# Patent

## Title
High level expression of recombinant toxin proteins

## Abstract

The present invention relates to the field of recombinant toxin protein production in bacterial hosts. In particular, the present invention relates to production processes for obtaining high levels of a recombinant CRM197, Diphtheria Toxin, Pertussis Toxin, Tetanus Toxoid Fragment C, Cholera Toxin B, Cholera holotoxin, and Pseudomonas Exotoxin A, from a bacterial host.

## Background
CLAIM OF PRIORITY
This application claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application Ser. No. 61/325,235 filed on Apr. 16, 2010, PCT/US10/30573 filed on Apr. 9, 2010, and U.S. Provisional Application Ser. No. 61/319,152 filed on Mar. 30, 2010, and is a continuation-in-part of PCT/US10/30573, filed on Apr. 9, 2010, which claims priority to U.S. Provisional Application Ser. No. 61/319,152 filed on Mar. 30, 2010. The contents of these applications are hereby incorporated by reference in their entirety.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Mar. 16, 2011, is named 38194201.txt and is 156,975 bytes in size.
BACKGROUND OF THE INVENTION
Microbial toxin proteins are used in medicine, as immunogens for vaccination against the toxin-producing microbe and as carrier proteins and adjuvants for other vaccines, and in scientific research as tools for studying molecular pathways.
Diphtheria toxin (DT) is a proteinaceous toxin that is synthesized and secreted by toxigenic strains of Corynebacterium diphtheriae. Toxigenic strains contain a bacteriophage lysogen carrying the toxin gene. DT is synthesized as a 535-amino-acid polypeptide, which undergoes proteolysis to form the mature toxin. The mature toxin comprises two subunits, A and B, joined by a disulfide bridge. The B subunit, formed from the C-terminal portion of intact DT, enables binding and entry of DT through the cell membrane and into the cytoplasm. Upon cell entry, the enzymatic A subunit, formed from the N terminal portion of intact DT, catalyzes ADP ribosylation of Elongation Factor 2 (EF-2). As a result, EF-2 is inactivated, protein synthesis stops, and the cell dies. Diphtheria toxin is highly cytotoxic; a single molecule can be lethal to a cell, and a dose of 10 ng/kg can kill animals and humans.
The CRM197 protein is a nontoxic, immunologically cross-reacting form of DT. It has been studied for its potential use as a DT booster or vaccine antigen. CRM197 is produced by C. diphtheriae that has been infected by the nontoxigenic phage β197tox-created by nitrosoguanidine mutagenesis of the toxigenic corynephage β. The CRM197 protein has the same molecular weight as DT but differs by a single base change (guanine to adenine) in the A subunit. This single base change results in an amino acid substitution (glutamic acid for glycine) and eliminates the toxic properties of DT.
Conjugated polysaccharide vaccines that use CRM197 as a carrier protein have been approved for human use. Vaccines include: Menveo® (Novartis Vaccines and Diagnostics), a vaccine indicated for preventing invasive meningococcal disease caused by Neisseria meningitidis subgroups A, C, Y, and W-135; Menjugate (Novartis Vaccines), a meningococcal group C conjugate vaccine; and Prevnar® (Wyeth Pharmaceuticals, Inc.), a childhood pneumonia vaccine that targets seven serotypes of Streptococcus pneumoniae, and HibTITER® (Wyeth), a Haemophilus influenzae type b vaccine. In addition, CRM197 has potential use as a boosting antigen for C. diphtheria vaccination and is being investigated as a carrier protein for use in other vaccines.
A method for high-level expression of CRM197 for approved therapeutics and investigational use has not been reported. CRM197 has been expressed in, e.g., C. diphtheriae, B. subtilis, and E. coli, at levels that range in the tens of mg/L. A single dose of the Prevnar conjugate vaccine contains about 20 μg of CRM197. Therefore, a method for economically producing CRM197 at levels of about 1 g/L or more would greatly facilitate vaccine research and manufacture.
Cholera Toxin (CTX), produced by Vibrio cholera, a bacterial pathogen that causes an infection characterized by diarrhea and vomiting, is also an ADP-ribosylating toxin. CTX is an oligomeric complex made up of six protein subunits: a single copy of the Cholera toxin A subunit (CTA), and five copies of the Cholera Toxin B subunit (CTB). The five B subunits, each weighing 12 kDa, form a five-membered ring. The A subunit has an A1 portion, CTA1, a globular enzyme that ADP-ribosylates G proteins, and an A2 chain, CTA2, that forms an extended alpha helix which sits snugly in the central pore of the B subunit ring. This ring binds to GM1 ganglioside receptors on the host cell surface, resulting in internalization of the entire complex. Once internalized, the CTA1 chain is released by reduction of a disulfide bridge. CTA1 is then activated and catalyzes ADP ribosylation of adenylate cyclase. The resulting increase in adenylate cyclase activity increases cyclic AMP synthesis, which causes massive fluid and electrolyte efflux and results in diarrhea.
The B subunit of CTX, though relatively harmless, retains its ability to bind to the GM1 ganglioside receptor. CTB therefore finds use in facilitating mucosal uptake of chemically or genetically conjugated foreign antigens. It has been demonstrated to induce both mucosal and systemic immunity, and is a candidate for use in edible vaccine production. Because of its binding preference, CTB also finds use as a neuronal tracer.
Pertussis toxin (PTX) is an exotoxin and virulence factor produced by Bordetella pertussis, a bacterial pathogen of the human respiratory tract that causes the disease whooping cough. The pertussis holotoxin is a multi-subunit complex with an AB 5 structure. The enzymatically active A subunit (S1) is an ADP-ribosyltransferase that modifies the alpha subunit of several heterotrimeric G proteins in mammalian cells, and the B oligomer (S2, S3, two copies of S4, and S5) binds glycoconjugate receptors on cells. The five subunits of the toxin are expressed from the Pertussis Toxoid operon.
Nontoxic variants of Pertussis toxin have been explored for use in protective vaccines and as a vaccine adjuvant. There is also a need for Pertussis toxin protein to use in research, e.g., for studies of G protein signaling pathways.
Tetanus Toxin, produced by Clostridium tetani, is a neurotoxin having a molecular weight of 150 kDa. It is made up of two parts: a 100 kDa heavy or B-chain and a 50 kDa light or A-chain. The chains are connected by a disulfide bond. The B-chain binds to disialogangliosides (GD2 and GD1b) on the neuronal membrane. The A-chain, a zinc endopeptidase, attacks the vesicle-associated membrane protein (VAMP).
The action of the A-chain stops the affected neurons from releasing the inhibitory neurotransmitters GABA (gamma-aminobutyric acid) and glycine by degrading the protein synaptobrevin. The consequence of this is dangerous overactivity in the muscles from the smallest stimulus—the failure of inhibition of motor reflexes by sensory stimulation. This causes generalized contractions of the agonist and antagonist musculature, termed a tetanic spasm.
Tetanus Toxin Fragment C (Tet C or TTC) is a 50 kD polypeptide generated by protease cleavage (e.g., with papain) of Tetanus toxin, or through recombinant expression of the fragment. It corresponds to the 451 amino acids at the C-terminus (amino acid positions 865-1315).
Fragment C has been shown to be non-toxic. Because it binds to neurons with high specificity and affinity, TTC finds use as a targeting molecule for neuronal drug delivery or for research purposes. TTC protein is also potentially useful as a vaccine carrier protein and for use in a vaccine to protect against C. tetani infection.
Clostridium difficile Toxin B (TcdB) is a virulence factor produced by Clostridium difficile, which causes hospital acquired diarrhea and pseudomembranous colitis. TcdB, and a second large clostridial toxin, TcdA, are involved in the development of pseudomembranous colitis.
TcdB is a glucosylating toxin of about 270 kD, and can be divided into enzymatic, translocation and receptor binding domains. The first 546 amino acids of TcdB contain the enzymatic region, which is followed by a putative translocation and receptor-binding domain. TcdB has potential use as a protective vaccine for C. difficile infection, as well as in diagnostic tests and their development.
Exotoxin A (ETA or PE) of Pseudomonas aeruginosa is a Type II ADPRT. Like its family members Diphtheria toxin and Cholera Toxin, it inhibits protein synthesis by the ADP-ribosylation of cellular elongation factor 2. P. aeruginosa Exotoxin A exists as a monomer, consisting of a single polypeptide chain of 613 amino acids (66 Kd).
ETA is potentially useful as a vaccine conjugate. Nontoxic mutants of ETA have been studied as vaccine conjugates for vaccinations that protect against Staphylococcus aureus, malaria, and Salmonella Typhi. 
Producing these toxins in amounts sufficient to meet expanding needs has presented significant challenges. When made in conventional protein overexpression systems, the toxin proteins are recovered in active form only at very low concentration due to degradation, improper folding, or both, depending on the specific characteristics, e.g., size and secondary structure, of the toxin. Therefore, methods for producing large amounts of these toxins, in soluble and/or active form, and at low cost is needed.
SUMMARY OF THE INVENTION
The present invention relates to a method for producing a recombinant toxin protein in a Pseudomonad host cell, said method comprising: ligating into an expression vector a nucleotide sequence encoding a toxin protein; transforming the Pseudomonas host cell with the expression vector; and culturing the transformed Pseudomonas host cell in a culture media suitable for the expression of the recombinant toxin protein; wherein the recombinant toxin protein is CRM197, Diphtheria Toxin, Cholera holotoxin, Cholera Toxin B, Pertussis toxin, Tetanus Toxin Fragment C, C. difficile Toxin B, or P. aeruginosa Exotoxin A.
In embodiments, the recombinant toxin protein is Cholera Toxin B, Cholera holotoxin, Pertussis toxin, Tetanus Toxin Fragment C, C. difficile Toxin B, or P. aeruginosa Exotoxin A.
In other embodiments, the recombinant toxin protein is Cholera Toxin B, Cholera holotoxin, Pertussis toxin, Tetanus Toxin Fragment C, or C. difficile Toxin B.
In other embodiments, the recombinant toxin protein is CRM197, Diphtheria Toxin, Cholera holotoxin, Cholera Toxin B, Pertussis toxin, Tetanus Toxin Fragment C, or C. difficile Toxin B.
In certain embodiments, the recombinant protein is produced at a yield of soluble and/or active toxin protein of about 0.2 grams per liter to about 12 grams per liter. In specific embodiments, the yield of soluble and/or active toxin protein is about 0.2 g/L, about 0.3 g/L, about 0.4 g/L, about 0.5 g/L, about 0.6 g/L, about 0.7 g/L, about 0.8 g/L, about 0.9 g/L, about 1 g/L, about 1.5 g/L, about 2 g/L, about 2.5 g/L, about 3 g/L, about 3.5 g/L, about 4 g/L, about 4.5 g/L, about 5 g/L, about 5.5 g/L, about 6 g/L, about 6.5 g/L, about 7 g/L, about 7.5 g/L, about 8 g/L, about 8.5 g/L, about 9 g/L, about 9.5 g/L, about 10 g/L, about 10.5 g/L, about 11 g/L, about 12 g/L, about 0.2 g/L to about 0.5 g/L, about 0.2 g/L to about 1 g/L, about 0.2 to about 2 g/L, about 0.3 g/L to about 0.6 g/L, about 0.3 g/L to about 1 g/L, about 0.3 to about 2 g/L, about 0.4 to about 0.7 g/L, about 0.4 to about 1 g/L about 0.4 to about 2 g/L, about 0.4 to about 3 g/L, about 0.5 g/L to about 1 g/L, about 0.5 g/L to about 2 g/L, about 0.5 g/L to about 3 g/L, about 0.5 g/L to about 4 g/L, about 0.5 g/L to about 5 g/L, about 0.5 g/L to about 6 g/L, about 0.5 g/L to about 7 g/L, about 0.5 g/L to about 8 g/L, about 0.5 g/L to about 9 g/L, about 0.5 g/L to about 10 g/L, about 0.5 g/L to about 11 g/L, about 0.5 g/L to about 12 g/L, about 1 g/L to about 2 g/L, about 1 g/L to about 3 g/L, about 1 g/L to about 4 g/L, about 1 g/L to about 5 g/L, about 1 g/L to about 6 g/L, about 1 g/L to about 7 g/L, about 1 g/L to about 8 g/L, about 1 g/L to about 9 g/L, about 1 g/L to about 10 g/L, about 1 g/L to about 11 g/L, about 1 g/L to about 12 g/L, about 2 g/L to about 3 g/L, about 2 g/L to about 4 g/L, about 2 g/L to about 5 g/L, about 2 g/L to about 6 g/L, about 2 g/L to about 7 g/L, about 2 g/L to about 8 g/L, about 2 g/L to about 9 g/L, about 2 g/L to about 10 g/L, about 2 g/L to about 11 g/L, about 2 g/L to about 12 g/L, about 3 g/L to about 4 g/L, about 3 g/L to about 5 g/L, about 3 g/L to about 6 g/L, about 3 g/L to about 7 g/L, about 3 g/L to about 8 g/L, about 3 g/L to about 9 g/L, about 3 g/L to about 10 g/L, about 3 g/L to about 11 g/L, about 3 g/L to about 12 g/L, about 4 g/L to about 5 g/L, about 4 g/L to about 6 g/L, about 4 g/L to about 7 g/L, about 4 g/L to about 8 g/L, about 4 g/L to about 9 g/L, about 4 g/L to about 10 g/L, about 4 g/L to about 11 g/L, about 4 g/L to about 12 g/L, about 5 g/L to about 6 g/L, about 5 g/L to about 7 g/L, about 5 g/L to about 8 g/L, about 5 g/L to about 9 g/L, about 5 g/L to about 10 g/L, about 5 g/L to about 11 g/L, about 5 g/L to about 12 g/L, about 6 g/L to about 7 g/L, about 6 g/L to about 8 g/L, about 6 g/L to about 9 g/L, about 6 g/L to about 10 g/L, about 6 g/L to about 11 g/L, about 6 g/L to about 12 g/L, about 7 g/L to about 8 g/L, about 7 g/L to about 9 g/L, about 7 g/L to about 10 g/L, about 7 g/L to about 11 g/L, about 7 g/L to about 12 g/L, about 8 g/L to about 9 g/L, about 8 g/L to about 10 g/L, about 8 g/L to about 11 g/L, about 8 g/L to about 12 g/L, about 9 g/L to about 10 g/L, about 9 g/L to about 11 g/L, about 9 g/L to about 12 g/L, about 10 g/L to about 11 g/L, about 10 g/L to about 12 g/L, or about 11 g/L to about 12 g/L.
In embodiments, the nucleotide sequence encoding the toxin protein is fused to a secretion signal coding sequence that when expressed directs transfer of the toxin protein to the periplasm. In embodiments, the host cell is defective in the expression of at least one protease or the host cell overexpresses at least one folding modulator, or a combination thereof.
In embodiments, the recombinant toxin protein is CRM197 and the host cell is defective in the expression of HslU, HslV, Prc1, DegP1, DegP2, and AprA. In related embodiments, the recombinant toxin protein is fused to a secretion leader that is Azu, IbpS31A, CupA2, PbpA20V, or Pbp. In embodiments, the recombinant toxin protein is CRM197 and the host cell is defective in the expression of HslU and HslV, or Prc1, or DegP1, or DegP2, or AprA. In specific embodiments, the recombinant toxin protein is CRM197 and the host cell is defective in the expression of Serralysin, HslU, HslV, Prc1, DegP1, DegP2, or AprA, or the host cell overexpresses DsbA, DsbB, DsbC, and DsbD. In embodiments, the host cell overexpresses DsbA, DsbB, DsbC, and DsbD, and the recombinant toxin protein is fused to the secretion leader Azu. In embodiments, the host cell is defective in the expression of Serralysin, and the recombinant toxin protein is fused to the secretion leader Pbp or Azu. In embodiments, the host cell is defective in the expression of HslU and HslV, and the recombinant toxin protein is fused to the secretion leader Pbp or Azu. In embodiments, the recombinant toxin protein is CRM197, the host cell is wild-type and wherein the recombinant toxin protein is fused to the secretion leader Pbp or Azu. In embodiments, the recombinant toxin protein is CRM197 and the recombinant toxin protein is fused to the secretion leader Azu, Pbp, IbpS31A, CupA2, or PbpA20V.
In other embodiments, the recombinant toxin protein is Cholera Toxin B and the host cell is defective in the expression of Lon, La, and AprA, or the host cell is defective in the expression of HslU, HslV, Prc1, DegP1, DegP2, and AprA. In related embodiments, the host cell is defective in the expression of Lon, La, and AprA and wherein the recombinant toxin protein is fused to the secretion leader Pbp A20V.
In other embodiments, the recombinant toxin protein is Pertussis toxin S1 E129A R9K and the host cell is defective in the expression of Lon, La, and AprA; GrpE, DnaK, and DnaJ; HtpX; RXF01590; or ppiB (RXF05345). In related embodiments, the recombinant toxin protein is fused to its native secretion leader.
In other embodiments, the recombinant toxin protein is Tetanus Toxin C and the host cell is defective in the expression of HslU, HslV, Prc1, DegP1, DegP2, and AprA. In related embodiments, the recombinant toxin protein is fused to the secretion leader DsbC, Pbp A20V, or CupA2.
In other embodiments, the recombinant toxin protein is Tetanus Toxin C and the host cell is defective in the expression of Lon, La, and AprA. In related embodiments, the recombinant toxin protein is fused to the secretion leader DsbA.
In other embodiments, the recombinant toxin protein is Tetanus Toxin C and the host cell is defective in the expression of GrpE, DnaK, and DnaJ. In related embodiments, the recombinant toxin protein is fused to the secretion leader NikA.
In other embodiments, the recombinant toxin protein is C. difficile Toxin B and the host cell is defective in the expression of: HtpX; DegP1; HslU, HslV, Prc1 and Prc2; or Lon and DegP2, or the host cell is both defective in the expression of Lon, Prc1, DegP2, AprA and overexpresses DegP2 S219A.
In embodiments, the activity of the recombinant toxin protein is measured in an activity assay, wherein about 40% to about 100% of the soluble toxin protein produced is determined to be active. In related embodiments, the activity assay is an immunological assay, a receptor-binding assay, or an enzyme assay.
In embodiments of the invention, the expression vector comprises a lac derivative promoter operatively linked to the protein coding sequence, and wherein the culturing comprises induction of the promoter using IPTG at a concentration of about 0.02 to about 1.0 mM, the cell density at induction is an optical density of about 40 to about 200 absorbance units (AU), the pH of the culture is from about 6 to about 7.5, and the growth temperature is about 20 to about 35° C.
In embodiments, the host cell is a Pseudomonas cell. In related embodiments, the host cell is Pseudomonas fluorescens. 
In embodiments of the invention, the nucleotide sequence has been optimized for expression in the Pseudomonad host cell. In related embodiments, the nucleotide sequence has been optimized for expression in the Pseudomonas host cell. In other related embodiments, the nucleotide sequence has been optimized for expression in the Pseudomonas fluorescens host cell.
In embodiments, the Pertussis toxin is wild-type or S1 E129A R9K. In embodiments, the P. aeruginosa Exotoxin A is wild-type, CRM66, or rEPA.
In embodiments of the invention, the expression vector further comprises a tag sequence adjacent to the coding sequence for the secretion signal. In embodiments, the expression vector further comprises a tag sequence adjacent to the coding sequence for the toxin protein.
The present invention also provides a recombinant toxin protein produced according to the methods described herein. In embodiments, the recombinant toxin protein is CRM197, Diphtheria Toxin, Cholera holotoxin, Cholera Toxin B, Pertussis Toxin, Tetanus Toxin fragment C, C. difficile Toxin B, or P. aeruginosa Exotoxin A. In embodiments, the Exotoxin A is wild-type, CRM66, or rEPA. In certain embodiments, the recombinant toxin protein is produced in a strain of P. fluorescens identified herein as producing a high yield of the toxin or producing high quality toxin. In certain embodiments, the recombinant toxin protein is produced in a strain of P. fluorescens described herein as producing the highest yield of the toxin protein. In other embodiments, the recombinant toxin protein is produced in a strain described herein as one used for fermentation production of the toxin.
INCORPORATION BY REFERENCE
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.



