Patent Application
20210040467
Botulinum neurotoxins (BoNTs) are lethal toxins produced by Clostridium botulinum. These toxins can specifically target neuronal terminals of various vertebrates, block the neuron transmitter release, and cause flaccid paralysis usually called “botulism.” The neuron blocking activity of the BoNTs can be utilized for therapeutic purpose, especially on neuron-related diseases, such as blepharospasm, strabismus, upper motor neuron syndrome, sweating, cervical dystonia, and chronic migraine. BoNTs are also widely used in the cosmetic industry.
Some aspects of the present disclosure provide methods of producing Botulinum neurotoxins (BoNTs) recombinantly in Bacillus, the method comprising culturing a Bacillus cell comprising a nucleotide sequence encoding a BoNT, under conditions suitable for expressing the BoNT.
In some embodiments, the nucleotide sequence encoding the BoNT is operably linked to a promoter. In some embodiments, the promoter is an inducible promoter.
In some embodiments, the nucleotide sequence encoding the BoNT is in an expression vector. In some embodiments, the expression vector is selected from the group consisting of: pHT01, pHT08, pHT09, pHT10, pHT43, pHT253, pHT254, pHT 255, pNZ8901, pNZ8902, pNZ8910, pNZ8911, pWH1520, pMM1522, pMM1525, pHIS1522, pHIS1525, pSTREP1525, pSTREPHIS1525, pC-His1622, pC-Strep1622, pN-His-TEV1622, pN-Strep-TEV1622, pN-StrepXa1622, pSTOP1622, p3STOP1623 hp, pC-HIS1623 hp, pN-His-TEV1623 hp, pSP-LipA-hp, pSP-YocH-hp, p3STOP1623-2RBShp, pC-STREP1623 hp, pN-STREP-Xa1623 hp, pN-STREP_TEV1623 hp, pMGBm19, pPT7, pPT7-SPlipA, pPconst1326, pBP26, pBP27, pBQ200, pGP380, pGP382, pGP886, pGP888, pGP1459, pGP1460, pGP1389, pBE-S, and pRB374.
In some embodiments, the BoNT is fused to a fusion domain at the N- or C-terminus. In some embodiments, the fusion domain is an affinity tag. In some embodiments, the affinity tag is selected from the group consisting of: His6, GST, Avi, Strep, S, MBP, Sumo, FLAG, HA, Myc, SBP, E, Calmodulin, Softag 1, Softag 3, TC, V5, VSV, Xpress, Halo, and Fc.
In some embodiments, the nucleotide sequence encoding the BoNT is codon optimized for expression in Bacillus.
In some embodiments, the BoNT is selected from the group consisting of: BoNT/A, BoNT/B, BoNT/C, BoNT/D, BoNT/E, BoNT/F, BoNT/G, BoNT/X, BoNT/En, and variants thereof. In some embodiments, the BoNT is a catalytically inactive BoNT. In some embodiments, the BoNT is a full-length BoNT. In some embodiments, the BoNT is a chimeric BoNT. In some embodiments, the BoNT comprises an amino acid sequence that is at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of SEQ ID NOs: 1-139. In some embodiments, the BoNT comprises the amino acid sequence of any one of SEQ ID NOs: 1-139.
In some embodiments, the method further comprises delivering the nucleotide sequence encoding the BoNT into the Bacillus cell. In some embodiments, the nucleotide sequence encoding the BoNT is delivered via transformation, transduction, conjugation, and electroporation.
In some embodiments, the method further comprises purifying the BoNT from the Bacillus cell. In some embodiments, the BoNT is purified via affinity chromatography, ion exchange chromatography, size-exclusion chromatography, or combinations thereof.
In some embodiments, the Bacillus cell is selected from the group consisting of: Bacillus subtilis, Bacillus megaterium, Bacillus anthracis, and Bacillus brevis. In some embodiments, the Bacillus cell is a wild type cell. In some embodiments, the Bacillus cell is an engineered cell. In some embodiments, the Bacillus is a protease deficient Bacillus cell.
Other aspects of the present disclosure provide a Bacillus cell comprising a nucleotide sequence encoding a Botulinum neurotoxin (BoNT). In some embodiments, the nucleotide sequence encoding the BoNT is operably linked to a promoter. In some embodiments, the promoter is an inducible promoter.
In some embodiments, the nucleotide sequence encoding the BoNT is in an expression vector. In some embodiments, the expression vector is selected from the group consisting of: pHT01, pHT08, pHT09, pHT10, pHT43, pHT253, pHT254, pHT 255, pNZ8901, pNZ8902, pNZ8910, pNZ8911, pWH1520, pMM1522, pMM1525, pHIS1522, pHIS1525, pSTREP1525, pSTREPHIS1525, pC-His1622, pC-Strep1622, pN-His-TEV1622, pN-Strep-TEV1622, pN-StrepXa1622, pSTOP1622, p3STOP1623 hp, pC-HIS1623 hp, pN-His-TEV1623 hp, pSP-LipA-hp, pSP-YocH-hp, p3STOP1623-2RBShp, pC-STREP1623 hp, pN-STREP-Xa1623 hp, pN-STREP_TEV1623 hp, pMGBm19, pPT7, pPT7-SPlipA, pPconst1326, pBP26, pBP27, pBQ200, pGP380, pGP382, pGP886, pGP888, pGP1459, pGP1460, pGP1389, pBE-S, and pRB374.
