Patent Application
20160326220
Pursuant to 37 C.F.R. §1.821(c) or (e), a file containing an electronic version of the Sequence Listing has been submitted concomitant with this application, the contents of which are hereby incorporated by reference. One file titled “V484_ST25” that is 42 KB and created on Jun. 14, 2016, is submitted electronically.
This application relates to the display of proteins and peptides on cellular or non-biotic surfaces in the form of multivalent filamentous polymers. In particular, the disclosure provides for tools and methods for the secretion and functional display of chimeric polypeptides on the surface of cells, in particular, bacterial cells, as well as on foreign substrates, both biological and synthetic. Further envisaged are biotechnological applications using the same.
A wide variety of biotechnological applications seek the immobilization of polypeptides on biological or synthetic surfaces.
The display of polypeptides on a cellular surface has been a subject of investigation for several years. Cellular surface display bears considerable advantages for numerous biotechnical applications including recombinant vaccines, combinatorial library screening, reagents for diagnostics, and whole-cell biocatalysts and biosorbents (Lee et al., 2003; Wernerus and Stahl, 2004). An attractive way to present proteins (or segments thereof) on the bacterial surface is to graft them into permissible positions on naturally occurring surface proteins. The first papers to describe microbial surface display fall within the field of vaccine development using the E. coli outer membrane proteins LamB (Charbit et al., 1986), OmpA (Ruppert et al., 1994) and PhoE (Agterberg and Tommassen, 1991) to display short gene fragments. Since then, a variety of anchoring motifs have been developed for the display of heterologous peptides and proteins, including S-layer proteins, lipoproteins, autotransporters and subunits of surface appendages (Samuelson et al., 2002; Lee et al., 2003). Among these various mechanisms, fibrillar structures such as flagella, pili and curli are especially attractive candidates because of their natural function and/or highly organized multi-subunit features. Both the major and minor structural subunits of flagella and pili were employed to transport passenger proteins onto the cell surface (reviewed in: Van Gerven et al., 2011).
While shown successful for several, not all proteins can be efficiently exposed on the bacterial surface using multi-subunit fibers. One of the problems usually encountered with flagellar or fimbrial display systems is the limited size of heterologous grafts that can be displayed without causing detrimental effects on the structure and/or function of the carrier protein. For pili of the chaperone-usher pathway (also referred to as fimbriae), the upper size limit seems to be relatively low, being 34 AA and 52 AA for, respectively, the major and minor tip subunits (Samuelson et al., 2002). Studies addressing the mechanisms of curli display are sporadic, with only short sequences being displayed (White et al., 1999; White et al., 2000; Huang et al., 2009; Meng et al., 2010). In these studies, regions within the major Salmonella curli subunit, AgfA, were replaced by different T-cell epitopes, as was also described in a patent application published as WO2008/124646.
High-density surface expression of recombinant proteins is a prerequisite for successfully using cellular surface display in several areas of biotechnological applications, including the construction of oral live vaccines and whole-cell biocatalysts in the fields of pharmaceutical, fine chemical, bioconversion, waste treatment and agrochemical production. An ideal display system should combine the ability to accommodate large inserts with a high copy number and a broad host range.
In addition, a range of biotechnological applications make use of the coating or activation of synthetic surfaces with polypeptides. Usually, this coating occurs through the covalent coupling or through (affinity-based) adsorption of the polypeptides to the desired material. Both approaches can have a number of problems or disadvantages: (1) for both strategies, the coating procedure is rather non-specific, requiring that the polypeptide samples are of a high degree of purity prior to the coating procedure in order to avoid the inclusion of contaminants, which would dilute the density of the desired polypeptide and which may add undesired properties to the coating. This need for a purification step often adds to the production expense; (2) the chemical composition of the material or the conditions required for covalent or adsorption-based coating of polypeptides can lead to the loss of the active conformation of the polypeptides; (3) the chemical build-up of the materials or the conditions required to allow polypeptide adsorption may not be compatible with downstream usage; and (4) adsorption-based coatings can lose polypeptides to the soluble fraction, leading to a depletion of the polypeptide density over time.
Therefore, a system that couples the bio-production of the desired polypeptides with a self-assembling property that leads to the formation of thread-like polymers onto a synthetic surface and that displays the polypeptide in an active conformation would alleviate a number of these disadvantages.
This disclosure is based on the unexpected finding that fusion of intact proteins (“passenger polypeptide” as defined further herein) to carrier proteins derived from bacterial fiber subunit proteins from the curli family (“carrier polypeptide” as defined further herein) is feasible and can successfully be used for the display of correctly folded and active proteins into filamentous threads, either on the bacterial cell surface or on foreign (synthetic) substrates. Bacterial fiber subunit proteins of the curli family can act as a versatile scaffold for secretion and surface display of heterologous proteinaceous inserts, which offers a number of advantages. First of all, the carriage of passenger proteins does not interfere with the correct secretion of the fiber subunit to the extracellular environment by the producing bacterium. Second, the fiber subunit carrier protein is competent for self-assembly into curli-like fibers and can accommodate and display entire and functionally active proteins into the fibers. Third, fibers are a high-valency display system, as the high copy number of the fiber subunit does not seem to be significantly affected by most foreign inserts. As a comparison, the major structural proteins of various fimbriae can only contain modest-sized inserts (in the 10-30 amino acid range) without detrimental effects on organelle structure and surface display. The minor adhesin component at the tip seems to be more accommodating but is still only capable of displaying peptides of around 100 amino acids (Pallesen et al., 1995), and results in single-copy display at the tip of the organelle. Thus, display using curli-like fibers is a promising tool for various approaches in biotechnology and biomedicine, demonstrating that, in addition to the export of peptides, proteins retaining their activity can be displayed successfully into the amyloid fibers on the bacterial cell surface or on foreign substrates, both biologically and synthetically.
Typically, curli fiber subunit proteins have strongly conserved motifs. Another unexpected finding of this disclosure is that the presence of a particularly conserved motif in the carrier protein seems to be sufficient for secretion and fiber formation, as well as for the carriage of passenger proteins and the display of correctly folded functional proteins into the fibers. This is particularly advantageous since it allows designing a fusion protein of choice in view of the desired characteristics of either the fiber and/or the display of the heterologous inserts.
Another unexpected finding of this disclosure is that a bacterial Type VIII secretion system is amenable for the transport and secretion of correctly folded and active proteins outside a bacterial cell.
Another unexpected finding is that curli subunits can be secreted from a non-native host, including a Gram-positive bacterium, and that these secreted subunits are competent to form extracellular curli fibers. Production of curli fibers by a non-native host bacterium includes the secretion and assembly of heterologous proteins and peptides fused to the curli subunit CsgA or to defined peptide fragments derived thereof.
One aspect of the present application relates to a method of producing a functionalized fiber, the method comprising the steps of:
In one embodiment of the above method, step c) occurs on or near the extracellular surface of the same or another host cell. In another embodiment, step c) occurs on or near an artificial surface. In yet another embodiment, step c) occurs in solution.
In one embodiment of the above method, the expressed chimeric polypeptide is secreted.
Also, the above method may further comprise the step of:
Preferably, for the above method, the passenger polypeptide of the chimeric polypeptide is maintained as a functionally active polypeptide after secretion or isolation.
In a particular embodiment of the above method, the host cell is a bacterial host cell, in particular a Gram-negative bacterial host cell, or a Gram-positive bacterial host cell.
In yet another embodiment of the above method, the host cell expresses, either endogenously or exogenously, a nucleic acid sequence encoding CsgG, and at least one nucleic acid sequence encoding one or more of CsgB, CsgC, CsgE, CsgF, or variants or fragments of any thereof.
In a particular embodiment of the above method, the recombinant nucleic acid molecule encoding the chimeric polypeptide and the one or more nucleic acid sequences are expressed simultaneously.
According to a preferred embodiment of the above method, the carrier polypeptide of the chimeric polypeptide has the following structure: (Y2i-1-Xi-Y2i)n, wherein:
In a particular embodiment of the above method, n is 1.
Also envisaged is the above method wherein the carrier polypeptide of the chimeric polypeptide is selected from the group consisting of:
In the above method, the chimeric polypeptide may further comprise a signal peptide.
In one embodiment of the above method, the passenger polypeptide comprised in the chimeric polypeptide is an enzyme or a binding domain. Particularly, the passenger polypeptide comprised in the chimeric polypeptide is between 100 amino acids and 250 amino acids.
Another aspect of the application encompasses a functionalized fiber obtained by any of the above methods.
A further aspect relates to a recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a chimeric polypeptide, the chimeric polypeptide comprising:
More particularly, the carrier polypeptide of the chimeric polypeptide has the following structure:
(Y2i-1-Xi-Y2i)n, wherein
In one embodiment of the above recombinant nucleic acid molecule, n is 1.
In another embodiment of the recombinant nucleic acid molecule, the carrier polypeptide of the chimeric polypeptide is selected from the group consisting of:
In another embodiment of the above recombinant nucleic acid molecule, the chimeric polypeptide further comprises a signal peptide.
In another embodiment of the above recombinant nucleic acid molecule, the passenger polypeptide comprised in the chimeric polypeptide is an enzyme or a binding domain.
Also envisaged in this application is a vector comprising any of the above recombinant nucleic acid molecules, as well as a host cell comprising any of the above recombinant nucleic acid molecules or vectors. Preferably, the host cell is a bacterial host cell, in particular a Gram-negative bacterial host cell or a Gram-positive bacterial host cell.
In one embodiment, the above host cell is genetically engineered to express, either endogenously or exogenously, a nucleic acid sequence encoding CsgG, and at least one nucleic acid sequence encoding one or more of CsgB, CsgC, CsgE, CsgF, or variants or fragments of any thereof.
In another embodiment of the above host cells, the recombinant nucleic acid molecule encoding any of the above-described chimeric polypeptides and nucleic acid sequences are expressed simultaneously.
Also, the host cell may be a component of a bacterial biofilm.
Another aspect of the application relates to a chimeric polypeptide encoded by any of the above-described recombinant nucleic acid molecules.
Also envisaged is a composition comprising one or more chimeric polypeptides encoded by one or more of the above-described recombinant nucleic acid molecules, whereby the passenger polypeptide of each chimeric polypeptide in the composition is a functionally active polypeptide. Preferably, the composition is a fiber composition. The composition may be attached to a surface, in particular, a cell surface or an artificial surface.
In yet another aspect, the application also encompasses the use of the above compositions for detecting and/or capturing of a substance, such as a protein, an organic or inorganic compound, a heavy metal, or a pollutant, in particular, the use of the composition for the chemical and/or enzymatic conversion of a substance, such as a protein, an organic or inorganic compound, a heavy metal, or a pollutant.
The application also relates to a method for producing a chimeric polypeptide in the extracellular medium of a host cell culture, the method comprising the steps of:
In the above method, the host cell may be genetically engineered to simultaneously express CsgE, or a variant or a fragment thereof.
In one embodiment of the above method, the method comprises the step of isolating the chimeric polypeptide from the culture medium.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
This disclosure will be described with respect to particular embodiments and with reference to certain drawings but the disclosure is not limited thereto but only by the claims. Any reference signs in the claims shall not be construed as limiting the scope. The drawings described are only schematic and are non-limiting. In the drawings, the size of some of the elements may be exaggerated and not drawn to scale for illustrative purposes. Where the term “comprising” is used in the present description and claims, it does not exclude other elements or steps. Where an indefinite or definite article is used when referring to a singular noun, e.g., “a,” “an,” or “the,” this includes a plural of that noun unless something else is specifically stated. Furthermore, the terms “first,” “second,” “third,” and the like, in the description and in the claims, are used for distinguishing between similar elements and not necessarily for describing a sequential or chronological order. It is to be understood that the terms so used are interchangeable under appropriate circumstances and that the embodiments of the disclosure described herein are capable of operation in other sequences than described or illustrated herein.