BRIEF DESCRIPTION OF THE DRAWINGS
The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings.
FIG. 1. CRM197 Amino Acid and DNA Sequences. A. Amino acid sequence (SEQ ID NO: 1). B. An optimized DNA sequence (SEQ ID NO:2) encoding the CRM197 protein, with translation shown. This optimized sequence is a non-limiting example of an optimized sequence useful in the methods of the present invention.
FIG. 2. High Throughput Expression Analysis of CRM197. CRM197 protein expressed using the DNA sequence shown in FIG. 1B was analyzed using capillary gel electrophoresis (SDS-CGE). Soluble fractions of 40 CRM197-expression strains tested are shown in a gel-like image generated from the SDS-CGE data. Strain names as described in Table 10 are listed above each lane. P. fluorescens-expressed CRM197 migrated as a single band at  ̃58 kDa on SDS-CGE (arrow at left). Molecular weight markers in first and last lanes are 16, 20, 29, 48, 69 and 119 kDa.
FIG. 3. Cholera Toxin B Amino Acid and DNA Sequences. A. Amino acid sequence (SEQ ID NO: 22). B. An optimized DNA sequence (SEQ ID NO: 23) encoding the CTB protein, with translation. This optimized sequence is a non-limiting example of an optimized sequence useful in the methods of the present invention.
FIG. 4. High Throughput Expression Analysis of Cholera Toxin B. Cholera Toxin B protein expressed using the DNA sequence shown in FIG. 3B was analyzed using capillary gel electrophoresis (SDS-CGE). Soluble fractions from 40 cholera toxin-expression strains tested are shown in a gel-like image generated from the SDS-CGE data. Strain names as described in Table 11 are listed above each lane. Induced CTB migrated as a single band at  ̃11.5 kDa on SDS-CGE (arrow at left). Molecular weight markers in first and last lanes are 16, 20, 29, 48, 69 and 119 kDa.
FIG. 5. Pertussis Toxoid Operon. BPETOX_S1-R9K & E129A, having 4210 basepairs, is shown.
FIG. 6. DNA Sequence of the Pertussis Toxoid. The Pertussis toxin S1 R9K E129A DNA sequence with translation is shown (SEQ ID NO:24). The sequence is derived from Genebank entry M13223. Subunits S1-S5 and signal sequences are indicated above the sequences. The R9K and E129A mutations in 51 are underlined. Encoded proteins are disclosed as SEQ ID NOS 25, 26, 28, 29, and 27, respectively, in order of appearance.
FIG. 7. Amino Acid Sequences of Pertussis Toxoid Subunits. Secretion signals are underlined. FIG. 7A. S1 subunit (R9K E129A) (SEQ ID NO:25). FIG. 7B. S2 subunit (SEQ ID NO:26). FIG. 7C. S3 subunit (SEQ ID NO:27). FIG. 7D. S4 subunit (SEQ ID NO:28). FIG. 7E. S5 subunit (SEQ ID NO:29).
FIG. 8. Western blot analysis of Pertussis Toxoid expression samples. Strain names are listed above each lane. Induced Ptx migrated as multiple bands range from 11 to 26 kDa (S1: 26.1 Kda, S2: 20.9 Kda, S3: 21.8 KDa, S4 (2×): 12 KDa, S5: 11 KDa) A. Reduced samples. B. Non-reduced samples. Both panels: Lane 1—molecular weight markers (10, 15, 20, 25, 37, 50, 75, 100, 150, 250 kDa); Lane 2—Null; Lane 3—strain 321; Lane 4—strain 322; Lane 5—strain 323; Lane 6—strain 324; Lane 7—strain 325; Lane 8—strain 326; Lane 9—strain 327; Lane 10—strain 328.
FIG. 9. Tetanus Toxin C Amino Acid and DNA Sequences. A. Amino acid sequence (SEQ ID NO:30). B. An optimized DNA sequence encoding the Tetanus Toxin C protein, with translation (SEQ ID NO:31). This optimized sequence is a non-limiting example of an optimized sequence useful in the methods of the present invention.
FIG. 10. Tetanus Toxin C Fragment Expression. Tetanus Toxin C Fragment expressed in P. fluorescens was analyzed using capillary gel electrophoresis (SDS-CGE). Soluble fractions from 40 tetanus toxin-expression strains tested are shown in a gel-like image generated from the SDS-CGE data. Strain names as described in Table 15 are listed above each lane. Induced Tetanus Toxin C Fragment migrated as a single band at  ̃51.6 kDa on SDS-CGE (arrow at left). Molecular weight markers in first and last lanes are 16, 20, 29, 48, 69 and 119 kDa.
FIG. 11. TcdB Amino Acid and DNA Sequences. A. Amino acid sequence (SEQ ID NO:32). B. An optimized DNA sequence encoding the TcdB protein, with translation (SEQ ID NO:33). This optimized sequence is a non-limiting example of an optimized sequence useful in the methods of the present invention.
FIG. 12. TcdB Expression. TcdB expressed in P. fluorescens was analyzed using capillary gel electrophoresis (SDS-CGE). Soluble fractions from 24 TcdB-expression strains tested are shown in a gel-like image generated from the SDS-CGE data. Strain names as described in Table 18 as well as null extract and reference standard (List Biologicals) are listed above each lane. Induced TcdB migrated as a single band at  ̃300 kDa on SDS-CGE (arrow at left). Molecular weight markers in first and last lanes are 16, 20, 29, 48, 69 and 119 kDa.
FIG. 13. Exotoxin A Amino Acid Sequence. The amino acid sequence of P. aeruginosa Exotoxin A is shown (SEQ ID NO:34). Three Exotoxin A proteins are indicated by the drawing: wild-type, CRM66, and rEPA. In variant CRM66, His 426 (bold, underlined text) is replaced by a Tyr as indicated above the sequence. In rEPA, Glu 553 (bold, underlined text) is deleted as indicated above the sequence.
FIG. 14. Soluble Tetanus Toxin C and Cholera Toxin B Production in P. fluorescens Fermentation Cultures. SDS-CGE Analysis. Lane 1-16, 20, 29, 48, 69 and 119 kDa molecular weight markers. Lanes 2 and 4-pre-induction samples and lanes 3 and 5 post-induction samples, respectively, of PS538-088 U5 and U6 fermentations expressing Cholera Toxin B, indicated by arrow at right.
FIG. 15. Soluble Tetanus Toxin Fragment C Production in P. fluorescens Fermentation Cultures. A. SDS-CGE Analysis. Lane 1-16, 20, 29, 48, 69 and 119 kDa molecular markers. Lanes 2, 3 and 4 are post-induction samples of PS538-529 U1 PS538-546 U5 and PS538-547 U7 fermentations, respectively, expressing Tetanus Toxin Fragment C, indicated by arrow at right. B. Western Blot Analysis. Fermentation samples from strains PS538-538 (U1 and U2), PS538-548 (U3 and U4), PS538-558 (U5 and U6) and PS538-568 (U7 and U8) were evaluated by Westen blot. Fermentation unit and hours post induction (I0, I8, I24) are indicated above each lane. Molecular weight (MW) standards are shown on the left of the blot and Tetanus Toxin C reference standard (Std; List Biological, Cat#193) is shown on the right. Blots were probed with Polyclonal Anti-Tetanus Toxin C Fragment, derived in Rabbit (Abcam, Cat#: ab34890) followed by Anti-Rabbit IgG Peroxidase, derived in Goat (Pierce, Cat#: 31460). Immunopure Metal Enhanced DAB (Pierce 34065) was used for detection.
FIG. 16. Soluble C. difficile B Toxin Protein Production in P. fluorescens Fermentation Cultures. Lane 1-16, 20, 29, 48, 69 and 119 kDa molecular weight markers. The marker sizes are also indicated in their respective positions at the right, based on migration in Lane 1. Lanes 2, 3 and 4 are post-induction samples of PS538-671 U5 and U6, and PS538-674 U7 fermentations, respectively, expressing C. difficile B Toxin Protein, indicated by arrow at right.
FIG. 17. DNA Sequence of Wild-Type Pertussis Toxoid. The wild-type Pertussis toxin DNA sequence with translation is shown (SEQ ID NO:35). The sequence is from Genebank entry M13223. Subunits S1-S5 and signal sequences are indicated above the sequences. The encoded proteins are disclosed as SEQ ID NOS 41-45, respectively, in order of appearance.
FIG. 18. Amino Acid and DNA Sequence of Wild-Type Diphtheria toxin. A. Amino acid sequence (SEQ ID NO: 36). B. An optimized DNA sequence (SEQ ID NO:37) encoding the DT protein, with translation shown. This optimized sequence is a non-limiting example of an optimized sequence useful in the methods of the present invention. The encoded protein is disclosed as residues 1-320 of SEQ ID NO: 36.
FIG. 19. Amino Acid and DNA Sequence of Cholera Holotoxin. A. CTA amino acid sequence (SEQ ID NO: 38), with secretion leader (underlined) (AE003852; Protein ID AAF94614.1). B. CTB amino acid sequence (SEQ ID NO: 39), with secretion leader (underlined) (GenBank AE003852; Protein ID AAF94613.1). C. CTX DNA sequence (SEQ ID NO:40) indicating the A and B subunits, with translation shown (Genbank AE003852). The encoded proteins are disclosed as SEQ ID NOS 38 and 39, respectively, in order of appearance.
FIG. 20. SDS-CGE Gel-like Image of Soluble rEPA Production in P. fluorescens Fermentation Cultures. Soluble rEPA expressed in fermentation cultures of P. fluorescens was analyzed using capillary gel electrophoresis (SDS-CGE). Soluble fractions from fermentations of expression strains PS538-1633 (u1 and u2), PS538-1640 (u3 and u5) and PS538-1670 (u6, u7 and u8) at 0 and 24 hours post-induction tested are shown in a gel-like image generated from the SDS-CGE data. Mw=molecular weight standards (16, 20, 29, 48, and 69 kilodaltons).
FIG. 21. Soluble rEPA Production Trends in P. fluorescens Fermentation Cultures. Soluble rEPA expression levels, as determined by SDS-CGE analysis of strains (PS538-1633, PS538-1640 and PS538-1670) in their respective fermentations (u1, u2, u3, u6, u7 and u8), are plotted against post-induction times.
FIG. 22. Western Blot of Soluble rEPA Production in P. fluorescens Fermentation Cultures. Soluble rEPA expressed in fermentation cultures of P. fluorescens were analyzed using Western blot analysis. Soluble fractions from fermentations of expression strains PS538-1633 (u1), PS538-1640 (u3 and u5) and PS538-1670 (u6 and u8) at 0 and 24 hours post-induction are shown in a Western blot analysis using an antibody specific for P. aeruginosa Exotoxin A. Mw=molecular weight standards. std=rEPA standard.
FIG. 23. SDS-CGE Gel-like Image of Soluble CRM197 Production in P. fluorescens Fermentation Cultures. CRM197 expressed in fermentation cultures of P. fluorescens was analyzed using capillary gel electrophoresis (SDS-CGE). Soluble fractions from various fermentations of expression strains PS538-772 (u1 and u2), PS538-776 (u3 and u5) and PS538-782 (u6 and u7) at various times post-induction (0, 16, 21 and 23 hours) tested are shown in a gel-like image generated from the SDS-CGE data. Mw=molecular weight standards (16, 20, 29, 48, 68, and 119 kilodaltons).
FIG. 24. Soluble CRM197 Production Trends in P. fluorescens Fermentation Cultures. Soluble CRM197 expression levels as determined by SDS-CGE from the different strains (PS538-772, PS538-776 and PS538-782) in their respective fermentations (u1, u2, u3, u6 and u7) are plotted against post-induction times.
FIG. 25. Western Blot of Soluble CRM197 Production in P. fluorescens Fermentation Cultures. CRM197 expressed in fermentation cultures of P. fluorescens were analyzed using Western blot analysis. Soluble fractions from various fermentations of expression strains PS538-772 (u1 and u2), PS538-776 (u3 and u5) and PS538-782 (u6 and u7) at various times post-induction (0, 16, 21 and 23 hours) tested are shown in a Western blot analysis using a diphtheria toxin specific antibody. Mw=molecular weight standards (37, 50, 75, 100, 150, and 250 kilodaltons). STD=CRM197 standard.



DETAILED DESCRIPTION OF THE INVENTION
Toxins
ADP-Ribosylating Toxins
ADP-ribosylating toxins (ADPRTs) facilitate scission of the N-glycosyl bond between nicotinamide and the N-ribose of NAD and transfer the ADP-ribose moiety to target proteins. ADPRTs are classified into four families based on their respective targets. Type I ADPRTs target heteromeric GTP-binding proteins. They include Cholera Toxin (CTX), Pertussis toxin (PTX), and Escherichia coli heat-labile enterotoxin (LT). Type II ADPRTs (Diphtheria toxin and Pseudomonas Exotoxin A) modify elongation factor 2 (EF2). Type III ADPRTs (Clostridium botulinum C3 exoenzyme) ADP-ribosylate small GTP-binding proteins. Type IV ADPRTs ADP-ribosylate actin. These actin-specific ADPRTs include a family of binary toxins comprising C. botulinum C2 toxin, C. perfringens l-toxin, C. difficile toxin (a toxin distinct from TcdA and TcdB, described by Popoff, et al., 1988, “Actin-specific ADP-ribosyltransferase produced by a Clostridium difficile strain,” Infection and Immunity 56(9):2299-2306, incorporated herein by reference), C. spiroforme toxin, and Bacillus cereus vegetative insecticidal protein (VIP).
The structures of several enzymatic components from each type of ADPRT have been determined with or without NAD, and are discussed by, e.g., Tsuge, et al., 2008, “Structural basis of actin recognition and arginine ADP-ribosylation by Clostridium perfringens-toxin,” PNAS 105(21):7399-7404, incorporated herein by reference. Typical actin-specific ADPRTs possess two similar domains: the C domain, which is essential for catalytic activity; and the N domain, which is important for the interaction with the binding and translocation subunit. By contrast, SpvB from Salmonella and the type III ADPRT C3 have only one ADP-ribosyltransferase domain and lack the N-terminal adaptor domain. In all type IV ADPRTs, the EXE motif, including two key glutamate residues, is present at the catalytic center. The former glutamate of the EXE motif is thought to be a key residue for ADP-ribosyltransferase, which is deprotonated from Arg-177 in actin. The latter glutamate forms a hydrogen bond with the O′2 on N-ribose, which is thought to stabilize the oxocarbenium cation.
ADPRTs are further described by Barth, et al., 2004, “Binary Bacterial Toxins: Biochemistry, Biology, and Application of Common Clostridium and Bacillus Proteins,” Microbiology and Molecular Biology Reviews 68(3):373-402; Mueller-Dieckmann, et al., “Structure of mouse ADP-ribosylhydrolase 3 (mARH3),” Acta Cryst F64:156-162; Kulich, et al., 1995, “Expression of Recombinant Exoenzyme S of Pseudomonas aeruginosa,” Infection and Immunity 63(1):1-8; Sakurai, et al., 2009, “Clostridium perfringens Iota-Toxin: Structure and Function,” Toxins 1:208-228; and Schirmer, et al., 2002, “The ADP-ribosylating Mosquitocidal Toxin from Bacillus sphaericus,” The Journal of Biological Chemistry 277(14): 11941-11948, all incorporated herein by reference.
In embodiments of the present invention, a recombinant toxin protein selected from a group including ADPRTs is produced. In embodiments, the group of ADPRTs consists of CTX (CTA and/or CTB), PTX, DT (CRM197 and/or WT), and Pseudomonas Exotoxin A. In embodiments, the group of ADPRTs consists of CTX(CTA and/or CTB), PTX, and Pseudomonas Exotoxin A. In other embodiments, a recombinant toxin protein selected from a group including Type I ADPRTs is produced. In embodiments, the group of Type I ADPRTs consists of CTX (CTA and/or CTB), and PTX. In other embodiments, a recombinant toxin protein selected from a group including Type II ADPRTs is produced. In embodiments, the group of Type II ADPRTs consists of DT (CRM197 and/or WT), and Pseudomonas Exotoxin A. In other embodiments, a recombinant toxin protein selected from a group including Type IV ADPRTs is produced. In embodiments, the Type IV ADPRT is TcdB.
CRM197 and DT
Cross-reacting material 197 (CRM197) is a Diphtheria toxin (DT) variant produced from a DT gene having a missense mutation. DT is an ADP-ribosylating toxin; CRM197 lacks the ADP-ribosyltransferase (ADPRT) activity of DT, and is thus nontoxic. The gene for CRM197 has a single base substitution, resulting in the incorporation of glutamic acid instead of glycine at residue 52. (See, e.g., Bishai, et al., 1987, “High-Level Expression of a Proteolytically Sensitive Diphtheria toxin Fragment in Escherichia coli,” J. Bact. 169(11):5140-51, Giannini, et al., 1984, “The Amino-Acid Sequence of Two Non-Toxic Mutants of Diphtheria toxin: CRM45 and CRM197,” Nucleic Acids Research 12(10): 4063-9, and GenBank Acc. No. 1007216A, all incorporated herein by reference.)
CRM197 protein may be prepared at low levels by methods known in the art or by expression in C. diphtheriae or other microorganisms. The naturally occurring, or wild-type, Diphtheria toxin may be obtained from toxin producing strains available from a variety of public sources including the American Type Culture Collection. A plasmid system for producing CRM197 protein in C. diphtheriae is described by, e.g., U.S. Pat. No. 5,614,382, “Plasmid for Production of CRM Protein and Diphtheria toxin,” incorporated herein by reference in its entirety.
The nucleotide sequence may be prepared using the techniques of recombinant DNA technology (described by, e.g., Sambrook et al, Molecular Cloning, a Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989), and also by site-directed mutagenesis, based on the known DT nucleotide sequence of the wild type structural gene for Diphtheria toxin carried by corynebacteriophage β. (See, e.g., Greenfield, et al., 1993, “Nucleotide Sequence of the Structural Gene for Diphtheria toxin Carried by Corynebacteriophage 18,” Proc Nat Acad Sci 80:6953-7, incorporated herein by reference.) The nucleotide sequence can be optimized as described elsewhere herein.
In embodiments of the present invention, CRM197 or DT are produced using any of the host strains described herein in Example 1, in combination with any of the expression vectors (plasmids) described in Example 1. In embodiments, the nucleic acid sequence is optimized for expression in the Pseudomonad host cell. In embodiments, the expression vectors used contain constructs expressing any of the secretion leaders described in Table 8 and Table 3 fused to the recombinant CRM197 or DT protein. In embodiments, the native secretion leader is used. In certain embodiments, the CRM197 or DT protein is expressed with a tag, e.g., a purification tag. In embodiments, the methods of the invention are used to produce CRM197 or DT at a yield of about 0.5 g/L to at least about 12 g/L.
Cholera Toxin
Cholera toxin (CTX), produced by Vibrio cholera, is also an ADP-ribosylating toxin. The Cholera toxin (CTX) is an oligomeric complex made up of six protein subunits: a single copy of the Cholera toxin A subunit (CTA), and five copies of the Cholera toxin B subunit (CTB). The five B subunits, each weighing 12 kDa, form a five-membered ring. The A subunit has an A1 portion, CTA1, a globular enzyme that ADP-ribosylates G proteins, and an A2 chain, CTA2, that forms an extended alpha helix which sits snugly in the central pore of the B subunit ring. This ring binds to GM1 ganglioside receptors on the host cell surface, resulting in internalization of the entire complex. Once internalized, the CTA1 chain is released by reduction of a disulfide bridge. CTA1 is then activated and catalyzes ADP ribosylation of adenylate cyclase. The resulting increase in adenylate cyclase activity increases cyclic AMP synthesis, which causes massive fluid and electrolyte efflux and results in diarrhea.
The B subunit of CTX, though relatively harmless, retains its ability to bind to the GM1 ganglioside receptor. CTB therefore finds use in facilitating mucosal uptake of chemically or genetically conjugated foreign antigens. It has been demonstrated to induce both mucosal and systemic immunity, and is a candidate for use in edible vaccine production. Because of its binding preference, CTB also finds use as a neuronal tracer.
The use of CTB, as well as its structural features, have been described, e.g., by: Nozoye, et al., 2009, “Production of Ascaris suum As14 Protein and Its Fusion Protein with Cholera Toxin B Subunit in Rice Seeds,” Parasitology 995-1000; Harakuni, et al., 2005, “Heteropentameric Cholera Toxin B Subunit Chimeric Molecules Genetically Fused to a Vaccine Antigen Induce Systemic and Mucosal Immune Responses: a Potential New Strategy to Target Recombinant Vaccine Antigens to Mucosal Immune Systems,” Infection and Immunity 73(9):5654-5665; Price, et al., 2005, “Intranasal Administration of Recombinant Neisseria gonorrhoeae Transferrin Binding Proteins A and B Conjugated to the Cholera Toxin B Subunit Induces Systemic and Vaginal Antibodies in Mice,” Infection and Immunity 73(7):3945-3953; and Sun, et al., 1999, “Intranasal Administration of a Schistosoma mansoni Glutathione S-Transferase-Cholera Toxoid Conjugate Vaccine Evokes Antiparasitic and Antipathological Immunity in Mice,” J. Immunol. 163:1045-1052, all incorporated herein by reference.
In embodiments of the present invention, CTB or CTX is produced using any of the host strains described herein in Example 1, in combination with any of the expression vectors described in Example 3. In embodiments, the nucleic acid sequence is optimized for expression in the Pseudomonad host cell. In embodiments, the expression vectors used contain constructs expressing any of the secretion leaders described in Table 8 and Table 3 fused to the recombinant CTB or CTX protein. In embodiments, the native secretion leader is used. In certain embodiments, the CTB or CTX protein is expressed with a tag, e.g., a purification tag. In embodiments, the methods of the invention are used to produce CTB or CTX at a yield of about 0.2 g/L to at least about 5 g/L.
Pertussis Toxin
Pertussis toxin is an exotoxin and virulence factor produced by Bordetella pertussis, a bacterial pathogen of the human respiratory tract that causes the disease whooping cough. The pertussis holotoxin is a multi-subunit complex with an AB 5 structure. The enzymatically active A subunit (S1) is an ADP-ribosyltransferase that modifies the alpha subunit of several heterotrimeric G proteins (primarily G i proteins) in mammalian cells, and the B oligomer (S2, S3, 2 copies of S4, and S5) binds glycoconjugate receptors on cells. S1 is proteolytically processed after cell entry. Carbonetti, et al., 2005, “Proteolytic Cleavage of Pertussis Toxin S1 Subunit is Not Essential for Its Activity in Mammalian Cells,” BMC Microbiology 5:7, incorporated herein by reference, reported that processing of S1 is not essential for its cytotoxic activity in mammalian cells.
Nontoxic variants of Pertussis toxin have been explored for use in vaccines. Pertussis toxin protein produced using the methods of the present invention is contemplated for use in a vaccine to protect against pertussis. Pertussis toxin has also been tested as a vaccine adjuvant, e.g., as described by Roberts, et al., 1995, “A Mutant Pertussis Toxin Molecule That Lacks ADP-Ribosyltransferase Activity, PT-9K/129G, Is an Effective Mucosal Adjuvant for Intranasally Delivered Proteins,” Infection and Immunity 63(6):2100-2108, incorporated herein by reference. Further, Pertussis toxin is also useful for research purposes, e.g., for studies of G protein signaling pathways (e.g., McCoy, et al., 2010, “PAR1 and PAR2 couple to overlapping and distinct sets of G proteins and linked signaling pathways to differentially regulate cell physiology,” Molecular Pharmacology Fast Forward MOL 62018, incorporated herein by reference) and as an adjuvant to enhance induction of autoimmune diseases, e.g., experimental autoimmune encephalomyelitis (EAE), experimental autoimmune orchitis, experimental autoimmune uveitis, etc. (Su, et al., 2001, “Pertussis Toxin Inhibits Induction of Tissue-Specific Autoimmune Disease by Disrupting G Protein-Coupled Signals,” J Immunol 167:250-256. incorporated herein by reference).
The five subunits of the toxin are expressed from the Pertussis Toxoid operon, shown in FIG. 5. The expression and structure of Pertussis toxin proteins, including certain variants, are described by above-cited reports, as well as by Burnette, et al., 1992, “Properties of Pertussis Toxin B Oligomer Assembled In Vitro from Recombinant Polypeptides Produced by Escherichia coli,” Infection and Immunity 60(6):2252-2256; U.S. Pat. No. 5,085,862, “Genetic detoxification of pertussis toxin;” and Kaslow, et al., 1987, “Structure-Activity Analysis of the Activation of Pertussis Toxin,” Biochemistry 26(1):123-7; all incorporated by reference herein in their entirety.
Pertussis Toxin or PTX as used herein refers to Pertussis Toxin mutant S1 R9K E129A or the wild-type protein. Wild-type Pertussis toxin and Pertussis toxin mutant S1 R9K E129A are described by, e.g.: Roberts, et al., 1995 (cited above); U.S. Pat. No. 7,427,404 and U.S. Pat. No. 7,666,436, both titled, “Pertussis Toxin Mutants, Bordetella Strains Capable of Producing Such Mutants and Their Use in the Development of Antipertussis Vaccines;” U.S. Pat. No. 5,935,580, “Recombinant Mutants for Inducing Specific Immune Responses;” U.S. Pat. No. 7,169,399, “Non-Toxic Double Mutant Forms of Pertussis Toxin as Adjuvants;” U.S. Pat. No. 5,785,971 and U.S. Pat. No. 5,427,788, both titled, “Pertussis Toxin and Use in Vaccines;” and U.S. Pat. No. 5,773,600, “DNA Encoding Pertussis Toxin Muteins,” all incorporated herein by reference in their entirety.
In embodiments of the present invention, Pertussis toxin mutant S1 E129A or wild-type Pertussis toxin is produced using any of the host strains described herein in Example 1, 5 and 7. In embodiments, the expression vectors used contain constructs expressing any of the secretion leaders described in Table 8 and Table 3 fused to the recombinant PTX protein. In embodiments, the native secretion leader is used. In embodiments, any or all of the subunit encoding sequences are optimized for expression in the Pseudomonad host selected, as described elsewhere herein. In certain embodiments, the subunits are expressed from two or more constructs, for example, by subcloning the individual sequences according to methods well-known in the art. In certain embodiments, the PTX protein is expressed with a tag, e.g., a purification tag. In embodiments, the methods of the invention are used to produce PTX or each individual subunit of PTX at a yield of about 0.2 g/L to at least about 5 g/L.
Tetanus Toxin Fragment C
Tetanus Toxin, produced by Clostridium tetani, is a neurotoxin having a molecular weight of 150 kDa. It is made up of two parts: a 100 kDa heavy or B-chain and a 50 kDa light or A-chain. The chains are connected by a disulfide bond. The B-chain binds to disialogangliosides (GD2 and GD1b) on the neuronal membrane. The A-chain, a zinc endopeptidase, attacks the vesicle-associated membrane protein (VAMP).
The action of the A-chain stops the affected neurons from releasing the inhibitory neurotransmitters GABA (gamma-aminobutyric acid) and glycine by degrading the protein synaptobrevin. The consequence of this is dangerous overactivity in the muscles from the smallest stimulus—the failure of inhibition of motor reflexes by sensory stimulation. This causes generalized contractions of the agonist and antagonist musculature, termed a tetanic spasm.
Tetanus Toxin Fragment C (Tet C or TTC) is a 50 kD polypeptide generated by protease cleavage (e.g., with papain) of Tetanus toxin, or through recombinant expression of the fragment. It corresponds to the 451 amino acids at the C-terminus (amino acid positions 865-1315). Recombinant expression of Fragment C is disclosed in, e.g., U.S. Pat. No. 5,443,966, “Expression of Tetanus Toxin Fragment C,” WO/2005/000346, “Carrier Proteins for Vaccines,” and U.S. Pat. No. 6,010,871, “Modification of Peptide and Protein,” all incorporated herein by reference in their entirety.
Fragment C has been shown to be non-toxic and capable of stimulating a protective immune response in mice and guinea pigs. U.S. Pat. No. 5,443,966 describes the sequence of Tetanus Toxin and production of Fragment C in E. coli. Expression of recombinant TTC in yeast has been described, e.g., in U.S. Pat. No. 5,571,694, “Expression of Tetanus Toxin Fragment C in Yeast,” incorporated herein by reference in its entirety.
Because it binds to neurons with high specificity and affinity, TTC finds use as a targeting molecule for neuronal drug delivery or for research purposes. Such use is described by, e.g., Townsend, et al., 2007, “Tetanus toxin C fragment conjugated nanoparticles for targeted drug delivery to neurons,” Biomaterials 28(34):5176-5184, incorporated herein by reference.
TTC protein is also potentially useful as a vaccine carrier protein, as described in, e.g., WO/2005/000346, and has been explored for use in a vaccine to protect against C. tetani infection.
In embodiments of the present invention, TTC is produced using any of the host strains described herein in Example 1, in combination with any of the expression vectors described in Example 8. In embodiments, the nucleic acid sequence is optimized for expression in the Pseudomonad host cell. In embodiments, the expression vectors used have constructs expressing any of the secretion leaders described in Table 8 and Table 3 fused to the recombinant TTC protein. In certain embodiments, the TTC protein is expressed with a tag, e.g., a purification tag. In embodiments, the native secretion leader is used. In embodiments, the methods of the invention are used to produce TTC at a yield of about 0.5 g/L to at least about 12 g/L.
C. difficile Toxin B
Clostridium difficile Toxin B (TcdB) is a virulence factor produced by Clostridium difficile, which causes hospital acquired diarrhea and pseudomembranous colitis. TcdB, and a second large clostridial toxin, TcdA, are involved in the development of pseudomembranous colitis.
TcdB, a glucosylating toxin of about 270 kD, can be divided into enzymatic, translocation and receptor binding domains. The first 546 amino acids of TcdB contain the enzymatic region, which is followed by a putative translocation and receptor-binding domain. Enzymatic activity has been reported to require the amino-terminal 546 residues, as amino or carboxy-terminal deletions of this fragment decrease activity. Within the enzymatic region, tryptophan 102 has been shown to be essential for UDP-glucose binding. A conserved DXD motif within LCTs is essential for LCT glucosyltransferase activity. Studies involving analysis of chimeras of the TcdB and TcsL enzymatic domain suggest that residues 364 to 516 confer substrate specificity.
The structure of TcdB and its expression and potential use as a protective vaccine for C. difficile infection are discussed in, e.g.: U.S. Pat. No. 7,226,597, “Mutants of Clostridium Difficile Toxin B and Methods of Use;” Jank, et al., 2008, “Structure and mode of action of clostridial glucosylating toxins: the ABCD model,” Trends in Microbiology 16(5):222-229; Sullivan, et al., 1982, “Purification and Characterization of Toxins A and B of Clostridium difficile,” Infection and Immunity 35(3):1032-1040; and Yang, et al., 2008, “Expression of recombinant Clostridium difficile toxin A and B in Bacillus megaterium,” BMC Microbiology 8:192, all incorporated herein by reference in their entirety.
In embodiments of the present invention, TcdB is produced using any of the host strains described herein in Examples 1, 5 and 7. In embodiments, the nucleic acid sequence is optimized for expression in the Pseudomonad host cell. In embodiments, the expression vectors used contain constructs expressing any of the secretion leaders described in Table 8 and Table 3 fused to the recombinant TcdB protein. In embodiments, the native secretion leader is used. In certain embodiments, the TcdB protein is expressed with a tag, e.g., a purification tag. In embodiments, the methods of the invention are used to produce TcdB at a yield of about 0.5 g/L to at least about 10 g/L.
Pseudomonas Aeruginosa Exotoxin A
Exotoxin A (ETA or PE) of Pseudomonas aeruginosa is a Type II ADPRT. It is one member of a family of secreted bacterial toxins capable of translocating a catalytic domain into mammalian cells and inhibiting protein synthesis by the ADP-ribosylation of cellular elongation factor 2. The protein exists as a monomer, consisting of a single polypeptide chain of 613 amino acids (66 Kd). The x-ray crystallographic structure of exotoxin A, determined to 3.0-A resolution, shows an amino-terminal domain, composed primarily of antiparallel beta-structure and comprising approximately half of the molecule; a middle domain composed of alpha-helices; and a carboxyl-terminal domain comprising approximately one-third of the molecule. The carboxyl-terminal domain is the ADP-ribosyltransferase of the toxin. The other two domains are presumably involved in cell receptor binding and membrane translocation.
The toxin binds to cells through a specific receptor on the cell surface, then the toxin-receptor complex is internalized into the cell. Finally, ETA is transferred to the cytosol where it enzymatically inhibits protein synthesis. The transfer process is believed to occur from an acidic compartment, since cellular intoxication is prevented by weak bases such as NH4+, which raises the pH in acidic vesicles. Upon exposure to acidic conditions, the hydrophobic domain of PE enters into the membrane, resulting in the formation of a channel through which the enzymatic domain, in extended form, passes into the cytosol. The activity of PE and mutants having reduced toxicity are described in, e.g., U.S. Pat. No. 4,892,827, “Recombinant Pseudomonas Exotoxins: Construction of an Active Immunotoxin with Low Side Effects,” and by Lukac, et al., 1988, “Toxoid of Pseudomonas aeruginosa Exotoxin A Generated by Deletion of an Active-Site Residue,” Infection and Immunity 56(12): 3095-3098, both incorporated herein by reference in their entirety.
Use of Exotoxin A mutant rEPA as a vaccine conjugate is described by, e.g.: Fattom, et al., 1993, “Laboratory and Clinical Evaluation of Conjugate Vaccines Composed of Staphylococcus aureus Type 5 and Type 8 Capsular Polysaccharides Bound to Pseudomonas aeruginosa Recombinant Exoprotein A,” Infection and Immunity 61(3):1023-1032; Qian, et al., 2007, “Conjugating recombinant proteins to Pseudomonas aeruginosa ExoProtein A: a strategy for enhancing immunogenicity of malaria vaccine candidates,” Vaccine 25(20):3923-3933; and Lin, et al., 2001. “The Efficacy of a Salmonella Typhi Vi Conjugate Vaccine in Two-To-Five-Year-Old Children,” N Engl J Med 344(17): 1263-1269, both incorporated herein by reference.
Pseudomonas aeruginosa Exotoxin A as used herein refers to Pseudomonas aeruginosa Exotoxin A mutant CRM66, deletion rEPA, or the wild-type protein. In embodiments of the present invention, Exotoxin A is produced using any of the host strains described herein in Examples 1, 5 and 7, and using expression vectors having constructs expressing any of the secretion leaders described in Table 8 and Table 3 fused to the recombinant Exotoxin A protein. In embodiments, the nucleic acid sequence is optimized for expression in the Pseudomonad host cell. In embodiments, the native secretion leader is used. In certain embodiments, the ETA protein is expressed with a tag, e.g., a purification tag. In embodiments, the methods of the invention are used to produce Exotoxin A at a yield of about 0.5 g/L to at least about 12 g/L.
Exemplary toxin proteins produced using the methods of the invention are listed in Table 1. It is understood that this list is not limiting. In embodiments of the invention, any of the nucleic acid sequences of the toxins described herein for production using the methods of the invention can be optimized for expression in the Pseudomonad host cell selected. As described elsewhere herein, there are multiple options for optimization of any given sequence. Any of the options as described are contemplated for use in optimizing the sequences of the toxins produced using the methods of the present invention. The optimized sequences provided herein are non-limiting examples of optimized sequences useful in the methods of the present invention.







