buffer B. Samples were analyzed at 2400 V in the positive ion mode with an ion transfer tube temperature of 275 degrees C. using the EASY-Spray™ source (Thermo Fisher Scientific). MS1 scans were obtained from 400-1600 m/z at 120K resolution with an AGC (automatic gain control) of 400,000 and a maximum injection time of 50 ins. Targeted MS/MS was conducted at 742.8330 m/z (z=4) representing the following sequences: QCCTSICSLYQLE (SEQ ID NO:58) and FVNQHLGSHLVE (SEQ ID NO:59) with one interchain and one intrachain disulfide bond. Masses were calculated to four decimal points for calculations (eg. H+=1.0073). Targeted MS/MS settings included a 3 m/z quadrupole isolation, HCD activation at 30%, and detection in the Orbitrap mass analyzer at 15K resolution from 100-2000 m/z with a maximum injection time of 250 ms and an AGC target of 50,000. Additional data-dependent or targeted MS/MS events can optionally be scheduled as desired, provided that a MS1 survey scan occurs at least every 2 seconds. The results of this liquid chromatography-mass spectrometry (LC-MS) analysis are shown in
D. Further Purification and Solubility of CPBpro_glargine Proinsulin
Additional variant CPBpro_glargine proinsulins were prepared (PN3.15, PN3.16, and PN3.17), each having a propeptide portion corresponding to SEQ ID NOs 33, 34, and 35 respectively, with one or more acid-cleavable DP (Asp-Pro) sequences inserted before the arginine present at the C-terminal end of the propeptide. Modifications were made to the expression construct (SEQ ID NO:56) encoding PN3.13 CPBpro_glargine proinsulin (SEQ ID NO:55) to produce expression constructs (SEQ ID NOs 63, 65, and 67, respectively, shown from the ribosome binding site (RBS) to the termination codon, plus 18 bp of downstream nucleotide sequence) encoding PN3.15 CPBpro_glargine proinsulin (SEQ ID NO:62), PN3.16 CPBpro_glargine proinsulin (SEQ ID NO:64), and PN3.17 CPBpro_glargine proinsulin (SEQ ID NO:66), with each expression construct having the polynucleotide encoding CPBpro_glargine proinsulin located downstream of the araBAD promoter in the pSOL expression vector, and a polynucleotide (SEQ ID NO:57) encoding Erv1p (SEQ ID NO:38) downstream of the prpBCDE promoter, as described in Example 2A. These pSOL:PN3.15-CPBpro-glargine/Erv1p, pSOL:PN3.16-CPBpro-glargine/Erv1p, and pSOL:PN3.17-CPBpro-glargine/Erv1p expression constructs were transformed into E. coli EB0001 cells. The PN3.15, PN3.16, and PN3.17 CPBpro_glargine proinsulins were produced by fermentation essentially as described in Example 2B, with lysis of host cells followed by centrifugation at 20K×g at 4 degrees C. for 30 minutes. The resulting pellets, comprising solubilizable complexes of CPBpro_glargine proinsulin, were solubilized in 8M urea in 1× phosphate-buffered saline (PBS) pH 7.5.
A portion of the PN3.15 CPBpro_glargine proinsulin (SEQ ID NO:62) prepared from solubilizable complexes was loaded on a 5-mL Ni-NTA column, washed with 8M urea and 10 mM imidazole in 1×PBS pH 7.5, then eluted in 500 mM imidazole in 1×PBS pH 7.5. The PN3.15 CPBpro_glargine proinsulin was stable and soluble in the nondenaturing conditions of the Ni-NTA column purification and elution into 500 mM imidazole in 1×PBS at neutral pH 7.5. Following elution from the Ni-NTA column, PN3.15, PN3.16, and PN3.17 CPBpro_glargine proinsulin samples in 500 mM imidazole in 1×PBS pH 7.5 were each adjusted to pH 6 with formic acid to precipitate the purified CPBpro_glargine proinsulin 16K×g at 4 degrees C. for 10 minutes, and the pellets were resuspended in 0.1M acetic acid at pH 2 and incubated at 65 degrees C. for 12 hours to cleave each propeptide at the DP (Asp-Pro) sequence present in each of the PN3.15, PN3.16, and PN3.17 propeptides. Following incubation the samples were neutralized with 2M NH4HCO3 (ammonium bicarbonate) to a final pH between 7.0 and 8.0. Cleavage of the propeptides was observed by polyacrylamide gel electrophoresis.
Separation of the cleaved N-terminal portion of the PN3.17 propeptide from the remainder of the PN3.17 CPBpro_glargine proinsulin (SEQ ID NO:66) was achieved by cation-exchange chromatography (‘CEX’) using a Capto S medium (GE Healthcare, Pittsburgh, Pa.). A cleavage reaction, in which PN3.17 CPBpro_glargine proinsulin was treated with 0.1M acetic acid at pH 2 and incubated at 60 degrees C. for 24 hours with shaking at 275 RPM, was adjusted to pH 4 with 1M hydrochloric acid and loaded onto the cation-exchange column, then equilibrated with 8M urea in 20 mM NaOAc pH 6.5, and eluted with increasing salt concentrations, from 0M to 0.35M NaCl, in 8M urea 20 mM NaOAc pH 6.5. LC-MS analysis of the CEX-purified glargine proinsulin fragment determined that the mass of the fragment was as expected for a glargine proinsulin with all its double bonds intact. Trypsin digestion of the CEX-purified glargine proinsulin produced a mature glargine insulin molecule with intact disulfide bonds, as indicated by LC-MS analysis.
To further investigate the precipitation of PN3.15 CPBpro_glargine proinsulin (SEQ ID NO:62) by acidic conditions, samples of PN3.15 CPBpro_glargine proinsulin prepared by solubilization of solubilizable complexes and elution from a Ni-NTA column with 500 mM imidazole in 1×PBS pH 7.8, as described above, were adjusted to the following pH values using 10% formic acid: pH 7.5, 7.2, 7.0, 6.7, 6.5, 6.0, 5.5, and 5.0. The samples were then centrifuged at 14K×g at 4 degrees C. for 15 minutes, and the supernatants were removed and dried by centrifugal evaporation. The pellets and dried supernatants were then resuspended in 8M urea in 1×PBS pH 7.5, and analyzed by polyacrylamide gel electrophoresis under denaturing conditions. At pH values between 7.8 and 7.2, the majority of the PN3.15 CPBpro_glargine proinsulin remained soluble. At pH 7.0, approximately equal amounts of PN3.15 CPBpro_glargine proinsulin was observed in the supernatant and the pellet. As the pH was decreased, increasing portions of the PN3.15 CPBpro_glargine proinsulin were present in the pellet, until almost all was precipitated at pH 5.0. The ability to precipitate proteins by altering the pH of the protein solution is useful, for example, for resuspension of the protein in a smaller, more concentrated volume, and/or in a different buffer. This effect of pH on solubility was also observed for PN3.17 CPBpro_glargine proinsulin, and is considered likely to be a characteristic of other polypeptide gene products that form solubilizable complexes.