Unless otherwise defined herein, scientific and technical terms and phrases used in connection with this disclosure shall have the meanings that are commonly understood by those of ordinary skill in the art. Generally, nomenclatures used in connection with, and techniques of molecular and cellular biology, genetics and protein and nucleic acid chemistry and hybridization described herein are those well-known and commonly used in the art. The methods and techniques of this disclosure are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated. See, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989); Ausubel et al., Current Protocols in Molecular Biology, Greene Publishing Associates (1992, and Supplements to 2002).
As used herein, the terms “polypeptide,” “protein,” and “peptide” are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. Throughout the application, the standard one letter notation of amino acids will be used. Typically, the term “amino acid” will refer to “proteinogenic amino acid,” i.e., those amino acids that are naturally present in proteins. Most particularly, the amino acids are in the L isomeric form, but D amino acids are also envisaged.
As used herein, the terms “nucleic acid molecule,” “polynucleotide,” “polynucleic acid,” and “nucleic acid” are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown. Non-limiting examples of polynucleotides include a gene, a gene fragment, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, control regions, isolated RNA of any sequence, nucleic acid probes, and primers. The nucleic acid molecule may be linear or circular.
Any of the peptides, polypeptides, nucleic acids, etc., disclosed herein may be “isolated” or “purified.” “Isolated” is used herein to indicate that the material referred to is (i) separated from one or more substances with which it exists in nature (e.g., is separated from at least some cellular material, separated from other polypeptides, separated from its natural sequence context), and/or (ii) is produced by a process that involves the hand of man such as recombinant DNA technology, chemical synthesis, etc.; and/or (iii) has a sequence, structure, or chemical composition not found in nature. “Purified” as used herein denote that the indicated nucleic acid or polypeptide is present in the substantial absence of other biological macromolecules, e.g., polynucleotides, proteins, and the like. In one embodiment, the polynucleotide or polypeptide is purified such that it constitutes at least 90% by weight, e.g., at least 95% by weight, e.g., at least 99% by weight, of the polynucleotide(s) or polypeptide(s) present (but water, buffers, ions, and other small molecules, especially molecules having a molecular weight of less than 1000 Daltons, can be present).
The term “sequence identity” as used herein refers to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison. Thus, a “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, Ile, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gln, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. Determining the percentage of sequence identity can be done manually, or by making use of computer programs that are available in the art. Examples of useful algorithms are PILEUP (Higgins & Sharp, CABIOS 5:151 (1989), BLAST and BLAST 2.0 (Altschul et al., J. Mol. Biol. 215:403 (1990)) and ClustalW and ClustalW2 (Larkin et al., Bioinformatics 23:2947 (2007)) or Multalin (F. Corpet, Nucl. Acids Res. 16:10881 (1988)). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (World Wide Web at ncbi.nlm.nih.gov/), multiple sequence alignments using ClustalW or ClustalW2 can be performed through the public tools provided by the European Bioinformatics Institute (World Wide Web at ebi.ac.uk/Tools).
“Similarity” refers to the percentage number of amino acids that are identical or constitute conservative substitutions. Similarity may be determined using sequence comparison programs such as GAP (Deveraux et al. 1984, Nucleic Acids Research 12:387-395) or FASTA (World Wide Web at fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml; Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85:2444 (1988)). In this way, sequences of a similar or substantially different length to those cited herein might be compared by insertion of gaps into the alignment, such gaps being determined, for example, by the comparison algorithm used by GAP.
As used herein, “conservative substitution” is the substitution of amino acids with other amino acids whose side chains have similar biochemical properties (e.g., are aliphatic, are aromatic, are positively charged, . . . ) and is well known to the skilled person. Non-conservative substitution is then the substitution of amino acids with other amino acids whose side chains do not have similar biochemical properties (e.g., replacement of a hydrophobic with a polar residue). Conservative substitutions will typically yield sequences that are not identical anymore, but still highly similar. As used herein, the term “hydrophobic amino acids” refers to the following 13 amino acids: isoleucine (I), leucine (L), valine (V), phenylalanine (F), tyrosine (Y), tryptophan (W), histidine (H), methionine (M), threonine (T), lysine (K), alanine (A), cysteine (C), and glycine (G). The term “aliphatic amino acids” refers to I, L or V residues. The term “charged amino acids” refers to arginine (R), lysine (K)—both positively charged; and aspartic acid (D), glutamic acid (E)—both negatively charged. The term “aromatic amino acids” refers to phenylalanine (F), tryptophan (W), tyrosine (Y), and histidine (H).
The term “recombinant” or “heterologous” when used in reference to a cell, nucleic acid, protein or vector, indicates that the cell, nucleic acid, protein or vector has been modified by the introduction of a non-native nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express nucleic acids or polypeptides that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed, over expressed or not expressed at all. The non-native nucleic acids or polypeptides are referred to as being heterologous, e.g., of a non-native origin.
As used herein, the term “carrier polypeptide” or “carrier protein” refers to a polypeptide that is secreted by an appropriate secretion system of a host cell and that has the capability and characteristics to, but does not need to, polymerize into a fiber structure. Within the context of this disclosure, the carrier polypeptide is derived from a naturally occurring bacterial protein, in particular, a fiber subunit protein, which is all defined in more detail further herein. It will be appreciated that a carrier polypeptide as used herein can be identical to a naturally occurring bacterial protein or can be a variant or a fragment derived thereof (as defined further herein), as long as it retains the capability to polymerize in vivo or in vitro. A fiber may comprise identical or different fiber subunits. In nature, a fiber is typically composed of a major and minor fiber subunit, reflecting either a high or low copy number in the fiber, respectively.
As used herein, the term “passenger polypeptide” or “passenger protein” is defined as a polypeptide that, when fused to a carrier polypeptide, is co-secreted and, if applicable, co-polymerized into a fiber structure.
The terms “chimeric polypeptide,” “chimeric protein,” “fusion polypeptide,” and “fusion protein” are used interchangeably herein and refer to a protein that comprises at least two separate and distinct regions that may or may not originate from the same protein. For example, a signal peptide linked to a protein of interest, wherein the signal peptide is not normally associated with the protein of interest, would be termed a “chimeric polypeptide” or “chimeric protein.” Or, two proteins or two protein domains that are not normally associated with each other, are other examples of chimeric polypeptides. A convenient means for linking or fusing two polypeptides is by expressing them as a fusion protein from a recombinant nucleic acid molecule, which comprises, for example, and within the present scope, a first polynucleotide encoding a carrier polypeptide operably linked to a second polynucleotide encoding a passenger polypeptide. Otherwise, the polypeptides comprised in a fusion protein can be linked through peptide bonds or may even be chemically linked. Typically, such a chimeric polypeptide will not exist as a contiguous polypeptide in a protein encoded by a gene in a non-recombinant genome. The term “chimeric polypeptide” and equivalents thus refers to a non-naturally occurring molecule, which means that it is manmade.
As used herein, the term “expression” refers to the process by which a polypeptide is produced based on the nucleic acid sequence of a gene. The process includes both transcription and translation.
The term “operably linked” as used herein refers to a linkage in which a regulatory sequence is contiguous with the gene of interest to control the gene of interest, as well as regulatory sequences that act in trans or at a distance to control the gene of interest. For example, a DNA sequence is operably linked to a promoter when it is ligated to the promoter downstream with respect to the transcription initiation site of the promoter and allows transcription elongation to proceed through the DNA sequence. A DNA for a signal sequence is operably linked to DNA coding for a polypeptide if it is expressed as a pre-protein that participates in the transport of the polypeptide. Linkage of DNA sequences to regulatory sequences is typically accomplished by ligation at suitable restriction sites or adapters or linkers inserted in lieu thereof using restriction endonucleases known to one of skill in the art. In a “fusion protein” or “chimeric polypeptide,” within the scope of this disclosure, a DNA sequence for a carrier polypeptide is operably linked to a DNA sequence of a passenger polypeptide when both are transcribed to a continuous messenger RNA and when both coding sequences are translated into a continuous polypeptide.
The term “regulatory sequence” as used herein refers to polynucleotide sequences that are necessary to affect the expression of coding sequences to which they are operably linked. Expression control sequences are sequences that control the transcription, post-transcriptional events and translation of nucleic acid sequences. Expression control sequences include appropriate transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (e.g., ribosome binding sites); sequences that enhance protein stability; and, when desired, sequences that enhance protein secretion. The nature of such control sequences differs depending upon the host organism. The term “control sequences” is intended to include, at a minimum, all components whose presence is essential for expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences.
The term “conformation” or “conformational state” of a protein refers generally to the range of tridimensional structures that a polypeptide may adopt at any instant in time. One of skill in the art will recognize that determinants of conformation or conformational state include a protein's primary structure as reflected in a protein's amino acid sequence (including modified amino acids) and the environment surrounding the protein. The conformation or conformational state of a protein also relates to structural features such as protein secondary structures (e.g., α-helix, β-sheet, among others), tertiary structure (e.g., the three-dimensional folding of a polypeptide chain), and quaternary structure (e.g., interactions of a polypeptide chain with other protein subunits). Post-translational and other modifications to a polypeptide chain such as ligand binding, phosphorylation, sulfation, glycosylation, or attachments of hydrophobic groups, among others, can influence the conformation of a protein. Furthermore, environmental factors, such as pH, salt concentration, ionic strength, and osmolality of the surrounding solution, and interaction with other proteins and co-factors, among others, can affect protein conformation. The conformational state of a protein may be determined by either functional assay for activity or binding to another molecule or by means of physical methods such as X-ray crystallography, FTIR, circular dichroism, NMR, or spin labeling, among other methods. For a general discussion of protein conformation and conformational states, one is referred to Cantor and Schimmel, Biophysical Chemistry, Part I: The Conformation of Biological Macromolecules, W.H. Freeman and Company, 1980, and Creighton, Proteins: Structures and Molecular Properties, W.H. Freeman and Company, 1993.
As used herein, the phrase “polypeptide in a functional conformation” or “functional polypeptide” or a “functionally active polypeptide” refers to a polypeptide that has adopted a particular functional conformational state, including a native conformation. As used herein, a “functional conformation” or a “functional conformational state” refers to the fact that a protein or polypeptide possesses a particular structural conformation that determines a particular protein activity (e.g., antigen binding activity, ligand binding activity, chemical activity, enzymatic activity, etc.). It should thus be clear that “a functional conformation” is meant to cover any conformation, having any activity, and is not meant to cover the denatured states of proteins. As used herein, the phrase “polypeptide in its native conformation” refers to the functional conformation of the polypeptide as adopted under its native conditions, e.g., as found under physiological conditions in its natural host and localization. It should be noted that the “native conformation” of a polypeptide is not per se restricted to a single conformation, but can encompass a dynamic range of conformations or a number of discrete conformations. The term “polypeptide in a functional conformation” is not meant to include linear epitopes or linear peptides.
As used herein, the term “transverse diameter” is defined as the diameter measured perpendicular to the longitudinal axis of an object, e.g., a protein in its tertiary or quaternary state. As used herein, an object's maximum transverse diameter can be understood to be equal to the minimal inner diameter of a hollow cylinder that allows inclusion or passage of the object.
As used herein, the terms “determining,” “measuring,” “assessing,” “monitoring,” and “assaying” are used interchangeably and include both quantitative and qualitative determinations.
The term “signal peptide” as used herein is defined as a short peptide of between 5 and 40 amino acids long, that when located at the N-terminus, directs the newly synthesized polypeptide toward the general secretory pathway or the Twin Arginine Transport (TAT) pathway. Synonyms include “signal sequence,” “leader sequence,” and “leader peptide”; these terms are used interchangeably herein. The signal peptide can or cannot be removed from the translocated polypeptide by post-translational, proteolytic processing. Examples are provided further in the specification.