In some embodiments, the BoNT is fused to a fusion domain at the N- or C-terminus. In some embodiments, the fusion domain is an affinity tag. In some embodiments, the affinity tag is selected from the group consisting of: His6, GST, Avi, Strep, S, MBP, Sumo, FLAG, HA, Myc, SBP, E, Calmodulin, Softag 1, Softag 3, TC, V5, VSV, Xpress, Halo, and Fc.
In some embodiments, the nucleotide sequence encoding the BoNT is codon optimized for expression in Bacillus. In some embodiments, the BoNT is selected from the group consisting of: BoNT/A, BoNT/B, BoNT/C, BoNT/D, BoNT/E, BoNT/F, BoNT/G, BoNT/X, BoNT/En, and variants thereof. In some embodiments, the BoNT is a catalytically inactive BoNT. In some embodiments, the BoNT is a full-length BoNT. In some embodiments, the BoNT is a chimeric BoNT. In some embodiments, the BoNT comprises an amino acid sequence that is at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of SEQ ID NOs: 1-139. In some embodiments, the BoNT comprises the amino acid sequence of any one of SEQ ID NOs: 1-139.
In some embodiments, the Bacillus cell is selected from the group consisting of: Bacillus subtilis, Bacillus megaterium, and Bacillus anthracis, and Bacillus brevis. In some embodiments, the Bacillus cell is a wild type cell. In some embodiments, the Bacillus cell is an engineered cell. In some embodiments, the Bacillus is a protease deficient Bacillus cell.
The accompanying drawings are not intended to be drawn to scale. In the drawings, each identical or nearly identical component that is illustrated in various figures is represented by a like numeral. For purposes of clarity, not every component may be labeled in every drawing. In the drawings:
Botulinum neurotoxins (BoNTs) are lethal toxins produced by Clostridium botulinum. These toxins can specifically target neuronal terminals of various vertebrates, block the neuron transmitter release, and cause flaccid paralysis usually called “botulism”. On the other hand, this property of the toxins can be utilized for therapeutic purpose, especially for neuron-related diseases. Starting from the 1960s, the efficacy of BoNTs in treating neuronal diseases has been explored and BoNTs are now widely used to treat a number of neuronal diseases including, without limitation, blepharospasm, strabismus, upper motor neuron syndrome, sweating, cervical dystonia, and chronic migraine. BoNTs are also widely used in the cosmetic industry. In December 1989, BOTOX, the first BoNT product, was proved by US Food and Drug Administration (FDA) for clinical treatment.
All commercial BoNT products for medical and cosmetic purpose are purified from their natural host C. botulinum. The procedure is time consuming and costly. Moreover, genetic operation is extremely difficult in C. botulinum, which is always an obstacle for developing engineered full length BoNTs. Escherichia coli cells are most commonly used bacterial hosts for expressing engineered proteins. After testing expression and production of BoNTs in E. coli, it was found that E. coli lack the ability to well express large proteins like BoNTs, especially for certain subtypes and engineered/chimeric toxins, which could be a hindrance for large-scale industrial production.
Provided herein are Bacillus cells comprising a nucleotide sequence encoding a Botulinum neurotoxin (BoNT) and methods of producing the BoNT by culturing said Bacillus cell under conditions suitable for expressing the BoNT.
“Botulinum neurotoxins (BoNTs),” as described herein, refer to a family of bacterial toxins that act by blocking neurotransmitter release from neurons, thus causing paralysis. As described herein, the term “BoNT” encompasses neurotoxins produced by Clostridium Botulinum and by other bacterial species but structurally and functionally belong to the BoNT family, and any fragments or variants thereof. BoNTs produced by Clostridium Botulinum include eight major serotypes: BoNT/A-G (e.g., as described in Schiavo et al., Physiol Rev 80, 717-766 (2000), incorporated herein by reference), and BoNT/X (e.g., as described in Zhang et al., Nature Communications, 8, Article number: 14130 (2017), incorporated herein by reference). Each BoNT serotype may have subtypes. For example, BoNT/A has 8 subtypes, BoNT/A1, BoNT/A2, BoNT/A3, BoNT/A4, BoNT/A5, BoNT/A6, BoNT/A7, and BoNT/A8. Similarly, BoNT/B also has 8 subtypes, BoNT/B1, BoNT/B2, BoNT/B3, BoNT/B4, BoNT/B5, BoNT/B6, BoNT/B7, and BoNT/B8. It has been found that bacterial species other than Clostridium Botulinum also produce neurotoxins that belong to the BoNT family, i.e., have similar structure or function as a BoNT produced by Clostridium Botulinum. For example, a BoNT family neurotoxin was identified in Enterococcus faecium and was designated “BoNT/En” (e.g., as described in Zhang et al., 2018, Cell Host and Microbe, 23: 1-8, Doi:10.1016/j.chom.2017.12.018, incorporated herein by reference).
In some embodiments, the BoNT is a full-length BoNT. A “full-length” BoNT refers to a BoNT that does not have any truncations, compared to a wild-type BoNT. A full-length BoNT may contain other types of mutations, compared to a wild-type BoNT, e.g., amino acid substitutions or fusion domains. In some embodiments, the BoNT is a naturally occurring, wild-type BoNT, e.g., any of the BoNTs described herein and known in the art. In some embodiments, the BoNT is a variant of a wild-type BoNT. BoNT variants have been previously described. For example, BoNT variants that have enhanced binding to target cells are described in PCT Application Publication WO 2017214447, incorporated herein by reference. In another example, the BoNT is a catalytically inactive variant, e.g., as described in PCT Application Publication WO 2018009903, incorporated herein by reference.