To obtain purified PN3.17 CPBpro_glargine proinsulin (SEQ ID NO:66) for further analysis, the PN3.17 CPBpro_glargine proinsulin was produced by fermentation essentially as described in Example 2B, with lysis of host cells followed by centrifugation at 20K×g at 4 degrees C. for 30 minutes. The pelleted material was solubilized in 8M urea in 1× phosphate-buffered saline (PBS) pH 7.5, at 10 mL of resuspension buffer per 1 g wet cell weight of harvested host cells, with vortexing and incubation at room temperature for 20 to 30 minutes, followed by a clarification spin at 4000×g at 4 degrees C. for 5 minutes. The solubilized PN3.17 CPBpro_glargine proinsulin was run over a 5-mL Ni-NTA column. Five column volumes (CV) of 8M urea in PBS pH 7.5 were used to equilibrate the column, the sample was loaded, followed by wash 1 (5CV 8M urea and 20 mM imidazole in PBS pH 7.5), wash 2 (1.25CV 20 mM imidazole in PBS pH 7.5), elution (5CV 500 mM imidazole in PBS pH 7.5), and cleaning (1.25CV 0.2N NaOH, 6CV 20% EtOH). To investigate the solubility of PN3.17 CPBpro_glargine proinsulin in various buffers, samples of the Ni-NTA-purified PN3.17 CPBpro_glargine proinsulin corresponding to 0.5 g wet cell weight of harvested host cells were run through 5-mL Zeba™ spin desalting columns with a 7K molecular weight cut-off (MWCO) (Thermo Fisher Scientific Inc., Waltham, Mass.). The buffers that the samples were spun into were: 500 mM imidazole in PBS pH 7.5, 200 mM imidazole in PBS pH 7.5, PBS pH 7.5, 50 mM EDTA in PBS pH 7.5, and 25 mM L-arginine in 10 mM K phosphate pH 7.5. A Bradford protein assay was used to measure the protein concentration of the PN3.17 CPBpro_glargine proinsulin solution as eluted in 500 mM imidazole in PBS pH 7.5, and the protein concentration of the PN3.17 CPBpro_glargine proinsulin solutions after spin desalting into the various buffers. The yield of PN3.17 CPBpro_glargine proinsulin in the experiment where the starting buffer, 500 mM imidazole in PBS pH 7.5, was replaced with the same buffer represents the efficiency of the spin desalting procedure, and was approximately 80%. The yield of the other samples, each transferred by spin desalting into a different buffer, ranged from 77% to 91% and were not significantly different from the yields expected from the spin desalting procedure itself, suggesting that there was no additional loss of PN3.17 CPBpro_glargine proinsulin from precipitation when transferred into a different buffer. The desalted PN3.17 CPBpro_glargine proinsulin samples were also analyzed by polyacrylamide gel electrophoresis under reducing and nonreducing conditions, and the shift in the electrophoretic mobility of the PN3.17 CPBpro_glargine proinsulin bands when exposed to reducing conditions indicates that the PN3.17 CPBpro_glargine proinsulin, as eluted from the Ni-NTA column and desalted, contained disulfide bonds.
Use of Variant Propeptides and C-Peptides in the Production of Glargine Proinsulin
A. Preparation of Glargine Proinsulin
Additional glargine proinsulins were prepared (PN3.62, PN3.116, PN3.165, PN3.172, and PN3.185), each having a variant propeptide portion corresponding to either SEQ ID NO:36 or SEQ ID NO:37, and a variant C-peptide corresponding to one of SEQ ID NOs 12, 13, and 14 (see Table 4).
Polynucleotides encoding each of the glargine proinsulin polypeptides were inserted downstream of the araBAD promoter in the pSOL expression vector (SEQ ID NO:42). These expression constructs each also contained the coding sequence for protein disulfide isomerase (PDI, SEQ ID NO:41) downstream of the prpBCDE promoter within the pSOL expression vector.
Each of the expression vectors encoding the glargine proinsulin polypeptides were used to transform E. coli EB0001 host cells, to form the following:
Each of the five types of host cells above was grown in fermentation culture and induced for protein expression, then harvested, generally as described in Example 2B. Two factors that varied between samples during the fermentation process was whether the fermentation was carried out in a DASbox or an NLF apparatus, and whether or not MnCl2 was added to the fermentation as a component of the Korz trace metals (see Example 2B). These factors are indicated for each of the glargine proinsulin samples that were purified and analyzed, as described in Example 3B.
B. Purification of Glargine Proinsulin by Direct Solubilization
In order to prepare highly purified samples of properly folded glargine proinsulin with correctly placed disulfide bonds, for the purpose of transversion to mature glargine insulin as described in Example 3C, the host cells harvested above were subjected to a direct solubilization treatment following lysis that does not use an initial centrifugation step to separate the soluble and insoluble fraction in order to collect the glargine proinsulin in the form of solubilizable complexes.
The samples of harvested host cells that were purified are referred to as shown in the following list, noting the fermentation apparatus and whether MnCl2 was added (+) or was absent (−) during fermentation.
For lysis, the ‘main sample group’ included PN3.62 A, B, and C; PN3.116; PN3.165 A; PN3.172; and PN3.185 A. For the main sample group, the harvested host cells were suspended in 7M urea, 50 mM Tris pH 8 at a 10-fold dilution relative to fermentation culture volume. The additional samples (PN3.165 B and C, and PN3.185 B and C) were suspended in 7M urea, 2.5 mM L-Cys, 50 mM Tris pH 9.5 at a 2-fold dilution relative to fermentation culture volume. All samples were homogenized at 8,000 psi for a total of five passes, lysing the cells. The lysates were diluted 3.5-fold in 50 mM Tris pH 8 (main sample group), or 2.5 mM L-Cys, 50 mM Tris pH 9.5 (PN3.165 B and C, and PN3.185 B and C), so that all samples were in 2M urea solutions. All samples except PN3.165 C and PN3.185 C were incubated at 16 degrees C. with shaking at 120 RPM for 48-72 hours, or for PN3.165 C and PN3.185 C, for 24 hours.
Following the incubation, for purification using immobilized metal affinity chromatography (IMAC), the lysate samples were all clarified via centrifugation at 3300×g, and the soluble lysates were filtered through 0.45 micrometer polyethersulfone (PES) membranes and collected, with imidazole added to the lysates for a final concentration of 10 mM. The centrifugation step in the clarification can also be performed at 7000 to 20,000×g for 30-60 minutes, and the soluble lysates can also be filtered by glass fiber filtration (0.7 micrometer particle retention in liquid). Additives to the clarified lysate, to prevent nonspecific binding during IMAC, can include 10-20 mM imidazole and/or 0-300 mM NaCl.
The IMAC columns were equilibrated with 2-4 column volumes (CVs) of 7 M urea, 0.3 M NaCl, 10 mM imidazole, 25 mM Tris pH 8, then washed with 2-4 CVs of 0.1 M NaCl, 40 mM Tris pH 10. For one sample group (PN3.62 A and B, PN3.165 A, PN3.172, and PN3.185 A), each sample was loaded onto a Ni Sepharose Fast Flow column (GE Healthcare Life Sciences, Pittsburgh, Pa.). For a second sample group (PN3.62 C, PN3.116, PN3.165 B and C, and PN3.185 B and C), each sample was loaded onto a Ni HisTrap High Performance column (GE Healthcare Life Sciences, Pittsburgh, Pa.). The samples were loaded at the equivalent of 0.5-1 mL fermentation culture volume per mL resin. All samples were eluted using 2-4 CVs 0.5 M imidazole, 40 mM Tris, 0.1 M NaCl pH 10. The columns were cleaned in place with 2 CVs 0.5 M NaOH, and stripped with 7 M urea, 0.3 M NaCl, 0.5 M imidazole, and 25 mM Tris pH 8.