TABLE 1







Exemplary Toxin Proteins










Exemplary Sequence



Target
Source/Reference
Origin





CRM197
GenBank Acc. No.
Corynebacterium



1007216A
diphtheriae




NCTC 13129


Diphtheria
GenBank NC_002935.2
Corynebacterium


toxin (WT)
GenBank CAA00374.1
diphtheriae


Cholera
GenBank NC_002505.1;
Vibrio cholerae


Holotoxin
NP231099.1 and NP23110.1


Cholera
GenBank ACH70471 (E1
Vibrio cholerae


Toxin B
Tor strain)
O1 biovar E1 tor


Pertussis
GenBank M13223.1 with
Bordetella


Toxin
mutations in S1
pertussis


Tetanus Toxin
GenBank 1A8D_A
Clostridium


C Fragment

tetani


C. difficile
GenBank CAA63562
Clostridium


Tox B VPI (TcdB)

difficile


P. aeruginosa
GenBank NP_249839
Pseudomonas


Exotoxin A

aeruginosa PAO1









Codon Optimization

In heterologous expression systems, optimization steps may improve the ability of the host to produce the foreign protein. Protein expression is governed by a host of factors including those that affect transcription, mRNA processing, and stability and initiation of translation. The polynucleotide optimization steps may include steps to improve the ability of the host to produce the foreign protein as well as steps to assist the researcher in efficiently designing expression constructs. Optimization strategies may include, for example, the modification of translation initiation regions, alteration of mRNA structural elements, and the use of different codon biases. Methods for optimizing the nucleic acid sequence of to improve expression of a heterologous protein in a bacterial host are known in the art and described in the literature. For example, optimization of codons for expression in a Pseudomonas host strain is described, e.g., in U.S. Pat. App. Pub. No. 2007/0292918, “Codon Optimization Method,” incorporated herein by reference in its entirety.
Optimization can thus address any of a number of sequence features of the heterologous gene. As a specific example, a rare codon-induced translational pause can result in reduced heterologous protein expression. A rare codon-induced translational pause includes the presence of codons in the polynucleotide of interest that are rarely used in the host organism may have a negative effect on protein translation due to their scarcity in the available tRNA pool. One method of improving optimal translation in the host organism includes performing codon optimization which can result in rare host codons being removed from the synthetic polynucleotide sequence.
Alternate translational initiation also can result in reduced heterologous protein expression. Alternate translational initiation can include a synthetic polynucleotide sequence inadvertently containing motifs capable of functioning as a ribosome binding site (RBS). These sites can result in initiating translation of a truncated protein from a gene-internal site. One method of reducing the possibility of producing a truncated protein, which can be difficult to remove during purification, includes eliminating putative internal RBS sequences from an optimized polynucleotide sequence.
Repeat-induced polymerase slippage can result in reduced heterologous protein expression. Repeat-induced polymerase slippage involves nucleotide sequence repeats that have been shown to cause slippage or stuttering of DNA polymerase which can result in frameshift mutations. Such repeats can also cause slippage of RNA polymerase. In an organism with a high G+C content bias, there can be a higher degree of repeats composed of G or C nucleotide repeats. Therefore, one method of reducing the possibility of inducing RNA polymerase slippage, includes altering extended repeats of G or C nucleotides.
Interfering secondary structures also can result in reduced heterologous protein expression. Secondary structures can sequester the RBS sequence or initiation codon and have been correlated to a reduction in protein expression. Stemloop structures can also be involved in transcriptional pausing and attenuation. An optimized polynucleotide sequence can contain minimal secondary structures in the RBS and gene coding regions of the nucleotide sequence to allow for improved transcription and translation.
Another feature that can effect heterologous protein expression is the presence of restriction sites. By removing restriction sites that could interfere with subsequent sub-cloning of transcription units into host expression vectors a polynucleotide sequence can be optimized.
For example, the optimization process can begin by identifying the desired amino acid sequence to be heterologously expressed by the host. From the amino acid sequence a candidate polynucleotide or DNA sequence can be designed. During the design of the synthetic DNA sequence, the frequency of codon usage can be compared to the codon usage of the host expression organism and rare host codons can be removed from the synthetic sequence. Additionally, the synthetic candidate DNA sequence can be modified in order to remove undesirable enzyme restriction sites and add or remove any desired signal sequences, linkers or untranslated regions. The synthetic DNA sequence can be analyzed for the presence of secondary structure that may interfere with the translation process, such as G/C repeats and stem-loop structures. Before the candidate DNA sequence is synthesized, the optimized sequence design can be checked to verify that the sequence correctly encodes the desired amino acid sequence. Finally, the candidate DNA sequence can be synthesized using DNA synthesis techniques, such as those known in the art.
In another embodiment of the invention, the general codon usage in a host organism, such as P. fluorescens, can be utilized to optimize the expression of the heterologous polynucleotide sequence. The percentage and distribution of codons that rarely would be considered as preferred for a particular amino acid in the host expression system can be evaluated. Values of 5% and 10% usage can be used as cutoff values for the determination of rare codons. For example, the codons listed in Table 2 have a calculated occurrence of less than 5% in the P. fluorescens MB214 genome and would be generally avoided in an optimized gene expressed in a P. fluorescens host.







TABLE 2







Codons occurring at less than 5% in P. fluorescens MB214











Amino Acid(s)
Codon(s) Used
% Occurrence







G Gly
GGA
3.26



I Ile
ATA
3.05



L Leu
CTA
1.78




CTT
4.57




TTA
1.89



R Arg
AGA
1.39




AGG
2.72




CGA
4.99



S Ser
TCT
4.28










The present invention contemplates the use of any coding sequence for the toxins produced, including any sequence that has been optimized for expression in the Pseudomonas host cell being used. Sequences contemplated for use can be optimized to any degree as desired, including, but not limited to, optimization to eliminate: codons occurring at less than 5% in the Pseudomonas host cell, codons occurring at less than 10% in the Pseudomonas host cell, a rare codon-induced translational pause, a putative internal RBS sequence, an extended repeat of G or C nucleotides, an interfering secondary structure, a restriction site, or combinations thereof.
Furthermore, the amino acid sequence of any secretion leader useful in practicing the methods of the present invention can be encoded by any appropriate nucleic acid sequence.
Expression Systems
Methods for expressing heterologous proteins, including useful regulatory sequences (e.g., promoters, secretion leaders, and ribosome binding sites), in Pseudomonas host cells, as well as host cells useful in the methods of the present invention, are described, e.g., in U.S. Pat. App. Pub. No. 2008/0269070 and U.S. patent application Ser. No. 12/610,207, both titled “Method for Rapidly Screening Microbial Hosts to Identify Certain Strains with Improved Yield and/or Quality in the Expression of Heterologous Proteins,” U.S. Pat. App. Pub. No. 2006/0040352, “Expression of Mammalian Proteins in Pseudomonas Fluorescens,” and U.S. Pat. App. Pub. No. 2006/0110747, “Process for Improved Protein Expression by Strain Engineering,” all incorporated herein by reference in their entirety. These publications also describe bacterial host strains useful in practicing the methods of the invention, that have been engineered to overexpress folding modulators or wherein protease mutations, including deletions, have been introduced, in order to increase heterologous protein expression.
Leaders
Sequence leaders are described in detail in U.S. Patent App. Pub. Nos. 2008/0193974 and 2010/0048864, both titled, “Bacterial Leader Sequences for Increased Expression,” and U.S. Pat. App. Pub. No. 2006/0008877, “Expression systems with Sec-secretion,” all incorporated herein by reference in their entirety, as well as in U.S. Pat. App. Pub. No. 2008/0269070 and U.S. patent application Ser. No. 12/610,207.
In embodiments, a sequence encoding a secretion leader is fused to the sequence encoding the toxin protein. In embodiments, the secretion leader is a periplasmic secretion leader. In embodiments, the secretion leader is the native secretion leader.







TABLE 3







Exemplary Secretion Leader Sequences









Secre-

SEQ


tion

ID


Leader
Amino Acid Sequence
NO:












DsbA
MRNLILSAALVTASLFGMTAQA
3


 


Azu
MFAKLVAVSLLTLASGQLLA
4


 


Ibp-S31A
MIRDNRLKTSLLRGLTLTLLSLTLLSPAAHA
5


 


Tpr
MNRSSALLLAFVFLSGCQAMA
6


 


CupB2
MLFRTLLASLTFAVIAGLPSTAHA
7


 


CupA2
MSCTRAFKPLLLIGLATLMCSHAFA
8


 


NikA
MRLAALPLLLAPLFIAPMAVA
9


 


Pbp A20V
MKLKRLMAAMTFVAAGVATVNAVA
10


 


DsbC
MRLTQIIAAAAIALVSTFALA
11


 


TolB
MRNLLRGMLVVICCMAGIAAA
12


 


Pbp
MKLKRLMAAMTFVAAGVATANAVA
13


 


Lao
MQNYKKFLLAAAVSMAFSATAMA
14


 


CupC2
MPPRSIAACLGLLGLLMATQAAA
15


 


PorE
MKKSTLAVAVTLGAIAQQAGA
16


 


Pbp
MKLKRLMAAMTFVAAGVATANAVA
17


 


FlgI
MKFKQLMAMALLLALSAVAQA
18


 


ttg2C
MQNRTVEIGVGLFLLAGILALLLLALRVSGLSA
19


 


CRM197
MSRKLFASXLIGALLGIGAPPSAHA
20


native




leader









It is understood that the secretion leaders useful in the methods of the present invention are not limited to those disclosed in Table 3.
In embodiments, the secretion leader is Azu, IbpS31A, CupA2, or PbpA20V. In other embodiments, the secretion leader is Azu, IbpS31A, CupA2, PbpA20V, or Pbp.
Native CRM197 is transported from C. diptheriae to the extracellular space via a secretion leader that is cleaved, leaving an amino terminal sequence of GADD (SEQ ID NO: 21). In order to preserve the natural amino terminus of CRM197 following expression in P. fluorescens and ensure disulfide bond formation, the protein is targeted to the periplasmic space.
Promoters
The promoters used in accordance with the present invention may be constitutive promoters or regulated promoters. Common examples of useful regulated promoters include those of the family derived from the lac promoter (i.e. the lacZ promoter), especially the tac and trc promoters described in U.S. Pat. No. 4,551,433 to DeBoer, as well as Ptac16, Ptac17, PtacII, PlacUV5, and the T7lac promoter. In one embodiment, the promoter is not derived from the host cell organism. In certain embodiments, the promoter is derived from an E. coli organism.
Inducible promoter sequences can be used to regulate expression of the toxins in accordance with the methods of the invention. In embodiments, inducible promoters useful in the methods of the present invention include those of the family derived from the lac promoter (i.e. the lacZ promoter), especially the tac and trc promoters described in U.S. Pat. No. 4,551,433 to DeBoer, as well as Ptac16, Ptac17, PtacII, PlacUV5, and the T7lac promoter. In one embodiment, the promoter is not derived from the host cell organism. In certain embodiments, the promoter is derived from an E. coli organism.
Common examples of non-lac-type promoters useful in expression systems according to the present invention include, e.g., those listed in Table 4.







TABLE 4







Examples of non-lac Promoters










Promoter
Inducer







PR
High temperature



PL
High temperature



Pm
Alkyl- or halo-benzoates



Pu
Alkyl- or halo-toluenes



Psal
Salicylates










See, e.g.: J. Sanchez-Romero & V. De Lorenzo (1999) Manual of Industrial Microbiology and Biotechnology (A. Demain & J. Davies, eds.) pp. 460-74 (ASM Press, Washington, D.C.); H. Schweizer (2001) Current Opinion in Biotechnology, 12:439-445; and R. Slater & R. Williams (2000 Molecular Biology and Biotechnology (J. Walker & R. Rapley, eds.) pp. 125-54 (The Royal Society of Chemistry, Cambridge, UK)). A promoter having the nucleotide sequence of a promoter native to the selected bacterial host cell also may be used to control expression of the transgene encoding the target polypeptide, e.g, a Pseudomonas anthranilate or benzoate operon promoter (Pant, Pben). Tandem promoters may also be used in which more than one promoter is covalently attached to another, whether the same or different in sequence, e.g., a Pant-Pben tandem promoter (interpromoter hybrid) or a Plac-Plac tandem promoter, or whether derived from the same or different organisms.
Regulated promoters utilize promoter regulatory proteins in order to control transcription of the gene of which the promoter is a part. Where a regulated promoter is used herein, a corresponding promoter regulatory protein will also be part of an expression system according to the present invention. Examples of promoter regulatory proteins include: activator proteins, e.g., E. coli catabolite activator protein, MalT protein; AraC family transcriptional activators; repressor proteins, e.g., E. coli Lad proteins; and dual-function regulatory proteins, e.g., E. coli NagC protein. Many regulated-promoter/promoter-regulatory-protein pairs are known in the art. In one embodiment, the expression construct for the target protein(s) and the heterologous protein of interest are under the control of the same regulatory element.
Promoter regulatory proteins interact with an effector compound, i.e., a compound that reversibly or irreversibly associates with the regulatory protein so as to enable the protein to either release or bind to at least one DNA transcription regulatory region of the gene that is under the control of the promoter, thereby permitting or blocking the action of a transcriptase enzyme in initiating transcription of the gene. Effector compounds are classified as either inducers or co-repressors, and these compounds include native effector compounds and gratuitous inducer compounds. Many regulated-promoter/promoter-regulatory-protein/effector-compound trios are known in the art. Although an effector compound can be used throughout the cell culture or fermentation, in a preferred embodiment in which a regulated promoter is used, after growth of a desired quantity or density of host cell biomass, an appropriate effector compound is added to the culture to directly or indirectly result in expression of the desired gene(s) encoding the protein or polypeptide of interest.
In embodiments wherein a lac family promoter is utilized, a lad gene can also be present in the system. The lad gene, which is normally a constitutively expressed gene, encodes the Lac repressor protein Lad protein, which binds to the lac operator of lac family promoters. Thus, where a lac family promoter is utilized, the lad gene can also be included and expressed in the expression system.
Promoter systems useful in Pseudomonas are described in the literature, e.g., in U.S. Pat. App. Pub. No. 2008/0269070, also referenced above.
Other Regulatory Elements
In embodiments, soluble proteins are present in either the cytoplasm or periplasm of the cell during production. Secretion leaders useful for targeting proteins are described elsewhere herein, and in U.S. Pat. App. Pub. No. 2008/0193974, U.S. Pat. App. Pub. No. 2006/0008877, and in U.S. patent application Ser. No. 12/610,207.
Other elements include, but are not limited to, transcriptional enhancer sequences, translational enhancer sequences, other promoters, activators, translational start and stop signals, transcription terminators, cistronic regulators, polycistronic regulators, tag sequences, such as nucleotide sequence “tags” and “tag” polypeptide coding sequences, which facilitates identification, separation, purification, and/or isolation of an expressed polypeptide.
In embodiments, the expression vector further comprises a tag sequence adjacent to the coding sequence for the secretion signal or to the coding sequence for the protein or polypeptide of interest. In one embodiment, this tag sequence allows for purification of the protein. The tag sequence can be an affinity tag, such as a hexa-histidine affinity tag (SEQ ID NO: 46). In another embodiment, the affinity tag can be a glutathione-S-transferase molecule. The tag can also be a fluorescent molecule, such as YFP or GFP, or analogs of such fluorescent proteins. The tag can also be a portion of an antibody molecule, or a known antigen or ligand for a known binding partner useful for purification.
An expression construct useful in practicing the methods of the present invention can include, in addition to the protein coding sequence, the following regulatory elements operably linked thereto: a promoter, a ribosome binding site (RBS), a transcription terminator, and translational start and stop signals. Useful RBSs can be obtained from any of the species useful as host cells in expression systems according to, e.g., U.S. Pat. App. Pub. No. 2008/0269070 and U.S. patent application Ser. No. 12/610,207. Many specific and a variety of consensus RBSs are known, e.g., those described in and referenced by D. Frishman et al., Gene 234(2):257-65 (8 Jul. 1999); and B. E. Suzek et al., Bioinformatics 17(12):1123-30 (December 2001). In addition, either native or synthetic RBSs may be used, e.g., those described in: EP 0207459 (synthetic RBSs); O. Ikehata et al., Eur. J. Biochem. 181(3):563-70 (1989) (native RBS sequence of AAGGAAG). Further examples of methods, vectors, and translation and transcription elements, and other elements useful in the present invention are well known in the art and described in, e.g.: U.S. Pat. No. 5,055,294 to Gilroy and U.S. Pat. No. 5,128,130 to Gilroy et al.; U.S. Pat. No. 5,281,532 to Rammler et al.; U.S. Pat. Nos. 4,695,455 and 4,861,595 to Barnes et al.; U.S. Pat. No. 4,755,465 to Gray et al.; and U.S. Pat. No. 5,169,760 to Wilcox, all incorporated herein by reference, as well as in many of the other publications incorporated herein by reference.
Host Strains
Bacterial hosts, including Pseudomonads, and closely related bacterial organisms are contemplated for use in practicing the methods of the invention. In certain embodiments, the Pseudomonad host cell is Pseudomonas fluorescens. The host cell can also be an E. coli cell.
Host cells and constructs useful in practicing the methods of the invention can be identified or made using reagents and methods known in the art and described in the literature, e.g., in U.S. Pat. App. Pub. No. 2009/0325230, “Protein Expression Systems,” incorporated herein by reference in its entirety. This publication describes production of a recombinant polypeptide by introduction of a nucleic acid construct into an auxotrophic Pseudomonas fluorescens host cell comprising a chromosomal lacI gene insert. The nucleic acid construct comprises a nucleotide sequence encoding the recombinant polypeptide operably linked to a promoter capable of directing expression of the nucleic acid in the host cell, and also comprises a nucleotide sequence encoding an auxotrophic selection marker. The auxotrophic selection marker is a polypeptide that restores prototrophy to the auxotrophic host cell. In embodiments, the cell is auxotrophic for proline, uracil, or combinations thereof. In embodiments, the host cell is derived from MB101 (ATCC deposit PTA-7841). U.S. Pat. App. Pub. No. 2009/0325230, “Protein Expression Systems,” and in Schneider, et al., 2005, “Auxotrophic markers pyrF and proC can replace antibiotic markers on protein production plasmids in high-cell-density Pseudomonas fluorescens fermentation,” Biotechnol. Progress 21(2): 343-8, both incorporated herein by reference in their entirety, describe a production host strain auxotrophic for uracil that was constructed by deleting the pyrF gene in strain MB101. The pyrF gene was cloned from strain MB214 (ATCC deposit PTA-7840) to generate a plasmid that can complement the pyrF deletion to restore prototropy. In particular embodiments, a dual pyrF-proC dual auxotrophic selection marker system in a P. fluorescens host cell is used. A PyrF production host strain as described can be used as the background for introducing other desired genomic changes, including those described herein as useful in practicing the methods of the invention.
In embodiments, the host cell is of the order Pseudomonadales. Where the host cell is of the order Pseudomonadales, it may be a member of the family Pseudomonadaceae, including the genus Pseudomonas. Gamma Proteobacterial hosts include members of the species Escherichia coli and members of the species Pseudomonas fluorescens. 
Other Pseudomonas organisms may also be useful. Pseudomonads and closely related species include Gram-negative Proteobacteria Subgroup 1, which include the group of Proteobacteria belonging to the families and/or genera described as “Gram-Negative Aerobic Rods and Cocci” by R. E. Buchanan and N. E. Gibbons (eds.), Bergey's Manual of Determinative Bacteriology, pp. 217-289 (8th ed., 1974) (The Williams & Wilkins Co., Baltimore, Md., USA) (hereinafter “Bergey (1974)”). Table 5 presents these families and genera of organisms.