A BoNT comprises a heavy chain (herein termed “BoNT-HC”) and a light chain (herein termed “BoNT-LC”) linked by a linker region. A proteolytic cleavage occurs in the linker region when a BoNT is processed into its mature form. The BoNT-LC comprises a protease domain that cleaves the substrates of the BoNT, while the BoNT-HC comprises a translocation domain at the N terminus of the heavy chain (HN) and a receptor binding domain at the C terminus of the heavy chain (HC), which mediate the entering of the BoNT into a cell. It has been shown that chimeric BoNTs can exert the function of a naturally occurring BoNT. A “chimeric BoNT” refers to a BoNT comprising domains from different BoNT serotypes. In some embodiments, a chimeric BoNT may contain the protease domain (LC) and the translocation domain (HN) from one BoNT (e.g., any one of BoNT/A-G, BoNT/X, and BoNT/En) and the receptor binding domain (HC) from a different BoNT (e.g., from any one of BoNT/A-G, BoNT/X, and BoNT/En, except where the LC and HN are from). In some embodiments, a chimeric BoNT comprises other variations, e.g., amino acid substations. Non-limiting, exemplary chimeric BoNTs are provided in Table 1.
In some embodiments, the BoNT produced using the method described herein comprises an amino acid sequence that is at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of SEQ ID NOs: 1-139. In some embodiments, the BoNT produced using the method described herein comprises the amino acid sequence of any one of SEQ ID NOs: 1-139. In some embodiments, the BoNT produced using the method described herein consists of the amino acid sequence of any one of SEQ ID NOs: 1-139. Non-limiting, exemplary amino acid sequences of the BoNTs that can be produced using the methods described herein are provided in Table 1.
In some embodiments, the BoNT is fused to a fusion domain at the N- or C-terminus. A “fusion domain” refers to a polypeptide sequence that is appended to the BoNT via an amide bond. In some embodiments, the fusion domain is an affinity tag. An “affinity tag,” as used herein, refers to a polypeptide sequence that can bind specifically to a substance or a moiety, e.g., a tag comprising six Histidines bind specifically to Ni2+. Affinity tags may be appended to proteins to facilitate their isolation. The affinity tags are typically fused to proteins via recombinant DNA techniques known by those skilled in the art. The use of affinity tags to facilitate protein isolate is also well known in the art. Suitable affinity tags that may be used in accordance with the present disclosure include, without limitation, His6, GST, Avi, Strep, S, MBP, Sumo, FLAG, HA, Myc, SBP, E, Calmodulin, Softag 1, Softag 3, TC, V5, VSV, Xpress, Halo, and Fc.
Other aspects of the present disclosure provide nucleotide sequences encoding the BoNTs described herein. A “nucleotide sequence” is at least two nucleotides covalently linked together, and in some instances, may contain phosphodiester bonds (e.g., a phosphodiester “backbone”). A nucleotide sequence may be DNA, both genomic and/or cDNA, RNA or a hybrid, where the nucleotide sequence contains any combination of deoxyribonucleotides and ribonucleotides (e.g., artificial or natural), and any combination of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine, hypoxanthine, isocytosine and isoguanine.
In some embodiments, the nucleotide sequence encoding the BoNT is at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5%, or 100% identical to any one of SEQ ID NOs: 1-139. In some embodiments, the nucleotide sequence encoding the BoNT is 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to any one of SEQ ID NOs: 1-139.
In some embodiments, the nucleotide sequence encoding the BoNT is codon optimized for expression in a Bacillus cell. Codon optimization methods are known in the art and may be used as provided herein. Codon optimization, in some embodiments, may be used to match codon frequencies in target and host organisms to ensure proper folding; bias GC content to increase mRNA stability or reduce secondary structures; minimize tandem repeat codons or base runs that may impair gene construction or expression; customize transcriptional and translational control regions; insert or remove protein trafficking sequences; remove/add post translation modification sites in encoded protein (e.g. glycosylation sites); add, remove or shuffle protein domains; insert or delete restriction sites; modify ribosome binding sites and mRNA degradation sites; adjust translational rates to allow the various domains of the protein to fold properly; or to reduce or eliminate problem secondary structures within the polynucleotide. Codon optimization tools, algorithms and services are known in the art—non-limiting examples include services from GeneArt (Life Technologies), DNA2.0 (Menlo Park Calif.) and/or proprietary methods. In some embodiments, the open reading frame (ORF) sequence is optimized using optimization algorithms.
In some embodiments, a codon optimized sequence shares less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, or less than 60% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a BoNT). In some embodiments, a codon optimized sequence shares 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a BoNT).
In some embodiments, the nucleotide sequence encoding the BoNT is operably linked to a promoter. A “promoter” refers to a control region of a nucleotide sequence at which initiation and rate of transcription of the remainder of a nucleotide sequence are controlled. A promoter drives expression or drives transcription of the nucleotide sequence that it regulates. A promoter may also contain sub-regions at which regulatory proteins and molecules may bind, such as RNA polymerase and other transcription factors. Promoters may be constitutive, inducible, activatable, repressible, tissue-specific or any combination thereof. A promoter is considered to be “operably linked” when it is in a correct functional location and orientation in relation to a nucleotide sequence it regulates to control (“drive”) transcriptional initiation and/or expression of that sequence.
A promoter may be one naturally associated with a gene or sequence, as may be obtained by isolating the 5′ non-coding sequences located upstream of the coding segment of a given gene or sequence. Such a promoter can be referred to as “endogenous.”