Following the IMAC, the samples were concentrated and desalted. For one sample group (PN3.62 A, PN3.165 A, PN3.172, and PN3.185 A), each sample was concentrated using a 3-kDa molecular weight cut-off (MWCO) Amicon® centrifugal concentrator (Sigma-Aldrich, St. Louis, Mo.), adding distilled water to return each sample to its starting volume for 2-3 exchanges using the same centrifugal concentrator. For the other sample group (PN3.62 B and C, PN3.116, PN3.165 B and C, and PN3.185 B and C), each sample was concentrated by tangential flow filtration and discontinuous diafiltration on a 3-kDa MWCO Vivaflow 50 tangential concentrator (Sartorius, Goettingen, Germany), with the volume in the feed reservoir concentrated to about one tenth the starting volume, then adding distilled water to return each sample to its starting volume, and repeating that process 2-3 times.
C. Transversion of Glargine Proinsulin to Mature Glargine Insulin
Experiments were performed to identify optimal conditions for transversion, by digestion with trypsin, of various forms of glargine proinsulin to mature glargine insulin (‘B32 glargine’). Following treatment protocols, the results were analyzed by solid-phase extraction mass spectrometry (SPE-MS).
The SPE-MS parameters were as follows:
The condition for each glargine proinsulin that produced optimal B32 glargine, according to the SPE-MS results, was selected and the corresponding sample was run by quadrupole time-of-flight (QTOF) liquid chromatography mass spectrometry (LCMS). An authentic standard of USP glargine was used for an external standard curve to quantitate the percentage of material that had undergone transversion. The percentage of transversion (% Transversion) equals the concentration of B32 glargine, as determined via A280 LC integration versus the USP glargine standard, divided by the starting concentration of glargine proinsulin, as determined via A280 LC integration versus an amino acid analyzed standard, multiplied by 100%. Integrations at A214 and via extracted ion chromatograms, versus the same glargine external standard curve, were in agreement with the integrations at A280.
The QTOF-LCMS parameters were as follows:
with the following gradient table:
In Experiment 1, 5 microliters of each glargine proinsulin sample were mixed with 5 microliters of NiCl2 solution of varying concentration, and 5 microliters of a trypsin solution (4.5 g/L trypsin in 120 mM Tris 300 mM NaCl pH 9, 15 mM CaCl2). The combined volumes were spun at 500×g for 1 minute, then incubated at room temperature with shaking at 100 RPM for variable amounts of time, then the reaction was stopped by addition of 8M urea with 1% formic acid (pH 3-3.5).
In Experiment 2, varying concentrations of NiCl2, FeCl2, NaCl, and CaCl2 were added to the trypsin reaction mixture, and the reaction was carried out for varying amounts of time, but otherwise generally as described above.
In Experiment 3, varying concentrations of NaCl or of Tris buffer were added to the trypsin reaction mixture, which had constant amounts of 1.5 g/L trypsin, 50 mM CaCl2, and 7 micromolar NiCl2, and the reaction was carried out for varying amounts of time, but otherwise generally as described for Experiment 1.
In Experiment 4, varying concentrations of NiCl2 and reaction times were tested, in a trypsin reaction mixture than contained 1.5 g/L trypsin, 5 mM CaCl2, 120 mM Tris, 300 mM NaCl.
In Experiment 5, two trypsin reaction conditions were tested, containing 1.5 g/L trypsin, for varying lengths of reaction time. Each condition produced a comparable maximum result, as indicated in the table below.
In Experiment 6, varying concentrations of NaCl and pH were tested for varying amounts of time, in a trypsin reaction mixture that contained 1.5 g/L trypsin and 7 micromolar NiCl2.
For each experiment, the best reaction conditions for each of the glargine proinsulins of interest that were tested are indicated below, along with the percent transversion.
These results demonstrate that high transversion frequencies can be obtained for the variant glargine proinsulin polypeptides of the invention, using the methods disclosed herein.
Determination of Solubility of Expression Products; Methods of Detecting Inclusion Bodies
When methods of the invention are used to express gene products in the cytoplasm of host cells, the following procedures can be used to determine the degree to which the gene products are produced in the cell in soluble form.
The most straightforward approach is to lyse cells using any effective method, such as enzymatic lysis with lysozyme, as described in more detail in Example 1, or by cell disruption with a microfluidizer. A sample of the cell lysate can be retained as a measure of the total gene product, soluble and insoluble, produced by the host cells. The lysed cells are then centrifuged at 20,000×g for 15 minutes at room temperature to separate out the insoluble fraction as a pellet; the soluble fraction (the supernatant) is collected. The amount of total gene product present in the cell lysate, minus the amount of soluble gene product recovered in the supernatant, represents the total amount of insoluble gene product present in the pellet. The methods for solubilization described herein can be used to determine what portion of the insoluble fraction in the pellet is solubilizable. Any method, such as ELISA or capillary electrophoresis Western blots, that can be used to detect the gene product, and preferably to specifically and quantifiably detect the gene product in each fraction, is employed and the amounts present in the soluble and insoluble fractions are compared. To test the effectiveness of this approach, endogenous host cell proteins, known to be soluble and present only in the host cell cytoplasm, are detected in both the soluble and insoluble fractions to determine whether the lysis and fractionation methods are trapping detectable amounts of soluble cytoplasmic products in the insoluble fraction.
It is also possible to directly assess whether cells contain inclusion bodies. Inclusion bodies can be harvested by centrifugation of lysed host cells, stained with dyes such as Congo Red, and visualized using bright-field or cross-polarized light microscopy at modest (10×) magnification (Wang et al., “Bacterial inclusion bodies contain amyloid-like structure”, PLoS Biol 2008 Aug. 5; 6(8): e195; doi: 10.1371/journal.pbio.0060195). Such inclusion bodies can also be resolubilized (Singh and Panda, “Solubilization and refolding of bacterial inclusion body proteins”, J Biosci Bioeng 2005 April; 99(4): 303-310; Review) and tested, using specific binding assays or other methods of protein identification, for example, to determine if they include particular gene products. Inclusion bodies can be distinguished from the solubilizable complexes described herein, in that the majority of the gene product recovered from inclusion bodies by solubilization will not be in an active or properly folded form, and will require at least one additional refolding step to obtain a majority of gene product that is active and/or properly folded.
Determining Additional Methods for Solubilization of Solubilizable Gene Product Complexes
The buffers used for solubilization of gene product complexes produced by the methods of the invention can include several different types of components, as described below. To optimize solubilization of any gene product of interest, experiments can be undertaken to identify the most effective combinations of solubilization buffer components. Initial experiments are performed to identify which combinations of buffer components can be readily prepared in the laboratory, using commercially available compounds. Once a test buffer has been prepared, it can be used in solubilization experiments with the gene product complexes of interest, and optionally with control gene product complexes that are known to be solubilizable to different extents in reference solubilization buffers. Examples of solubilization protocols for use with gene product complexes are provided herein, such as those described in Examples 1 and 2.
Components of Solubilization Buffers:
The following description of buffer components, summarized in Table 5, is intended to provide examples of the different types of components that can be used in combination in solubilization buffers, without limitation on either possible buffer components or the combinations thereof. For example, chaotropic agents include n-butanol, ethanol, guanidinium chloride, guanidine hydrochloride, lithium perchlorate, lithium acetate, magnesium chloride, phenol, 2-propanol, sodium dodecyl sulfate, thiourea, and/or urea. One or more compound of each type of buffer component can be used in combination with one or more compound of any or all other component types, in the preparation of solubilization buffers to be tested for effectiveness in solubilizing gene product complexes. The concentrations of buffer components shown in Table 5 include ranges of concentrations and also particular examples of concentrations that can be tested for effectiveness.