TABLE 5





Families and Genera Listed in the Part, “Gram-Negative


Aerobic Rods and Cocci” (Bergey, 1974)


















Family I. Pseudomonaceae
Gluconobacter




Pseudomonas




Xanthomonas




Zoogloea



Family II. Azotobacteraceae
Azomonas




Azotobacter




Beijerinckia




Derxia



Family III. Rhizobiaceae
Agrobacterium




Rhizobium



Family IV. Methylomonadaceae
Methylococcus




Methylomonas



Family V. Halobacteriaceae
Halobacterium




Halococcus



Other Genera
Acetobacter




Alcaligenes




Bordetella




Brucella




Francisella




Thermus










Pseudomonas and closely related bacteria are generally part of the group defined as “Gram(−) Proteobacteria Subgroup 1” or “Gram-Negative Aerobic Rods and Cocci” (Buchanan and Gibbons (eds.) (1974) Bergey's Manual of Determinative Bacteriology, pp. 217-289). Pseudomonas host strains are described in the literature, e.g., in U.S. Pat. App. Pub. No. 2006/0040352, cited above.
“Gram-negative Proteobacteria Subgroup 1” also includes Proteobacteria that would be classified in this heading according to the criteria used in the classification. The heading also includes groups that were previously classified in this section but are no longer, such as the genera Acidovorax, Brevundimonas, Burkholderia, Hydrogenophaga, Oceanimonas, Ralstonia, and Stenotrophomonas, the genus Sphingomonas (and the genus Blastomonas, derived therefrom), which was created by regrouping organisms belonging to (and previously called species of) the genus Xanthomonas, the genus Acidomonas, which was created by regrouping organisms belonging to the genus Acetobacter as defined in Bergey (1974). In addition hosts can include cells from the genus Pseudomonas, Pseudomonas enalia (ATCC 14393), Pseudomonas nigrifaciensi (ATCC 19375), and Pseudomonas putrefaciens (ATCC 8071), which have been reclassified respectively as Alteromonas haloplanktis, Alteromonas nigrifaciens, and Alteromonas putrefaciens. Similarly, e.g., Pseudomonas acidovorans (ATCC 15668) and Pseudomonas testosteroni (ATCC 11996) have since been reclassified as Comamonas acidovorans and Comamonas testosteroni, respectively; and Pseudomonas nigrifaciens (ATCC 19375) and Pseudomonas piscicida (ATCC 15057) have been reclassified respectively as Pseudoalteromonas nigrifaciens and Pseudoalteromonas piscicida. “Gram-negative Proteobacteria Subgroup 1” also includes Proteobacteria classified as belonging to any of the families: Pseudomonadaceae, Azotobacteraceae (now often called by the synonym, the “Azotobacter group” of Pseudomonadaceae), Rhizobiaceae, and Methylomonadaceae (now often called by the synonym, “Methylococcaceae”). Consequently, in addition to those genera otherwise described herein, further Proteobacterial genera falling within “Gram-negative Proteobacteria Subgroup 1” include: 1) Azotobacter group bacteria of the genus Azorhizophilus; 2) Pseudomonadaceae family bacteria of the genera Cellvibrio, Oligella, and Teredinibacter; 3) Rhizobiaceae family bacteria of the genera Chelatobacter, Ensifer, Liberibacter (also called “Candidatus Liberibacter”), and Sinorhizobium; and 4) Methylococcaceae family bacteria of the genera Methylobacter, Methylocaldum, Methylomicrobium, Methylosarcina, and Methylosphaera. 
The host cell can be selected from “Gram-negative Proteobacteria Subgroup 16.” “Gram-negative Proteobacteria Subgroup 16” is defined as the group of Proteobacteria of the following Pseudomonas species (with the ATCC or other deposit numbers of exemplary strain(s) shown in parenthesis): Pseudomonas abietaniphila (ATCC 700689); Pseudomonas aeruginosa (ATCC 10145); Pseudomonas alcaligenes (ATCC 14909); Pseudomonas anguilliseptica (ATCC 33660); Pseudomonas citronellolis (ATCC 13674); Pseudomonas flavescens (ATCC 51555); Pseudomonas mendocina (ATCC 25411); Pseudomonas nitroreducens (ATCC 33634); Pseudomonas oleovorans (ATCC 8062); Pseudomonas pseudoalcaligenes (ATCC 17440); Pseudomonas resinovorans (ATCC 14235); Pseudomonas straminea (ATCC 33636); Pseudomonas agarici (ATCC 25941); Pseudomonas alcaliphila; Pseudomonas alginovora; Pseudomonas andersonii; Pseudomonas asplenii (ATCC 23835); Pseudomonas azelaica (ATCC 27162); Pseudomonas beyerinckii (ATCC 19372); Pseudomonas borealis; Pseudomonas boreopolis (ATCC 33662); Pseudomonas brassicacearum; Pseudomonas butanovora (ATCC 43655); Pseudomonas cellulosa (ATCC 55703); Pseudomonas aurantiaca (ATCC 33663); Pseudomonas chlororaphis (ATCC 9446, ATCC 13985, ATCC 17418, ATCC 17461); Pseudomonas fragi (ATCC 4973); Pseudomonas lundensis (ATCC 49968); Pseudomonas taetrolens (ATCC 4683); Pseudomonas cissicola (ATCC 33616); Pseudomonas coronafaciens; Pseudomonas diterpeniphila; Pseudomonas elongata (ATCC 10144); Pseudomonas flectens (ATCC 12775); Pseudomonas azotoformans; Pseudomonas brenneri; Pseudomonas cedrella; Pseudomonas corrugata (ATCC 29736); Pseudomonas extremorientalis; Pseudomonas fluorescens (ATCC 35858); Pseudomonas gessardii; Pseudomonas libanensis; Pseudomonas mandelii (ATCC 700871); Pseudomonas marginalis (ATCC 10844); Pseudomonas migulae; Pseudomonas mucidolens (ATCC 4685); Pseudomonas orientalis; Pseudomonas rhodesiae; Pseudomonas synxantha (ATCC 9890); Pseudomonas tolaasii (ATCC 33618); Pseudomonas veronii (ATCC 700474); Pseudomonas frederiksbergensis; Pseudomonas geniculata (ATCC 19374); Pseudomonas gingeri; Pseudomonas graminis; Pseudomonas grimontii; Pseudomonas halodenitrificans; Pseudomonas halophila; Pseudomonas hibiscicola (ATCC 19867); Pseudomonas huttiensis (ATCC 14670); Pseudomonas hydrogenovora; Pseudomonas jessenii (ATCC 700870); Pseudomonas kilonensis; Pseudomonas lanceolata (ATCC 14669); Pseudomonas lini; Pseudomonas marginate (ATCC 25417); Pseudomonas mephitica (ATCC 33665); Pseudomonas denitrificans (ATCC 19244); Pseudomonas pertucinogena (ATCC 190); Pseudomonas pictorum (ATCC 23328); Pseudomonas psychrophila; Pseudomonas filva (ATCC 31418); Pseudomonas monteilii (ATCC 700476); Pseudomonas mosselii; Pseudomonas oryzihabitans (ATCC 43272); Pseudomonas plecoglossicida (ATCC 700383); Pseudomonas putida (ATCC 12633); Pseudomonas reactans; Pseudomonas spinosa (ATCC 14606); Pseudomonas balearica; Pseudomonas luteola (ATCC 43273); Pseudomonas stutzeri (ATCC 17588); Pseudomonas amygdali (ATCC 33614); Pseudomonas avellanae (ATCC 700331); Pseudomonas caricapapayae (ATCC 33615); Pseudomonas cichorii (ATCC 10857); Pseudomonas ficuserectae (ATCC 35104); Pseudomonas fuscovaginae; Pseudomonas meliae (ATCC 33050); Pseudomonas syringae (ATCC 19310); Pseudomonas viridiflava (ATCC 13223); Pseudomonas thermocarboxydovorans (ATCC 35961); Pseudomonas thermotolerans; Pseudomonas thivervalensis; Pseudomonas vancouverensis (ATCC 700688); Pseudomonas wisconsinensis; and Pseudomonas xiamenensis. In one embodiment, the host cell is Pseudomonas fluorescens. 
The host cell can also be selected from “Gram-negative Proteobacteria Subgroup 17.” “Gram-negative Proteobacteria Subgroup 17” is defined as the group of Proteobacteria known in the art as the “fluorescent Pseudomonads” including those belonging, e.g., to the following Pseudomonas species: Pseudomonas azotoformans; Pseudomonas brenneri; Pseudomonas cedrella; Pseudomonas corrugata; Pseudomonas extremorientalis; Pseudomonas fluorescens; Pseudomonas gessardii; Pseudomonas libanensis; Pseudomonas mandelii; Pseudomonas marginalis; Pseudomonas migulae; Pseudomonas mucidolens; Pseudomonas orientalis; Pseudomonas rhodesiae; Pseudomonas synxantha; Pseudomonas tolaasii; and Pseudomonas veronii. 
In embodiments, the Pseudomonas host cell is defective in the expression of HslU, HslV, Prc1, DegP1, DegP2, AprA, or a combination thereof. In embodiments, the host cell is defective in proteases HslU, HslV, Prc1, DegP1, DegP2, and AprA, and overexpresses DegP2 S219A. An example of such a strain is disclosed herein as Host Strain 2. These proteases are known in the art and described in, e.g., U.S. Pat. App. Pub. No. 2006/0110747. AprA, an extracellular serralysin-type metalloprotease metalloproteinase, is described by, e.g., Maunsell, et al., 2006, “Complex regulation of AprA metalloprotease in Pseudomonas fluorescens M114: evidence for the involvement of iron, the ECF sigma factor, PbrA and pseudobactin M114 siderophore, Microbiology 152(Pt 1):29-42, incorporated herein by reference, and in U.S. Patent App. Pub. Nos. 2008/0193974 and 2010/0048864.
In other embodiments, the Pseudomonas host cell overexpresses DsbA, DsbB, DsbC, and DsbD. DsbA, B, C, and D are disulfide bond isomerases, described, e.g., in U.S. Pat. App. Pub. No. 2008/0269070 and U.S. patent application Ser. No. 12/610,207.
In other embodiments, the Pseudomonas host cell is wild-type, i.e., having no protease expression defects and not overexpressing any folding modulator.
A host cell that is defective in the expression of a protease can have any modification that results in a decrease in the normal activity or expression level of that protease relative to a wild-type host. For example, a missense or nonsense mutation can lead to expression of protein that not active, and a gene deletion can result in no protein expression at all. A change in the upstream regulatory region of the gene can result in reduced or no protein expression. Other gene defects can affect translation of the protein. The expression of a protease can also be defective if the activity of a protein needed for processing the protease is defective.
Examples of proteases and folding modulators useful in the methods of the present invention are shown in Tables 6 and 7, respectively. RXF numbers refer to the open reading frame. (See, e.g., U.S. Pat. App. Pub. No. 2008/0269070 and U.S. patent application Ser. No. 12/610,207.)







TABLE 6







P. fluorescens strain MB214 proteases












Class
Family
RXF
Gene
Curated Function
Location





Aspartic Peptidases
A8 (signal peptidase II family)
RXF05383.2

Lipoprotein signal peptidase (ec
Cytoplasmic






3.4.23.36)
Membrane



A24 (type IV prepilin peptidase
RXF05379.1

type 4 prepilin peptidase pild (ec
Cytoplasmic



family)


3.4.99.—)
Membrane


Cysteine Peptidases
C15 (pyroglutamyl peptidase I
RXF02161.1

Pyrrolidone-carboxylate peptidase
Cytoplasmic



family)


(ec 3.4.19.3)



C40
RXF01968.1

invasion-associated protein, P60
Signal peptide




RXF04920.1

invasion-associated protein, P60
Cytoplasmic




RXF04923.1

phosphatase-associated protein
Signal peptide






papq



C56 (PfpI endopeptidase family)
RXF01816.1

protease I (ec 3.4.—.—)
Non-secretory


Metallopeptidases
M1
RXF08773.1

Membrane alanine aminopeptidase
Non-secretory






(ec 3.4.11.2)



M3
RXF00561.2
prlC
Oligopeptidase A (ec 3.4.24.70)
Cytoplasmic




RXF04631.2

Zn-dependent oligopeptidases
Cytoplasmic



M4 (thermolysin family)
RXF05113.2

Extracellular metalloprotease
Extracellular






precursor (ec 3.4.24.—)



M41 (FtsH endopeptidase family)
RXF05400.2

Cell division protein ftsH (ec
Cytoplasmic






3.4.24.—)
Membrane



M10
RXF04304.1

Serralysin (ec 3.4.24.40)
Extracellular




RXF04500.1

Serralysin (ec 3.4.24.40)
Extracellular




RXF01590.2

Serralysin (ec 3.4.24.40)
Extracellular




RXF04497.2

Serralysin (ec 3.4.24.40)
Extracellular




RXF04495.2

Serralysin (ec 3.4.24.40)
Extracellular




RXF02796.1

Serralysin (ec 3.4.24.40)
Extracellular



M14 (carboxypeptidase A family)
RXF09091.1

Zinc-carboxypeptidase precursor
Cytoplasmic






(ec 3.4.17.—)



M16 (pitrilysin family)
RXF03441.1

Coenzyme pqq synthesis protein F
Non-secretory






(ec 3.4.99.—)




RXF01918.1

zinc protease (ec 3.4.99.—)
Signal peptide




RXF01919.1

zinc protease (ec 3.4.99.—)
Periplasmic




RXF03699.2

processing peptidase (ec 3.4.24.64)
Signal peptide



M17 (leucyl aminopeptidase
RXF00285.2

Cytosol aminopeptidase (ec
Non-secretory



family)


3.4.11.1)



M18
RXF07879.1

Aspartyl aminopeptidase (ec
Cytoplasmic






3.4.11.21)



M20
RXF00811.1
dapE
Succinyl-diaminopimelate
Cytoplasmic






desuccinylase (ec 3.5.1.18)




RXF04052.2

Xaa-His dipeptidase (ec 3.4.13.3)
Signal peptide




RXF01822.2

Carboxypeptidase G2 precursor (ec
Signal peptide






3.4.17.11)




RXF09831.2::

N-acyl-L-amino acid
Signal peptide




RXF04892.1

amidohydrolase (ec 3.5.1.14)



M28 (aminopeptidase Y family)
RXF03488.2

Alkaline phosphatase isozyme
OuterMembrane






conversion protein precursor (ec






3.4.11.—)



M42 (glutamyl aminopeptidase
RXF05615.1

Deblocking aminopeptidase (ec
Non-secretory



family)


3.4.11.—)



M22
RXF05817.1

O-sialoglycoprotein endopeptidase
Extracellular






(ec 3.4.24.57)




RXF03065.2

Glycoprotease protein family
Non-secretory



M23
RXF01291.2

Cell wall endopeptidase, family
Signal peptide






M23/M37




RXF03916.1

Membrane proteins related to
Signal peptide






metalloendopeptidases




RXF09147.2

Cell wall endopeptidase, family
Signal peptide






M23/M37



M24
RXF04693.1

Methionine aminopeptidase (ec
Cytoplasmic






3.4.11.18)




RXF03364.1

Methionine aminopeptidase (ec
Non-secretory






3.4.11.18)




RXF02980.1

Xaa-Pro aminopeptidase (ec
Cytoplasmic






3.4.11.9)




RXF06564.1

Xaa-Pro aminopeptidase (ec
Cytoplasmic






3.4.11.9)



M48 (Ste24 endopeptidase family)
RXF05137.1

Heat shock protein HtpX
Cytoplasmic







Membrane




RXF05081.1

Zinc metalloprotease (ec 3.4.24.—)
Signal peptide



M50 (S2P protease family)
RXF04692.1

Membrane metalloprotease
Cytoplasmic







Membrane


Serine Peptidases
S1 (chymotrypsin family)
RXF01250.2

protease do (ec 3.4.21.—)
Periplasmic




RXF07210.1

protease do (ec 3.4.21.—)
Periplasmic



S8 (subtilisin family)
RXF06755.2

serine protease (ec 3.4.21.—)
Non-secretory




RXF08517.1

serine protease (ec 3.4.21.—)
Extracellular




RXF08627.2

extracellular serine protease (ec
Signal peptide






3.4.21.—)




RXF06281.1

Extracellular serine protease
Non-secretory






precursor (ec 3.4.21.—)




RXF08978.1

extracellular serine protease (ec
OuterMembrane






3.4.21.—)




RXF06451.1

serine protease (ec 3.4.21.—)
Signal peptide



S9 (prolyl oligopeptidase family)
RXF02003.2

Protease ii (ec 3.4.21.83)
Periplasmic




RXF00458.2

Hydrolase
Non-secretory



S11 (D-Ala-D-Ala carboxypeptidase
RXF04657.2

D-alanyl-D-alanine-endopeptidase
Periplasmic



A family)


(ec 3.4.99.—)




RXF00670.1

D-alanyl-D-alanine
Cytoplasmic






carboxypeptidase (ec 3.4.16.4)
Membrane



S13 (D-Ala-D-Ala peptidase C
RXF00133.1

D-alanyl-meso-diaminopimelate
OuterMembrane



family)


endopeptidase (ec 3.4.—.—)




RXF04960.2

D-alanyl-meso-diaminopimelate
Signal peptide






endopeptidase (ec 3.4.—.—)



S14 (ClpP endopeptidase family)
RXF04567.1
clpP
atp-dependent Clp protease
Non-secretory






proteolytic subunit (ec 3.4.21.92)




RXF04663.1
clpP
atp-dependent Clp protease
Cytoplasmic






proteolytic subunit (ec 3.4.21.92)



S16 (lon protease family)
RXF04653.2

atp-dependent protease La (ec
Cytoplasmic






3.4.21.53)




RXF08653.1

atp-dependent protease La (ec
Cytoplasmic






3.4.21.53)




RXF05943.1

atp-dependent protease La (ec
Cytoplasmic






3.4.21.53)



S24 (LexA family)
RXF00449.1

LexA repressor (ec 3.4.21.88)
Non-secretory




RXF03397.1

LexA repressor (ec 3.4.21.88)
Cytoplasmic



S26 (signal peptidase I family)
RXF01181.1

Signal peptidase I (ec 3.4.21.89)
Cytoplasmic







Membrane



S33
RXF05236.1
pip3
Proline iminopeptidase (ec 3.4.11.5)
Non-secretory




RXF04802.1
pip1
Proline iminopeptidase (ec 3.4.11.5)
Non-secretory




RXF04808.2
pip2
Proline iminopeptidase (ec 3.4.11.5)
Cytoplasmic



S41 (C-terminal processing
RXF06586.1

Tail-specific protease (ec 3.4.21.—)
Signal peptide



peptidase family)
RXF01037.1

Tail-specific protease (ec 3.4.21.—)
Signal peptide



S45
RXF07170.1
pacB2
Penicillin acylase (ec 3.5.1.11)
Signal peptide




RXF06399.2
pacB1
Penicillin acylase ii (ec 3.5.1.11)
Signal peptide



S49 (protease IV family)
RXF06993.2

possible protease sohb (ec 3.4.—.—)
Non-secretory




RXF01418.1

protease iv (ec 3.4.—.—)
Non-secretory



S58 (DmpA aminopeptidase family)
RXF06308.2

D-aminopeptidase (ec 3.4.11.19)
Cytoplasmic







Membrane


Threonine Peptidases
T1 (proteasome family)
RXF01961.2
hslV
atp-dependent protease hslV (ec
Cytoplasmic






3.4.25.—)



T3 (gamma-glutamyltransferase
RXF02342.1
ggt1
Gamma-glutamyltranspeptidase (ec
Periplasmic



family)


2.3.2.2)




RXF04424.2
ggt2
Gamma-glutamyltranspeptidase (ec
Periplasmic






2.3.2.2)


Unclassified Peptidases
U32
RXF00428.1

protease (ec 3.4.—.—)
Cytoplasmic




RXF02151.2

protease (ec 3.4.—.—)
Cytoplasmic



U61
RXF04715.1

Muramoyltetrapeptide
Non-secretory






carboxypeptidase (ec 3.4.17.13)



U62
RXF04971.2
pmbA
PmbA protein
Cytoplasmic




RXF04968.2

TldD protein
Cytoplasmic


Non MEROPS Proteases

RXF00325.1

Repressor protein C2
Non-secretory




RXF02689.2

Microsomal dipeptidase (ec
Cytoplasmic






3.4.13.19)




RXF02739.1

membrane dipeptidase (3.4.13.19)
Signal peptide




RXF03329.2

Hypothetical Cytosolic Protein
Cytoplasmic




RXF02492.1

Xaa-Pro dipeptidase (ec 3.4.13.9)
Cytoplasmic




RXF04047.2

caax amino terminal protease
Cytoplasmic






family
Membrane




RXF08136.2

protease (transglutaminase-like
Cytoplasmic






protein)




RXF09487.1

Zinc metalloprotease (ec 3.4.24.—)
Non-secretory









Certain proteases can have both protease and chaperone-like activity. When these proteases are negatively affecting protein yield and/or quality it can be useful to delete them, and they can be overexpressed when their chaperone activity may positively affect protein yield and/or quality. These proteases include, but are not limited to: Hsp100(Clp/Hsl) family members RXF04587.1 (clpA), RXF08347.1, RXF04654.2 (clpX), RXF04663.1, RXF01957.2 (hslU), RXF01961.2 (hslV); Peptidyl-prolyl cis-trans isomerase family member RXF05345.2 (ppiB); Metallopeptidase M20 family member RXF04892.1 (aminohydrolase); Metallopeptidase M24 family members RXF04693.1 (methionine aminopeptidase) and RXF03364.1 (methionine aminopeptidase); and Serine Peptidase S26 signal peptidase I family member RXF01181.1 (signal peptidase).