In some embodiments, a coding nucleotide sequence may be positioned under the control of a recombinant or heterologous promoter, which refers to a promoter that is not normally associated with the encoded sequence in its natural environment. Such promoters may include promoters of other genes; promoters isolated from any other cell; and synthetic promoters or enhancers that are not “naturally occurring” such as, for example, those that contain different elements of different transcriptional regulatory regions and/or mutations that alter expression through methods of genetic engineering that are known in the art. In addition to producing nucleic acid sequences of promoters and enhancers synthetically, sequences may be produced using recombinant cloning and/or nucleic acid amplification technology, including polymerase chain reaction (PCR) (see U.S. Pat. Nos. 4,683,202 and 5,928,906).
In some embodiments, a promoter is an “inducible promoter,” which refers to a promoter that is characterized by regulating (e.g., initiating or activating) transcriptional activity when in the presence of, influenced by or contacted by an inducer signal. An inducer signal may be endogenous or a normally exogenous condition (e.g., light), compound (e.g., chemical or non-chemical compound) or protein that contacts an inducible promoter in such a way as to be active in regulating transcriptional activity from the inducible promoter. Thus, a “signal that regulates transcription” of a nucleic acid refers to an inducer signal that acts on an inducible promoter. A signal that regulates transcription may activate or inactivate transcription, depending on the regulatory system used. Activation of transcription may involve directly acting on a promoter to drive transcription or indirectly acting on a promoter by inactivation a repressor that is preventing the promoter from driving transcription. Conversely, deactivation of transcription may involve directly acting on a promoter to prevent transcription or indirectly acting on a promoter by activating a repressor that then acts on the promoter. In some embodiments, using inducible promoters in the genetic circuits of the cell state classifier results in the conditional expression or a “delayed” expression of a gene product.
The administration or removal of an inducer signal results in a switch between activation and inactivation of the transcription of the operably linked nucleotide sequence. Thus, the active state of a promoter operably linked to a nucleotide sequence refers to the state when the promoter is actively regulating transcription of the nucleotide sequence (i.e., the linked nucleotide sequence is expressed). Conversely, the inactive state of a promoter operably linked to a nucleotide sequence refers to the state when the promoter is not actively regulating transcription of the nucleotide sequence (i.e., the linked nucleotide sequence is not expressed).
An inducible promoter of the present disclosure may be induced by (or repressed by) one or more physiological condition(s), such as changes in light, pH, temperature, radiation, osmotic pressure, saline gradients, cell surface binding, and the concentration of one or more extrinsic or intrinsic inducing agent(s). An extrinsic inducer signal or inducing agent may comprise, without limitation, amino acids and amino acid analogs, saccharides and polysaccharides, nucleic acids, protein transcriptional activators and repressors, cytokines, toxins, petroleum-based compounds, metal containing compounds, salts, ions, enzyme substrate analogs, hormones or combinations thereof.
Inducible promoters of the present disclosure include any inducible promoter described herein or known to one of ordinary skill in the art. Examples of inducible promoters include, without limitation, chemically/biochemically-regulated and physically-regulated promoters such as alcohol-regulated promoters, tetracycline-regulated promoters (e.g., anhydrotetracycline (aTc)-responsive promoters and other tetracycline-responsive promoter systems, which include a tetracycline repressor protein (tetR), a tetracycline operator sequence (tetO) and a tetracycline transactivator fusion protein (tTA)), steroid-regulated promoters (e.g., promoters based on the rat glucocorticoid receptor, human estrogen receptor, moth ecdysone receptors, and promoters from the steroid/retinoid/thyroid receptor superfamily), metal-regulated promoters (e.g., promoters derived from metallothionein (proteins that bind and sequester metal ions) genes from yeast, mouse and human), pathogenesis-regulated promoters (e.g., induced by salicylic acid, ethylene or benzothiadiazole (BTH)), temperature/heat-inducible promoters (e.g., heat shock promoters), and light-regulated promoters (e.g., light responsive promoters from plant cells).
In some embodiments, an inducer signal of the present disclosure is an N-acyl homoserine lactone (AHL), which is a class of signaling molecules involved in bacterial quorum sensing. Quorum sensing is a method of communication between bacteria that enables the coordination of group based behavior based on population density. AHL can diffuse across cell membranes and is stable in growth media over a range of pH values. AHL can bind to transcriptional activators such as LuxR and stimulate transcription from cognate promoters.
In some embodiments, an inducer signal of the present disclosure is anhydrotetracycline (aTc), which is a derivative of tetracycline that exhibits no antibiotic activity and is designed for use with tetracycline-controlled gene expression systems, for example, in bacteria.
In some embodiments, an inducer signal of the present disclosure is isopropyl β-D-1-thiogalactopyranoside (IPTG), which is a molecular mimic of allolactose, a lactose metabolite that triggers transcription of the lac operon, and it is therefore used to induce protein expression where the gene is under the control of the lac operator. IPTG binds to the lac repressor and releases the tetrameric repressor from the lac operator in an allosteric manner, thereby allowing the transcription of genes in the lac operon, such as the gene coding for beta-galactosidase, a hydrolase enzyme that catalyzes the hydrolysis of β-galactosides into monosaccharides. The sulfur (S) atom creates a chemical bond which is non-hydrolyzable by the cell, preventing the cell from metabolizing or degrading the inducer. IPTG is an effective inducer of protein expression, for example, in the concentration range of 100 μM to 1.0 mM. Concentration used depends on the strength of induction required, as well as the genotype of cells or plasmid used. If lacIq, a mutant that over-produces the lac repressor, is present, then a higher concentration of IPTG may be necessary. In blue-white screen, IPTG is used together with X-gal. Blue-white screen allows colonies that have been transformed with the recombinant plasmid rather than a non-recombinant one to be identified in cloning experiments.
Other inducible promoter systems are known in the art and may be used in accordance with the present disclosure.