For preparation of a gene product of interest in a way that retains a properly folded gene product conformation, retains properly formed disulfide bonds, and/or retains protein activity, reducing agents would not be included in the solubilization buffer. However, certain analytic assays, such as capillary electrophoresis Western blots (see Example 6), are preferably performed with the solubilized gene product samples in a reduced state. For the purpose of preparing samples for such assays, reducing agents (for example, DTE (dithioerythritol), DTT (dithiothreitol), and/or TCEP (tris(2-carboxyethyl)phosphine)) can be included in the buffer at a concentration of 10 mM, for example, or up to 100 mM.
Characterization by Capillary Electrophoresis Western Blot
Gene products can be detected and quantified as described below, using as an example soluble or solubilized protein gene products, by a capillary electrophoresis Western blot run on a WES system (ProteinSimple, San Jose, Calif.) according to the manufacturer's instructions. Soluble protein extracts are loaded into the capillary set, and the proteins are electrophoretically separated by size. The protein of interest in the samples is detected with a primary antibody that is specific for that protein, and incubation with an HRP-conjugated secondary antibody, such as a goat anti-human or anti-mouse secondary antibody, that recognizes the heavy and/or light chains of the primary antibody. Detection of the presence of the HRP-conjugated secondary antibody is accomplished by addition of the chemiluminescent substrate to the capillary and the direct capture of the light emitted during the enzyme-catalyzed reaction. Molecular weight estimates are calculated using a standard curve generated using six biotinylated proteins ranging from 12 k to 230 kDa for each run. Fluorescent standards are included in the sample loading buffer, giving each sample an internal standard that is used to align the sample with the molecular weight standard.
To determine the amount of protein present at a given molecular weight, known amounts of a standard preparation of the protein of interest are run in some of the capillaries, and detected using the same primary and secondary antibodies as for the experimental samples. Serial dilutions are prepared of the standard for the protein of interest having a known concentration, such as a commercially available protein standard, starting for example at 10 micrograms/mL and diluted down to 1.0 nanograms/mL Approximately five WES system capillaries are used to run the serial dilution. For each protein band in both the experimental and the serial dilution capillaries, a curve is generated by the WES system software representing the protein band's chemiluminescence intensity, and the area under each curve is evaluated, with a standard curve of these areas plotted for the protein bands in the serial dilution capillaries. To determine the concentration of the experimental samples, the area under each curve representing the chemiluminescence intensity of an experimental sample can be compared to the standard curve generated for the samples of known concentration.
Determining the Yield and Recovery of Gene Products Produced Using the Solubilization and Purification Methods of the Invention
The following method can be used to calculate the amount of gene product recovered at different stages of the solubilization and purification process, as compared to the total amount present in the cell lysate.
A standard sample for the gene product is required. This could be a commercially available sample of the gene product that has a known concentration, or an amino acid analyzed (AAA) completely purified sample of the gene product.
The cell lysate from a host cell culture, such as a fermentation culture, is prepared at a known level of dilution from the host cell culture. An SDS-PAGE gel, such as a 4-12% gel, is prepared and a serial-dilution set of samples of both the cell lysate and of the standard sample of the gene product are run on the SDS-PAGE gel under reducing conditions, followed by staining with SimplyBlue SafeStain (Thermo Fisher Scientific Inc., Waltham, Mass.). The use of reducing conditions is needed to allow the total amount of gene product in the cell lysate to be measured. A densitometry measurement of the gene product band on the SDS-PAGE gel is performed for each of the samples, and curves based on the densitometry data are plotted a follows.
For the standard samples of the gene product, the band density of the gene product band of each standard sample run on the gel is plotted on the y-axis, and the sample volume (in microliters) is plotted on the x-axis. For the sample volume, the volume of the standard sample solution present in the least-diluted sample (for example, 6 microliters) is plotted. For each serially diluted standard sample, its volume is plotted as the volume of the standard in the least-diluted sample (e.g. 6 microliters) divided by each dilution factor (e.g. 2). For these values, the sample volumes (in microliters) would be 6, 3, 1.5, 0.75, etc. A best-fit linear standard curve is created based on the plotted data, which can be expressed using the formula y=m(standard)x+k, where in is the slope of the standard curve and k is the y-intercept.
For determining the yield (or titer, in g/L) of the gene product present in the cell lysate, the band density of the gene product band for each cell lysate sample is plotted on the y-axis against the sample volumes on the x-axis, in the same manner as for the standard samples, described above. A best-fit linear curve for the cell lysate samples is also created, in the form y=m(experimental)x+k. To calculate the yield of the gene product in the cell lysate, the slope for the cell lysate samples is divided by the slope for the standard samples, and then multiplied by the concentration of the standard sample solution and multiplied by the degree to which the cell lysate samples were diluted relative to the host cell culture (for example, 100 for a 100-fold dilution).
To illustrate the use of this method, the following example is the determination of the total gene product yield of PN3.172 proglargine from a fermentation process. A highly purified and amino acid analyzed (AAA) standard sample of PN3.172 had been prepared, which had a concentration of 0.266 micrograms/microliter, which is equivalent to 0.266 g/L. The PN3.172 proglargine polypeptide was expressed in host cell fermentation culture and lysed generally according to the methods described in Examples 2B and 3A above. The cell lysate that was analyzed was diluted 80-fold relative to the host cell fermentation culture, so the dilution factor is 80. Samples of both the AAA PN3.172 standard and the PN3.172 cell lysate were prepared as sets of samples serially diluted by a factor of 1.25, having volumes of 6.0, 4.8, 3.8, 3.1, and 2.5 microliters, and these samples were run on a 4-12% SDS-PAGE gel under reducing conditions, followed by staining with SimplyBlue SafeStain (Thermo Fisher Scientific Inc., Waltham, Mass.). The band densitometry was performed for each of the AAA PN3.172 standard and the PN3.172 cell lysate samples, and the best-fit linear curves were plotted. For the AAA PN3.172 standard, the curve was y=93,899x−129,917, with the slope or m(standard) equal to 93,899. For the PN3.172 cell lysate, the curve was y=72,614x−228,763, with the slope or m(experimental) equal to 72,614. The calculation of the yield of PN3.172 in the cell lysate was: (m(experimental)/m(standard))×dilution factor×concentration of standard=(72,614/93,899)×80×0.266 g/L=16.5 g/L. In additional experiments, yields of proinsulin gene product in the cell lysate have ranged from 5 to 20 g/L.
When the optical density (for example, the OD600) of the host cell growth culture is measured at the time of lysis, it is also possible to calculate the yield of a gene product as g/L/OD, by dividing the yield in g/L as calculated above by the optical density.