The term “biofilm,” as used herein, is an aggregate of microorganisms in which cells adhere to each other and/or to a surface. These adherent cells are frequently embedded within a self-produced matrix generally composed of extracellular DNA, proteins, and polysaccharides in various configurations. Biofilms can contain many different types of microorganism, e.g., bacteria, archaea, protozoa, fungi and algae. However, monospecies biofilms occur as well. Microorganisms living in a biofilm usually have significantly different properties from free-floating (planktonic) microorganisms of the same species, as a result of the dense and protected environment of the film. For example, increased resistance to detergents and antibiotics is often observed, as the dense extracellular matrix and the outer layer of cells protect the interior of the community.
The term “vector” as used herein is intended to refer to a nucleic acid molecule capable of transporting another nucleic acid molecule to which it has been linked. The vector may be of any suitable type including, but not limited to, a phage, virus, plasmid, phagemid, cosmid, bacmid or even an artificial chromosome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., vectors having an origin of replication that functions in the host cell). Other vectors can be integrated into the genome of a host cell upon introduction into the host cell, and are thereby replicated along with the host genome. Moreover, certain preferred vectors are capable of directing the expression of certain genes of interest. Such vectors are referred to herein as “recombinant expression vectors” (or simply, “expression vectors”). Suitable vectors have regulatory sequences, such as promoters, enhancers, terminator sequences, and the like as desired and according to a particular host organism (e.g., bacterial cell, yeast cell). Typically, a recombinant vector according to this disclosure comprises at least one “chimeric gene” or “expression cassette.” Expression cassettes are generally DNA constructs preferably including (5′ to 3′ in the direction of transcription): a promoter region, a polynucleotide sequence, homologue, variant or fragment thereof of this disclosure, operably linked with the transcription initiation region, and a termination sequence including a stop signal for RNA polymerase and a polyadenylation signal. It is understood that all of these regions should be capable of operating in biological cells, in particular, bacterial cells, to be transformed. The promoter region comprising the transcription initiation region, which preferably includes the RNA polymerase binding site, and the polyadenylation signal may be native to the biological cell to be transformed or may be derived from an alternative source, where the region is functional in the biological cell.
The term “host cell,” as used herein, is intended to refer to a cell into which a recombinant vector has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell but also to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. A host cell may be an isolated cell or cell line grown in culture or may be a cell that resides in a living tissue or organism. In particular, host cells are of bacterial or fungal origin, but may also be of plant or mammalian origin. The wordings “host cell,” “recombinant host cell,” “expression host cell,” “expression host system,” and “expression system,” are intended to have the same meaning and are used interchangeably herein.
This disclosure provides tools and methods for the recombinant production, transport and secretion of chimeric polypeptides by bacterial host cells. The chimeric polypeptides as described herein comprise a carrier polypeptide moiety characterized by its ability to self-polymerize into a fiber and a passenger polypeptide moiety that is carried along with the carrier polypeptide moiety. The chimeric polypeptides thus essentially comprise a passenger polypeptide that is fused to a carrier polypeptide. The carrier polypeptides are designed polypeptides that hold properties and sequence characteristics from the curlin repeat family of proteins. The chimeric polypeptides are produced by a bacterial cell, either a Gram-positive or a Gram-negative bacterial cell. When produced by a Gram-negative (diderm) bacterial cell, they can be isolated from the bacterial cell or secreted to the extracellular environment by virtue of the secretion machinery responsible for the assembly of curli-like fibers (also called Type VIII secretion system or nucleation-precipitation pathway), which minimally encompasses a CsgG-like lipoprotein and can include the accessory proteins CsgE or CsgF. Upon secretion, the chimeric polypeptides may self-assemble into curli-like fibers by virtue of the polymerizing nature of the carrier polypeptide. The tools and methods as described herein additionally provide for the functional display of polypeptides along filamentous fibers on the producing host cell surface or on foreign surfaces.
Thus, one aspect of this disclosure relates to a recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a chimeric polypeptide which is a fusion protein of different moieties, in particular, comprising at least a carrier polypeptide moiety and a passenger polypeptide moiety.
In particular, the disclosure provides for a recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a chimeric polypeptide, the chimeric polypeptide comprising:
In general, several naturally occurring bacterial surface proteins can be used to present proteins on the bacterial surface, including S-layer proteins, lipoproteins, autotransporters and subunits of surface appendages. Structural subunits of fibrillar structures such as flagella and pili are particularly useful to transport proteins onto the cell surface because of their natural function and/or their highly organized multi-subunit features. The terms pili (hair-like structures) and fimbriae (threads), collectively referred to as “pili,” are generally being used to indicate exterior appendages formed by any of the following biosynthetic pathways: the chaperone-usher and alternate chaperone-usher pathways, Type II-like secretion systems (Type IV pili), Type III secretion systems, Type IV secretion systems, Type VIII secretion system (also called extracellular nucleation-precipitation), or by sortase-mediated assembly pathways. Pili are involved in numerous essential biological processes such as, for example, recognition and colonization of target surfaces, biofilm formation, shielding and host subversion, motility, protein and nucleic acid secretion and/or uptake, and signaling events. “Flagella” represent the other main type of filamentous multi-subunit surface organelles on bacteria. They are considered unique motility organelles not only used for swimming but also essential for swarming. Visualized by electron microscopy (EM), flagella are thicker, longer, and less numerous than pili. Invariably, these two types of surface appendages are built up of one or a few repeating (glyco)protein subunits that are covalently or noncovalently attached to linear or branched structures. The various classes of bacterial surface appendages along with their biosynthetic pathways and structural properties are reviewed by Van Gerven et al. (2011), the content of which is incorporated herein by reference.
Within the scope of the disclosure, a preferred class of bacterial fiber subunits for the design of carrier proteins for functional display of proteins is the class of fiber subunit components of “curli fibers” or “curli.” As used herein, the term “curli” refers to unbranched, highly aggregative flexible filaments of 4-7 nm diameter and are the major proteinaceous component of the extracellular matrix produced by many bacteria, e.g., many Enterobacteriaceae such as E. coli and Salmonella spp. (Barnhart et al. 2006). In Salmonella typhymurium, these are called thin aggregative fimbriae (Tafi) (Collinson et al. 1991). Curli are formed by means of the extracellular nucleation-precipitation (ENP) pathway, also referred to as Type VIII secretion system (T8SS). Native curli fibers exhibit structural and biochemical properties of amyloids, e.g., they are non-branching, cross-beta sheet rich fibers (e.g., showing characteristic fiber diffraction signals at 4.7 Å and 10 Å) that are resistant to protease digestion and denaturation by 10% SDS, and bind to amyloid-specific moieties such as thioflavin T, which fluoresces when bound to amyloid, and Congo red, which produces a unique spectral pattern (“red shift”) in the presence of amyloid. Native curli fibers require formic acid treatment for depolymerization, unlike amorphous or colloidal protein aggregates or other filamentous organelles such as pili and flagella. Curli fibers are involved in adhesion to surfaces, cell aggregation, and biofilm formation. Curli also mediate host cell adhesion and invasion, and they are potent inducers of the host inflammatory response. It will be appreciated that the term “curli” also includes native-like curli fibers whereby the filamentous threads can have a different fibrillous structure but that retain the characteristic to be resistant to denaturation by 10% SDS.
In nature, curli subunits are secreted as monomeric subunits that polymerize on the extracellular surface upon contact with growing fibers or a surface-exposed nucleator protein (Chapman et al. 2002). Taking the curli biogenesis pathway in Escherichia coli as a non-limiting example, curli are assembled by a process in which the major fiber subunit polypeptide, CsgA (SEQ ID NO: 1), is nucleated into a fiber by the minor fiber subunit polypeptide, CsgB (SEQ ID NO: 24), or by pre-existing CsgA polymers. CsgA and CsgB are about 30% identical at the amino acid level and contain an imperfect five-fold internal repeat symmetry characterized by conserved polar residues. The assembly process is believed to involve addition of soluble polypeptides to the growing fiber tip. Thus, both subunits are incorporated into the fiber, although CsgA is the major protein constituent. In living bacteria, curli formation likely involves activities of several additional polypeptides encoded by other Csg genes (CsgD (SEQ ID NO: 25), CsgE (SEQ ID NO: 26), CsgF (SEQ ID NO: 27), CsgG (SEQ ID NO: 28)), whereas these polypeptides are not required for curli formation in vitro. CsgG forms a pore in the outer membrane and is important for the stability and secretion of CsgA, CsgB and CsgF. The latter plays a role in the stability and nucleation activity of CsgB. Other curli proteins are CsgD, the transcriptional activator for the csgBAC-operon, CsgE, which potentially has chaperone properties and CsgC, which possibly has oxido-reductase activity and may possibly bind CsgG.
“CsgA polypeptide” or simply “CsgA,” as used herein, encompasses any polypeptide having an amino acid sequence of a naturally occurring bacterial CsgA polypeptide as well as variants of a polypeptide having an amino acid sequence of a naturally occurring bacterial CsgA polypeptide. A CsgA polypeptide variant is at least 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identical to or similar (as defined herein) to a naturally occurring CsgA polypeptide. Naturally occurring CsgA polypeptides are known in the art and amino acid sequences of CsgA polypeptides from a large number of bacteria have been identified. One of skill in the art will readily be able to find CsgA sequences by searching databases such as GenBank, which are publicly available through the National Center for Biotechnology Information (NCBI; see the World Wide Web at ncbi.nlm.nih.gov). CsgA polypeptides characteristically encompass multiple copies of a 20-30 amino acid repeat known as curlin repeat (PFAM domain PF07012: World Wide Web at pfam.sanger.ac.uk/family/PF07012), herein incorporated by reference. In general, CsgA polypeptides have an N-terminal secretion signal for transport through the SEC-system, which is cleaved off, followed by multiple copies of imperfect repeats containing an S-(X)5-Q-(X)4-N-(X)5-Q motif (SXXXXXQXXXXNXXXXXQ, SEQ ID NO: 29, wherein X means any amino acid) and providing the amyloidogenic core of the protein (Collison et al. 1999; Wang and Chapman 2008). As an illustration, E. coli CsgA (SEQ ID NO: 1) consists of an N-terminal secretion signal (MKLLKVAAIAAIVFSGSALA; SEQ ID NO: 30) that is cleaved off, an N-terminal domain of 22 amino acids (GVVPQYGGGGNHGGGGNNSGPN, SEQ ID NO: 31) that is believed to provide the targeting sequence for CsgG-mediated secretion, and a C-terminal amyloidogenic core (SEQ ID NO: 3), containing five strongly conserved repeats, R1-R5 (SEQ ID NO: 4 to 8). See also Table 1.
It is shown in this disclosure that carrier polypeptides derived from CsgA polypeptide subunits of bacterial curli fibers are versatile tools and allow the secretion of a fused passenger polypeptide to the extracellular environment of the producing bacterium and allows for its incorporation into fibers, where it is displayed along the length of the fiber and retains its functional conformation. These are referred to herein as “functionalized fibers.” Such functionalized fibers of the fusion protein can be formed on the cell surface of the producing bacterium, or can be nucleated onto a foreign surface that is exposed to a solution containing the fusion protein. In this disclosure, it is shown that the carrier polypeptide derived from CsgA at least comprises the following amino acid sequence: V/I/L-X-Q-X-G-X-X-N/Q-X-A/V/I/L-X-X-X-Q (SEQ ID NO: 32), wherein X means any amino acid, and minimal sequences needed for a carrier polypeptide to be secreted by a bacterial host cell and to allow subsequent polymerization into fibers are defined (as described further herein). Advantageously, the fiber composition can thus be designed according to needs and applications, by (1) adapting the sequence of the carrier polypeptide at permissive sites (e.g., where the amino acid can be freely chosen), and/or (2) varying the nature and number of the passenger polypeptides, and/or (3) designing a suitable fusion construct, and/or (4) co-production and secretion of multiple carrier-passenger fusion proteins with different passenger polypeptides in order to obtain fibers of mixed passenger composition, and/or (5) co-production and secretion of the carrier-passenger fusion polypeptide(s) with a carrier polypeptide in order to modulate the density of the passenger display in the fiber.