In some embodiments, inducible promoters of the present disclosure are from prokaryotic cells (e.g., bacterial cells). Examples of inducible promoters for use prokaryotic cells include, without limitation, bacteriophage promoters (e.g. Pls1con, T3, T7, SP6, PL) and bacterial promoters (e.g., Pbad, PmgrB, Ptrc2, Plac/ara, Ptac, Pm), or hybrids thereof (e.g. PLlacO, PLtetO). Examples of bacterial promoters for use in accordance with the present disclosure include, without limitation, positively regulated E. coli promoters such as positively regulated σ70 promoters (e.g., inducible pBad/araC promoter, Lux cassette right promoter, modified lamdba Prm promote, plac Or2-62 (positive), pBad/AraC with extra REN sites, pBad, P(Las) TetO, P(Las) CIO, P(Rhl), Pu, FecA, pRE, cadC, hns, pLas, pLux), σS promoters (e.g., Pdps), σ32 promoters (e.g., heat shock) and σ54 promoters (e.g., glnAp2); negatively regulated E. coli promoters such as negatively regulated σ70 promoters (e.g., Promoter (PRM+), modified lamdba Prm promoter, TetR-TetR-4C P(Las) TetO, P(Las) CIO, P(Lac) IQ, RecA_DlexO_DLacO1, dapAp, FecA, Pspac-hy, pcI, plux-cI, plux-lac, CinR, CinL, glucose controlled, modified Pr, modified Prm+, FecA, Pcya, rec A (SOS), Rec A (SOS), EmrR_regulated, BetI_regulated, pLac_lux, pTet_Lac, pLac/Mnt, pTet/Mnt, LsrA/cI, pLux/cI, LacI, LacIQ, pLacIQ1, pLas/cI, pLas/Lux, pLux/Las, pRecA with LexA binding site, reverse BBa_R0011, pLacI/ara-1, pLacIq, rrnB P1, cadC, hns, PfhuA, pBad/araC, nhaA, OmpF, RcnR), σS promoters (e.g., Lutz-Bujard LacO with alternative sigma factor σ38), σ32 promoters (e.g., Lutz-Bujard LacO with alternative sigma factor σ32), and σ54 promoters (e.g., glnAp2); negatively regulated B. subtilis promoters such as repressible B. subtilis GA promoters (e.g., Gram-positive IPTG-inducible, Xyl, hyper-spank) and GB promoters. Other inducible microbial promoters may be used in accordance with the present disclosure.
The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. In addition, a host cell strain (e.g., Bacillus) may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products may be important for the function of the protein. For example, the BoNT described herein is expressed as a single gene product (e.g., as a single polypeptide chain), and is then proteolytic cleavage in the linker region to be processed into its mature form.
In some embodiments, the nucleotide sequence encoding the BoNT is incorporated into vectors (e.g., cloning vectors or expression vectors). A “vector” refers to a nucleic acid (e.g., DNA) used as a vehicle to artificially carry genetic material (e.g., an engineered nucleic acid) into a cell where, for example, it can be replicated and/or expressed. In some embodiments, a vector is an episomal vector (see, e.g., Van Craenenbroeck K. et al. Eur. J. Biochem. 267, 5665, 2000, incorporated by reference herein). A non-limiting example of a vector is a plasmid. Plasmids are double-stranded generally circular DNA sequences that are capable of automatically replicating in a host cell. Plasmid vectors typically contain an origin of replication that allows for semi-independent replication of the plasmid in the host and also the transgene insert. Plasmids may have more features, including, for example, a “multiple cloning site,” which includes nucleotide overhangs for insertion of a nucleic acid insert, and multiple restriction enzyme consensus sites to either side of the insert. Another non-limiting example of a vector is a viral vector (e.g., retroviral, adenoviral, adeno-association, helper-dependent adenoviral systems, hybrid adenoviral systems, herpes simplex, pox virus, lentivirus, Epstein-Barr virus). In some embodiments, the viral vector is derived from an adeno-associated virus (AAV). In some embodiments, the viral vector is derived from an herpes simplex virus (HSV).
Additionally, the vector may contain, for example, some or all of the following: a selectable marker gene, e.g., genes that confer antibiotic resistance to the Bacillus cell. Suitable vectors and methods for producing vectors containing transgenes are well known and available in the art.
In bacterial systems, a number of expression vectors may be advantageously selected depending upon the use intended for the polypeptides being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of pharmaceutical compositions of polypeptides described herein, vectors which direct the expression of high levels of fusion protein products that are readily purified may be desirable. Such vectors include, but are not limited, to the E. coli expression vector pUR278 (Rüther et al. (1983) “Easy Identification Of cDNA Clones,” EMBO J. 2:1791-1794), in which the coding sequence may be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye et al. (1985) “Up-Promoter Mutations In The 1pp Gene Of Escherichia Coli,” Nucleic Acids Res. 13:3101-3110; Van Heeke et al. (1989) “Expression Of Human Asparagine Synthetase In Escherichia Coli,” J. Biol. Chem. 24:5503-5509); and the like. pGEX vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption and binding to a matrix glutathione-agarose beads followed by elution in the presence of free glutathione.
The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety. In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The coding sequence may be cloned individually into non-essential regions (e.g., the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (e.g., the polyhedrin promoter).