This method for calculating yield can also be used at later steps in the solubilization and purification process. For example, an SDS-PAGE gel can be run with standard samples and with experimental samples solubilized by one of the methods described herein, and the post-solubilization yield of the experimental samples can be determined. Also, this yield calculation method can be used to determine the yield of gene product following purification by column chromatography, such as Ni-IMAC purification, preferably using an RP-UPLC analysis of standard sample peaks and experimental sample peaks. When RP-UPLC analysis is used, the calculated area under the chromatogram peak(s) at the expected retention time(s) for the desired gene product is used in much the same way as band density in the yield calculation method described above. A serial dilution of the standard sample is made and those samples of known gene product quantity are run through the chromatography column one at a time, the areas under the gene product peaks are calculated, and a standard curve is plotted. For the experimental sample, the calculated area under the chromatogram peak(s) at the expected retention time(s) from any single run through the RP-UPLC column can be compared to the standard curve calculated from the serial dilution of the standard sample, to obtain the amount of gene product in the experimental sample.
The percentage of the gene product that is recovered between successive process steps can be determined by dividing the yield at the later process step by the yield at the earlier process step, and multiplying by 100%. Purification processes were performed on PN3.172 proglargine, in which the yield at the cell lysate stage was determined using the above method, and the PN3.172 proglargine was solubilized either by centrifuging solubilizable complexes to form a pellet, and then solubilizing PN3.172 proglargine from the pellet (as in Examples 1 and 2), or by the direct solubilization method (as in Example 3). The yields of soluble PN3.172 proglargine were determined using the above method, and the percent recovery of soluble PN3.172 proglargine was calculated for each solubilization method. The ‘pelleting and solubilization’ method of Examples 1 and 2 produced PN3.172 proglargine with 84.7% recovery, with the recovered material being 75.3% pure PN3.172 proglargine protein as determined by RP-UPLC analysis, using a BEH 300A 1.7 μm 2.1×150 mm C4 protein column (product number 186006549, Waters, Milford, Mass.). The ‘direct solubilization’ method of Example 3 produced PN3.172 proglargine with a comparable 81.4% recovery, however the recovered material was 30.4% pure PN3.172 proglargine protein as determined by RP-UPLC analysis. Subsequent purification of the PN3.172 proglargine prepared by each solubilization method, using a Ni-IMAC column and a buffer-exchange step, resulted in a 70.8% total recovery for the ‘pelleting and solubilization’ PN3.172 proglargine, with 98.2% purity, and a 71.0% total recovery for the ‘direct solubilization’ PN3.172 proglargine, with 94.7% purity. This experiment demonstrated that the ‘pelleting and solubilization’ method of Examples 1 and 2 recovers as much gene product as the direct solubilization method of Example 3, and results in a higher purity of material both before and after the subsequent chromatography step.
Characterizing the Disulfide Bonds Present in Expression Products
The number and location of disulfide bonds in protein expression products can be determined by digestion of the protein with a protease, such as trypsin, under nonreducing conditions, and subjecting the resulting peptide fragments to mass spectrometry (MS) combining sequential electron transfer dissociation (ETD) and collision-induced dissociation (CID) MS steps (MS2, MS3) (Nili et al., “Defining the disulfide bonds of insulin-like growth factor-binding protein-5 by tandem mass spectrometry with electron transfer dissociation and collision-induced dissociation”, J Biol Chem 2012 Jan. 6; 287(2): 1510-1519; Epub 2011 Nov. 22).
Digestion of Expressed Protein.
To prevent disulfide bond rearrangements, any free cysteine residues are first blocked by alkylation: the expressed protein is incubated protected from light with the alkylating agent iodoacetamide (5 mM) with shaking for 30 minutes at 20° C. in buffer with 4 M urea. Alternatively and preferably, NEM is used as the alkylating reagent, with trypsin proteolysis in combination with reduction/alkylation conducted under denaturing conditions (6M GuaHCl). Following alkylation, the expressed protein is separated by nonreducing SDS-PAGE using precast gels. Alternatively, the expressed protein is incubated in the gel after electrophoresis with iodoacetamide or NEM, or without as a control. Protein bands are stained, de-stained with double-deionized water, excised, and incubated twice in 500 microliters of 50 mM ammonium bicarbonate, 50% (v/v) acetonitrile while shaking for 30 minutes at 20° C. Protein samples are dehydrated in 100% acetonitrile for 2 minutes, dried by vacuum centrifugation, and rehydrated with 10 mg/ml of trypsin or chymotrypsin in buffer containing 50 mM ammonium bicarbonate and 5 mM calcium chloride for 15 minutes on ice. Excess buffer is removed and replaced with 50 microliters of the same buffer without enzyme, followed by incubation for 16 hours at 37° C. or 20° C., for trypsin and chymotrypsin, respectively, with shaking. Digestions are stopped by addition of 3 microliters of 88% formic acid, and after brief vortexing, the supernatant is removed and stored at −20° C. until analysis. Alternative protein fragmentation methods (LysC, Glu-C, or CNBr) are used if trypsinolysis provides insufficient sequence coverage (<75%). Using the reducing agent TCEP (tris(2-carboxyethyl)phosphine) under acidic conditions in the presence of NEM provides access to fragments with partly intact disulfide linkages. The disulfide-intact digest map is compared to the reduced (DTT or TCEP) digest map.
Localization of Disulfide Bonds by Mass Spectrometry.
Peptides are injected onto a 1 mm×8 mm trap column (Michrom BioResources, Inc., Auburn, Calif.) at 20 microliters/minute in a mobile phase containing 0.1% formic acid. The trap cartridge is then placed in-line with a 0.5 mm×250 mm column containing 5 mm Zorbax SB-C18 stationary phase (Agilent Technologies, Santa Clara, Calif.), and peptides separated by a 2-30% acetonitrile gradient over 90 minutes at 10 micro-liters/minute with a 1100 series capillary HPLC (Agilent Technologies); alternatively, a C18 column suitable for UPLC is used. Peptides are analyzed using a LTQ Velos linear ion trap with an ETD source (Thermo Fisher Scientific Inc., Waltham, Mass.). Electrospray ionization is performed using a Captive Spray source (Michrom Bioresources, Inc.), or preferably, an uncoated, pulled fused silica emitter (New Objective Inc., Woburn, Massachuetts) at 3.0 kV. Alternatively, analysis of medium-sized proteolytic fragments is performed using a Thermo LTQ-FT MS (7 Tesla) instrument, or a Synapt G2-Si quadrupole traveling wave ion mobility time-of-flight (ToF) mass spectrometer (Waters Corp., Milford, Mass.). Preferably, peptides are analyzed using an Orbitrap Fusion™ Tribrid™ mass spectrometer (Thermo Fisher Scientific). Disulfide-linked peptides have charge states of +4 or greater following trypsinization due to the presence of two N-termini and two basic residues (arginine or lysine) at the carboxy termini. These disulfide-linked peptides are preferentially isolated by the Orbitrap Fusion™ instrument so that the disulfide bonds can be broken using ETD fragmentation. Survey MS scans are followed by seven data-dependant scans consisting of CID and ETD MS2 scans on the most intense ion in the survey scan, followed by five MS3 CID scans on the first- to fifth-most intense ions in the ETD MS2 scan. CID scans use normalized collision energy of 35, and ETD scans use a 100 ins activation time with supplemental activation enabled. Minimum signals to initiate MS2 CID and ETD scans are 10,000, minimum signals for initiation of MS3 CID scans are 1000, and isolation widths for all MS2 and MS3 scans are 3.0 m/z. The dynamic exclusion feature of the software is enabled with a repeat count of 1, exclusion list size of 100, and exclusion duration of 30 seconds. Inclusion lists to target specific cross-linked species for collection of ETD MS2 scans are used. Separate data files for MS2 and MS3 scans are created by Bioworks 3.3 (Thermo Fisher Scientific) using ZSA charge state analysis. Matching of MS2 and MS3 scans to peptide sequences is performed by Sequest (V27, Rev 12, Thermo Fisher Scientific). The analysis is performed without enzyme specificity, a parent ion mass tolerance of 2.5, fragment mass tolerance of 1.0, and a variable mass of +16 for oxidized methionine residues. Results are then analyzed using the program Scaffold (V3_00_08, Proteome Software, Portland, Oreg.) with minimum peptide and protein probabilities of 95 and 99% being used. Software tools for data interpretation also include Proteome Discoverer™ 2.0 with the Disulfinator node (Thermo Fisher Scientific). Peptides from MS3 results are sorted by scan number, and cysteine containing peptides are identified from groups of MS3 scans produced from the five most intense ions observed in ETD MS2 scans. The identities of cysteine peptides participating in disulfide-linked species are further confirmed by manual examination of the parent ion masses observed in the survey scan and the ETD MS2 scan.