It will thus be understood that the carrier polypeptide moiety of this disclosure refers to a polypeptide derived from a curlin repeat polypeptide as defined hereinbefore. Here, the sequence constraints of the carrier polypeptide that forms part of the chimeric polypeptide as described herein will be explained in more detail.
According to a preferred embodiment, the carrier polypeptide of the chimeric polypeptide as described herein has the following structure: (Y2i-1-Xi-Y2i)n, wherein:
As mentioned, in the above formula, n is an integer from 1 to 20 and i increases from 1 to n with each repeat. In other words, i starts at 1 and is increased with 1 with each repeat until n is reached; or i is the number of the repeat (and is an integer from 1 to n).
The formula thus encompasses the following structures:
Y1-X1-Y2 (i.e., n=1),
Y1-X1-Y2-Y3-X2-Y4 (i.e., n=2),
Y1-X1-Y2-Y3-X2-Y4-Y5-X3-Y6 (i.e., n=3),
Y1-X1-Y2-Y3-X2-Y4-Y5-X3-Z3-Y7-X4-Y8 (i.e., n=4), and
Y1-X1-Y2-Y3-X2-y4-Y5-X3-Y6-Y7-X4-Y8-Y9-X5-Y10 (i.e., n=5), etc. wherein each numbered X and Y are as defined above.
Non-limiting examples of suitable carrier polypeptides that have the structure (Y2i-1-Xi-Y2i)n as defined above include:
In more specific embodiments, the carrier polypeptide of the chimeric polypeptide as described herein has the following structure: (Y2i-1-Xi-Y2i)n, as defined above, wherein n is an integer from 1 to 15, from 1 to 10, from 1 to 9, from 1 to 8, from 1 to 7, from 1 to 6, from 1 to 5, from 1 to 4, from 1 to 3, from 1 to 2. In one particular embodiment, n is 1.
In other specific embodiments, the carrier polypeptide of the chimeric polypeptide as described herein has the following structure: (Y2i-1-Xi-Y2i)n, as defined above, wherein each Y2i-1 and Y2i are independently selected from 0 to 20 contiguous amino acids, from 0 to 18 contiguous amino acids, from 0 to 15 contiguous amino acids, from 0 to 10 contiguous amino acids, from 0 to 5 contiguous amino acids, and/or wherein the total length of each Y2i-1-Xi-Y2i is not more than 50 amino acids, not more than 45 amino acids, not more than 40 amino acids, not more than 35 amino acids, not more than 30 amino acids, not more than 25 amino acids.
In still other specific embodiments, the carrier polypeptide of the chimeric polypeptide as described herein has the following structure: (Y2i-1-Xi-Y2i)n, as defined above, wherein each Xi corresponds to an amino acid sequence selected from the group consisting of:
As an alternative embodiment, the carrier polypeptide moiety of the chimeric polypeptide as described herein is selected from the group consisting of:
In particular, the disclosure provides embodiments that specifically relate to polypeptides whose sequence comprises or consists of the sequence of a naturally occurring bacterial CsgA polypeptide (as defined hereinbefore), as well as to variants and fragments of such naturally occurring bacterial CsgA polypeptide. As used herein, “variant” refers to any polypeptide or peptide differing from a naturally occurring polypeptide by amino acid insertion(s), deletion(s), and/or substitution(s), created using, e g., recombinant DNA techniques. In some embodiments, amino acid “substitutions” are the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, i.e., conservative amino acid replacements. “Conservative” amino acid substitutions may be made on the basis of similarity in any of a variety or properties such as side chain size, polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or amphipathicity of the residues involved. For example, the non-polar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, glycine, proline, phenylalanine, tryptophan and methionine. The polar (hydrophilic), neutral amino acids include serine, threonine, tyrosine, asparagine, and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. In some embodiments, cysteine is considered a non-polar amino acid. In some embodiments, insertions or deletions may range in size from about 1 to 20 amino acids, e.g., 1 to 10 amino acids. In some instances, larger domains may be removed without substantially affecting function. In certain embodiments, the sequence of a variant can be obtained by making no more than a total of 1, 2, 3, 5, 10, 15, or 20 amino acid additions, deletions, or substitutions to the sequence of a naturally occurring polypeptide. In some embodiments, not more than 1%, 5%, 10%, or 20% of the amino acids in a polypeptide or fragment thereof are insertions, deletions, or substitutions relative to the original polypeptide. In some embodiments, guidance in determining which amino acid residues may be replaced, added, or deleted without eliminating or substantially reducing activities of interest (i.e., retaining the capability to polymerize in vivo), may be obtained by comparing the sequence of the particular polypeptide with that of orthologous polypeptides from other organisms and avoiding sequence changes in regions of high conservation or by replacing amino acids with those found in orthologous sequences since amino acid residues that are conserved among various species may more likely be important for activity than amino acids that are not conserved. Thus, according to a particularly preferred embodiment of this disclosure, a variant should at least comprise the amino acid sequence V/I/L-X-Q-X-G-X-X-N/Q-X-A/V/I/L-X-X-X-Q (SEQ ID NO: 32), wherein X means any amino acid.
A “fragment” of a polypeptide refers to a subsequence of the polypeptide. Fragments may vary in size from as few as 10 amino acids to the length of the intact polypeptide, but are preferably at least 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150 amino acids in length. If desired, the fragment may be fused at either terminus to additional amino acids, which may number from 1 to 20, typically 50 to 100, but up to 250 to 500 or more. According to a preferred embodiment, a fragment as described herein is a “functional fragment,” which means a carrier polypeptide fragment retaining the capability to polymerize in vivo and in vitro. Thus, according to a particularly preferred embodiment of this disclosure, a fragment will at least comprise the amino acid sequence V/I/L-X-Q-X-G-X-X-N/Q-X-A/V/I/L-X-X-X-Q, wherein X means any amino acid.
According to a specific embodiment, the carrier polypeptide derived from a bacterial fiber subunit for displaying proteins is not derived from a subunit of flagella. According to other specific embodiments, the carrier polypeptide derived from bacterial fiber subunit for displaying proteins is not derived from a subunit of the chaperone/usher family pili, of Type IV pili, of Type III secretion-related organelles, or of Type IV secretion pili. According to yet another specific embodiment, the carrier polypeptide derived from bacterial fiber subunit as carrier protein for displaying proteins is not derived from a subunit of pili of Gram-positive bacteria.
In general, the nature of the passenger polypeptide is not critical to the disclosure, however, the size and structural features of the passenger polypeptide will determine whether a passenger polypeptide will be secreted by the Type VIII secretion system and attain its native fold. Particular embodiments of the passenger polypeptides that form part of the chimeric polypeptides are described further herein.
It will be understood that the passenger polypeptides differ from the carrier polypeptides as described hereinbefore, in that the passenger polypeptides of this disclosure do not comprise amino acid sequence VII/L-X-Q-X-G-X-X-N/Q-X-A/V/I/L-X-X-X-Q (SEQ ID NO: 32), wherein X means any amino acid. Accordingly, and in contrast with the carrier polypeptide, it will be clear that the passenger polypeptide in itself has no self-polymerizing properties. Whereas the carrier polypeptide moiety is meant for the passage through the type VIII secretion system and, if applicable, for the self-polymerizing property of the chimeric polypeptide, the passenger polypeptide moiety does not contribute to the formation of a polymeric structure. Instead, the passenger polypeptide moiety is co-secreted, and if applicable, can be displayed on the fiber surface as a functional protein and does not form part of the backbone of the fiber.
In particular embodiments, the passenger polypeptide that forms part of the chimeric polypeptide has an amino acid sequence of less than 800 amino acids, less than 700 amino acids, less than 600 amino acids, less than 500 amino acids, less than 400 amino acids, less than 350 amino acids, or less than 300 amino acids. Preferably, the passenger polypeptide that forms part of the chimeric polypeptide has an amino acid sequence of less than 250 amino acids, less than 200 amino acids, less than 150 amino acids, less than 100 amino acids, or less than 80 amino acids; and/or according to other preferred embodiments, the passenger polypeptide that forms part of the chimeric polypeptide has an amino acid sequence of at least 40 amino acids long, at least 50 amino acids, at least 60 amino acids, at least 80 amino acids, at least 100 amino acids, at least 110 amino acids, at least 120 amino acids, at least 150 amino acids, or at least 200 amino acids in length.
In other embodiments, the passenger polypeptide that forms part of the chimeric polypeptide has an amino acid sequence between 40 and 800 amino acids, between 50 and 700 amino acids, between 60 and 600 amino acids, between 80 and 350 amino acids, preferably between 100 and 300 amino acids, between 100 and 250 amino acids, between 110 and 250 amino acids, between 120 and 250 amino acids, or between 150 and 250 amino acids.
In other embodiments, the passenger polypeptide that forms part of the chimeric polypeptide preferably has particular structural features that depend on its folded dimensions. In particular, the passenger polypeptide as described herein has a transverse diameter of 4 nm or less, 3 nm or less, preferably 2.5 nm or less, when present in its folded conformation. In still other embodiments, the passenger polypeptide as described herein has at least four cysteines, preferably at least two cysteines that are involved in disulphide bridge formation.
Other particular embodiments of the passenger polypeptide relating to size and structural features are described in the Example section.
According to specific embodiments, the passenger polypeptide of the chimeric polypeptide is a binding domain (as defined hereafter). In particular, the passenger polypeptide of the chimeric polypeptide can also be a fusion of at least two binding domains, at least three binding domains, at least four binding domains. The at least two or more binding domains may be identical or not. According to other specific embodiments, the passenger polypeptide of the chimeric polypeptide is an enzyme. In particular, the passenger polypeptide of the chimeric polypeptide can also be a fusion of least two enzymes, at least three enzymes, or at least four enzymes. The at least two or more enzymes may be identical or not. Also envisaged are chimeric polypeptides of the disclosure, wherein the passenger polypeptide is fusion of at least one binding domain and at least one enzyme.