In some embodiments, the vectors are adapted for expressing the BoNT in a Bacillus cell. Expression vectors suitable for expressing proteins (e.g., BoNT) in a Bacillus cell are commercially available. For example, Mibitec GmbH (Germany) provides numberous expression vectors suitable for protein expression in Bacillus, including, pHT01 (#PBS001), pHT08 (#PBS003), pHT09 (#PBS004), pHT10 (#PBS005), pHT43 (#PBS002), pHT253 (#PBS013), pHT254 (#PBS014), pHT255 (#PBS015), pNZ8901 (#PBS031), pNZ8902 (#PBS032), pNZ8910 (#PBS033), pNZ8911 (#PBS034), pWH1520 (#BMEG03), pMM1522 (#BMEG10), pMM1525 (#BMEG 11), pHIS1522 (#BMEG 12), pHIS1525 (#BMEG 13), pSTREP1525 (#BMEG 14), pSTREPHIS1525 (#BMEG 15), pC-His1622 (#BMEG 20), pC-Strep1622 (#BMEG 21), pN-His-TEV1622 (#BMEG 22), pN-Strep-TEV1622 (#BMEG 23), pN-StrepXa1622 (#BMEG 24), pSTOP1622 (#BMEG 25), p3STOP1623 hp (#BMEG 30), pC-HIS1623 hp (#BMEG31), pN-His-TEV1623 hp (#BMEG 32), pSP-LipA-hp (#BMEG 33), pSP-YocH-hp (#BMEG 34), p3STOP1623-2RBShp (#BMEG 35), pC-STREP1623 hp (#BMEG 36), pN-STREP-Xa1623 hp (#BMEG 37), pN-STREP_TEV1623 hp (#BMEG 38), pMGBm19 (#BMEG 39), pPT7 (#BMEG T710), pPT7-SPlipA (#BMEG T711), and pPconst1326 (#BMEG 45). Takara Bio Inc. (Japan) provides a Bacillus subtilis secretory protein expression system (#3380) including an expression vector pBES. Further, ATCC provides vector pRB374 (#ATCC77374) for Bacillus expression. One skilled in the art is able to choose the appropriate expression vector.
The method of producing a BoNT described herein comprises culturing a Bacillus cell comprising the nucleotide sequence encoding the BoNT under conditions suitable for expressing the BoNT. In some embodiments, the method further comprises delivering the nucleotide sequence encoding the BoNT to a Bacillus cell. Standard molecular biology techniques are used to prepare and deliver the recombinant expression vector, and culture the Bacillus cells. An expression vector comprising the nucleotide sequence encoding the BoNT can be transferred to a host cell by conventional techniques (e.g., electroporation, transformation, transduction, or conjugation) and the resulting Bacillus cells are then cultured by conventional techniques to produce the BoNT described herein.
The Bacillus cells may be cultured at an appropriate temperature (e.g., 16° C.-42° C.) for an appropriate amount of time (e.g., 4-72 hours). In some embodiments, the Bacillus cells are cultured at 16, 18, 20, 25, 30, 35, 37, 40, or 42° C. In some embodiments, the Bacillus cells are cultured for 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 36, 48, 60, 72 hours or longer. Any standard culturing media (e.g., Luria-Bertani (LB) media) suitable for Bacillus cells can be used. If the expression of the BoNT is driven by an inducible promoter, the media may further contain an inducer at an appropriate concentration that activates the inducible promoter.
Once the BoNT has been recombinantly expressed, it may be purified by any method known in the art for example, by chromatography (e.g., affinity chromatography, ion exchange chromatography, size-exclusion chromatography, or combinations thereof), centrifugation, differential solubility, or by any other standard technique for the purification of polypeptides.
The BoNT produced using the method described herein is substantially free of (e.g., at least 80%, 90%, 95%, 97%, 99%, or 99.5% free of), other protein(s) and/or other polypeptide(s) (e.g., other Bacillus proteins). In some embodiments, the isolated polypeptides is 100% free of other protein(s) and/or other polypeptide(s) (e.g., Bacillus proteins). The methods described herein provide high yield of intact BoNTs. Being “intact” means that the BoNT products are substantially free of truncated products (e.g., those produced due to aborted translation or protease cleavage). As demonstrated herein, in some embodiments, about 5-10 mg protein can be obtained from one litter LB cultured B. subtilis.
The BoNT produced using the methods herein have comparable biological activities as a naturally occurring BoNT (e.g., in target cell recognition, translocation, and/or substrate cleavage). Having “comparable biological activity” means that the BoNT produced using the methods described herein are have at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of the biological activity (e.g., in target cell recognition, translocation, and substrate cleavage) of a naturally occurring BoNT. In some embodiments, the BoNT produced using the methods described herein are have 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or more of the biological activity (e.g., in target cell recognition, translocation, and substrate cleavage) of a naturally occurring BoNT.