Solubilization and Purification of Expression Products from Bacterial Cell Periplasm, from Spheroplasts, and from Whole Cells
The solubilization and purification methods of the invention can be used in the production of gene products that accumulate in different compartments of the cell, such as the cytoplasm or periplasm. Host cells such as E. coli or S. cerevisiae have an outer cell membrane or cell wall, and can form spheroplasts when the outer membrane or wall is removed. Expressed proteins made in such hosts can be purified specifically from the periplasm, or from spheroplasts, or from whole cells, using the following method (Schoenfeld, “Convenient, rapid enrichment of periplasmic and spheroplasmic protein fractions using the new PeriPreps™ Periplasting Kit”, Epicentre Forum 1998 5(1): 5; available at epibio.com/docs/default-source/forum-archive/forum-05-1---convenient-rapid-enrichment-of-periplasmic-and-spheroplasmic-protein-fractions-using-the-new-peripreps-periplasting-kit.pdf). This method is designed for E. coli and other grain negative bacteria, but the general approach can be modified for other host cells such as S. cerevisiae.
1. The bacterial host cell culture is grown to late log phase only, as older cell cultures in stationary phase commonly demonstrate some resistance to lysozyme treatment. If the expression of recombinant protein is excessive, cells may prematurely lyse; therefore, cell cultures are not grown in rich medium or at higher growth temperatures that might induce excessive protein synthesis. Protein expression is then induced; the cells should be in log phase or early stationary phase.
2. The cell culture is pelleted by centrifugation at a minimum of 1,000×g for 10 minutes at room temperature. Note: the cells must be fresh, not frozen. The wet weight of the cell pellet is determined in order to calculate the amount of reagents required for this protocol.
3. The cells are thoroughly resuspended in a minimum of 2 ml of PeriPreps Periplasting Buffer (200 mM Tris-HCl pH 7.5, 20% sucrose, 1 mM EDTA, and 30 U/microliter Ready-Lyse Lysozyme) for each gram of cells, either by vortex mixing or by pipetting until the cell suspension is homogeneous. Note: excessive agitation may cause premature lysing of the spheroplasts resulting in contamination of the periplasmic fraction with cytoplasmic proteins.
4. Incubate for five minutes at room temperature. Ready-Lyse Lysozyme is optimally active at room temperature. Lysis at lower temperatures (0° C.-4° C.) requires additional incubation time; at such temperatures incubation times are extended 2- to 4-fold.
5. Add 3 ml of purified water at 4° C. for each grain of original cell pellet weight (Step 2) and mix by inversion.
6. Incubate for 10 minutes on ice.
7. The lysed cells are pelleted by centrifugation at a minimum of 4,000×g for 15 minutes at room temperature.
8. The supernatant containing the periplasmic fraction is transferred to a clean tube.
9. To degrade contaminating nucleic acids, OmniCleave Endonuclease is optionally added to PeriPreps Lysis Buffer. Inclusion of a nuclease will generally improve the yield of protein and the ease of handling of the lysates, but addition of a nuclease is undesirable in some cases: for example, the use of a nuclease should be avoided if residual nuclease activity or transient exposure to the magnesium cofactor will interfere with subsequent assays or uses of the purified protein. The addition of EDTA to the lysate to inactivate OmniCleave Endonuclease, likewise, may interfere with subsequent assay or use of the purified protein. If nuclease is to be added, 2 microliters of OmniCleave Endonuclease and 10 microliters of 1.0 M MgCl2 are diluted up to 1 ml with PeriPreps Lysis Buffer (10 mM Tris-HCl pH 7.5, 50 mM KCl, 1 mM EDTA, and 0.1% deoxycholate) for each milliliter of Lysis Buffer needed in Step 10.
10. The pellet is resuspended in 5 ml of PeriPreps Lysis Buffer for each gram of original cell pellet weight.
11. The pellet is incubated at room temperature for 10 minutes (if included, OmniCleave Endonuclease activity will cause a significant decrease in viscosity; the incubation is continued until the cellular suspension has the consistency of water).
12. The cellular debris is pelleted by centrifugation at a minimum of 4,000×g for 15 minutes at 4° C.
13. The supernatant containing the spheroplast fraction is transferred to a clean tube.
14. If OmniCleave Endonuclease was added to the PeriPreps Lysis Buffer, 20 microliters of 500 mM EDTA is added for each milliliter of the resultant spheroplastic fraction, to chelate the magnesium (the final concentration of EDTA in the lysate is 10 mM). Following hydrolysis of nucleic acids with OmniCleave Endonuclease, lysates may contain substantial amounts of mono- or oligonucleotides. The presence of these degradation products may affect further processing of the lysate: for example, nucleotides may decrease the binding capacity of anion exchange resins by interacting with the resin.
The above protocol can be used to prepare total cellular protein with the following modifications. The cells pelleted in Step 2 can be fresh or frozen; at Step 4, the cells are incubated for 15 minutes; Steps 5 through 8 are omitted; at Step 10, 3 ml of PeriPreps Lysis Buffer is added for each grain of original cell pellet weight.
After preparation of periplasmic, or spheroplastic, or whole-cell protein samples, the samples can be analyzed by any of a number of protein characterization and/or quantification methods. In one example, the successful fractionation of periplasmic and spheroplastic proteins is confirmed by analyzing an aliquot of both the periplasmic and spheroplastic fractions by SDS-PAGE (two microliters of each fraction is generally sufficient for visualization by staining with Coomassie Brilliant Blue). The presence of unique proteins or the enrichment of specific proteins in a given fraction indicates successful fractionation. For example, if the host cell contains a high-copy number plasmid with the ampicillin resistance marker, then the presence of β-lactamase (31.5 kDa) mainly in the periplasmic fraction indicates successful fractionation. Other E. coli proteins found in the periplasmic space include alkaline phosphatase (50 kDa) and elongation factor Tu (43 kDa). The amount of protein found in a given fraction can be quantified using any of a number of methods (such as SDS-PAGE and densitometry analysis of stained or labeled protein bands, scintillation counting of radiolabeled proteins, enzyme-linked immunosorbent assay (ELISA), or scintillation proximity assay, among other methods.) Comparing the amounts of a protein found in the periplasmic fraction as compared to the spheroplastic fraction indicates the degree to which the protein has been exported from the cytoplasm into the periplasm.