The term “binding domain,” as used herein, refers to a molecule that has the capability of interacting with a molecule of interest, for example, specific a target protein, a carbohydrate, a nucleic acid, a lipid, a small organic or small inorganic molecule. Within the scope of this disclosure, a binding domain is a polypeptide, more particularly, a protein domain. A protein domain is an element of overall protein structure that is self-stabilizing and often folds independently of the rest of the protein chain. Binding domains vary in length from between about 25 amino acids up to 500 amino acids and more. Many binding domains can be classified into folds and are recognizable, identifiable, 3-D structures. Some folds are so common in many different proteins that they are given special names. Non-limiting examples are binding domains selected from a 3- or 4-helix bundle, an armadillo repeat domain, a leucine-rich repeat domain, a PDZ domain, a SUMO or SUMO-like domain, an immunoglobulin-like domain, phosphotyrosine-binding domain, pleckstrin homology domain, src homology 2 domain, a lectin domain, and a metal-binding domain, amongst others. Antibodies are the natural prototype of specifically binding proteins with specificity mediated through hypervariable loop regions, so-called complementarity-determining regions (CDR). Although, in general, antibody-like scaffolds have proven to work well as specific binders, it has become apparent that it is not compulsory to stick strictly to the paradigm of a rigid scaffold that displays CDR-like loops. In addition to antibodies, many other natural proteins mediate specific high-affinity interactions between domains. Alternatives to immunoglobulins have provided attractive starting points for the design of novel binding (recognition) molecules. “Scaffold,” as used in this disclosure, refers to a protein framework that can carry altered amino acids or sequence insertions that confer binding to specific target proteins, carbohydrate, nucleic acids, lipids, and small organic or small inorganic molecules. Engineering scaffolds and designing libraries are mutually interdependent processes. In order to obtain specific binders, a combinatorial library of the scaffold has to be generated. This is usually done at the DNA level by randomizing the codons at appropriate amino acid positions, by using either degenerate codons or trinucleotides. A wide range of different non-immunoglobulin scaffolds with widely diverse origins and characteristics are currently used for combinatorial library display. Some of them are comparable in size to an scFv of an antibody (about 30 kDa), while the majority of them are much smaller. Modular scaffolds based on repeat proteins vary in size depending on the number of repetitive units. Frequently, when generating a particular type of binding domain using selection methods, combinatorial libraries comprising a consensus or framework sequence containing randomized potential interaction residues are used to screen for binding to a molecule of interest, such as a protein, a carbohydrate, a nucleic acid, a lipid, a small organic or small inorganic molecule.
A non-limiting list of examples comprise binding domains or scaffolds based on the human 10th fibronectin type III domain, binders based on lipocalins, binders based on SH3 domains, binders based on members of the knottin family, binders based on CTLA-4, T-cell receptors, neocarzinostatin, carbohydrate binding module 4-2, tendamistat, kunitz domain inhibitors, PDZ domains, Src homology domain 2 (SH2), scorpion toxins, insect defensin A, plant homeodomain finger proteins, bacterial enzyme TEM-1 beta-lactamase, Ig-binding domain of Staphylococcus aureus protein A, E. coli colicin E7 immunity protein, E. coli cytochrome b562, designed ankyrin-repeat domains (DARPins), alphabodies, lipopeptides (e.g., pepducins), anticalins, and affibodies.
Also included as binding domains are compounds with a specificity for a given target protein, cyclic and linear peptide binders, peptide aptamers, multivalent avimer proteins or small modular immunopharmaceutical drugs, ligands with a specificity for a receptor or a co-receptor, protein binding partners identified in a two-hybrid analysis, binding domains based on the specificity of the biotin-avidin high affinity interaction, and binding domains based on the specificity of cyclophilin-FK506 binding proteins. Also included are lectins with an affinity for a specific carbohydrate structure. Also included are metal-binding domains with an affinity for a specific metal.
For more examples, see also, e.g., Gebauer and Skerra, 2009; Skerra, 2000; Starovasnik et al., 1997; Binz et al., 2004; Koide et al., 1998; Dimitrov, 2009; Nygren et al. 2008; and WO2010/066740.
In one embodiment, the passenger polypeptide is a binding domain that is derived from an immunoglobulin. Preferably, the passenger polypeptide according to the disclosure is a binding domain that is derived from an antibody or an antibody fragment. Non-limiting examples of immunoglobulin-based binding domains include antibodies, heavy chain antibodies (hcAb), single domain antibodies (sdAb), minibodies, the variable domain derived from camelid heavy chain antibodies (VHH or nanobodies), the variable domain of the new antigen receptors derived from shark antibodies (VNAR), and engineered CH2 domains (nano-antibodies).
The term “antibody” (Ab) refers generally to a polypeptide encoded by an immunoglobulin gene, or a functional fragment thereof, that specifically binds and recognizes an antigen, and is known to the person skilled in the art. The term “antibody” is meant to include whole antibodies, including single-chain whole antibodies, and antigen-binding fragments. In some embodiments, antigen-binding fragments may be antigen-binding antibody fragments that include, but are not limited to, Fab, Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (dsFv) and fragments comprising or consisting of either a VL or VH domain, and any combination of those or any other functional portion of an immunoglobulin peptide capable of binding to the target antigen. The term “antibodies” is also meant to include heavy chain antibodies, or functional fragments thereof, such as single domain antibodies, more specifically, immunoglobulin single variable domains such as VHHs or nanobodies, as defined further herein.
In a particular embodiment, the passenger polypeptide is a binding domain that is an immunoglobulin single variable domain that comprises an amino acid sequence comprising four framework regions (FR1 to FR4) and three complementarity-determining regions (CDR1 to CDR3), preferably according to the following formula (1):
FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4 (1),
or any suitable fragment thereof (which will then usually contain at least some of the amino acid residues that form at least one of the complementarity-determining regions).
Binding domains comprising four FRs and three CDRs are known to the person skilled in the art and have been described, as a non-limiting example, in Wesolowski et al. (2009, Med. Microbiol. Immunol. 198:157). Typical, but non-limiting, examples of immunoglobulin single variable domains include light chain variable domain sequences (e.g., a VL domain sequence), or heavy chain variable domain sequences (e.g., a VH domain sequence), which are usually derived from conventional four-chain antibodies. Preferably, the immunoglobulin single variable domains are derived from camelid antibodies, preferably from heavy chain camelid antibodies, devoid of light chains, and are known as VHH domain sequences or nanobodies (as described further herein). Thus, in a preferred embodiment, the passenger polypeptide is a nanobody. In another embodiment, the passenger polypeptide is a fusion of at least two nanobodies, at least three nanobodies, or more.
The term “nanobody” (Nb), as used herein, refers to the smallest antigen binding fragment or single variable domain (VHH) derived from naturally occurring heavy chain only antibody and is known to the person skilled in the art. They are derived from heavy chain only antibodies, seen in camelids (Hamers-Casterman et al. 1993; Desmyter et al. 1996). The single variable domain heavy chain antibody is herein designated as a Nanobody or a VHH antibody. Nanobody™ and Nanobodies™ are trademarks of Ablynx NV (Belgium).
The delineation of the CDR sequences (and, thus, also the FR sequences) is based on the IMGT unique numbering system for V-domains and V-like domains (Lefranc et al. 2003). Alternatively, the delineation of the FR and CDR sequences can be done by using the Kabat numbering system as applied to VHH domains from Camelids in the article of Riechmann and Muyldermans (2000). As will be known by the person skilled in the art, the immunoglobulin single variable domains, in particular, the nanobodies, can, in particular, be characterized by the presence of one or more Camelidae hallmark residues in one or more of the framework sequences (according to Kabat numbering), as described, for example, in WO 08/020079, on page 75, Table A-3, incorporated herein by reference.
According to another embodiment, the chimeric polypeptide encoded by the recombinant nucleic acid molecule as described above further comprises a linker moiety. In particular, the carrier polypeptide and passenger polypeptide as comprised in the chimeric polypeptide as described hereinabove, can be fused to each other either directly or through a linker moiety. The nature and/or length of the linker moieties are not critical to the disclosure. According to particular embodiments, the linker is selected from a stretch of between 0 and 20 identical or non-identical units, wherein a unit preferably is an amino acid, but can also be a monosaccharide, a nucleotide or a monomer (in the case where a chimeric polypeptide would be synthetically designed, see further herein).
Typically, “linker molecules” or “linkers” are peptides of 0 to 20 amino acids length and are typically chosen or designed to be unstructured and flexible. For instance, one can choose amino acids that form no particular secondary structure. Or, amino acids can be chosen so that they do not form a stable tertiary structure. Or, the amino acid linkers may form a random coil. Such linkers include, but are not limited to, synthetic peptides rich in Gly, Ser. Thr, Gin, Glu or further amino acids that are frequently associated with unstructured regions in natural proteins (Dosztanyi et al. 2005). Non-limiting examples include (GS)5 or (GS)10.
Preferably, the amino acid linker sequence is relatively short, has a low susceptibility to proteolytic cleavage and does not interfere with the biological activity of chimeric polypeptide. According to specific embodiments, an amino acid linker sequence is a peptide of between 0 and 20 amino acids, between 0 and 10 amino acids, particularly between 0 and 5 amino acids. Particularly envisaged sequences of short linkers include, but are not limited to, PPP, PP or GS.
For certain applications, it may be advantageous that the linker molecule comprises or consists of one or more particular sequence motifs. For example, at least one proteolytic cleavage site can be introduced into the linker molecule such that the displayed passenger protein can be released after surface display. Useful cleavage sites are known in the art, and include a protease cleavage site such as Factor Xa cleavage site having the sequence IEGR (SEQ ID NO: 74), the thrombin cleavage site having the sequence LVPR (SEQ ID NO: 75), the enterokinase cleaving site having the sequence DDDDK (SEQ ID NO: 76), or the PreScission cleavage site LEVLFQGP (SEQ ID NO: 77).
Non-limiting examples of suitable linker sequences are also described in the Example section.
According to a preferred embodiment, the chimeric polypeptide encoded by the recombinant nucleic acid molecule as described above further comprises a signal peptide moiety.
In bacteria, a signal peptide (as defined herein) is a prerequisite for proteins to be translocated across the cytoplasmic membrane to the periplasm in Gram-negatives (diderms) or extracellular space in Gram-positives (monoderms). Suitable signal peptides will typically depend on the host cell and the protein to be translocated, and are known by the person skilled in the art. For example, signal peptides may be chosen such that they direct the proteins to the Sec secretion system. Other signal peptides will direct the proteins to the Tat (the Twin arginine translocase) secretion pathway. Thus, depending on the host cell and the protein to be translocated, the skilled person can easily select a suitable signal peptide, for example, by using the SignalP webserver (on the World Wide Web at cbs.dtu.dk/services/SignalP/), which predicts the presence and location of signal peptides and there cleavage sites in amino acid sequences from different organisms, including Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.
Non-limiting examples of signal peptide sequences include OmpA, PelB, LamB, SurA, DsbA, TolB, and PhoA leader sequences.
According to specific embodiments, signal peptides of naturally occurring CsgA polypeptides may also be used, for example, SEQ ID NO: 30. Non-limiting examples of suitable signal peptides are also described in the Example section.
This disclosure also provides for a vector comprising the recombinant nucleic acid molecule as described hereinbefore.
The vector generally contains elements required for replication in a prokaryotic host system. Such vectors, which include plasmid vectors and viral vectors such as bacteriophage, are well known and can be purchased from a commercial source (e.g., Promega, Madison Wis.; Stratagene, La Jolla Calif.; GIBCO/BRL, Gaithersburg Md.) or can be constructed by one skilled in the art. The construction of expression vectors and the expression of a polynucleotide in transformed or transfected cells involves the use of molecular cloning techniques also well known in the art (see Sambrook et al., in Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press 1989); Current Protocols in Molecular Biology (eds., Ausubel et al.; Greene Publishing Associates, Inc., and John Wiley & Sons, Inc. 1990 and supplements)).
This disclosure also provides for a host cell comprising the vector or recombinant nucleic acid molecule as described hereinbefore. It will be appreciated that in some embodiments, the recombinant nucleic acid molecule as described herein can be integrated in the genome of the host cell. Within the context of this disclosure, preferably host cells of bacterial origin are transformed with any of the recombinant nucleic acid sequences or vectors as described herein. In particular, the bacterial host cells as provided herein may be Gram-positive bacterial host cells or Gram-negative bacterial host cells, which are terms commonly used in the art for the classification of Bacteria. Essentially, any bacterial host cell can be chosen. When a Gram-negative bacterial host cell is chosen, the secretion machinery responsible for the assembly of curli fibers (as defined hereinbefore) needs to be present (also called Type VIII secretion system or nucleation-precipitation pathway), which minimally encompasses a CsgG protein, and preferably also the accessory proteins CsgE or CsgF. Further, within the context of this disclosure, the bacterial host cell is engineered so that the expression of genes encoding the proteins of the Type VIII secretion system and the expression of the recombinant nucleic acid molecule encoding the chimeric polypeptide is synchronized. A typical way of achieving this is by using an appropriate set of (inducible) promoters. The choice of a promoter will typically depend on the nature of the host cell. The choice further depends on the desired temporal expression of a particular fusion protein as described herein. In this regard, promoters include constitutive promoters, inducible promoters and repressible promoters. According to specific embodiments, the conditions for inducing or repressing any of the promoters are selected from the group consisting of metabolic, or stress, or pH, or temperature, or drug-inducing or repressing conditions, or other inducing or repressing conditions. Examples of suitable promoters are described in “Useful proteins from recombinant bacteria” in Gilbert et al., 1980, Scientific American 242:74-94; and in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual.