TABLE 7







P. fluorescens strain MB214 protein folding modulators











ORF ID
GENE
FUNCTION
FAMILY
LOCATION










GroES/EL











RXF02095.1
groES
Chaperone
Hsp10
Cytoplasmic


RXF06767.1::
groEL
Chaperone
Hsp60
Cytoplasmic


Rxf02090


RXF01748.1
ibpA
Small heat-shock protein (sHSP) IbpA
Hsp20
Cytoplasmic




PA3126; Acts as a holder for GroESL folding


RXF03385.1
hscB
Chaperone protein hscB
Hsp20
Cytoplasmic







Hsp70 (DnaK/J)











RXF05399.1
dnaK
Chaperone
Hsp70
Periplasmic


RXF06954.1
dnaK
Chaperone
Hsp70
Cytoplasmic


RXF03376.1
hscA
Chaperone
Hsp70
Cytoplasmic


RXF03987.2
cbpA
Curved dna-binding protein, dnaJ like activity
Hsp40
Cytoplasmic


RXF05406.2
dnaJ
Chaperone protein dnaJ
Hsp40
Cytoplasmic


RXF03346.2
dnaJ
Molecular chaperones (DnaJ family)
Hsp40
Non-secretory


RXF05413.1
grpE
heat shock protein GrpE PA4762
GrpE
Cytoplasmic







Hsp100 (Clp/Hsl)











RXF04587.1
clpA
atp-dependent clp protease atp-binding subunit
Hsp100
Cytoplasmic




clpA


RXF08347.1
clpB
ClpB protein
Hsp100
Cytoplasmic


RXF04654.2
clpX
atp-dependent clp protease atp-binding subunit
Hsp100
Cytoplasmic




clpX


RXF04663.1
clpP
atp-dependent Clp protease proteolytic subunit
MEROPS
Cytoplasmic




(ec 3.4.21.92)
peptidase





family S14


RXF01957.2
hslU
atp-dependent hsl protease atp-binding subunit
Hsp100
Cytoplasmic




hslU


RXF01961.2
hslV
atp-dependent hsl protease proteolytic subunit
MEROPS
Cytoplasmic





peptidase





subfamily





T1B







Hsp33











RXF04254.2
yrfI
33 kDa chaperonin (Heat shock protein 33
Hsp33
Cytoplasmic




homolog) (HSP33).







Hsp90











RXF05455.2
htpG
Chaperone protein htpG
Hsp90
Cytoplasmic







SecB











RXF02231.1
secB
secretion specific chaperone SecB
SecB
Non-secretory







Disulfide Bond Isomerases











RXF07017.2
dsbA
disulfide isomerase
DSBA oxido-
Cytoplasmic





reductase


RXF08657.2
dsbA/
disulfide isomerase
DSBA oxido-
Cytoplasmic



dsbC/

reductase



dsbG/



fernA


RXF01002.1
dsbA/
disulfide isomerase
DSBA oxido-
Periplasmic



dsbC

reductase/





Thioredoxin


RXF03307.1
dsbC
disulfide isomerase
Glutaredoxin/
Periplasmic





Thioredoxin


RXF04890.2
dsbG
disulfide isomerase
Glutaredoxin/
Periplasmic





Thioredoxin


RXF03204.1
dsbB
Disulfide bond formation protein B (Disulfide
DSBA oxido-
Periplasmic




oxidoreductase).
reductase


RXF04886.2
dsbD
Thiol:disulfide interchange protein dsbD
DSBA oxido-
Periplasmic





reductase







Peptidyl-prolyl cis-trans isomerases











RXF03768.1
ppiA
Peptidyl-prolyl cis-trans isomerase A (ec 5.2.1.8)
PPIase:
Periplasmic





cyclophilin





type


RXF05345.2
ppiB
Peptidyl-prolyl cis-trans isomerase B.
PPIase:
Cytoplasmic





cyclophilin





type


RXF06034.2
fklB
Peptidyl-prolyl cis-trans isomerase FklB.
PPIase:
OuterMembrane





FKBP type


RXF06591.1
fklB/
fk506 binding protein Peptidyl-prolyl cis-trans
PPIase:
Periplasmic



fkbP
isomerase (EC 5.2.1.8)
FKBP type


RXF05753.2
fklB;
Peptidyl-prolyl cis-trans isomerase (ec 5.2.1.8)
PPIase:
OuterMembrane



fkbP

FKBP type


RXF01833.2
slyD
Peptidyl-prolyl cis-trans isomerase SlyD.
PPIase:
Non-secretory





FKBP type


RXF04655.2
tig
Trigger factor, ppiase (ec 5.2.1.8)
PPIase:
Cytoplasmic





FKBP type


RXF05385.1
yaad
Probable FKBP-type 16 kDa peptidyl-prolyl cis-
PPIase:
Non-secretory




trans isomerase (EC 5.2.1.8) (PPiase)
FKBP type




(Rotamase).


RXF00271.1

Peptidyl-prolyl cis-trans isomerase (ec 5.2.1.8)
PPIase:
Non-secretory





FKBP type







pili assembly chaperones (papD like)











RXF06068.1
cup
Chaperone protein cup
pili assembly
Periplasmic





papD


RXF05719.1
ecpD
Chaperone protein ecpD
pili assembly
Signal peptide





papD


RXF05319.1
ecpD
Hnr protein
pili assembly
Periplasmic





chaperone


RXF03406.2
ecpD;
Chaperone protein ecpD
pili assembly
Signal peptide



csuC

papD


RXF04296.1
ecpD;
Chaperone protein ecpD
pili assembly
Periplasmic



cup

papD


RXF04553.1
ecpD;
Chaperone protein ecpD
pili assembly
Periplasmic



cup

papD


RXF04554.2
ecpD;
Chaperone protein ecpD
pili assembly
Periplasmic



cup

papD


RXF05310.2
ecpD;
Chaperone protein ecpD
pili assembly
Periplasmic



cup

papD


RXF05304.1
ecpD;
Chaperone protein ecpD
pili assembly
Periplasmic



cup

papD


RXF05073.1
gltF
Gram-negative pili assembly chaperone
pili assembly
Signal peptide




periplasmic function
papD







Type II Secretion Complex











RXF05445.1
YacJ
Histidinol-phosphate aminotransferase (ec
Class-II pyridoxal-
Membrane




2.6.1.9)
phosphate-dependent





aminotransferase





family. Histidinol-





phosphate amino-





transferase subfamily.


RXF05426.1
SecD
Protein translocase subunit secd
Type II
Membrane





secretion





complex


RXF05432.1
SecF
protein translocase subunit secf
Type II
Membrane





secretion





complex







Disulfide Bond Reductases











RXF08122.2
trxC
Thioredoxin 2
Disulfide
Cytoplasmic





Bond





Reductase


RXF06751.1
Gor
Glutathione reductase (EC 1.8.1.7) (GR) (GRase)
Disulfide
Cytoplasmic




PA2025
Bond





Reductase


RXF00922.1
gshA
Glutamate--cysteine ligase (ec 6.3.2.2) PA5203
Disulfide
Cytoplasmic





Bond





Reductase









High Throughput Screens

In some embodiments, a high throughput screen can be conducted to determine optimal conditions for expressing a soluble recombinant toxin protein. The conditions that be varied in the screen include, for example, the host cell, genetic background of the host cell (e.g., deletions of different proteases), type of promoter in an expression construct, type of secretion leader fused to the sequence encoding the recombinant protein, growth temperature, OD at induction when an inducible promoter is used, concentration of IPTG used for induction when a lacZ promoter is used, duration of protein induction, growth temperature following addition of an inducing agent to a culture, rate of agitation of culture, method of selection for plasmid maintenance, volume of culture in a vessel, and method of cell lysing.
In some embodiments, a library (or “array”) of host strains is provided, wherein each strain (or “population of host cells”) in the library has been genetically modified to modulate the expression of one or more target genes in the host cell. An “optimal host strain” or “optimal expression system” can be identified or selected based on the quantity, quality, and/or location of the expressed protein of interest compared to other populations of phenotypically distinct host cells in the array. Thus, an optimal host strain is the strain that produces the polypeptide of interest according to a desired specification. While the desired specification will vary depending on the polypeptide being produced, the specification includes the quality and/or quantity of protein, e.g., whether the protein is sequestered or secreted, and in what quantities, whether the protein is properly or desirably processed and/or folded, and the like. In embodiments, improved or desirable quality can be production of toxin protein with high fidelity cleavage of the secretion leader and low levels of degradation. In embodiments, the optimal host strain or optimal expression system produces a yield, characterized by the amount or quantity of soluble heterologous protein, the amount or quantity of recoverable heterologous protein, the amount or quantity of properly processed heterologous protein, the amount or quantity of properly folded heterologous protein, the amount or quantity of active heterologous protein, and/or the total amount or quantity of heterologous protein, of a certain absolute level or a certain level relative to that produced by an indicator strain, i.e., a strain used for comparison.
Methods of screening microbial hosts to identify strains with improved yield and/or quality in the expression of heterologous proteins are described, for example, in U.S. Patent Application Publication No. 20080269070.
Fermentation Format
The expression system according to the present invention can be cultured in any fermentation format. For example, batch, fed-batch, semi-continuous, and continuous fermentation modes may be employed herein.
In embodiments, the fermentation medium may be selected from among rich media, minimal media, and mineral salts media. In other embodiments either a minimal medium or a mineral salts medium is selected. In certain embodiments, a mineral salts medium is selected.
Mineral salts media consists of mineral salts and a carbon source such as, e.g., glucose, sucrose, or glycerol. Examples of mineral salts media include, e.g., M9 medium, Pseudomonas medium (ATCC 179), and Davis and Mingioli medium (see, B D Davis & E S Mingioli (1950) J. Bact. 60:17-28). The mineral salts used to make mineral salts media include those selected from among, e.g., potassium phosphates, ammonium sulfate or chloride, magnesium sulfate or chloride, and trace minerals such as calcium chloride, borate, and sulfates of iron, copper, manganese, and zinc. Typically, no organic nitrogen source, such as peptone, tryptone, amino acids, or a yeast extract, is included in a mineral salts medium. Instead, an inorganic nitrogen source is used and this may be selected from among, e.g., ammonium salts, aqueous ammonia, and gaseous ammonia. A mineral salts medium will typically contain glucose or glycerol as the carbon source. In comparison to mineral salts media, minimal media can also contain mineral salts and a carbon source, but can be supplemented with, e.g., low levels of amino acids, vitamins, peptones, or other ingredients, though these are added at very minimal levels. Media can be prepared using the methods described in the art, e.g., in U.S. Pat. App. Pub. No. 2006/0040352, referenced and incorporated by reference above. Details of cultivation procedures and mineral salts media useful in the methods of the present invention are described by Riesenberg, D et al., 1991, “High cell density cultivation of Escherichia coli at controlled specific growth rate,” J. Biotechnol. 20 (1):17-27.
In embodiments, production can be achieved in bioreactor cultures. Cultures can be grown in, e.g., up to 2 liter bioreactors containing a mineral salts medium, and maintained at 32° C. and pH 6.5 through the addition of ammonia. Dissolved oxygen can be maintained in excess through increases in agitation and flow of sparged air and oxygen into the fermentor. Glycerol can be delivered to the culture throughout the fermentation to maintain excess levels. In embodiments, these conditions are maintained until a target culture cell density, e.g., optical density at 575 nm (A575), for induction is reached, at which time IPTG is added to initiate the target protein production. It is understood that the cell density at induction, the concentration of IPTG, pH and temperature each can be varied to determine optimal conditions for expression. In embodiments, cell density at induction can be varied from A575 of 40 to 200 absorbance units (AU). IPTG concentrations can be varied in the range from 0.02 to 1.0 mM, pH from 6 to 7.5, and temperature from 20 to 35° C. After 16-24 hours, the culture from each bioreactor can be harvested by centrifugation and the cell pellet frozen at −80° C. Samples can then be analyzed, e.g., by SDS-CGE, for product formation.
Fermentation may be performed at any scale. The expression systems according to the present invention are useful for recombinant protein expression at any scale. Thus, e.g., microliter-scale, milliliter scale, centiliter scale, and deciliter scale fermentation volumes may be used, and 1 Liter scale and larger fermentation volumes can be used.
In embodiments, the fermentation volume is at or above about 1 Liter. In embodiments, the fermentation volume is about 1 liter to about 100 liters. In embodiments, the fermentation volume is about 1 liter, about 2 liters, about 3 liters, about 4 liters, about 5 liters, about 6 liters, about 7 liters, about 8 liters, about 9 liters, or about 10 liters. In embodiments, the fermentation volume is about 1 liter to about 5 liters, about 1 liter to about 10 liters, about 1 liter to about 25 liters, about 1 liter to about 50 liters, about 1 liter to about 75 liters, about 10 liters to about 25 liters, about 25 liters to about 50 liters, or about 50 liters to about 100 liters In other embodiments, the fermentation volume is at or above 5 Liters, 10 Liters, 15 Liters, 20 Liters, 25 Liters, 50 Liters, 75 Liters, 100 Liters, 200 Liters, 500 Liters, 1,000 Liters, 2,000 Liters, 5,000 Liters, 10,000 Liters, or 50,000 Liters.
Bacterial Growth Conditions
Growth conditions useful in the methods of the provided invention can comprise a temperature of about 4° C. to about 42° C. and a pH of about 5.7 to about 8.8. When an expression construct with a lacZ promoter is used, expression can be induced by adding IPTG to a culture at a final concentration of about 0.01 mM to about 1.0 mM.
The pH of the culture can be maintained using pH buffers and methods known to those of skill in the art. Control of pH during culturing also can be achieved using aqueous ammonia. In embodiments, the pH of the culture is about 5.7 to about 8.8. In certain embodiments, the pH is about 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, or 8.8 In other embodiments, the pH is about 5.7 to 5.9, 5.8 to 6.0, 5.9 to 6.1, 6.0 to 6.2, 6.1 to 6.3, 6.2 to 6.5, 6.4 to 6.7, 6.5 to 6.8, 6.6 to 6.9, 6.7 to 7.0, 6.8 to 7.1, 6.9 to 7.2, 7.0 to 7.3, 7.1 to 7.4, 7.2 to 7.5, 7.3 to 7.6, 7.4 to 7.7, 7.5 to 7.8, 7.6 to 7.9, 7.7 to 8.0, 7.8 to 8.1, 7.9 to 8.2, 8.0 to 8.3, 8.1 to 8.4, 8.2 to 8.5, 8.3 to 8.6, 8.4 to 8.7, or 8.5 to 8.8. In yet other embodiments, the pH is about 5.7 to 6.0, 5.8 to 6.1, 5.9 to 6.2, 6.0 to 6.3, 6.1 to 6.4, or 6.2 to 6.5. In certain embodiments, the pH is about 5.7 to about 6.25.
In embodiments, the growth temperature is maintained at about 4° C. to about 42° C. In certain embodiments, the growth temperature is about 4° C., about 5° C., about 6° C., about 7° C., about 8° C., about 9° C., about 10° C., about 11° C., about 12° C., about 13° C., about 14° C., about 15° C., about 16° C., about 17° C., about 18° C., about 19° C., about 20° C., about 21° C., about 22° C., about 23° C., about 24° C., about 25° C., about 26° C., about 27° C., about 28° C., about 29° C., about 30° C., about 31° C., about 32° C., about 33° C., about 34° C., about 35° C., about 36° C., about 37° C., about 38° C., about 39° C., about 40° C., about 41° C., or about 42° C. In other embodiments, the growth temperature is maintained at about 25° C. to about 27° C., about 25° C. to about 28° C., about 25° C. to about 29° C., about 25° C. to about 30° C., about 25° C. to about 31° C., about 25° C. to about 32° C., about 25° C. to about 33° C., about 26° C. to about 28° C., about 26° C. to about 29° C., about 26° C. to about 30° C., about 26° C. to about 31° C., about 26° C. to about 32° C., about 27° C. to about 29° C., about 27° C. to about 30° C., about 27° C. to about 31° C., about 27° C. to about 32° C., about 26° C. to about 33° C., about 28° C. to about 30° C., about 28° C. to about 31° C., about 28° C. to about 32° C., about 29° C. to about 31° C., about 29° C. to about 32° C., about 29° C. to about 33° C., about 30° C. to about 32° C., about 30° C. to about 33° C., about 31° C. to about 33° C., about 31° C. to about 32° C., about 30° C. to about 33° C., or about 32° C. to about 33° C. In other embodiments, the temperature is changed during culturing. In one embodiment, the temperature is maintained at about 30° C. before an agent to induce expression from the construct, e.g., IPTG, is added to the culture. After adding the induction agent, the temperature is reduced to about 25° C.
Induction
As described elsewhere herein, inducible promoters can be used in the expression construct to control expression of the recombinant toxin protein, e.g., a lac promoter. In the case of the lac promoter derivatives or family members, e.g., the tac promoter, the effector compound is an inducer, such as a gratuitous inducer like IPTG (isopropyl-β-D-1-thiogalactopyranoside, also called “isopropylthiogalactoside”). In embodiments, a lac promoter derivative is used, and recombinant protein expression is induced by the addition of IPTG to a final concentration of about 0.01 mM to about 1.0 mM, when the cell density has reached a level identified by an OD575 of about 80 to about 160. In embodiments, the OD575 at the time of culture induction for the recombinant protein can be about 80, about 90, about 100, about 110, about 120, about 130, about 140, about 150, about 160, about 170 about 180. In other embodiments, the OD575 is about 80 to about 100, about 100 to about 120, about 120 to about 140, about 140 to about 160. In other embodiments, the OD575 is about 80 to about 120, about 100 to about 140, or about 120 to about 160. In other embodiments, the OD575 is about 80 to about 140, or about 100 to 160. The cell density can be measured by other methods and expressed in other units, e.g., in cells per unit volume. For example, an OD575 of about 80 to about 160 of a Pseudomonas fluorescens culture is equivalent to approximately 8×1010 to about 1.6×1011 colony forming units per mL or 35 to 70 g/L dry cell weight. In embodiments, the cell density at the time of culture induction is equivalent to the cell density as specified herein by the absorbance at OD575, regardless of the method used for determining cell density or the units of measurement. One of skill in the art will know how to make the appropriate conversion for any cell culture.
In embodiments, the final IPTG concentration of the culture is about 0.01 mM, about 0.02 mM, about 0.03 mM, about 0.04 mM, about 0.05 mM, about 0.06 mM, about 0.07 mM, about 0.08 mM, about 0.09 mM, about 0.1 mM, about 0.2 mM, about 0.3 mM, about 0.4 mM, about 0.5 mM, about 0.6 mM, about 0.7 mM, about 0.8 mM, about 0.9 mM, or about 1 mM. In other embodiments, the final IPTG concentration of the culture is about 0.08 mM to about 0.1 mM, about 0.1 mM to about 0.2 mM, about 0.2 mM to about 0.3 mM, about 0.3 mM to about 0.4 mM, about 0.2 mM to about 0.4 mM, about 0.08 to about 0.2 mM, or about 0.1 to 1 mM.
In embodiments wherein a non-lac type promoter is used, as described herein and in the literature, other inducers or effectors can be used. In one embodiment, the promoter is a constitutive promoter.
After adding and inducing agent, cultures can be grown for a period of time, for example about 24 hours, during which time the recombinant protein is expressed. After adding an inducing agent, a culture can be grown for about 1 hr, about 2 hr, about 3 hr, about 4 hr, about 5 hr, about 6 hr, about 7 hr, about 8 hr, about 9 hr, about 10 hr, about 11 hr, about 12 hr, about 13 hr, about 14 hr, about 15 hr, about 16 hr, about 17 hr, about 18 hr, about 19 hr, about 20 hr, about 21 hr, about 22 hr, about 23 hr, about 24 hr, about 36 hr, or about 48 hr. After an inducing agent is added to a culture, the culture can be grown for about 1 to 48 hrs, about 1 to 24 hrs, about 10 to 24 hrs, about 15 to 24 hrs, or about 20 to 24 hrs. Cell cultures can be concentrated by centrifugation, and the culture pellet resuspended in a buffer or solution appropriate for the subsequent lysis procedure.
In embodiments, cells are disrupted using equipment for high pressure mechanical cell disruption (which are available commercially, e.g., Microfluidics Micro fluidizer, Constant Cell Disruptor, Niro-Soavi homogenizer or APV-Gaulin homogenizer). Cells expressing the recombinant protein can be disrupted, for example, using sonication. Any appropriate method known in the art for lysing cells can be used to release the soluble fraction. For example, in embodiments, chemical and/or enzymatic cell lysis reagents, such as cell-wall lytic enzyme and EDTA, can be used. Use of frozen or previously stored cultures is also contemplated in the methods of the invention. Cultures can be OD-normalized prior to lysis. For example, cells can be normalized to an OD600 of about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or about 20.
Centrifugation can be performed using any appropriate equipment and method. Centrifugation of cell culture or lysate for the purposes of separating a soluble fraction from an insoluble fraction is well-known in the art. For example, lysed cells can be centrifuged at 20,800×g for 20 minutes (at 4° C.), and the supernatants removed using manual or automated liquid handling. The pellet (insoluble) fraction is resuspended in a buffered solution, e.g., phosphate buffered saline (PBS), pH 7.4. Resuspension can be carried out using, e.g., equipment such as impellers connected to an overhead mixer, magnetic stir-bars, rocking shakers, etc.
A “soluble fraction,” i.e., the soluble supernatant obtained after centrifugation of a lysate, and an “insoluble fraction,” i.e., the pellet obtained after centrifugation of a lysate, result from lysing and centrifuging the cultures. These two fractions also can be referred to as a “first soluble fraction” and a “first insoluble fraction,” respectively.
Evaluation of Product
Numerous assay methods are known in the art for characterizing proteins. Use of any appropriate method for characterizing the yield or quality of the recombinant toxin protein is contemplated herein.
Protein Yield
Protein yield in any purification fraction as described herein can be determined by methods known to those of skill in the art, for example, by capillary gel electrophoresis (CGE), and Western blot analysis. Activity assays, as described herein and known in the art, also can provide information regarding protein yield. In embodiments, these or any other methods known in the art are used to evaluate proper processing of a protein, e.g., proper secretion leader cleavage.
Useful measures of protein yield include, e.g., the amount of recombinant protein per culture volume (e.g., grams or milligrams of protein/liter of culture), percent or fraction of recombinant protein measured in the insoluble pellet obtained after cell lysis (e.g., amount of recombinant protein in extract supernatant/amount of protein in insoluble fraction), percent or fraction of active protein (e.g., amount of active protein/amount protein used in the assay), percent or fraction of total cell protein (tcp), amount of protein/cell, and percent or proportion of dry biomass. In embodiments, the measure of protein yield as described herein is based on the amount of soluble protein or the amount of active protein, or both, obtained.
In embodiments wherein yield is expressed in terms of culture volume the culture cell density may be taken into account, particularly when yields between different cultures are being compared.
In embodiments, the methods of the present invention can be used to obtain a soluble and/or active and/or properly processed (e.g., having the secretion leader cleaved properly) recombinant toxin protein or subunit protein yield of about 0.2 grams per liter to about 12 grams per liter. In embodiments, the yield is about 0.5 grams per liter to about 12 grams per liter. In certain embodiments, the recombinant protein or subunit protein yield is about 0.2 g/L, about 0.3 g/L, about 0.4 g/L, about 0.5 g/L, about 0.6 g/L, about 0.7 g/L, about 0.8 g/L, about 0.9 g/L, about 1 g/L, about 1.5 g/L, about 2 g/L, about 2.5 g/L, about 3 g/L, about 3.5 g/L, about 4 g/L, about 4.5 g/L, about 5 g/L, about 5.5 g/L, about 6 g/L, about 6.5 g/L, about 7 g/L, about 7.5 g/L, about 8 g/L, about 8.5 g/L, about 9 g/L, about 9.5 g/L, about 10 g/L, about 10.5 g/L, about 11 g/L, about 12 g/L, about 0.2 g/L to about 0.5 g/L, about 0.2 g/L to about 1 g/L, about 0.2 to about 2 g/L, about 0.3 g/L to about 0.6 g/L, about 0.3 g/L to about 1 g/L, about 0.3 to about 2 g/L, about 0.4 to about 0.7 g/L, about 0.4 to about 1 g/L about 0.4 to about 2 g/L, about 0.4 to about 3 g/L, about 0.5 g/L to about 1 g/L, about 0.5 g/L to about 1 g/L, about 0.5 g/L to about 2 g/L, about 0.5 g/L to about 3 g/L, about 0.5 g/L to about 4 g/L, about 0.5 g/L to about 5 g/L, about 0.5 g/L to about 6 g/L, about 0.5 g/L to about 7 g/L, about 0.5 g/L to about 8 g/L, about 0.5 g/L to about 9 g/L, about 0.5 g/L to about 10 g/L, about 0.5 g/L to about 11 g/L, about 0.5 g/L to about 12 g/L, about 1 g/L to about 2 g/L, about 1 g/L to about 3 g/L, about 1 g/L to about 4 g/L, about 1 g/L to about 5 g/L, about 1 g/L to about 6 g/L, about 1 g/L to about 7 g/L, about 1 g/L to about 8 g/L, about 1 g/L to about 9 g/L, about 1 g/L to about 10 g/L, about 1 g/L to about 11 g/L, about 1 g/L to about 12 g/L, about 2 g/L to about 3 g/L, about 2 g/L to about 4 g/L, about 2 g/L to about 5 g/L, about 2 g/L to about 6 g/L, about 2 g/L to about 7 g/L, about 2 g/L to about 8 g/L, about 2 g/L to about 9 g/L, about 2 g/L to about 10 g/L, about 2 g/L to about 11 g/L, about 2 g/L to about 12 g/L, about 3 g/L to about 4 g/L, about 3 g/L to about 5 g/L, about 3 g/L to about 6 g/L, about 3 g/L to about 7 g/L, about 3 g/L to about 8 g/L, about 3 g/L to about 9 g/L, about 3 g/L to about 10 g/L, about 3 g/L to about 11 g/L, about 3 g/L to about 12 g/L, about 4 g/L to about 5 g/L, about 4 g/L to about 6 g/L, about 4 g/L to about 7 g/L, about 4 g/L to about 8 g/L, about 4 g/L to about 9 g/L, about 4 g/L to about 10 g/L, about 4 g/L to about 11 g/L, about 4 g/L to about 12 g/L, about 5 g/L to about 6 g/L, about 5 g/L to about 7 g/L, about 5 g/L to about 8 g/L, about 5 g/L to about 9 g/L, about 5 g/L to about 10 g/L, about 5 g/L to about 11 g/L, about 5 g/L to about 12 g/L, about 6 g/L to about 7 g/L, about 6 g/L to about 8 g/L, about 6 g/L to about 9 g/L, about 6 g/L to about 10 g/L, about 6 g/L to about 11 g/L, about 6 g/L to about 12 g/L, about 7 g/L to about 8 g/L, about 7 g/L to about 9 g/L, about 7 g/L to about 10 g/L, about 7 g/L to about 11 g/L, about 7 g/L to about 12 g/L, about 8 g/L to about 9 g/L, about 8 g/L to about 10 g/L, about 8 g/L to about 11 g/L, about 8 g/L to about 12 g/L, about 9 g/L to about 10 g/L, about 9 g/L to about 11 g/L, about 9 g/L to about 12 g/L, about 10 g/L to about 11 g/L, about 10 g/L to about 12 g/L, or about 11 g/L to about 12 g/L.
In embodiments, the amount of recombinant toxin protein or subunit protein produced is about 1% to 75% of the total cell protein. In certain embodiments, the amount of toxin protein or subunit protein produced is about 1%, about 2%, about 3%, about 4%, about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 1% to about 5%, about 1% to about 10%, about 1% to about 20%, about 1% to about 30%, about 1% to about 40%, about 1% to about 50%, about 1% to about 60%, about 1% to about 75%, about 2% to about 5%, about 2% to about 10%, about 2% to about 20%, about 2% to about 30%, about 2% to about 40%, about 2% to about 50%, about 2% to about 60%, about 2% to about 75%, about 3% to about 5%, about 3% to about 10%, about 3% to about 20%, about 3% to about 30%, about 3% to about 40%, about 3% to about 50%, about 3% to about 60%, about 3% to about 75%, about 4% to about 10%, about 4% to about 20%, about 4% to about 30%, about 4% to about 40%, about 4% to about 50%, about 4% to about 60%, about 4% to about 75%, about 5% to about 10%, about 5% to about 20%, about 5% to about 30%, about 5% to about 40%, about 5% to about 50%, about 5% to about 60%, about 5% to about 75%, about 10% to about 20%, about 10% to about 30%, about 10% to about 40%, about 10% to about 50%, about 10% to about 60%, about 10% to about 75%, about 20% to about 30%, about 20% to about 40%, about 20% to about 50%, about 20% to about 60%, about 20% to about 75%, about 30% to about 40%, about 30% to about 50%, about 30% to about 60%, about 30% to about 75%, about 40% to about 50%, about 40% to about 60%, about 40% to about 75%, about 50% to about 60%, about 50% to about 75%, about 60% to about 75%, or about 70% to about 75%, of the total cell protein.
In certain embodiments, multiple proteins are produced from the same host cell. For example, in embodiments, all five subunits of Pertussis toxin are made from the same host cell grown in a single culture. In such embodiments the concentration, % total cell protein, or activity observed is that for each individual toxin subunit or for all the subunits taken together. That is, in embodiments, the methods of the invention are used to obtain a yield of the S1, S2, S3, S4, or S5 subunit of Pertussis toxin protein of about 1 gram per liter to about 12 grams per liter. In embodiments, the amount of S1, S2, S3, S4, or S5 subunit protein produced is 1% to 75% of the total cell protein. Alternatively, the methods of the invention are used to obtain a yield of S1, S2, S3, S4, and S5 subunit protein of about 1 gram per liter to about 12 grams per liter. In embodiments, the amount of S1, S2, S3, S4, and S5 subunit protein produced is 1% to 75% of the total cell protein. In certain embodiments, the amount of each subunit obtained, in grams per liter or % total cell protein, is approximately the same.
The “solubility” and “activity” of a protein, though related qualities, are generally determined by different means. The solubility of a protein, particularly a hydrophobic protein, typically relates to the folding of a protein; insolubility indicates that hydrophobic amino acid residues are improperly located on the outside of the folded protein. Protein activity, which can be evaluated using methods, e.g., those described below, is another indicator of proper protein conformation. “Soluble, active, or both,” or “soluble and/or active,” as used herein, refers to protein that is determined to be soluble, active, or both soluble and active, by methods known to those of skill in the art and described herein. The “activity” of a given protein can include binding activity, e.g., that represented by binding to a receptor, a specific antibody, or to another known substrate, or by enzymatic activity if relevant. Activity levels can be described, e.g., in absolute terms or in relative terms, as when compared with the activity of a standard or control sample, or any sample used as a reference.
Activity assays for evaluating toxins are known in the art and described in the literature. Activity assays include immunological or antibody binding assays, e.g., Western Blot analysis and ELISA, as well as receptor binding assays, e.g., CRM197 can be evaluated by Diptheria toxin receptor (proHB-EGF) binding assay. Antibodies useful in these assays are commercially available. Activity assays also include enzyme activity assays. Wild-type DT can be assayed immunologically and also by ADP-ribosylation activity, using methods known in the art and described elsewhere herein for P. aeruginosa Exotoxin A.
For example, Western blot analysis of CTB can be performed as described, e.g., in U.S. Pat. No. 6,140,082, “Expression of Gene Products from Genetically Manipulated Strains of Bordetella,” incorporated herein by reference. This patent describes expression of CTB in Bordetella. The proteins from culture supernatants were resolved by SDS-PAGE or boiled before being resolved to convert the CTB pentamer to the monomeric form. The proteins were transferred onto nylon membranes and probed with goat anti-choleragenoid IgG antibody (anti-CTB, List Biologicals #GAC-01C). Detection was performed with alkaline phosphatase-conjugated donkey anti-goat IgG, using dig chemiluminescence (Boehringer Mannheim). A Cholera toxin standard (Sigma) containing both CTA and CTB was used for comparison.
Western blot analysis of PTX can be performed, e.g., as described herein in the Examples, using commercially available antibodies. Monoclonal antibodies are available from, e.g., Abcam, Cambridge, Mass.
Tetanus Toxin C Fragment can be evaluated by Western Blot analysis, or by ELISA as described in, e.g., U.S. Pat. No. 5,443,966, “Expression of tetanus toxin fragment C,” incorporated herein by reference. Antibodies are available from multiple commercial sources, e.g., Abcam, Cambridge, Mass.
TcdB activity can be evaluated by Western Blot or other detection analysis, as described in the art. Enzymatic activity can be assayed, e.g., using glucosylhydrolase/glucosylation assay methods described in the art, for example in U.S. Pat. No. 7,226,597, incorporated herein by reference in its entirety. Specifically, glucosylation reactions can be carried out in a reaction mix containing 50 mM n-2hydroxyethylpiperazine-n′-2-ethane sulfonic acid, 100 mM KCl, 1 mM MnCl2, 1 mM MgCl2, 100 μgram/ml BSA, 0.2 mM GDP, 40 μM[14C]UDP-glucose (303 Ci/mol; ICN Pharmaceuticals), 100 μM UDP-glucose and 3 pmol of TcdB or 10 pmol of each fusion protein. The assay is allowed to incubate overnight at 37° C. and the cleaved glucose is separated using AG1-X2 anion exchange resin and counted in a liquid scintillation counter.
P. aeruginosa Exotoxin A activity can be evaluated using immunological methods, e.g., Western Blot analysis. Since ETA is an ADP-ribosylating toxin, it can be assayed for ADP-ribosylation activity, e.g., as described in U.S. Pat. No. 4,892,827, incorporated herein by reference. Specifically, rabbit reticulocyte preparations or wheat germ extracts enriched with elongation factor 2 (EF-2) are used as a source of EF-2. Assays (500 μl total volume) contain about 10 pmole of EF-2, 37 pmole of 14C-NAD (0.06 μCi), 0.25 to 1.25 μg of ETA and buffer (40 mM DTT, 1 mM EDTA, and 50 mM Tris, pH 8.1). Activity is measured as pmoles of NAD transferred to EF-2 in 30 minutes. A standard curve of known concentrations of PE is established and used to determine the activity of PE in extracts from E. coli. After incubation for 30 minutes at 37° C., 0.5 ml 12% TCA is added to each assay mixture. The assay mixtures are then set in an ice bath for 15 minutes, followed by centrifugation at 4° C., 3,000×g for 10 minutes. The pellet is washed with 1 ml 6% TCA and centrifuged as above. The pellet is then measured for 14C radioactivity in a liquid scintillation counter as the index of the ADP-ribosylation activity.
Therefore, a measure of activity can represent, e.g., antibody or receptor binding capacity, substrate binding capacity (as to a column material), or enzyme activity.
In embodiments, activity is represented by the % active recombinant toxin protein in the extract supernatant as compared with the total amount assayed. This is based on the amount of recombinant toxin protein determined to be active by the assay relative to the total amount of recombinant toxin protein used in the assay. In other embodiments, activity is represented by the % activity level of the protein compared to a standard, e.g., native protein. This is based on the amount of active recombinant toxin protein in supernatant extract sample relative to the amount of active protein in a standard sample (where the same amount of protein from each sample is used in assay).
In embodiments, about 40% to about 100% of the toxin protein or subunit is determined to be active. In embodiments, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100% of the recombinant toxin protein or protein subunit is determined to be active. In embodiments, about 40% to about 50%, about 50% to about 60%, about 60% to about 70%, about 70% to about 80%, about 80% to about 90%, about 90% to about 100%, about 50% to about 100%, about 60% to about 100%, about 70% to about 100%, about 80% to about 100%, about 40% to about 90%, about 40% to about 95%, about 50% to about 90%, about 50% to about 95%, about 50% to about 100%, about 60% to about 90%, about 60% to about 95%, about 60% to about 100%, about 70% to about 90%, about 70% to about 95%, about 70% to about 100%, or about 70% to about 100% of the recombinant toxin protein or subunit is determined to be active.
In other embodiments, about 75% to about 100% of the recombinant toxin protein or protein subunit is determined to be active. In embodiments, about 75% to about 80%, about 75% to about 85%, about 75% to about 90%, about 75% to about 95%, about 80% to about 85%, about 80% to about 90%, about 80% to about 95%, about 80% to about 100%, about 85% to about 90%, about 85% to about 95%, about 85% to about 100%, about 90% to about 95%, about 90% to about 100%, or about 95% to about 100% of the recombinant toxin protein or subunit is determined to be active.
Means of confirming the identity of the induced protein are also known in the art. For example, a protein can analyzed by peptide mass fingerprint using MALDI-TOF mass spectrometry, N-terminal sequencing analysis, or peptide mapping.
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
EXAMPLES
Example 1
High Throughput Expression of a Recombinant CRM197 Protein
CRM197 expression strains were constructed and the amount of soluble CRM197 protein produced in the strains was analyzed using capillary gel electrophoresis (SDS-CGE). Based on the resulting data, certain strains were selected for use in large-scale expression.
Construction and Growth of CRM197 Expression Strains
The CRM197 coding sequence was constructed using P. fluorescens preferred codons to encode the CRM197 amino acid sequence. FIG. 1 shows the amino acid and DNA sequences of the expressed synthetic CRM197 gene.
Plasmids carrying the optimized CRM197 sequence, fused to ten P. fluorescens secretion leaders as shown in Table 8, were constructed. The CRM197 coding sequence was fused in frame with that of P. fluorescens secretion leaders to target the protein to the periplasm for recovery in the properly folded and active form.