Titration of Expression by Varying Inducer Concentration
To optimize production of a gene product using the expression systems of the invention, it is possible to independently adjust or titrate the concentrations of the inducers. Host cells containing expression constructs comprising inducible promoters—such as L-arabinose-inducible, propionate-inducible, L-rhamnose-inducible, or D-xylose-inducible promoters—are grown to the desired density for small-volume titrations (such as an OD600 of approximately 0.5) in M9 minimal medium containing the appropriate antibiotics, then cells are aliquoted into small volumes of M9 minimal medium, optionally prepared with no carbon source such as glycerol, and with the appropriate antibiotics and varying concentrations of each inducer. Small-volume titrations can be performed in 200- to 500-ml shake flasks. The concentration of L-arabinose, L-rhamnose, or D-xylose necessary to induce expression is typically less (and is often substantially less) than 0.02% per OD unit of cells. In a titration experiment, the tested concentrations of L-arabinose can range from 2% to 1.5%, 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.005%, 0.002%, 0.001%, 0.0005%, 0.0002%, 0.0001%, 0.00005%, 0.00002%, 0.00001%, 0.000005%, 0.000002%, 0.000001%, 0.0000005%, 0.0000002%, 0.0000001%, 0.00000005%, 0.00000002%, and 0.00000001%, all per OD unit of cells. A concentration of 66.61 micromolar L-arabinose corresponds to 0.001% L-arabinose. An alternative titratation experiment for L-arabinose, L-rhamnose, or D-xylose would be to test the following concentrations, expressed in terms of molarity: 250 mM, 100 mM, 50 mM, 25 mM, 10 mM, 5 mM, 2.5 mM, 1.0 mM, 500 micromolar, 250 micromolar, 100 micromolar, 75 micromolar, 50 micromolar, 25 micromolar, 10 micromolar, 5.0 micromolar, 2.5 micromolar, 1.0 micromolar, 500 nM, 250 nM, 100 nM, 50 nM, 25 nM, 10 nM, 5.0 nM, 2.5 nM, 1.0 nM, 500 pM, 250 pM, 100 pM, 50 pM, 25 pM, 10 pM, 5.0 pM, 2.5 pM, and 1.0 pM, all per OD unit of cells. For propionate, concentrations to be tested can range from 1 M to 750 mM, 500 mM, 250 mM, 100 mM, 75 mM, 50 mM, 25 mM, 10 mM, 5 mM, 1 mM, 750 micromolar, 500 micromolar, 250 micromolar, 100 micromolar, 50 micromolar, 25 micromolar, 10 micromolar, 5.0 micromolar, 2.5 micromolar, 1.0 micromolar, 500 nM, 250 nM, 100 nM, 50 nM, 25 nM, 10 nM, 5.0 nM, 2.5 nM, and 1.0 nM all per OD unit of cells.
For each concentration ‘x’ of L-arabinose (or L-rhamnose or D-xylose) that is tested, the concentration of a different inducer such as propionate, added to each of the tubes containing concentration ‘x’ of the first inducer, is varied in each series of samples. Alternatively, titration experiments can start at a ‘standard’ combination of inducer concentrations, which for host cells having a reduced level of gene function of at least one gene encoding a protein that metabolizes the inducer is 0.0015% (100 micromolar) of any of L-arabinose, L-rhamnose, or D-xylose per OD unit of cells, and/or 100 micromolar propionate per OD unit of cells. For host cells in which the proteins that metabolize the inducer are functional, the ‘standard’ combination of inducer concentrations is 0.0033% (220 micromolar) of any of L-arabinose, L-rhamnose, or D-xylose per OD unit of cells, and/or 83 mM propionate per OD unit of cells. Additional combinations of inducer concentrations that vary from that of the ‘standard’ combination are tested; in a series of titration experiments, the results from initial experiments can be used to ‘fine-tune’ the inducer concentrations used in later experiments. Similar titration experiments can be performed with any combination of inducers used in an expression system of the invention, including but not limited to L-arabinose, propionate, L-rhamnose, and D-xylose. After growth in the presence of inducers for 6 hours, the cells are pelleted, the desired product is extracted from the cells, and the yield of product per mass value of cells is determined by a quantitative immunological assay such as ELISA, or by purification of the product and quantification by UV absorbance at 280 nm.
It is also possible to titrate inducer concentrations using a high-throughput assay, in which the proteins to be expressed are engineered to include a fluorescent protein moiety, such as that provided by the mKate2 red fluorescent protein (Evrogen, Moscow, Russia), or the enhanced green fluorescent proteins from Aequorea victoria and Bacillus cereus. Another approach to determining the amount and activity of gene products produced by different concentrations of inducers in a high-throughput titration experiment, is to use a sensor capable of measuring biomolecular binding interactions, such as a sensor that detects surface plasmon resonance, or a sensor that employs bio-layer interferometry (BLI) (for example, an Octet® QK system from forteBIO, Menlo Park, Calif.). If an antibody is available that binds with sufficient specificity to the gene product that is being expressed, the gene product can be detected and quantified using a capillary electrophoresis Western blot, such as that run on a WES system as described in Example 6.
Determination of Polynucleotide or Amino Acid Sequence Similarity
Percent polynucleotide sequence or amino acid sequence identity is defined as the number of aligned symbols, i.e. nucleotides or amino acids, that are identical in both aligned sequences, divided by the total number of symbols in the alignment of the two sequences, including gaps. The degree of similarity (percent identity) between two sequences may be determined by aligning the sequences using the global alignment method of Needleman and Wunsch (J. Mol. Biol. 48:443, 1970), as implemented by the National Center for Biotechnology Information (NCBI) in the Needleman-Wunsch Global Sequence Alignment Tool, available through the website blast.ncbi.nlm.nih.gov/Blast.cgi. In one embodiment, the Needleman and Wunsch alignment parameters are set to the default values (Match/Mismatch Scores of 2 and −3, respectively, and Gap Costs for Existence and Extension of 5 and 2, respectively). Other programs used by those skilled in the art of sequence comparison may also be used to align sequences, such as, for example, the basic local alignment search tool or BLAST® program (Altschul et al., “Basic local alignment search tool”, J Mol Biol 1990 Oct. 5; 215(3): 403-410), as implemented by NCBI, using the default parameter settings described at the blast.ncbi.nlm.nih.gov/Blast.cgi website. The BLAST algorithm has multiple optional parameters including two that may be used as follows: (A) inclusion of a filter to mask segments of the query sequence that have low compositional complexity or segments consisting of short-periodicity internal repeats, which is preferably not utilized or set to ‘off’, and (B) a statistical significance threshold for reporting matches against database sequences, called the ‘Expect’ or E-score (the expected probability of matches being found merely by chance; if the statistical significance ascribed to a match is greater than this E-score threshold, the match will not be reported). If this ‘Expect’ or E-score value is adjusted from the default value (10), preferred threshold values are 0.5, or in order of increasing preference, 0.25, 0.1, 0.05, 0.01, 0.001, 0.0001, 0.00001, and 0.000001.