In one specific embodiment, the bacterial host cell is a Gram-negative bacterial host cell. In accordance with a more systematic phylogenetic classification, particularly envisaged are bacteria belonging to the phylum Proteobacteria and Bacteroidetes, which constitute a major group of Gram-negative bacteria, including the genera Escherichia, Salmonella, Klebsiella, Shigella, Enterobacter, and other Enterobacteriaceae, Pseudomonas, Moraxella, Helicobacter, Stenotrophomonas, Bdellovibrio, acetic acid bacteria, Legionella and numerous others. Suitable bacterial hosts include Enterobacteria, such as Escherichia coli, Shigella dysenteriae, Klebsiella pneumoniae, and the like. Mutant cells of any of the above-mentioned bacteria may also be employed, as is also illustrated in the Example section.
In general, a Gram-negative bacterial host cell endogenously expresses the csgBAC and csgDEFG operons under the control of their natural promoter. In some embodiments, the csgBAC and/or csgDEFG operons, and/or csgA, csgB, CsgC, CsgD, CsgE, CsgF and/or CsgG individually or a combination of any thereof, can be exogenously expressed in the host cell on a plasmid under the control of its natural promoter or, alternatively, under the control of an inducible promoter. A variety of inducible promoters can be compatible with expression of one or more of the genes of the csgBAC and/or csgDEFG operons, and are known in the art. It will be appreciated that a cell that expresses such plasmids may also express endogenous copies of csgBAC and/or csgDEFG. In some embodiments, the endogenous copies of csgBAC and/or csgDEFG are mutated or deleted. According to one particular embodiment, the bacterial host cell does not endogenously express csgA.
For certain applications, it may be advantageous to express the recombinant nucleic acid molecules encoding the chimeric polypeptides of the disclosure in a non-pathogenic bacterial host cell or an attenuated strain.
According to other embodiments, the bacterial host cell encompasses a Gram-positive host cell comprising such a recombinant nucleic acid sequence or vectors as described herein. The host cell is, for instance, a lactic acid bacterium, preferably selected from Lactococcus lactis, Bacillus subtilis, Streptococcus pyogenes, Staphylococcus epidermis, Staphylococcus gallinarium, Staphylococcus aureus, Streptococcus mutans, Staphylococcus warneri, Streptococcus salivarius, Lactobacillus sakei, Lactobacillus plantarum, Carnobacterium piscicola, Enterococcus faecalis, Micrococcus varians, Streptomyces OH-4156, Streptomyces cinnamoneus, Streptomyces griseoluteus, Butyrivibrio fibriosolvens, Streptoverticillium hachijoense, Actinoplanes linguriae, Ruminococcus gnavus, Streptococcus macedonicus, and Streptococcus bovis, amongst others.
Upon expression and subsequent secretion from the host cell, the chimeric polypeptides may self-assemble into curli fibers by virtue of the polymerizing nature of the carrier polypeptide. Carrier polymerization encompasses a conformational transition from a disordered to a cross-β structure and is nucleated by pre-existing cross-β fibers (including curli or curli fragments) or a nucleation polypeptide exposed on the same bacterial host cell surface or a foreign surface (which can be another bacterial surface or an artificial surface). Notably, where surface display on the producing host cell is envisaged, any of the mentioned bacterial strains endogenously expresses (e.g. Gram-negative bacteria) or can be transformed with (e.g. Gram-positive bacteria) the genes needed to nucleate the chimeric polypeptide protein. Thus, according to the embodiment where polymerization occurs on the producing host cell, the bacterial host cell comprising the vector or recombinant nucleic acid molecule as described hereinbefore, also expresses a nucleation polypeptide, for example, CsgB. Alternatively, in the embodiment where the polymerization occurs on or near another bacterial surface, the corresponding other bacterial cell needs to present a nucleation polypeptide, for example, CsgB or pre-existing cross-β fibers, including curli or curli fragments. In the embodiment where the polymerization occurs on an artificial surface (as defined further herein), the artificial surface is activated with a nucleation agent, for example, surfaces activated with CsgB, a cross-β fiber, CsgA or a nucleating CsgA peptide to trigger the polymerization of chimeric polypeptides secreted from a bacterial host cell.
In general, the nucleic acid molecules as provided herein can be transferred into any host cell by conventional methods, which vary depending on the type of cellular host (see, generally, Maniatis et al., Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Press, 1982)). Selection of the appropriate vector system, regulatory regions and host cell is common knowledge within the level of ordinary skill in the art. It is expected that vectors, promoters, and the like can be similarly utilized and modified to permit expression of the chimeric polypeptides of the disclosure in other bacterial hosts. Replicability of the replicon in the bacteria is taken into consideration when selecting bacteria for use in the methods of the disclosure. Methods suitable for the maintenance and growth of bacterial cells are all well known.
Of particular interest and also envisaged herein, is a library of host cells, comprising a plurality of host cells according to the disclosure, wherein each member of the library displays at its cell surface a different passenger polypeptide. The library is particularly suitable to screen for agents that will bind to the displayed protein (as described further herein).
This disclosure also encompasses a composition comprising one or more chimeric polypeptides encoded by one or more recombinant nucleic acid molecules as described hereinabove, whereby the passenger polypeptide of each chimeric polypeptide in the composition is a functionally active polypeptide. According to one embodiment, the composition is a fiber. The composition may be attached to a surface, in particular, a cell surface or an artificial surface (as described further herein).
Within the context of this disclosure, it is envisaged to use the composition for detecting and/or capturing of a substance, such as a protein, an organic or inorganic compound, a heavy metal, or a pollutant. Or alternatively, it is envisaged to use the composition for the chemical and/or enzymatic conversion of a substance, such as a protein, an organic or inorganic compound, a heavy metal, or a pollutant.
Within the context of this disclosure, the capture of a substance (such as a protein, an organic or inorganic compound, a heavy metal, or a pollutant) encompasses its binding to the passenger polypeptide moiety fused to the carrier protein moiety, that form part of the chimeric polypeptide as described hereinbefore. In a particular embodiment, the chimeric polypeptide is displayed on a bacterial cell, which is freely suspended in solution, is adsorbed onto a solid or gel-like surface or a suspended particle, or is present in a bacterial biofilm. In a particular embodiment, the chimeric polypeptide is displayed directly on a solid surface, a suspended organic, anorganic or mixed organic—anorganic particle, or an organic or inorganic gel-like matrix. Capture of the substance entails the exposure of a solution holding the substance to the capture material, by suspension of the capture material to the substance solution or by contact of the capture medium and the substance solution in a continuous flow process. The substances are non-covalently or covalently bound by the capture material and thus retained from the solution carrying the substances. In the context of a chemical or enzymatic conversion by the capture material, the substances are modified and the resulting products are released back to the carrying solution.
One further aspect of this disclosure relates to a method for producing a chimeric polypeptide in the extracellular medium of a host cell culture, the method comprising the steps of:
In one embodiment, the method further comprises the step of isolating the chimeric polypeptide from the culture medium.
Further embodiments of chimeric polypeptides and suitable host cells and expressing conditions are described above and also apply here.
According to one aspect, this disclosure also envisages a method of producing a functionalized fiber, the method comprising the steps of:
In one particular embodiment, the above-described method further comprises the step of isolating the expressed chimeric polypeptide from the cell before step c). In the alternative, the expressed chimeric polypeptide is secreted from the cell. According to a specifically preferred embodiment of the above-described method, the passenger polypeptide of the chimeric polypeptide is maintained as a functionally active polypeptide after secretion or isolation.
According to one embodiment, step c) of the above-described method occurs on or near the extracellular surface of the same or another host cell. According to another embodiment, step c) occurs on or near an artificial surface. An artificial or synthetic surface may be a bead, a slide, a chip, a plate, or a column. More particularly, the artificial surface may be particulate (e.g., beads or granules) or in sheet form (e.g., membranes or filters, glass or plastic slides, microtiter assay plates, dipstick, or capillary devices), which can be flat, pleated, or hollow fibers or tubes.
In still another embodiment, step c) of the above-described method occurs in solution, for example, without limitation, in the extracellular medium of the producing bacterial host cell.
Further embodiments of chimeric polypeptides and suitable host cells and expressing conditions are described above and also apply here.
In previous studies, short peptide stretches (9 to 16 residues in length) within the major Salmonella curli subunit, AgfA, have been successfully replaced by different T-cell epitopes (White et al., 1999; White et al., 2000; Huang et al., 2009; Meng et al., 2010). To further explore whether there are sequence specific or structural restrictions for passage through the CsgG transmembrane pore, a more extensive heterologous sequence was fused to the CsgA C-terminus. Because CsgA is believed to be in an extended conformation during secretion, ERD10 (early response to dehydration), a 260-residue intrinsically disordered protein from plants (Kovacs et al., 2008), was used as passenger sequence. ERD10 was C-terminally 6×His-tagged and fused by its N-terminus to the major curli subunit CsgA. This fusion was cloned in the pBAD33 vector under the control of the PBAD promoter, resulting in plasmid pNA36 (
Next, a systematic investigation was carried out as to whether CsgA-targeted transport through the Type VIII secretion pathway was possible for folded passenger proteins. For this purpose, a range of well-characterized proteins or domains was selected, differing in size, secondary structure composition and disulfide bond content (
Anti-6×His immunoblot analysis of E. coli DH5α cells transformed with the different plasmids revealed that after a 45-minute induction in liquid LB medium at 37° C., the cultures produced the respective recombinant fusion proteins. Longer induction, however, caused lysis of the bacterial cells. This toxicity was gauged to be due to the absence of the curli assembly machinery, expression of which is restricted to prolonged growth (48 hours) on solid medium at low temperature (Olsen et al., 1989). Accordingly, in further experiments, induction of the fusion proteins was delayed by growth on two-layered glucose/arabinose agar plates at room temperature in order to synchronize with curli-promoting conditions. Except for CsgA-PhoA, delayed induction of the CsgA-fusions no longer resulted in cell lysis, suggesting that the Csg protein machinery protected cells from the cytotoxic species and/or CsgA fusion proteins were now transported outside the cell. As for the ERD10 fusion, anti-6×His antibodies were used in IF to get an initial observation of the display of the different fusion proteins.