TABLE 8







Secretion leaders used for CRM197 expression screen









Secretion Leader












1
DsbA


2
Azu


3
Ibp-S31A


4
Tpr


5
CupB2


6
CupA2


7
NikA


8
Pbp A20V


9
DsbC


10
TolB









Constructs containing the ten secretion leaders fused to the recombinant CRM197 coding sequence were tested in P. fluorescens hosts. Four hosts, listed in Table 9, were tested with each expression plasmid. Host cells were electroporated with the indicated plasmids, resuspended in HTP growth medium with trace minerals and 5% glycerol and then transferred to 96-well deep well plate with 400 μl M9 salts 1% glucose medium and trace elements. The 96-well plates were incubated at 30° C. with shaking for 48 hours. Ten microliters of each of the forty seed cultures were transferred into triplicate 96-well deep-well plates, each well containing 500 μl of HTP medium supplemented with trace elements and 5% glycerol, and incubated as before for 24 hours.







TABLE 9







Host strains used for CRM197 expression screen









Host Strain
Genotype
Type





1
lon, la, aprA
PD


2
hslUV prc1 degP1 degP2 aprA deletions;
PD + FMO



overexpresses DegP2 S219A



3
dsbABCD
FMO


4
grpE, dnaKJ
FMO





PD = Protease Deletion (listed proteases are deleted);


FMO = Folding Modulator Overexpressor (listed folding modulators are overexpressed.






Isopropyl-β-D-1-thiogalactopyranoside (IPTG) was added to each well to a final concentration of 0.3 mM to induce the expression of target proteins. Mannitol (Sigma, M1902) was added to each well to a final concentration of 1% to induce the expression of folding modulators in folding modulator over-expressing strains, and the temperature was reduced to 25° C. Twenty four hours after induction, cells were normalized to OD600=15 using PBS in a volume of 400 μl. Samples were frozen for later processing by sonication and centrifugation to generate soluble and insoluble fractions.
Sample Preparation and SDS-CGE Analysis
Soluble and insoluble cellular fractions were prepared by sonication of the normalized cultures followed by centrifugation. Frozen, normalized culture broth (400 μL) was thawed and sonicated for 3.5 minutes. The lysates were centrifuged at 20,800×g for 20 minutes (4° C.) and the supernatants removed using manual or automated liquid handling (soluble fraction). The pellets (insoluble fraction) were frozen and then thawed for re-centrifugation at 20,080×g for 20 minutes at 4 C, to remove residual supernatant. The pellets were then resuspended in 400 μL of 1× phosphate buffered saline (PBS), pH 7.4. Further dilutions of soluble and insoluble samples for SDS-CGE analysis were performed in 1× phosphate buffered saline (PBS), pH 7.4. Soluble and insoluble samples were prepared for SDS capillary gel electrophoresis (CGE) (Caliper Life Sciences, Protein Express LabChip Kit, Part 760301), in the presence of dithiothreitol (DTT).
Representative gel-like images showing the results of the reducing SDS-CGE analysis of the soluble fraction from each strain are shown in FIG. 2. Table 10 shows the mean soluble CRM197 yield and standard deviation of 3 replicates for each of the CRM197-expression strains constructed. The host strain and secretion leader screened for each strain are also indicated.
Both secretion leader and host strain showed a significant impact on CRM197 expression. Expression ranged from no detectable yield to more than 1.2 g/L at the 0.5 mL scale, with the highest expression levels observed in the Host Strain 2 background. The yield observed in PS538-776 was 1263 mg/L, and that in PS538-772 was 1241 mg/L, both well over the average yield of 340 mg/L. Both high and low yields were observed in the same host strain depending on the leader used, and both high and low yields were observed using the same leader in different host strains.
PS538-772, PS538-773, PS538-776, PS538-778, PS538-782 were selected for evaluation in large-scale fermentation.







TABLE 10







Mean CRM197 yield for CRM197-expression strains













Corresponding







Strain Number







in U.S. patent







application


Mean 



Strain
Ser. No.


Yield
Std Dev


Number
61/325,235
Host
Leader
(mg/L)
(3 replicates)















PS538-761
PS538-731
1
DsbA
205
162


PS538-762
PS538-732
1
Azu
427
186


PS538-763
PS538-733
1
Ibp-S31A
361
183


PS538-764
PS538-734
1
Tpr
298
106


PS538-765
PS538-735
1
CupB2
105
109


PS538-766
PS538-736
1
CupA2
175
99


PS538-767
PS538-737
1
NikA
314
85


PS538-768
PS538-738
1
Pbp A20V
291
204


PS538-769
PS538-739
1
DsbC
148
91


PS538-770
PS538-740
1
TolB
213
36


PS538-771
PS538-741
2
DsbA
407
218


PS538-772
PS538-742
2
Azu
1241
372


PS538-773
PS538-743
2
Ibp-S31A
1107
219


PS538-774
PS538-744
2
Tpr
280
285


PS538-775
PS538-745
2
CupB2
192
219


PS538-776
PS538-746
2
CupA2
1263
474


PS538-777
PS538-747
2
NikA
699
259


PS538-778
PS538-748
2
Pbp A20V
914
416


PS538-779
PS538-749
2
DsbC
567
141


PS538-780
PS538-750
2
TolB
382
217


PS538-781
PS538-751
3
DsbA
591
230


PS538-782
PS538-752
3
Azu
1094
543


PS538-783
PS538-753
3
Ibp-S31A
323
143


PS538-784
PS538-754
3
Tpr
419
70


PS538-785
PS538-755
3
CupB2
75
74


PS538-786
PS538-756
3
CupA2
309
214


PS538-787
PS538-757
3
NikA
52
73


PS538-788
PS538-758
3
Pbp A20V
356
295


PS538-789
PS538-759
3
DsbC
319
117


PS538-790
PS538-760
3
TolB
69
88


PS538-791
PS538-761
4
DsbA
270
106


PS538-792
PS538-762
4
Azu
0
14


PS538-793
PS538-763
4
Ibp-S31A
0
6


PS538-794
PS538-764
4
Tpr
0
0


PS538-795
PS538-765
4
CupB2
18
39


PS538-796
PS538-766
4
CupA2
118
134


PS538-797
PS538-767
4
NikA
0
9


PS538-798
PS538-768
4
Pbp A20V
0
0


PS538-799
PS538-769
4
DsbC
0
0


PS538-800
PS538-770
4
TolB
0
0









Example 2
Large-Scale Expression of a Recombinant Crm197 Protein
Recombinant CRM197 protein was produced in Pseudomonas fluorescens strains PS538-772, PS538-776, and PS538-782 in 2 liter fermentors. Cultures were grown in 2 liter fermentors containing a mineral salts medium as described herein and also by, e.g., Riesenberg, D., et al., 1991, and maintained at 32° C. and pH 6.5 through the addition of ammonia. Dissolved oxygen was maintained in excess through increases in agitation and flow of sparged air and oxygen into the fermentor. Glycerol was delivered to the culture throughout the fermentation to maintain excess levels. These conditions were maintained until a target culture cell density (optical density at 575 nm (A575)) for induction is reached, at which time IPTG is added to initiate CRM197 production. Cell density at induction could be varied from A575 of 40 to 200 absorbance units (AU). IPTG concentrations could be varied in the range from 0.02 to 0.4 mM. pH from 6 to 7.5 and temperature 20 to 35° C. After 16-24 hours, the culture from each bioreactor was harvested by centrifugation and the cell pellet frozen at −80° C. Samples were analyzed by SDS-CGE for product formation.
Multiple fermentation conditions were evaluated resulting in top CRM197 expression as determined by SDS-CGE of 1 to 2 g/L (see FIGS. 23 and 24). The identities of the induced proteins were confirmed by Western blot analysis using a diphtheria toxin specific antibody (FIG. 25).
Example 3
High Throughput Expression of a Recombinant Cholera Toxin B Protein
Construction and Growth of Cholera Toxin B Expression Strains
The Cholera Toxin B coding sequence was constructed using P. fluorescens preferred codons to encode the Cholera Toxin B amino acid sequence. FIG. 3 shows the amino acid and DNA sequences of the expressed synthetic Cholera Toxin B gene.
Plasmids carrying the optimized Cholera Toxin B sequence, fused to the same ten P. fluorescens secretion leader coding sequences used with CRM197 (shown in Table 8) were constructed. The secretion leaders were included to target the protein to the periplasm for recovery in the properly folded and active form.
Constructs expressing the ten secretion leaders fused to the recombinant Cholera Toxin B protein were tested in P. fluorescens hosts. The four hosts listed in Table 9 were tested with each expression plasmid. Host cells were electroporated with the indicated plasmids, and grown and induced in 96-well format as described above for the CRM197 high throughput expression. Samples were prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples.
Representative gel-like images showing the results of the reducing SDS-CGE analysis of the soluble fraction from each strain are shown in FIG. 4. Table 11 shows the mean soluble Cholera Toxin B yield and standard deviation of 3 replicates for each of the Cholera Toxin B-expression strains constructed.
Both secretion leader and host strain showed a significant impact on Cholera Toxin B expression. Expression ranged from no detectable yield to more than 0.2 g/L at the 0.5 mL scale, with the highest expression levels observed in the hslUV prc1 degP1 degP2 aprA deletion/DegP2 S219A overexpression host background. Expression of Cholera Toxin B fused to leaders 6 (CupA2) and 8 (PbpA20V) appeared to be consistently high in all four strains.