The host cells used for BoNT expression in the methods described herein are Bacillus cells. Exemplary Bacillus cells that may be used include, without limitation: B. acidiceler, B. acidicola, B. acidiproducens, B. acidocaldarius, B. acidoterrestris, B. aeolius, B. aerius, B. aerophilus, B. agaradhaerens, B. agri, B. aidingensis, B. akibai, B. alcalophilus, B. algicola, B. alginolyticus, B. alkalidiazotrophicus, B. alkalinitrilicus, B. alkalisediminis, B. alkalitelluris, B. altitudinis, B. alveayuensis, B. alvei, B. amyloliquefaciens, B. aminovorans[2], B. amylolyticus, B. andreesenii, B. aneurinilyticus, B. anthracis, B. aquimaris, B. arenosi, B. arseniciselenatis, B. arsenicus, B. aurantiacus, B. arvi, B. aryabhattai, B. asahii, B. atrophaeus, B. axarquiensis, B. azotofixans, B. azotoformans, B. badius, B. barbaricus, B. bataviensis, B. beijingensis, B. benzoevorans, B. beringensis, B. berkeleyi, B. beveridgei, B. bogoriensis, B. boroniphilus, B. borstelensis, B. brevis Migula, B. butanolivorans, B. canaveralius, B. carboniphilus, B. cecembensis, B. cellulosilyticus, B. centrosporus, B. cereus, B. chagannorensis, B. chitinolyticus, B. chondroitinus, B. choshinensis, B. chungangensis, B. cibi, B. circulans, B. clarkii, B. clausii, B. coagulans, B. coahuilensis, B. cohnii, B. composti, B. curdlanolyticus, B. cycloheptanicus, B. cytotoxicus, B. daliensis, B. decisifrondis, B. decolorationis, B. deserti, B. dipsosauri, B. drentensis, B. edaphicus, B. ehimensis, B. eiseniae, B. enclensis, B. endophyticus, B. endoradicis, B. farraginis, B. fastidiosus, B. fengqiuensis, B. firmus, B. flexus, B. foraminis, B. fordii, B. formosus, B. fortis, B. fumarioli, B. funiculus, B. fusiformis, B. galactophilus, B. galactosidilyticus, B. galliciensis, B. gelatini, B. gibsonii, B. ginsengi, B. ginsengihumi, B. ginsengisoli, B. glucanolyticus, B. gordonae, B. gottheilii, B. graminis, B. halmapalus, B. haloalkaliphilus, B. halochares, B. halodenitrificans, B. halodurans, B. halophilus, B. halosaccharovorans, B. hemicellulosilyticus, B. hemicentroti, B. herbersteinensis, B. horikoshii, B. horneckiae, B. horti, B. huizhouensis, B. humi, B. hwajinpoensis, B. idriensis, B. indicus, B. infantis, B. infernus, B. insolitus, B. invictae, B. iranensis, B. isabeliae, B. isronensis, B. jeotgali, B. kaustophilus, B. kobensis, B. kochii, B. kokeshiiformis, B. koreensis, B. korlensis, B. kribbensis, B. krulwichiae, B. laevolacticus, B. larvae, B. laterosporus, B. lautus, B. lehensis, B. lentimorbus, B. lentus, B. licheniformis, B. ligniniphilus, B. litoralis, B. locisalis, B. luciferensis, B. luteolus, B. luteus, B. macauensis, B. macerans, B. macquariensis, B. macyae, B. malacitensis, B. mannanilyticus, B. marisflavi, B. marismortui, B. marmarensis, B. massiliensis, B. megaterium, B. mesonae, B. methanolicus, B. methylotrophicus, B. migulanus, B. mojavensis, B. mucilaginosus, B. muralis, B. murimartini, B. mycoides, B. naganoensis, B. nanhaiensis, B. nanhaiisediminis, B. nealsonii, B. neidei, B. neizhouensis, B. niabensis, B. niacini, B. novalis, B. oceanisediminis, B. odysseyi, B. okhensis, B. okuhidensis, B. oleronius, B. oryzaecorticis, B. oshimensis, B. pabuli, B. pakistanensis, B. pallidus, B. pallidus, B. panacisoli, B. panaciterrae, B. pantothenticus, B. parabrevis, B. paraflexus, B. pasteurii, B. patagoniensis, B. peoriae, B. persepolensis, B. persicus, B. pervagus, B. plakortidis, B. pocheonensis, B. polygoni, B. polymyxa, B. popilliae, B. pseudalcalophilus, B. pseudofirmus, B. pseudomycoides, B. psychrodurans, B. psychrophilus, B. psychrosaccharolyticus, B. psychrotolerans, B. pulvifaciens, B. pumilus, B. purgationiresistens, B. pycnus, B. qingdaonensis, B. qingshengii, B. reuszeri, B. rhizosphaerae, B. rigui, B. runs, B. safensis, B. salarius, B. salexigens, B. saliphilus, B. schlegelii, B. sediminis, B. selenatarsenatis, B. selenitireducens, B. seohaeanensis, B. shacheensis, B. shackletonii, B. siamensis, B. silvestris, B. simplex, B. siralis, B. smithii, B. soli, B. solimangrovi, B. solisalsi, B. songklensis, B. sonorensis, B. sphaericus, B. sporothermodurans, B. stearothermophilus, B. stratosphericus, B. subterraneus, B. subtilis, B. taeanensis, B. tequilensis, B. thermantarcticus, B. thermoaerophilus, B. the rmoamylovorans, B. thermocatenulatus, B. thermocloacae, B. thermocopriae, B. the rmodenitrificans, B. thermoglucosidasius, B. thermolactis, B. thermoleovorans, B. thermophilus, B. thermoruber, B. thermosphaericus, B. thiaminolyticus, B. thioparans, B. thuringiensis, B. tianshenii, B. trypoxylicola, B. tusciae, B. validus, B. vallismortis, B. vedderi, B. velezensis, B. vietnamensis, B. vireti, B. vulcani, B. wakoensis, B. weihenstephanensis, B. xiamenensis, B. xiaoxiensis, and B. zhanjiangensis. In some embodiments, the Bacillus cell is Bacillus subtilis, Bacillus megaterium, Bacillus anthracis, or Bacillus brevis.
In some embodiments, the Bacillus subtilis, Bacillus megaterium, and Bacillus anthracis, and Bacillus brevis.
In some embodiments, the Bacillus cell is a wild-type cell (i.e., unmodified genetically). In some embodiments, the Bacillus cell is engineered to be protease deficient (e.g., by inactivating one or more genes encoding proteases in the Bacillus cell). Protease deficient Bacillus have been described for expressing recombinant proteins, e.g., in Fahnestock et al., Appl Environ Microbiol. 1987 February; 53(2): 379-384, incorporated herein by reference.