To acquire a more quantitative measure of secretion, the extracellular exposure of the fusion's C-terminal 6×His-tag was monitored using whole cell ELISA (
To obtain a further measure of secretion efficiency, the proportion of intra-versus extracellular material was monitored for a select number of CsgA-fusions (CsgA-ERD10, CsgA-Nb208, CsgA-FedF, CsgA-RNase1, CsgA-PhoA and CsgA-mCherry) by means of their protease susceptibility. As a control for cell envelope integrity, protease sensitivity of the endogenous, periplasmically located oxidoreductase DsbA was monitored in parallel. For all tested constructs, anti-6×His Western analysis of whole cell lysates showed the presence of both the full-length CsgA-fusions as well as bands corresponding to the passenger proteins only, stemming from fusions that had lost their N-terminal CsgA portion due to proteolitic processing (
Next, examination was carried out as to whether the CsgA-fused passenger proteins can attain their native fold following Type VIII-mediated secretion. Nb208 is a GFP-binding single domain antibody, a property that was used as reporter of its structural conformation on the bacterial cell surface. Like the CsgA-ERD10 fusion, LSR10 cells harboring plasmid pNA15 (csgA-Nb208) showed a marked pericellular fluorescence during anti-6×His immunostaining of the fusion protein in the surface-exposed material (
For CsgG, biochemical and EM structural studies point to the formation of a 2-nm wide oligomeric channel that transports its CsgA substrate in an extended, unfolded conformation (Chapman et al., 2002; Robinson et al., 2006). The observations above illustrate that when fused to CsgA, heterologous proteins can be accepted for secretion, but that secretion efficiencies are dependent on the folded dimensions of the passenger protein. Strikingly, whereas CsgA-FimC and CsgA-mCherry fusions show poor or no specific secretion, the similarly sized, but intrinsically unfolded, protein ERD10 is efficiently secreted and incorporated into surface-exposed CsgA-fusions. This suggests that rather than the linear size, the folding of the passenger protein prior to secretion and the size of its tertiary structure form the blockage for CsgG-mediated secretion. Notably, the transverse diameter of the passenger proteins that showed poor secretion ranges from 3.2 to 5 nm (
Nanobodies contain two cysteines that form a disulfide bridge between framework β-strands 1 and 3. In E. coli, disulfide bridge formation and isomerization is DsbA/DbsC-catalyzed and takes place in the periplasm (Nakamoto and Bardwell, 2004; Messens and Collet, 2006). In the case of autotransporters, the introduction of disulfide-bound “knots” in the passenger domain has been used to study the transport mechanism (Klauser et al., 1990). Such knotted passengers obstructed translocation unless disulfide bond formation in the E. coli periplasm was prevented, either by the addition of β-mercaptoethanol (2-ME) to the growth medium or by the use of an E. coli dsbA mutant (Klauser et al., 1990). Similarly, it was reasoned that the presence of an oxidized disulfide in surface-exposed CsgA-Nb208 fusion would indicate the substrate passed the CsgG transporter in a non-linear conformation. To confirm whether Nb208 in surface-exposed CsgA-Nb208 had an oxidized disulfide, Nb208 activity in a mutant where one of the two cysteines was mutated to serine (CsgA-Nb208C22S) was assessed. Although extracellular material containing CsgA-Nb208C22S was similarly displayed on the bacterial surface, as evidenced by anti-6×His IF staining (
The fimbrial lectin domain FedF15-165 contains two disulfide bonds that stabilize its R-sandwich fold and an elongated loop near its receptor binding site (Moonens et al., 2012). Using an anti-FedF nanobody that selectively recognizes a conformational epitope in the FedF sugar binding site (Nb231) (
Finally, though RNase1 gets partially secreted (
Secreted native CsgA is found as fibrillar filaments that show the physical characteristics of amyloids and can be seen as negatively staining fibrils of 6-12 nm by EM (Chapman et al., 2002). TEM analysis of LSR10 (pNA15) showed an abundant extracellular matrix associated with the cells (
Native curli fibrils are resistant to heating in SDS and require formic acid (FA) treatment for depolymerization, unlike amorphous or colloidal protein aggregates or other filamentous organelles such as pili and flagella (Chapman et al., 2002; Fronzes et al., 2008). To more quantitatively monitor to what extent the matrix of secreted CsgA-fusions contained fibrillar, SDS-insoluble material versus SDS-soluble aggregates, cell lysates were analyzed by SDS-PAGE with or without FA treatment. For all secreted fusions, anti-6×His Western blotting showed the presence of SDS-insoluble material that did not migrate into the stacking gel unless treated with FA (
In order to define minimal CsgA domains necessary for transport and functional display of heterologous polypeptides, several CsgA repeat (R1 up to R5) deletions were made in the CsgA-flex-NB208-His fusion construct. In practice, deletion of CsgA repeats in the CsgA-NB208 fusions were carried out by “outwards” PCR on pNA15, using primer combinations DelR5FW and DelR1Rev, DelR5FW and DelR2Rev, DelR5FW and DelR3Rev, DelR5FW and DelR4Rev, DelR5FW and DelR5, DelR1FW and DelR1Rev, or Rev DelN22FW and DelN22Rev, giving rise to pNA20, pNA21, pNA22, pNA23, pNA24, pNA25, pNA26, respectively (see Table 4). Δ1-5 (expressed from plasmid pNA20) represents the removal of CsgA repeats R1 to R5, leaving only the N22 sequence fused to NB208 in the mature protein. Δ2-5, Δ3-5, and Δ4-5 stand for the deletions of R2 to R5, R3 to R5 and R4 to R5, respectively, and their corresponding coding plasmids are pNA21, pNA22 and pNA23. Δ5, Δ1 and ΔN22 symbolize CsgA-NB208 fusions lacking R1, R5 or N22 and are coded on plasmids pNA24, pNA25 and pNA26. Except for ΔN22, all NB208 fusions above retain the N22 signal sequence.
Additionally, it was investigated whether the single CsgA repeats, without N22 present, would still be able to display NB208 at the cell surface and form fibers. Therefore, chimeric constructs of only one repeat of CsgA (without N22) fused to NB208 were made by “outwards” PCR. Starting from pNA21, pNA22, pNA23, pNA24. or pNA18 with primer combinations Rev DelN22FW and DelN22Rev, DelN22Rev and Del R1FW, DelN22Rev and R3 Fw, DelN22Rev and R4 Fw or DelN22Rev and R5 Fw, respectively, this PCR resulted in plasmids pSB1, pSB2, pSB3, pSB4 and pSB5 (see Table 4).
The presence of the CsgA repeat deletions seemed to have no influence on the level of fusion protein produced in DH5α, as determined in Western blotting (data not shown).
To test whether cells expressing the protein fusions were able to produce curli, LSR10 cells harboring the different deletion constructs were grown on Congo red agar under curli-expressing conditions. Curli production was monitored by the degree of colony staining and further examined using TEM. To evaluate whether the CsgA deletion-fused passenger protein was properly folded, the intrinsic property of NB208 to bind GFP was exploited using fluorescence microscopy.
On Congo red indicator plates, LSR10 cells expressing the different fusions looked pink to red, depending on the deletion (
Further, the necessity of N22 for transport through CsgG was evaluated. Although the N22 is said to be the secretion signal for CsgG, LSR10 cells harboring a CsgA-NB208 fusion lacking this N22 (ΔN22) still secreted curli fusion products, as determined by Congo red binding (
Further, the necessity of the different CsgA repeats R1 to R5 for transport through CsgG was evaluated. LSR10 (pNA21), i.e., Δ2-5, produced colonies that reacted stronger with Congo red than wild-type MC4100 or LSR10 cells expressing the CsgA-NB208 fusion protein. LSR10 (pNA25), i.e., Δ1, bound Congo red to the same extent as the intact CsgA-NB208 fusion. However, for both Δ2-5 and Δ1, TEM showed that curli were less abundant than in the wild-type and were architecturally distinct as they tended to arrange into thick bundled fibers (
For some applications, it might be beneficial to display different polypeptides, with different functionalities, in the same fiber structure. This can be achieved by co-expressing two or more different fusion polypeptides in the same bacterial cell, or by mixing two or more populations of cells, each harboring one single fusion polypeptide. For other applications, a combination of wild-type CsgA and CsgA fusion polypeptides might be beneficial. CsgA can then be co-expressed on a different or on the same plasmid as the fusion polypeptide in a csgA knockout strain. Otherwise, the chromosomal copy of csgA can also be used. As demonstrated in Example 6, the minimal amyloid repeating sequence of CsgA is sufficient as carrier polypeptide for display. Combinations of wild-type CsgA and one or more repeating units fused to different polypeptides are, therefore, also possible.
As a proof-of-principle, MC4100 (pNA15) was used to display hybrid fibers composed of a CsgA-Nb208 fusion and native CsgA as a spacer (see
Curli are also produced by Enterobacteriaceae other than E. coli (Barnhart et al., 2006). For example, in Salmonella spp., these curli fibers are called thin aggregative fimbriae (Tafi) (Collinson et al., 1991). To investigate the broadening of the host cell range, the CsgA-flex-NB208-His fusion (pNA15) was expressed in Salmonella enterica serovar Typhimurium c3000. Exogenously added GFP bound specifically to induced c3000 (pNA15), proving functional curli display across species (
Further testing was performed to ascertain if, apart from Gram-negative bacteria, Gram-positive bacteria could also be used to secrete CsgA fusion proteins that are able to form functional fibers. In this way, the problems caused by extensive folding of the passenger in the periplasm can be circumvented. For this purpose, the csgA-His, csgA-flex-NB208-His and csgA-flex-Bla-His fusions were cloned in vectors compatible with secreted expression in Lactococcus lactis, under the control of different constitutive promoters. Anti-histidine Western blotting proved the correct fusion proteins were produced in the supernatant (data not shown). For the Bla fusions, the correct folding of the Bla moiety was shown by growth of L. lactis harboring the CsgA-Bla fusion under the control of five different promoters (i.e., P9, Cplc, LacA1, SplA, P43, respectively, pEXP435, pEXP436, pEXP437, pEXP438, pEXP439) on agar plates containing ampicillin. All five promoters yielded enough CsgA-Bla to provide resistance to ampicillin (data not shown). In transmission electron microscopy (TEM), fibers were visible on L. lactis(pEXP424) and L. lactis(pEXP437) cells, harboring the csgA-NB208 or csgA-Bla fusions, respectively (
For some applications, it might be useful to grow functional hybrid fibers in vitro. As proof of this concept, CsgA-NB208-His was produced cytoplasmically in E. coli BL21DE3 cells and afterwards purified via nickel affinity chromatography. The ability to form amyloid fibers in vitro was demonstrated by ThT fluorescence and TEM (data not shown). Ni-NTA gold (5 nm) binding to CsgA-NB208-His fibers grown in vitro for 1 week shows the intact fusion is present in these fibers (
For some biotechnological applications, the display of proteins is desired on non-biotic surfaces. Here, CsgA fibers were coupled onto a synthetic surface, namely a magnetic bead. CsgA-6×His was expressed without signal peptide in E. coli BL21DE3 cells and, after production, purified via nickel affinity chromatography. In vitro produced CsgA-6×His fibers (formed in a concentrated CsgA-6×His solution in MES buffer over a three-week period) were sonicated to obtain nuclei, which were covalently coupled to carboxylate-modified magnetic microparticles via the direct EDAC procedure. These activated beads were added to a solution of purified CsgA-His. The coupling of the in vitro grown fibers to the particles was demonstrated by TEM and IF microscopy using an antibody directed to the 6×His-tag (
Bacteria were grown at 37° C. on solid Lysogeny Broth (LB) (Bertani, 2004) or in liquid LB medium supplemented with ampicillin (100 mg l−1) or chloramphenicol (25 mg l−1) when required. To induce curli expression, bacteria were grown for 48 hours at 26° C. on LB, supplemented with Congo red (CR) (100 mg l−1) to monitor curli assembly. For production of CsgA-fusion proteins, two-layered LB plates were used, with the upper and lower layer containing 0.2% (w/v) glucose and 0.2% (w/v) L-arabinose, respectively.