TABLE 11







Cholera Toxin B Expression Summary
















Mean



Strain
Host


Yield
Std Dev


Number
Strain
Plasmid
Leader
(mg/L)
(3 replicates)















PS538-081
1
p538-021
DsbA
25
8


PS538-082
1
p538-022
Azu
1
8


PS538-083
1
p538-023
Ibp-S31A
0
5


PS538-084
1
p538-024
Tpr
35
14


PS538-085
1
p538-025
CupB2
10
9


PS538-086
1
p538-026
CupA2
138
18


PS538-087
1
p538-027
NikA
0
5


PS538-088
1
p538-028
Pbp A20V
213
23


PS538-089
1
p538-029
DsbC
0
6


PS538-090
1
p538-030
TolB
0
4


PS538-091
2
p538-021
DsbA
133
62


PS538-092
2
p538-022
Azu
83
56


PS538-093
2
p538-023
Ibp-S31A
50
44


PS538-094
2
p538-024
Tpr
61
55


PS538-095
2
p538-025
CupB2
62
19


PS538-096
2
p538-026
CupA2
147
57


PS538-097
2
p538-027
NikA
31
28


PS538-098
2
p538-028
Pbp A20V
223
78


PS538-099
2
p538-029
DsbC
41
24


PS538-100
2
p538-030
TolB
6
5


PS538-101
3
p538-021
DsbA
1
7


PS538-102
3
p538-022
Azu
1
2


PS538-103
3
p538-023
Ibp-S31A
19
17


PS538-104
3
p538-024
Tpr
28
36


PS538-105
3
p538-025
CupB2
5
9


PS538-106
3
p538-026
CupA2
40
12


PS538-107
3
p538-027
NikA
5
10


PS538-108
3
p538-028
Pbp A20V
45
19


PS538-109
3
p538-029
DsbC
0
6


PS538-110
3
p538-030
TolB
0
3


PS538-111
4
p538-021
DsbA
0
5


PS538-112
4
p538-022
Azu
0
3


PS538-113
4
p538-023
Ibp-S31A
0
2


PS538-114
4
p538-024
Tpr
13
3


PS538-115
4
p538-025
CupB2
2
4


PS538-116
4
p538-026
CupA2
15
16


PS538-117
4
p538-027
NikA
0
2


PS538-118
4
p538-028
Pbp A20V
35
15


PS538-119
4
p538-029
DsbC
0
2


PS538-120
4
p538-030
TolB
0
2









Example 4
Large-Scale Expression of a Recombinant Cholera Toxin B Protein
Recombinant Cholera Toxin B protein was produced in Pseudomonas fluorescens Pfēnex Expression TechnologyTM strains PS538-088 and PS538-091. The selected strain was grown in 2 liter fermentors containing a mineral salts medium as described herein and also by, e.g., Riesenberg, D., et al., 1991, and maintained at 32° C. and pH 6.5 through the addition of ammonia. Dissolved oxygen was maintained in excess through increases in agitation and flow of sparged air and oxygen into the fermentor. Glycerol was delivered to the culture throughout the fermentation to maintain excess levels. These conditions were maintained until a target culture cell density (optical density at 575 nm (A575)) for induction was reached, at which time IPTG was added to initiate the target protein production. IPTG was added to initiate CTB production. After 16-24 hours, the culture from each bioreactor was harvested by centrifugation and the cell pellet was frozen at −80° C.
Multiple fermentation conditions were evaluated resulting in top CTB expression as determined by SDS-CGE of 0.6 to 1.0 g/L. The top performing fermentation cultures were induced at approximately 80-160 OD with 0.2 mM IPTG at pH 6.5-7.2 and 32° C. Soluble CTB concentrations were determined by SDS-CGE (see FIG. 14 and Table 12). The identities of the induced proteins were confirmed by peptide mass fingerprint using MALDI-TOF mass spectrometry.







TABLE 12







Soluble Cholera Toxin B Titers















Product



Strain
Fermentation
Product
concentration (g/L)
















PS538-088
U5
CTB
0.94 ± 0.03



PS538-088
U6
CTB
0.59 ± 0.01



PS538-091
U3
CTB
0.81 ± 0.09










Example 5
High Throughput Expression of a Recombinant Pertussis Toxin Protein
Construction and Growth of Pertussis Toxoid S1 E129A R9K Expression Strains
The sequence of the Pertussis toxoid operon encoding subunits S1, S2, S3, S4 and S5, with S1 mutations E129A and R9K was used for expression of recombinant Pertussis toxin. FIG. 5 shows a map of the operon. FIG. 6 shows the DNA sequence of the operon, with translation (SEQ ID NO:24). FIG. 7 shows the individual amino acid sequences of S1, S2, S3, S4 and S5.
The construct was expressed in eight P. fluorescens hosts, shown in Table 13. Host cells were electroporated with p538-081, and grown and induced in 96-well format as described above for CRM197 high throughput expression. Samples were prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples.







TABLE 13







Pertussis Toxin S1 E129A R9K Expression Strains











Strain






Number
Host
Genotype
Plasmid
Type














PS538-321
1
lon, la, aprA
p538-081
PD


PS538-322
2
hslUV, prc1, degP1, degP2
p538-081
PD




and aprA




PS538-323
3
dsbABCD
p538-081
FMO


PS538-324
4
grpE, dnaKJ
p538-081
FMO


PS538-325
5
htpX
p538-081
PD


PS538-326
6
RXF01590
p538-081
PD


PS538-327
7
lon, la, aprA deletions;
p538-081
PD + FMO




overexpresses grpE and dnaKJ




PS538-328
8
ppiB (RXF05345)
p538-081
FMO





PD = Protease Deletion (listed proteases are deleted);


FMO = Folding Modulator Overexpressor (listed folding modulators are overexpressed.






Western Blot Analysis of Expressed Pertussis Toxin

Soluble fractions from the eight cultures described above were analyzed by Western blot to evaluate Pertussis Toxoid expression. Twenty microliters of the soluble fractions (2× diluted, reduced and non-reduced) were run on Bio-Rad 12% Bis-Tris Gel in 1× Bio_Rad MES running buffer. For reduced Western analysis, 1× XT reducing agent was added. Proteins were transferred from SDS-PAGE at 100V for 60 minutes onto a 0.2 μm nitrocellulose membrane (Bio Rad, 162 0232) using 1× NuPAGE Transfer Buffer (Invitrogen, NP0006-1) with 20% methanol. Membranes were blocked for 1 hour at room temperature in BlockerTM 1% Casein in PBS (Pierce, 37528). For detection, the diluents were poured off and more was added containing the combination of 1:1000 dilution each of monoclonal antibodies directed against Bordetella pertussis toxin S4 and S1 (Abcam, cat# ab37686 and #37547). The blots were incubated with rocking overnight at 4° C. The blots were washed three times with PBS-Tween for 5 minutes each, and were then incubated in more diluent containing a 1:5,000 dilution of anti-Mouse IgG-Peroxidase derived in goat (Sigma, Cat#A4416) at room temperature for 1 hour. The blots were washed three times with PBS-Tween (Sigma, P3563) for 5 minutes each, before color development using Immunopure Metal Enhanced DAB substrate (Pierce, 34065). Multiple subunits were detected by the anti-S1 and anti-S4 antibodies under both reducing and non reducing conditions (FIG. 8). The banding pattern of reduced and nonreduced samples of the expressed toxoid observed was consistent with that observed for purified Pertussis toxin from strain 165 as reported by Sekura, et al. (J. Biological Chemistry 258: 14647, 1983).
Example 6
Large-Scale Expression of Recombinant Pertussis Toxin Protein
Recombinant Pertussis toxin protein is produced in Pseudomonas fluorescens Pfēnex Expression TechnologyTM strains PS538-321, PS538-324, PS538-325, PS538-326, and PS538-328. The selected strain is grown in 2 liter fermentors, induced with IPTG, and samples prepared for analysis, as described above for CTB large-scale expression. The samples are analyzed by SDS-CGE, for product formation and their activity analyzed by Western Blot.
Example 7
High Throughput Expression of Recombinant Wild-Type Pertussis Toxoid
Construction and Growth of Pertussis Toxoid Expression Strains
The sequence of the wild-type Pertussis toxin operon encoding subunits S1, S2, S3, S4 and S5, with S1 is used for expression of recombinant Pertussis Toxoid. FIG. 17 shows the DNA sequence of the operon, with translation (SEQ ID NO:35).
The construct is expressed in the P. fluorescens hosts shown in Table 14. Each strain listed that does not have an overexpression plasmid is tested a) as described (having no overexpression plasmid); b) including a GrpE DnaKJ overexpression plasmid, and c) including a DsbABCD overexpression plasmid. Host cells are electroporated with the PTX WT expression plasmid, and grown and induced in 96-well format as described above for PTX S1 R9K E129A high-throughput expression. Samples are prepared and analyzed by SDS-CGE also as described above.







TABLE 14







Pertussis Toxoid Wild-Type Expression Strains









Host*
Genotype
Type












9
hslUV prc2
PD


10
hslUV degP1
PD


11
la
PD


12
hslUV prc1 prc2
PD


13
lon la prc1 prc2
PD


14
RXF01590
PD


1
lon la aprA
PD


7
lon la prc1 degP2 aprA; overexpresses GrpE DnaKJ
PD + FMO


15
RXF02151 RXF00428
PD


16
lon la degP2
PD


17
overexpresses DsbAB
FMO


18
overexpresses DsbCD
FMO


19
prc1 degP2; overexpresses degP2 S219A
PD + FMO


20
prc1 degP2 clp1 aprA; overexpresses degP2 S219A
PD + FMO


21
prc1 degP2 lon aprA; overexpresses degP2 S219A
PD + FMO


22
prc1 degP2 degP1 aprA; overexpresses degP2 S219A
PD + FMO


23
lon prc1 degP2 degP1 aprA; overexpresses degP2 S219A
PD + FMO


2
hslUV prc1 degP2 degP1 aprA; overexpresses degP2
PD + FMO



S219A



25
lon la degP2 prc1 aprA; overexpresses degP2 S219A
PD + FMO


26
degP2; overexpresses SecB
PD + FMO


27
degP2; overexpresses FkbP
PD + FMO


28
degP2; overexpresses GroELES
PD + FMO


29
lon la aprA; overexpresses SecB
PD + FMO


30
lon la aprA; overexpresses FkbP
PD + FMO


31
lon la aprA; overexpresses GroELES
PD + FMO


32
dsbC
PD


33
dsbC; ovrexpresses DsbAB
PD + FMO


3
overexpresses DsbABCD
FMO


35
lexA aprA
PD


36
overexpresses SlyD
FMO


37
lon hslUV
PD


38
Wt
—


39
aprA
PD


4
overexpresses GrpE DnaKJ
FMO


5
htpX
PD


40
lon
PD


41
prc1
PD


42
hslUV
PD


43
degP2
PD


44
degP1
PD


45
prc2
PD


46
RXF6451
PD


6
RXF1590
PD


48
RXF4692
PD


49
hslUV mic
PD


50
RXF2161
PD


51
RXF00133
PD


52
RXF2796
PD


53
RXF4968
PD


54
overexpresses DsbC
FMO


55
overexpresses DsbAC
FMO


56
overexpresses LepB
FMO


57
overexpresses SecB
FMO


58
overexpresses ClpA
FMO


59
overexpresses FklB2
FMO


60
overexpresses DnaK-like
FMO


61
overexpresses FkbP
FMO


62
overexpresses PpiA
FMO


8
overexpresses PpiB
FMO


63
overexpresses HscA
FMO


64
overexpresses GshA
FMO


65
overexpresses Gor
FMO


66
overexpresses TrxC
FMO


67
overexpresses DsbG
FMO


68
overexpresses Ppi
FMO


69
overexpresses GroELES
FMO


70
prc1 aprA; overexpresses GrpE DnaKJ
PD +FMO


71
hypersecretion



72
overexpresses DsbD
FMO


73
hypersecretion



74
hypersecretion



75
prc1 prc2
PD


76
hslUV clpA
PD





*Each strain listed that does not have an overexpression plasmid is tested a) as described (having no overexpression plasmid); b) including a GrpE DnaKJ overexpression plasmid, and c) including a DsbABCD overexpression plasmid. PD = Protease Deletion (listed proteases are deleted); FMO = Folding Modulator Overexpressor (listed folding modulators are overexpressed.






Hypersecretion strains, also known as hyper-vesiculating strains, are described, e.g., in WO2010/008764, “Pseudomonas Fluorescens Strains for Production of Extracellular Recombinant Protein,” incorporated herein by reference in its entirety.
Example 8
High Throughput Expression of a Recombinant Tetanus Toxin Fragment C Protein
Construction and Growth of Tetanus Toxin C Expression Strains
The Tetanus Toxin C coding sequence was constructed using P. fluorescens preferred codons to encode the Tetanus Toxin C amino acid sequence. FIG. 9 shows the amino acid and DNA sequences of the expressed synthetic Tetanus Toxin C gene.
Plasmids carrying the optimized Tetanus Toxin C sequence, fused to the same ten P. fluorescens secretion leader coding sequences used with CRM197 (shown in Table 8) were constructed. The secretion leaders were included to target the protein to the periplasm for recovery in the properly folded and active form.
Constructs expressing the ten secretion leaders fused to the recombinant Tetanus Toxin C protein were tested in P. fluorescens hosts. The four hosts listed in Table 9 were tested with each leader. Host cells were electroporated with the indicated plasmids, and grown and induced in 96-well format as described above for the CRM197 high throughput expression. Samples were prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples.
Representative gel-like images showing the results of the reducing SDS-CGE analysis of the soluble fraction from each strain are shown in FIG. 10. Table 15 shows the mean soluble Tetanus Toxin C yield and standard deviation of 3 replicates for each of the Tetanus Toxin C-expression strains constructed. Tetanus Toxin C fragment appeared to be expressed well in most strains tested, with highest yields ranging up to 600 mg/L in the hslUV prc1 degP1 degP2 aprA deletion/DegP2 S219A overexpression expression host. Strains PS538-529, PS538-538, PS538-544, PS538-546, PS538-547, PS538-548, PS538-558, PS538-565 and PS538-568 were selected for further evaluation.







TABLE 15







Tetanus Toxin C Expression Summary.
















Mean



Strain



Yield
Std Dev


Number
Host
Plasmid
Leader
(mg/L)
(3 replicates)















PS538-529
1
p538-132 
DsbA
261
75


PS538-530
1
p538-133 
Azu
200
82


PS538-531
1
p538-134 
Ibp-531A
165
64


PS538-532
1
p538-135 
Tpr
207
107


PS538-533
1
p538-136 
CupB2
205
128


PS538-534
1
p538-137 
CupA2
200
117


PS538-535
1
p538-138 
NikA
174
96


PS538-536
1
p538-139 
Pbp A20V
311
156


PS538-537
1
p538-140 
DsbC
188
97


PS538-538
1
p538-141 
TolB
129
63


PS538-539
2
p538-132 
DsbA
486
89


PS538-540
2
p538-133 
Azu
495
93


PS538-541
2
p538-134 
Ibp-531A
568
68


PS538-542
2
p538-135 
Tpr
589
364


PS538-543
2
p538-136 
CupB2
534
318


PS538-544
2
p538-137 
CupA2
504
134


PS538-545
2
p538-138
NikA
444
145


PS538-546
2
p538-139
Pbp A20V
637
280


PS538-547
2
p538-140
DsbC
574
68


PS538-548
2
p538-141
TolB
438
61


PS538-549
3
p538-132
DsbA
174
37


PS538-550
3
p538-133
Azu
180
58


PS538-551
3
p538-134
Ibp-S31A
88
58


PS538-552
3
p538-135
Tpr
247
134


PS538-553
3
p538-136
CupB2
199
39


PS538-554
3
p538-137
CupA2
165
69


PS538-555
3
p538-138
NikA
97
90


PS538-556
3
p538-139
Pbp A20V
297
112


PS538-557
3
p538-140
DsbC
151
52


PS538-558
3
p538-141
TolB
35
13


PS538-559
4
p538-132
DsbA
39
39


PS538-560
4
p538-133
Azu
40
43


PS538-561
4
p538-134
Ibp-S31A
36
40


PS538-562
4
p538-135
Tpr
35
39


PS538-563
4
p538-136
CupB2
54
26


PS538-564
4
p538-137
CupA2
42
36


PS538-565
4
p538-138
NikA
44
37


PS538-566
4
p538-139
Pbp A20V
37
40


PS538-567
4
p538-140
DsbC
39
43


PS538-568
4
p538-141
TolB
45
38









Example 9
Large-Scale Expression of a Recombinant Tetanus Toxin Fragment C Protein
Recombinant Tetanus Toxin C protein was produced in Pseudomonas fluorescens Pfēnex Expression TechnologyTM strains PS538-529, PS538-538, PS538-544, PS538-546, PS538-547, PS538-548, PS538-558, PS538-565 and PS538-568. The selected strains were grown in 2 liter fermentors containing a mineral salts medium as described above for CRM197.
Multiple fermentation conditions were evaluated resulting in top soluble TTC expression from strains PS538-529, PS538-546, and PS538-547 of 6 to 10 g/L as determined by SDS-CGE (see FIG. 15 and Table 16). The top performing fermentation culture was induced at approximately 160 OD with 0.2 mM IPTG at pH 7.2 and 32° C. The identities of the induced proteins were confirmed by peptide mass fingerprint using MALDI-TOF mass spectrometry and Western Blot. Mass spectrometry and Western blot analyses indicated that the secretion leaders of PS538-529, PS538-546 and PS538-547 (DsbA, Pbp A20V and DsbC, respectively) were not processed from 100% of the expressed protein under these expression conditions. However, the TolB leader was identified as being precisely cleaved from the secreted protein (data not shown). TolB-TTC expression strains PS538-538, PS538-548, PS538-558 and PS538-568 were screened at the 2 L fermentation scale, using the conditions outlined above, to identify a strain that enabled production of TTC with high fidelity cleavage of the secretion leader and low levels of degradation. Strains PS538-538, PS538-548 and PS538-558 were observed to produce similar quality and yield of material by Western blot analysis (FIG. 15B).







TABLE 16







Soluble Tetanus Toxin C (TTC) Titers















Product



Strain
Fermentation
Product
concentration (g/L)
















PS538-529
U1 - FIG. 15A
TTC
5.7 ± 1.3



PS538-546
U7 - FIG. 15A
TTC
9.5 ± 1.1



PS538-547
U5 - FIG. 15A
TTC
6.2 ± 1.9



PS538-538
U1 - FIG. 15B
TTC
 2.5 ± 0.09



PS538-538
U2 - FIG. 15B
TTC
1.8 ± 0.2



PS538-548
U3 - FIG. 15B
TTC
5.3 ± 0.6



PS538-548
U4 - FIG. 15B
TTC
4.5 ± 0.2



PS538-558
U5 - FIG. 15B
TTC
1.1 ± 0.8



PS538-558
U6 - FIG. 15B
TTC
1.9 ± 0.1



PS538-568
U7 - FIG. 15B
TTC
 0.2 ± 0.01



PS538-568
U8 - FIG. 15B
TTC
 0.2 ± 0.01










Example 10
High Throughput Expression of a Recombinant C. Difficile B Protein Construction and Growth of TcdB Expression Strains
The TcdB coding sequence was constructed using P. fluorescens preferred codons to encode the TcdB amino acid sequence. FIG. 11 shows the amino acid and DNA sequences of the expressed synthetic TcdB gene.
Plasmids carrying the optimized TcdB sequence were tested in the P. fluorescens hosts having genotypes listed in Table 17. Host cells were electroporated with the cytoplasmic expression plasmid p538-211, and grown and induced in 96-well format as described above for the CRM197 high throughput expression. Samples were prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples.







TABLE 17







TcdB Host Strains









Host Strain
Genotype
Type












37
hslUV lon
PD


38

WT


4
dnaKJ grpE
FMO


5
htpX
PD


40
lon
PD


41
prc1
PD


42
hslUV
PD


43
degP2
PD


44
degP1
PD


45
prc2
PD


47
RXF01590
PD


49
hslUV mic
PD


53
RXF04968
PD


55
dsbAC
FMO


61
fkbP
FMO


66
trxC
FMO


72
dsbD
FMO


76
hslUV clpA
PD


12
hslUV prc1 prc2
PD


1
lon la aprA
PD


16
lon la degP2
PD


2
hslUV prc1 degP1 degP2 aprA
PD + FMO



deletions; overexpresses degP2 S219A



3
dsbABCD
FMO


21
lon prc1 degP2 aprA deletions with
PD + FMO



degP2 S219A overexpression









Representative gel-like images showing the results of the reducing SDS-CGE analysis of the soluble fraction from each of the 24 strains tested are shown in FIG. 12. Table 18 shows the mean soluble TcdB yield and standard deviation of 3 replicates for each of the TcdB-expression strains constructed. Strains PS538-654, PS538-659, PS538-669, PS538-671, and PS538-674 were selected for further evaluation.







TABLE 18







TcdB Expression Summary











Strain


Mean
St Dev


Number
Host
Plasmid
Yield (mg/L)
(3 replicates)














PS538-651
37
p538-211
103
7


PS538-652
38
p538-211
55
4


PS538-653
4
p538-211
57
1


PS538-654
5
p538-211
166
13


PS538-655
40
p538-211
88
3


PS538-656
41
p538-211
68
5


PS538-657
42
p538-211
90
14


PS538-658
43
p538-211
68
2


PS538-659
44
p538-211
109
8


PS538-660
45
p538-211
78
4


PS538-661
6
p538-211
98
15


PS538-662
49
p538-211
106
10


PS538-663
53
p538-211
91
6


PS538-664
55
p538-211
45
4


PS538-665
61
p538-211
63
6


PS538-666
66
p538-211
56
8


PS538-667
72
p538-211
70
8


PS538-668
76
p538-211
80
6


PS538-669
12
p538-211
117
39


PS538-670
1
p538-211
108
18


PS538-671
16
p538-211
247
65


PS538-672
2
p538-211
32
6


PS538-673
3
p538-211
52
2


PS538-674
21
p538-211
145
12









Example 11
Large-Scale Expression of Recombinant C. Difficile Toxin B Protein
Recombinant C. difficile toxin B protein was produced in Pseudomonas fluorescens Pfēnex Expression TechnologyTM strain PS538-654, PS538-659, PS538-669, PS538-671, and PS538-674. The selected strains were grown in 2 liter fermentors, induced with IPTG, and samples prepared for analysis, as described above for CTB large-scale expression.
Multiple fermentation conditions were evaluated resulting in top C. difficile B Toxin expression as determined by SDS-CGE of approximately 2 g/L. The top performing fermentation culture was induced at approximately 160 OD with 0.08 mM IPTG at pH 6.5 and 32° C. Soluble C. difficile B Toxin concentrations were determined by SDS-CGE (see FIG. 16 and Table 19). The identities of the induced proteins were confirmed by Western blot.







TABLE 19







Soluble C. difficile B Toxin (TcdB) Titers















Product



Strain
Fermentation
Product
concentration (g/L)
















PS538-671
U5
TcdB
1.6 ± 0.4



PS538-671
U6
TcdB
2.1 ± 0.2



PS538-674
U7
TcdB
1.8 ± 0.2










Example 12
High Throughput Expression of a Recombinant Exotoxin A Protein
Construction and Growth of P. Aeruginosa Exotoxin a Expression Strains
The P. aeruginosa Exotoxin A mutant rEPA coding sequence was constructed using P. fluorescens preferred codons to encode the rEPA amino acid sequence. FIG. 13 shows the amino acid and DNA sequences of the expressed synthetic rEPA gene.
Plasmids carrying the optimized sequences encoding either the deletion mutant rEPA, as indicated in FIG. 13, fused to the same ten P. fluorescens secretion leader coding sequences used with CRM197 (shown in Table 8) were constructed. The secretion leader coding sequences were included to target the protein to the periplasm for recovery in the properly folded and active form.
Constructs expressing the ten secretion leaders fused to the rEPA proteins were tested in eight P. fluorescens hosts, listed in Table 20. Host cells were electroporated with the indicated plasmids, and grown and induced in 96-well format as described above for the CRM197 high throughput expression. Samples were prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples. The highest yields ranged from 4.7-6.7 g/L of soluble rEPA.







TABLE 20







Exotoxin A Host Strains









Host Strain
Genotype
Type





5
htpX
PD


6
serralysin
PD


7
Lon La1 aprA ; with grpE dnaKJ
PD/FMO



overexpression



8
ppiB
PD


1
Lon-, La-, aprA-
PD


2
hslUV-, prc1-, degP1-, degP2-, aprA-
PD + FMO



with degP2 S219A overexpression



3
dsbABCD overexpression
FMO


4
grpE, dnaKJ overexpression
FMO









Host cells were electroporated with the indicated plasmids, and grown and induced in 96-well format as described above for the CRM197 high throughput expression. Samples were prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples. The highest yields ranged from 1.6 to 2.2 g/L of soluble Exotoxin A protein. Table 21 shows the soluble rEPA yield for each of the expression strains selected for further testing.