In practicing the present invention, many conventional techniques in molecular biology, microbiology, and recombinant DNA technology are optionally used. Such conventional techniques relate to vectors, host cells, and recombinant methods. These techniques are well known and are explained in, for example, Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Mc, San Diego, Calif.; Sambrook et al., Molecular Cloning—A Laboratory Manual (3rd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2000; and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2006). Other useful references, for example for cell isolation and culture and for subsequent nucleic acid or protein isolation, include Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique, third edition, Wiley-Liss, New York and the references cited therein; Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips (Eds.) (1995) Plant Cell, Tissue and Organ Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg N.Y.); and Atlas and Parks (Eds.) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, Fla. Methods of making nucleic acids (for example, by in vitro amplification, purification from cells, or chemical synthesis), methods for manipulating nucleic acids (for example, by site-directed mutagenesis, restriction enzyme digestion, ligation, etc.), and various vectors, cell lines, and the like useful in manipulating and making nucleic acids are described in the above references. In addition, essentially any polynucleotide (including labeled or biotinylated polynucleotides) can be custom or standard ordered from any of a variety of commercial sources.
The present invention has been described in terms of particular embodiments found or proposed to comprise certain modes for the practice of the invention. It will be appreciated by those of ordinary skill in the art that, in light of the present disclosure, numerous modifications and changes can be made in the particular embodiments exemplified without departing from the intended scope of the invention.
All cited references, including patent publications, are incorporated herein by reference in their entirety. Nucleotide and other genetic sequences, referred to by published genomic location or other description, are also expressly incorporated herein by reference.
Homo
sapiens
Homo
sapiens
Homo
sapiens
Caenorhabditis
elegans
Escherichia
coli
Thermotoga
maritima
Thermotoga maritima
Homo
sapiens
S. cerevisiae
Saccharomyces cerevisiae
Humicola insolens
Humicola insolens PDI
Saccharomyces cerevisiae
Homo
sapiens
Homo
sapiens
Homo
sapiens
Homo
sapiens
This application is a continuation of International Application No. PCT/US2019/052998, filed 25 Sep. 2019, which claims the benefit of priority of U.S. Provisional Application No. 62/735,861, filed on 25 Sep. 2018, the entire disclosures of which are incorporated by reference herein.
| Number | Name | Date | Kind |
|---|---|---|---|
| 9617335 | McClain et al. | Apr 2017 | B2 |
| 20150353940 | McClain et al. | Dec 2015 | A1 |
| Number | Date | Country |
|---|---|---|
| WO-200100245 | Jan 2001 | WO |
| WO-2009089154 | Jul 2009 | WO |
| WO 2012115638 | Aug 2012 | WO |
| WO 2013168178 | Nov 2013 | WO |
| WO-2014025663 | Feb 2014 | WO |
| WO-2016205570 | Dec 2016 | WO |
| WO 2017106583 | Jun 2017 | WO |
| Entry |
|---|
| Nguyen et al., “Pre-expression of a sulfhydryl oxidase significantly increases the yields of eukaryotic disulfide bond containing proteins expressed in the cytoplasm of E. coli,” Microbial Cell Factories, 10:1, 2011 (13 pages). |
| Amet et al., Insertion of the designed helical linker led to increased expression of Tf-based fusion proteins, Pharm. Res. Mar. 26(3): 523-528 (2009). |
| Chang et al., Human insulin production from a novel mini-proinsulin which has high receptor-binding activity, Biochem. J. 329(Pt 3): 631-635 (1998). |
| Chung et al., Recombinant production of biologically active giant grouper (Epinephelus lanceolatus) growth hormone from inclusion bodies of Escherichia coli by fed-batch culture, Protein Expr. Purif. 110: 79-88 (2015). |
| Coll et al., Three-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity, EMBO. J. 10(1): 1-9 (1991). |
| Cube Biotech, “Screening detergents for optimal solubilization and purification of membrane proteins”, 2013, retrieved from www.cube-biotech.com/files/protocols/Screening_Detergents.pdf www.cube-biotech.com/files/protocols/Screening_Detergents.pdf> on Mar. 29, 2017. |
| Datsenko et al., One-step inactivation of chromosomal genes in Escherichia colt K-12 using PCR products, Proc. Natl. Acad. Sci. U.S.A. 97(12): 6640-6645 (2000). |
| De Mey et al., Promoter knock-in: a novel rational method for the fine tuning of genes, BMC Biotechnol. 10: 26 (2010). |
| Farr et al., Oxidative stress responses in Escherichia coli and Salmonella typhimurium, Microbiol. Rev. 55(4): 561-585 (1991). |
| Faulkner et al., Functional plasticity of a peroxidase allows evolution of diverse disulfide-reducing pathways, Proc. Natl. Acad. Sci. U.S.A. 105(18): 6735-6740 (2008). |
| Khlebnikov et al., Regulatable arabinose-inducible gene expression system with consistent control in all cells of a culture, J. Bacteriol. 182(24): 7029-7034 (2000). |
| Kikuchi et al., The nucleotide sequence of the promoter and the amino-terminal region of alkaline phosphatase structural gene (phoA) of Escherichia coli, Nucleic Acids Res. 9(21): 5671-5678 (1981). |
| Lobstein et al., SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm, Microb. Cell Fact.11: 56 (2012). |
| Majewski et al., Simple constrained-optimization view of acetate overflow in E. coli, Biotechnol. Bioeng. 35(7): 732-738 (1990). |
| Makino et al., Strain engineering for improved expression of recombinant proteins in bacteria, Microb. Cell Fact. 14; 10: 32 (2011). |
| Man et al., Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria, Nucleic Acids Res. 39(8): e50 (2011). |
| Morgan-Kiss et al., Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity, Proc. Natl. Acad. Sci. U.S.A. 99(11): 7373-7377 (2002). |
| Muyrers et al., Rapid modification of bacterial artificial chromosomes by ET-recombination, Nucleic Acids Res. 27(6): 1555-1557 (1999). |
| NCBI Accession No. NC 000913.2, Escherichia coli str. K-12 substr. MG1655, complete genome, Mar. 9, 2022. |
| NCBI Accession No. NC 000913.3, Escherichia coli str. K-12 substr. MG1655, complete genome, Mar. 9, 2022. |
| NCBI Accession No. NP 001278826.1, insulin preproprotein [Homo sapiens], Feb. 2022. |
| Needleman et al., A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol. 48:443 (1970). |
| Nili et al., Defining the disulfide bonds of insulin-like growth factor-binding protein-5 by tandem mass spectrometry with electron transfer dissociation and collision-induced dissociation, J. Biol. Chem. 287(2): 1510-1519 (2012). |
| Notenboom et al., Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms, Biochemistry. 40(21): 6248-6256 (2001). |
| Schoenfeld, “Convenient, rapid enrichment of periplasmic and spheroplasmic protein fractions using the new PeriPrepsTM Peri-plasting Kit”, Epicentre Forum 1998 5(1): 5; available at epibio.com/docs/default-source/forum-archive/forum-05-1—convenient-rapid-enrichment-of-periplasmic-and-epibio.com/docs/default-source/forum-archive/forum-05-1—convenient-rapid-enrichment-of-periplasmic-and->spheropl asmic-protein-fractions-using-the-new-periprep s-periplasting-kit.pdf. |
| Song et al., Organization and regulation of the D-xylose operons in Escherichia coli K-12: XyIR acts as a transcriptional activator, J. Bacteriol. 179(22): 7025-7032 (1997). |
| Wickstrum et al., The AraC/XyIS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation, J. Bacteriol. 192(1): 225-232 (2010). |
| Yamaguchi et al., Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies, Biomolecules. 4(1): 235-251 (2014). |
| Number | Date | Country | |
|---|---|---|---|
| 20200299343 A1 | Sep 2020 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62735861 | Sep 2018 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US2019/052998 | Sep 2019 | US |
| Child | 16866361 | US |