E. coli DH5α was used for all cloning procedures. To create 6×His-tagged CsgA under the control of the arabinose-inducible PBAD promoter, a DNA fragment encoding the csgA gene, including its signal peptide (amino acids M1 to Y151, accession number P28307), was amplified by PCR with primers CsgA FW 1 and CsgA-HIS Rev 1, using chromosomal DNA of E. coli MC4100 as template. After restriction with Acc65I and XbaI, this fragment was ligated into the pBAD33 vector by standard techniques to create pNA1. The In-Fusion™ PCR cloning kit (ClonTech) was used for fusing the major curli subunit CsgA to the N-terminus of Nb208, a nanobody that recognizes green fluorescent protein (GFP). Nb208, without its signal peptide, was amplified by PCR from plasmid pCA0747 using primers NB208 IF flex FW and NB208 IF Rev. The obtained PCR fragment was inserted into the SmaI linearized pNaA1 plasmid, resulting in pNA15. The same strategy was followed to fuse CsgA to beta-lactamase (amino acids H24 to W286, accession number AAB59737.1, pET22b (Novagen) as template), phosphatase A (amino acids P27 to K471, accession number NP_414917, pGV4220 as template (Pattery et al., 1999)), FimC (amino acids G37 to E241, accession number P31697, K514 (Colson et al., 1965) total DNA as template), FedF (amino acids N35 to K185, accession number CAA81288, pExp62 (Moonens et al., 2012) as template), RNase1 (amino acids L1 to Y245, accession number 2PQX_A (Messens et al., 2007)), mCherry (amino acids V1 to K235, accession number ADV78248, psWU30gltFC (Luciano et al., 2011) as template) and ERD10 (amino acids A2 to D260, accession number AEE29973.1 (Kovacs et al., 2008)). pNA35, a C22S mutant of Nb208 in pNA15, was constructed by site-directed mutagenesis (QuikChange protocol, Stratagene) with primers FW mut ser and Rev mut ser starting from pNA15. pNA48, encoding 6×His-tagged ERD10 with the CsgA N-terminal signal peptide only (CsgAN1-A20), was created by outwards PCR with primers Delta A pNA36 FW and DelN22 Rev on pNA36. Deletions of csgA repeats in the csgA-NB208 fusions were carried out by “outwards” PCR on pNA15; primer combinations are described in Example 6. For cytoplasmic expression, csgA-His was amplified by PCR with primers CsgA FW2 and Csg-His Rev2, and cloned into the NdeI/EcoRI sites of pET22b, resulting in pNA9. Via mutagenesis PCR a BamHI restriction site was introduced between csgA and the His-tag in pNA9 (primers BamHI mut FW and BamHI mut Rev), giving rise to pNA52. Next, a PCR fragment of NB208 without signal peptide (primers NB208 IF petBamHI FW and NB208 IF petBamHI Rev on pNA15 as template) was inserted in the BamHI cut pNA52, resulting in pNA53. The gateway cloning system (Invitrogen) was used to generate the vectors for expression of CsgA fusion proteins in Lactococcus lactis cells. His-tagged csgA fusions were amplified from pNA15 and pNA31 to first generate “Entry” clones by BP recombination using primers CsgA-1 and CsgA-2. These Entry vectors were subsequently recombined with a Lactococcus shuttle vector, pTRKH3, harboring different promoters (i.e., Cplc, LacA1, P9, SplA, P43) (Mc Cracken et al., 2000, Rud et al., 2006). NVG1, a csgG deletion mutant of LSR10 was made as described (Datsenko and Wanner, 2000) using primers FwpKD3csgG and RevpKD3csgG. Bacterial strains, plasmids and primers utilized in this work are listed in Tables 4 and 5.
Recombinant gene expression was induced in E. coli DH5α at OD600 0.6, by adding L-arabinose to a final concentration of 0.2% (w/v) and incubating at 37° C. For induction in LSR10 cells, bacteria were grown on two-layered plates (described in bacterial growth conditions) for 48 hours at 26° C. Bacteria were scraped off, resuspended in PBS (pH 7.4) and normalized by optical density at 600 nm. For the in vitro fiber formation experiments, E. coli BL21DE3 (pNA53) cells, grown in LB medium at 37° C. till OD600nm 0.9, were induced with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 1 hour at 37° C.
The presence of the fusion proteins in bacterial whole-cell lysates was determined by SDS-PAGE and subsequent Western blotting (Sambrook and Russel, 2001), using a mouse anti-his monoclonal antibody (mAb) (MCA1396, AbD Serotec) as primary and an anti-mouse IgG alkaline phosphatase conjugated (Sigma) as secondary antibody.
For IF microscopy, bacteria were grown and induced as described above. Cells resuspended in PBS were coated onto poly-L-lysine treated microscope slides (Pallesen et al., 1995). Nonspecific binding was blocked by incubation with 5% (w/v) bovine serum albumin (BSA) for 15 minutes. The slides were subsequently incubated for 1 hour with a 1:400 dilution of an anti-6×His mAb (MCA1396, AbD Serotec), washed with PBS and incubated for 1 hour with a 1:250 dilution of ALEXA FLUOR® 594- or ALEXA FLUOR® 488-labeled goat anti-mouse antibody (Invitrogen). For GFP binding studies, after blocking with BSA, a 45 Ξg ml−1 solution of GFP in PBS was added for 1 hour. Slides were examined by a TE2000-U Nikon microscope with a 100 magnification oil immersion lens.
Bacteria were scraped from inducing plates, resuspended in PBS at an OD600nm of 1. Where indicated, lysozyme and EDTA were added to a final concentration of 1% (w/v) before incubation at 100° C. for 10 minutes. Five μl samples were spotted on a nitrocellulose membrane and air dried. Membrane blocking for non-specific binding was carried out with a 10% (w/v) skimmed milk (biorad) solution in PBS for 10 minutes. The accessibility of the fusion proteins was determined using a mouse anti-6×His mAb (MCA1396, AbD Serotec) as primary and an anti-mouse IgG alkaline phosphatase conjugated (Sigma) as secondary antibody.
Bacterial colonies were scraped from inducing plates, resuspended in PBS and 5 μl samples were absorbed onto formvar-coated copper grids (Agar Scientific) for 2 minutes, washed with deionized water, and negatively stained with 1% (w/v) uranyl acetate for 30 seconds. For immunogold labeling, specimens were blocked with 5% (w/v) BSA in PBS for 10 minutes, afterwards incubated with a 1:100 dilution of an anti-6×His mAb (MCA1396, AbD Serotec) for 30 minutes at RT, washed with PBS and finally incubated for 30 minutes with a 1:100 dilution of an anti-mouse 10 nm gold conjugated antibody (G7652, Sigma). Samples were rinsed with PBS followed by distilled water before negative staining. Alternatively, detection of the 6×His-tag in surface exposed fusion proteins was done using 5 nm Ni-NTA-NANOGOLD® (Nanoprobes). Bacteria absorbed onto the grids were incubated for 10 minutes with 20 μl Ni-NTA-NANOGOLD® solution. After washing three times with PBS, the samples were negatively stained. For TEM on SDS-stable fibers, whole cells scraped from inducing plates were boiled in SDS-sample buffer and loaded on an SDS-PAGE gel. After running, the SDS-stable material was recuperated from the slots, 5 μl was coated on the grids and negatively stained. Bacteria were visualized using a JEM-1400 Transmission Electron Microscope (JEOL).
Bacteria were grown and induced as described above. The cells were scraped off the plates and suspended in PBS at an OD600 of 1.0. One hundred μl of this cell suspension was coated on 96-well microtiter plates for 2 hours at 37° C. Wells were blocked for 1 hour at 37° C. with 10% skimmed milk powder (Biorad) in PBS prior to incubation with the primary antibodies, either a 1:500 dilution of mouse anti-His mAb (MCA1396, AbD Serotec), a 1:200 dilution of mouse anti-peptidoglycan mAb (7263-1006, AbD Serotec) or a 1:2000 dilution of anti-E. coli polyclonal antibody (4329-4906, AbD Serotec). Wells were subsequently washed and bound antibodies were detected by incubation with an anti-mouse IgG alkaline phosphatase conjugated (Sigma) or anti-rabbit IgG alkaline phosphatase conjugated (Sigma-Aldrich) secondary antibody. Binding was revealed by p-dinitrophenylphosphatase (p-DNPP) (Sigma) as substrate. Absorbance values were measured at 405 nm. To make a comparison between the different experiments and between the different fusion constructs, values obtained for anti-His and anti-pep were divided by the corresponding values for the anti-E. coli response. Statistics were done with the Mann-Whitney test (p-values of 0.05 or 0.001), using pBAD33 as reference.
Bacterial cells were resuspended in PBS and incubated for 2 hours at 37° C. with 50 Ξg ml−1 Proteinase K (Thermo Scientific). AEBSF was added to a final concentration of 1 mM to stop the reaction. After formic acid treatment, cell lysates were subjected to SDS-PAGE and subsequent Western blotting using an anti-6×His mAb (MCA1396, AbD Serotec), or an anti-DsbA antiserum (kindly provided by J. Messens) as primary antibody and an anti-mouse or anti-rabbit secondary antibody, respectively.
Curli were isolated by a protocol modified from Collinson et al. (1991) as described previously (Dueholm et al., 2013). Samples were subjected to formic acid treatment and evaluated in Western blotting using an anti-6×His mAb (MCA1396, AbD Serotec) or a rabbit anti-CsgA antiserum (kindly provided by M. R. Chapman).
CsgA-NB208-His without Sec signal sequence is expressed in the cytoplasm of E. coli BL21DE3 and purified via a denaturation method (Zhou et al., 2013). The polymerization kinetics of the purified proteins was followed by ThT fluorescence (Zhou et al., 2013).
CsgA-6×His was purified as described above and fibers were grown during 3 weeks at room temperature. Fibers were sonicated to obtain nuclei (Zhou et al., 2013), which were coupled onto Sera-mag magnetic carboxylate-modified microparticles (Thermo Scientific) via the direct EDAC procedure. After coupling, two washes were performed with an MES buffer. Pellets were resuspended between those washes by ultrasonication. The final pellet was resuspended again in MES buffer.
RNase1 and isolated CsgA-RNase1 curli were digested in solution overnight at 37° C. with sequencing grade-modified trypsin (Promega, Madison, Wis., USA) in 25 mM NH4HCO3. Prior to mass spectrometry analysis, the samples were desalted on ZipTip C18 (Millipore, Billerica, Mass., USA) and eluted in 50% CH3CN/1% HCOOH (v/v). The samples were loaded into gold-palladium-coated borosilicate nanoelectrospray capillaries (Thermo Fisher Scientific, Waltham, Mass., USA) and ESI mass spectra were acquired on a Q-Tof Ultima mass spectrometer (Waters, Milford, Mass., USA), equipped with a Z-spray nanoelectrospray source and operating in the positive ion mode. Capillary voltages of 1.5-1.8 kV and cone voltage of 50 V typically were used. The source temperature was held at 80° C. Data acquisition was performed using the MassLynx 4.1 software. The spectra represent the combination of 1 second scans. The tryptic peptides were initially identified by peptide mass fingerprinting (PMF). The identity of predicted disulphide-bound peptides was confirmed by tandem mass spectrometry (MS/MS). After processing of the MS/MS data by the maximum entropy data enhancement program MaxEnt 3, the amino acid sequences were semi-automatically determined using the peptide sequencing program PepSeq (Waters, Milford, Mass., USA).
S. Typhimurium
GGTACTGATGAGCGATCG
| Number | Date | Country | Kind |
|---|---|---|---|
| 13199513.6 | Dec 2013 | EP | regional |
This application is a national phase entry under 35 U.S.C. §371 of International Patent Application PCT/EP2014/079319, filed Dec. 24, 2014, designating the United States of America and published in English as International Patent Publication WO 2015/097289 A1 on Jul. 2, 2015, which claims the benefit under Article 8 of the Patent Cooperation Treaty to European Patent Application Serial No. 13199513.6, filed Dec. 24, 2013.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2014/079319 | 12/24/2014 | WO | 00 |