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Some of the embodiments, advantages, features, and uses of the technology disclosed herein will be more fully understood from the Examples below. The Examples are intended to illustrate some of the benefits of the present disclosure and to describe particular embodiments, but are not intended to exemplify the full scope of the disclosure and, accordingly, do not limit the scope of the disclosure.
C. botulinum is a gram-positive bacterium, which is evolutionary close to the model bacterium Bacillus subtilis, but is genetically far away from E. coli (
The crystal structure of full-length BoNT/A, BoNT/B and BoNT/E have been solved previously, giving an overall view of these molecules. Not many disulfide bonds were found within these 150-kd molecules, suggesting an oxidative environment or additional oxidative cofactors are not essential for the production of BoNTs; which is expected, because C. botulinum is an anaerobic bacterium. The surface distribution of the hydrophobic and hydrophilic residues are relatively even across these toxins like BoNT/A and BoNT/B (
iBoNT/B (“i” refers to the inactive form, which contains R370A/Y373F mutations at its enzymatic domain) was used as an example of BoNTs and the express pattern of it in E. coli was analyzed. Generally, very few products were obtained using E. coli, despite varying the expression conditions including growth temperature, inducer concentration, and culture medium. Therefore, the low yield of iBoNT/B in E. coli could be mainly because of the intrinsic defect of the host. To validate this, iBoNT/B fused with either N-terminal or C-terminal His-tag was expressed in E. coli. A large amount of the iBoNT/B products in the cell lysate were presented as shorter fragments wherever the tag was attached. For C-terminal tagged iBoNT/B, purification by Ni-NTA beads removed the majority of the shorter fragments. In contrast, all fragments of N-terminal tagged iBoNT/B remained after IMAC purification (
Next, the expression pattern of iBoNT/B was analyzed in B. subtilis by Western-blot. Unlike in E. coli, the majority of the expressed iBoNT/B existed as integrate full-length protein (
Next, the expression plasmids for other botulinum neurotoxins including iBoNT/A, iBoNT/C, iBoNT/D were created, and the expression of those proteins were tested in B. subtilis. As expected, all of these proteins were able to be produced in B. subtilis with decent yields (
Here, a new protocol has been developed to express full-length BoNTs in B. subtilis with improved protein quality and yield. This protocol could be used to produce full-length BoNTs and their variants for scientific study, to produce active toxins for medical therapy or cosmetics, and to develop natural/recombinant toxoids vaccines.
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents of the embodiments described herein. The scope of the present disclosure is not intended to be limited to the above description, but rather is as set forth in the appended claims.
Articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between two or more members of a group are considered satisfied if one, more than one, or all of the group members are present, unless indicated to the contrary or otherwise evident from the context. The disclosure of a group that includes “or” between two or more group members provides embodiments in which exactly one member of the group is present, embodiments in which more than one members of the group are present, and embodiments in which all of the group members are present. For purposes of brevity those embodiments have not been individually spelled out herein, but it will be understood that each of these embodiments is provided herein and may be specifically claimed or disclaimed.
It is to be understood that the disclosure encompasses all variations, combinations, and permutations in which one or more limitation, element, clause, or descriptive term, from one or more of the claims or from one or more relevant portion of the description, is introduced into another claim. For example, a claim that is dependent on another claim can be modified to include one or more of the limitations found in any other claim that is dependent on the same base claim. Furthermore, where the claims recite a composition, it is to be understood that methods of making or using the composition according to any of the methods of making or using disclosed herein or according to methods known in the art, if any, are included, unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise.
Where elements are presented as lists, e.g., in Markush group format, it is to be understood that every possible subgroup of the elements is also disclosed, and that any element or subgroup of elements can be removed from the group. It is also noted that the term “comprising” is intended to be open and permits the inclusion of additional elements or steps. It should be understood that, in general, where an embodiment, product, or method is referred to as comprising particular elements, features, or steps, embodiments, products, or methods that consist, or consist essentially of, such elements, features, or steps, are provided as well. For purposes of brevity those embodiments have not been individually spelled out herein, but it will be understood that each of these embodiments is provided herein and may be specifically claimed or disclaimed.
Where ranges are given, endpoints are included. Furthermore, it is to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value within the stated ranges in some embodiments, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise. For purposes of brevity, the values in each range have not been individually spelled out herein, but it will be understood that each of these values is provided herein and may be specifically claimed or disclaimed. It is also to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values expressed as ranges can assume any subrange within the given range, wherein the endpoints of the subrange are expressed to the same degree of accuracy as the tenth of the unit of the lower limit of the range.
Where websites are provided, URL addresses are provided as non-browser-executable codes, with periods of the respective web address in parentheses. The actual web addresses do not contain the parentheses.
In addition, it is to be understood that any particular embodiment of the present disclosure may be explicitly excluded from any one or more of the claims. Where ranges are given, any value within the range may explicitly be excluded from any one or more of the claims. Any embodiment, element, feature, application, or aspect of the compositions and/or methods of the disclosure, can be excluded from any one or more claims. For purposes of brevity, all of the embodiments in which one or more elements, features, purposes, or aspects is excluded are not set forth explicitly herein.
This application claims the benefit under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 62/623,715, filed Jan. 30, 2018, and entitled “PRODUCTION OF BOTULINUM NEUROTOXINS USING BACILLUS SYSTEMS,” the entire contents of which are incorporated herein by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2019/015594 | 1/29/2019 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62623715 | Jan 2018 | US |