TABLE 21







rEPA HTP Expression Summary













Strain


Secretion
Volumetric



Number
Host
Plasmid
Leader
Yield (g/L)

















PS538-1670
3
p538-250
DsbC
6.7



PS538-1663
3
p538-243
Ibp-s31a
5.7



PS538-1633
1
p538-243
Ibp-s31a
5.7



PS538-1640
1
p538-249
Pbp-A20V
4.7



PS538-1662
3
p538-242
Azu
4.2



PS538-1632
1
p538-242
Azu
3.2



PS538-1671
4
p538-241
DsbA
2.9



PS538-1665
3
p538-245
Tpr
2.7



PS538-1667
3
p538-247
CupA2
2.6



PS538-1674
4
p538-244
TolB
2.3



PS538-1672
4
p538-242
Azu
2.2



PS538-1676
4
p538-246
CupB2
2.2



PS538-1677
4
p538-247
CupA2
2.1



PS538-1635
1
p538-245
Tpr
2.0



PS538-1675
4
p538-245
Tpr
2.0



PS538-1673
4
p538-243
Ibp-s31a
2.0



PS538-1680
4
p538-250
DsbC
1.9



PS538-1679
4
p538-249
Pbp-A20V
1.7



PS538-1669
3
p538-249
Pbp-A20V
1.6



PS538-1678
4
p538-248
NikA
1.5



PS538-1652
2
p538-242
Azu
1.5



PS538-1653
2
p538-243
Ibp-s31a
1.4



PS538-1660
2
p538-250
DsbC
1.4



PS538-1637
1
p538-247
CupA2
1.3



PS538-1666
3
p538-246
CupB2
1.1



PS538-1636
1
p538-246
CupB2
1.0



PS538-1634
1
p538-244
TolB
1.0



PS538-1627
8
p538-247
CupA2
0.8



PS538-1631
1
p538-241
DsbA
0.8



PS538-1622
8
p538-242
Azu
0.8



PS538-1661
3
p538-241
DsbA
0.7



PS538-1603
5
p538-243
Ibp-s31a 
0.6



PS538-1630
8
p538-250
DsbC
0.6



PS538-1602
5
p538-242
Azu
0.6



PS538-1605
5
p538-245
Tpr
0.6



PS538-1623
8
p538-243
Ibp-s31a 
0.6



PS538-1664
3
p538-244
TolB
0.5



PS538-1668
3
p538-248
NikA
0.5



PS538-1610
5
p538-250
DsbC
0.5



PS538-1606
5
p538-246
CupB2
0.4



PS538-1659
2
p538-249
Pbp-A20V 
0.4



PS538-1607
5
p538-247
CupA2
0.4



PS538-1626
8
p538-246
CupB2
0.4



PS538-1625
8
p538-245
Tpr
0.4



PS538-1638
1
p538-248
NikA
0.3



PS538-1609
5
p538-249 
Pbp-A20V
0.3



PS538-1604
5
p538-244
TolB
0.3



PS538-1629
8
p538-249
Pbp-A20V 
0.3



PS538-1657
2
p538-247
CupA2
0.2



PS538-1651
2
p538-241
DsbA
0.2



PS538-1601
5
p538-241
DsbA
0.2



PS538-1624
8
p538-244
TolB
0.2



PS538-1621
5
p538-241
DsbA
0.2



PS538-1608
5
p538-248
NikA
0.2



PS538-1654
2
p538-244
TolB
0.2



PS538-1628
8
p538-248
NikA
0.1



PS538-1658
2
p538-248
NikA
0.1



PS538-1655
2
p538-245
Tpr
0.1



PS538-1641
7
p538-241
DsbA
0.1



PS538-1611
6
p538-241
DsbA
NQ



PS538-1612
6
p538-242
Azu
NQ



PS538-1613
6
p538-243
Ibp-s31a
NQ



PS538-1614
6
p538-244
TolB
NQ



PS538-1615
6
p538-245
Tpr
NQ



PS538-1616
6
p538-246
CupB2
NQ



PS538-1617
6
p538-247
CupA2
NQ



PS538-1618
6
p538-248
NikA
NQ



PS538-1619
6
p538-249
Pbp-A20V
NQ



PS538-1620
6
p538-250
DsbC
NQ



PS538-1642
7
p538-242
Azu
NQ



PS538-1643
7
p538-243
Ibp-s31a
NQ



PS538-1644
7
p538-244
TolB
NQ



PS538-1645
7
p538-245
Tpr
NQ



PS538-1646
7
p538-246
CupB2
NQ



PS538-1647
7
p538-247
CupA2
NQ



PS538-1648
7
p538-248
NikA
NQ



PS538-1649
7
p538-249
Pbp-A20V
NQ



PS538-1650
7
p538-250
DsbC
NQ



PS538-1656
2
p538-246
CupB2
NQ







NQ = not quantifiable






Example 13
Large-Scale Expression of a Recombinant Pseudomonas aeruginosa Exotoxin A Protein
Recombinant P. aeruginosa exotoxin A protein (rEPA) was produced in Pseudomonas fluorescens strains PS538-1633, PS538-1640 and PS538-1670 in 2 liter fermentors. Cultures were grown in 2 liter fermentors containing a mineral salts medium as described herein and also by, e.g., Riesenberg, D., et al., 1991, and maintained at 32° C. and pH 6.5 through the addition of ammonia. Dissolved oxygen was maintained in excess through increases in agitation and flow of sparged air and oxygen into the fermentor. Glycerol is delivered to the culture throughout the fermentation to maintain excess levels. These conditions were maintained until a target culture cell density (optical density at 575 nm (A575)) for induction is reached, at which time IPTG was added to initiate rEPA production. Cell density at induction can be varied from A575 of 40 to 200 absorbance units (AU). IPTG concentrations can be varied in the range from 0.02 to 0.4 mM. pH from 6 to 7.5 and temperature 20 to 35° C. After 16-24 hours, the culture from each bioreactor was harvested by centrifugation and the cell pellet frozen at −80° C. Samples were analyzed by SDS-CGE for product formation.
Multiple fermentation conditions were evaluated resulting in top rEPA expression as determined by SDS-CGE of up to 32 g/L (FIGS. 20 and 21). The identity of the induced protein was confirmed by Western blot analysis using an antibody specific for P. aeruginosa exotoxin A (FIG. 22). The yields obtained are shown in Table 22.







TABLE 22







rEPA Fermentation Analysis











Strain Number
Fermentation
Yield (g/L)







PS538-1633
Ul
15.5 ± 0.7



PS538-1633
U2
11.1 ± 0.6



PS538-1640
U3
20.1 ± 1.7



PS538-1640
U5
31.9 ± 1.6



PS538-1670
U6
20.0 ± 0.7



PS538-1670
U7
14.6 ± 1.1



PS538-1670
U8
31.0 ± 1.7










Example 14
High Throughput Expression of a Recombinant Wild-Type Diphtheria Toxin Protein
Construction and Growth of Wild-Type Diphtheria Toxin Expression Strains
A Diphtheria Toxin coding sequence is constructed using P. fluorescens preferred codons to encode the wild-type Diphtheria Toxin amino acid sequence. FIG. 18 shows the amino acid and DNA sequences of the expressed synthetic Diphtheria Toxin gene.
Plasmids carrying the optimized sequences encoding Diphtheria Toxin, fused to the ten P. fluorescens secretion leader coding sequences used with CRM197 (shown in Table 8) are constructed. The secretion leader coding sequences are included to target the protein to the periplasm for recovery in the properly folded and active form.
Constructs expressing the ten secretion leaders fused to the recombinant Diphtheria Toxin proteins are tested in P. fluorescens hosts. The four hosts listed in Table 9 are tested with each leader. Host cells are electroporated with the indicated plasmids, and grown and induced in 96-well format as described above for the CRM197 high throughput expression. Samples are prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples.
Example 15
Large-Scale Expression of a Recombinant Wild-Type Diphtheria Toxin Protein
Recombinant Wild-Type Diphtheria Toxin protein is produced in selected Pseudomonas fluorescens Pfēnex Expression TechnologyTM strains. The selected strains are grown in 2 liter fermentors, induced with IPTG, and samples prepared for analysis, as described above for CRM197 large-scale expression. The samples are analyzed by SDS-CGE.
Example 16
High Throughput Expression of a Recombinant Cholera Holotoxin Protein
Construction and Growth of CTX Expression Strains
The CTX coding sequence is constructed using P. fluorescens preferred codons to encode the CTX amino acid sequence. The coding sequence is based on the amino acid and DNA sequences of the CTX gene shown in FIG. 19.
Plasmids carrying the optimized CTX sequence, fused to the ten P. fluorescens secretion leader coding sequences used with CRM197 (shown in Table 8) are constructed. The secretion leaders are included to target the protein to the periplasm for recovery in the properly folded and active form.
Constructs expressing the ten secretion leaders fused to the recombinant CTX protein are tested in P. fluorescens hosts. The four hosts listed in Table 9 are tested with each expression plasmid. Host cells are electroporated with the indicated plasmids, and grown and induced in 96-well format as described above for the CRM197 high throughput expression. Samples are prepared and analyzed by SDS-CGE as described above for the CRM197 high throughput expression samples.
Example 17
Large-Scale Expression of a Recombinant Cholera Holotoxin Protein
Recombinant Cholera Holotoxin protein is produced in selected Pseudomonas fluorescens Pfēnex Expression TechnologyTM strains. The selected strains are grown in 2 liter fermentors, induced with IPTG, and samples prepared for analysis, as described above for CRM197 large-scale expression. The samples are analyzed by SDS-CGE.







TABLE 23







Sequence Listings








SEQ ID NO
DESCRIPTION











1
CRM197 Amino Acid Sequence


2
CRM197 DNA Sequence, optimized


3
DsbA Secretion Leader


4
Azu


5
Ibp-S31A


6
Tpr


7
CupB2


8
CupA2


9
NikA


10
Pbp A20V


11
DsbC


12
TolB


13
Pbp


14
Lao


15
CupC2


16
PorE


17
Pbp


18
FlgI


19
ttg2C


20
CRM197 native leader


21
Cleavage product GADD


22
Cholera Toxin B Amino Acid Sequence


23
Cholera Toxin B DNA Sequence, optimized


24
Pertussis toxin S1 R9K E129A DNA sequence


25
Pertussis toxin S1 R9K E129A Amino Acid Sequence


26
Pertussis toxin S2 Amino Acid Sequence


27
Pertussis toxin S3 Amino Acid Sequence


28
Pertussis toxin S4 Amino Acid Sequence


29
Pertussis toxin S5 Amino Acid Sequence


30
Tetanus Toxin C Amino Acid Sequence


31
Tetanus Toxin C DNA Sequence, optimized


32
TcdB Amino Acid Sequence


33
TcdB DNA Sequence, optimized


34
Exotoxin A Amino Acid Sequence


35
DNA Sequence of Wild-Type Pertussis Toxoid


36
Wild-Type Diphtheria Toxin Amino Acid Sequence


37
Wild-Type Diphtheria Toxin DNA Sequence, optimized


38
Cholera Toxin A Amino Acid Sequence


39
Cholera Toxin B Amino Acid Sequence


40
Cholera Holotoxin (CTX) DNA Sequence


41
Wild Type Pertussis toxin 51 Amino Acid Sequence


42
Pertussis toxin S2 Amino Acid Sequence


43
Pertussis toxin S4 Amino Acid Sequence


44
Pertussis toxin S5 Amino Acid Sequence


45
Pertussis toxin S3 Amino Acid Sequence


46
Hexa-histidine affinity tag

## Claims

1. A method for producing a recombinant toxin protein in a Pseudomonad host cell, said method comprising:
ligating into an expression vector a nucleotide sequence encoding the toxin protein;
transforming the Pseudomonad host cell with the expression vector; and
culturing the transformed Pseudomonad host cell in a culture media suitable for the expression of the recombinant toxin protein;
wherein the recombinant toxin protein is CRM 197, and wherein the recombinant protein is produced at a yield of soluble or active CRM197 protein of about 0.2 grams per liter to about 12 grams per liter.

2. The method of claim 1, wherein the yield of soluble or active toxin protein is 0.2 grams per liter to about 12 grams per liter, about 0.2 g/L, about 0.3 g/L, about 0.4 g/L, about 0.5 g/L, about 0.6 g/L, about 0.7 g/L, about 0.8 g/L, about 0.9 g/L, about 1 g/L, about 1.5 g/L, about 2 g/L, about 2.5 g/L, about 3 g/L, about 3.5 g/L, about 4 g/L, about 4.5 g/L, about 5 g/L, about 5.5 g/L, about 6 g/L, about 6.5 g/L, about 7 g/L, about 7.5 g/L, about 8 g/L, about 8.5 g/L, about 9 g/L, about 9.5 g/L, about 10 g/L, about 10.5 g/L, about 11 g/L, about 12 g/L, about 0.2 g/L to about 0.5 g/L, about 0.2 g/L to about 1 g/L, about 0.2 to about 2 g/L, about 0.3 g/L to about 0.6 g/L, about 0.3 g/L to about 1 g/L, about 0.3 to about 2 g/L, about 0.4 to about 0.7 g/L, about 0.4 to about 1 g/L, about 0.4 to about 2 g/L, about 0.4 to about 3 g/L, about 0.5 g/L to about 1 g/L, about 0.5 g/L to about 2 g/L, about 0.5 g/L to about 3 g/L, about 0.5 g/L to about 4 g/L, about 0.5 g/L to about 5 g/L, about 0.5 g/L to about 6 g/L, about 0.5 g/L to about 7 g/L, about 0.5 g/L to about 8 g/L, about 0.5 g/L to about 9 g/L, about 0.5 g/L to about 10 g/L, about 0.5 g/L to about 11 g/L, about 0.5 g/L to about 12 g/L, about 1 g/L to about 2 g/L, about 1 g/L to about 3 g/L, about 1 g/L to about 4 g/L, about 1 g/L to about 5 g/L, about 1 g/L to about 6 g/L, about 1 g/L to about 7 g/L, about 1 g/L to about 8 g/L, about 1 g/L to about 9 g/L, about 1 g/L to about 10 g/L, about 1 g/L to about 11 g/L, about 1 g/L to about 12 g/L, about 2 g/L to about 3 g/L, about 2 g/L to about 4 g/L, about 2 g/L to about 5 g/L, about 2 g/L to about 6 g/L, about 2 g/L to about 7 g/L, about 2 g/L to about 8 g/L, about 2 g/L to about 9 g/L, about 2 g/L to about 10 g/L, about 2 g/L to about 11 g/L, about 2 g/L to about 12 g/L, about 3 g/L to about 4 g/L, about 3 g/L to about 5 g/L, about 3 g/L to about 6 g/L, about 3 g/L to about 7 g/L, about 3 g/L to about 8 g/L, about 3 g/L to about 9 g/L, about 3 g/L to about 10 g/L, about 3 g/L to about 11 g/L, about 3 g/L to about 12 g/L, about 4 g/L to about 5 g/L, about 4 g/L to about 6 g/L, about 4 g/L to about 7 g/L, about 4 g/L to about 8 g/L, about 4 g/L to about 9 g/L, about 4 g/L to about 10 g/L, about 4 g/L to about 11 g/L, about 4 g/L to about 12 g/L, about 5 g/L to about 6 g/L, about 5 g/L to about 7 g/L, about 5 g/L to about 8 g/L, about 5 g/L to about 9 g/L, about 5 g/L to about 10 g/L, about 5 g/L to about 11 g/L, about 5 g/L to about 12 g/L, about 6 g/L to about 7 g/L, about 6 g/L to about 8 g/L, about 6 g/L to about 9 g/L, about 6 g/L to about 10 g/L, about 6 g/L to about 11 g/L, about 6 g/L to about 12 g/L, about 7 g/L to about 8 g/L, about 7 g/L to about 9 g/L, about 7 g/L to about 10 g/L, about 7 g/L to about 11 g/L, about 7 g/L to about 12 g/L, about 8 g/L to about 9 g/L, about 8 g/L to about 10 g/L, about 8 g/L to about 11 g/L, about 8 g/L to about 12 g/L, about 9 g/L to about 10 g/L, about 9 g/L to about 11 g/L, about 9 g/L to about 12 g/L, about 10 g/L to about 11 g/L, about 10 g/L to about 12 g/L, or about 11 g/L to about 12 g/L.

3. The method of claim 1, wherein the nucleotide sequence encoding the toxin protein is fused to a secretion signal coding sequence that when expressed directs transfer of the toxin protein to the periplasm.

4. The method of claim 3, wherein the expression vector further comprises a tag sequence adjacent to the coding sequence for the secretion signal.

5. The method of claim 1, wherein the host cell is defective in the expression of at least one protease or wherein the host cell overexpresses at least one folding modulator, or a combination thereof.

6. The method of claim 1, wherein the recombinant toxin protein is CRM197 and the host cell is defective in the expression of the proteases HslU, HslV, Prc1, DegP1, DegP2, and AprA.

7. The method of claim 6, wherein the recombinant toxin protein is fused to a secretion leader that is Azu, IbpS31A, CupA2, PbpA20V, or Pbp.

8. The method of claim 1, wherein the recombinant toxin protein is CRM197 and the host cell is defective in the expression of a protease that is Serralysin, HslU, HslV, Prc1, DegP1, DegP2, or AprA, or a combination thereof, or wherein the host cell overexpresses folding modulators DsbA, DsbB, DsbC, and DsbD, and further wherein the recombinant toxin protein is fused to the Azu, Pbp, or native secretion leader.

9. The method of claim 1, wherein the recombinant toxin protein is CRM197, the host cell is wild-type and wherein the recombinant toxin protein is fused to the secretion leader Pbp or Azu.

10. The method of claim 4, wherein the recombinant toxin protein is CRM197 and wherein the recombinant toxin protein is fused to the secretion leader Azu, Pbp, IbpS31A, CupA2, or PbpA20V.

11. The method of claim 1, further comprising measuring the activity of the recombinant toxin protein in an activity assay, wherein about 40% to about 100% of the soluble toxin protein produced is determined to be active.

12. The method of claim 11, wherein the activity assay is an immunological assay, a receptor-binding assay, or an enzyme assay.

13. The method of claim 1, wherein the expression vector comprises a lac promoter operatively linked to the protein coding sequence, and wherein the culturing comprises induction of the promoter using IPTG at a concentration of about 0.02 to about 1.0 mM, the cell density at induction is an optical density of about 40 to about 200 absorbance units (AU), the pH of the culture is from about 6 to about 7.5, and the growth temperature is about 20 to about 35° C.

14. The method of claim 13, wherein the lac promoter is selected from the following promoters: tac, trc, Ptac16, Ptac17, PtacII, PlacUV5 and T7lac.

15. The method of claim 1, wherein the host cell is a Pseudomonas cell.

16. The method of claim 15, wherein the nucleotide sequence has been optimized for expression in the Pseudomonas host cell.

17. The method of claim 1, wherein the host cell is Pseudomonas fluorescens.

18. The method of claim 17, wherein the nucleotide sequence has been optimized for expression in the Pseudomonas fluorescens host cell.

19. The method of claim 1, wherein the nucleotide sequence has been optimized for expression in the Pseudomonad host cell.

20. The method of claim 1, wherein the expression vector further comprises a tag sequence adjacent to the coding sequence for the toxin protein.

21. The method of claim 1, wherein the recombinant protein is produced at a yield of soluble and active CRM197 protein of about 0.2 grams per liter to about 12 grams per liter.

22. The method of claim 21, wherein the yield of soluble and active toxin protein is about 0.2 grams per liter to 12 grams per liter, about 0.2 g/L, about 0.3 g/L, about 0.4 g/L, about 0.5 g/L, about 0.6 g/L, about 0.7 g/L, about 0.8 g/L, about 0.9 g/L, about 1 g/L, about 1.5 g/L, about 2 g/L, about 2.5 g/L, about 3 g/L, about 3.5 g/L, about 4 g/L, about 4.5 g/L, about 5 g/L, about 5.5 g/L, about 6 g/L, about 6.5 g/L, about 7 g/L, about 7.5 g/L, about 8 g/L, about 8.5 g/L, about 9 g/L, about 9.5 g/L, about 10 g/L, about 10.5 g/L, about 11 g/L, about 12 g/L, about 0.2 g/L to about 0.5 g/L, about 0.2 g/L to about 1 g/L, about 0.2 to about 2 g/L, about 0.3 g/L to about 0.6 g/L, about 0.3 g/L to about 1 g/L, about 0.3 to about 2 g/L, about 0.4 to about 0.7 g/L, about 0.4 to about 1 g/L, about 0.4 to about 2 g/L, about 0.4 to about 3 g/L, about 0.5 g/L to about 1 g/L, about 0.5 g/L to about 2 g/L, about 0.5 g/L to about 3 g/L, about 0.5 g/L to about 4 g/L, about 0.5 g/L to about 5 g/L, about 0.5 g/L to about 6 g/L, about 0.5 g/L to about 7 g/L, about 0.5 g/L to about 8 g/L, about 0.5 g/L to about 9 g/L, about 0.5 g/L to about 10 g/L, about 0.5 g/L to about 11 g/L, about 0.5 g/L to about 12 g/L, about 1 g/L to about 2 g/L, about 1 g/L to about 3 g/L, about 1 g/L to about 4 g/L, about 1 g/L to about 5 g/L, about 1 g/L to about 6 g/L, about 1 g/L to about 7 g/L, about 1 g/L to about 8 g/L, about 1 g/L to about 9 g/L, about 1 g/L to about 10 g/L, about 1 g/L to about 11 g/L, about 1 g/L to about 12 g/L, about 2 g/L to about 3 g/L, about 2 g/L to about 4 g/L, about 2 g/L to about 5 g/L, about 2 g/L to about 6 g/L, about 2 g/L to about 7 g/L, about 2 g/L to about 8 g/L, about 2 g/L to about 9 g/L, about 2 g/L to about 10 g/L, about 2 g/L to about 11 g/L, about 2 g/L to about 12 g/L, about 3 g/L to about 4 g/L, about 3 g/L to about 5 g/L, about 3 g/L to about 6 g/L, about 3 g/L to about 7 g/L, about 3 g/L to about 8 g/L, about 3 g/L to about 9 g/L, about 3 g/L to about 10 g/L, about 3 g/L to about 11 g/L, about 3 g/L to about 12 g/L, about 4 g/L to about 5 g/L, about 4 g/L to about 6 g/L, about 4 g/L to about 7 g/L, about 4 g/L to about 8 g/L, about 4 g/L to about 9 g/L, about 4 g/L to about 10 g/L, about 4 g/L to about 11 g/L, about 4 g/L to about 12 g/L, about 5 g/L to about 6 g/L, about 5 g/L to about 7 g/L, about 5 g/L to about 8 g/L, about 5 g/L to about 9 g/L, about 5 g/L to about 10 g/L, about 5 g/L to about 11 g/L, about 5 g/L to about 12 g/L, about 6 g/L to about 7 g/L, about 6 g/L to about 8 g/L, about 6 g/L to about 9 g/L, about 6 g/L to about 10 g/L, about 6 g/L to about 11 g/L, about 6 g/L to about 12 g/L, about 7 g/L to about 8 g/L, about 7 g/L to about 9 g/L, about 7 g/L to about 10 g/L, about 7 g/L to about 11 g/L, about 7 g/L to about 12 g/L, about 8 g/L to about 9 g/L, about 8 g/L to about 10 g/L, about 8 g/L to about 11 g/L, about 8 g/L to about 12 g/L, about 9 g/L to about 10 g/L, about 9 g/L to about 11 g/L, about 9 g/L to about 12 g/L, about 10 g/L to about 11 g/L, about 10 g/L to about 12 g/L, or about 11 g/L to about 12 g/L.

23. The method of claim 21, wherein the nucleotide sequence encoding the toxin protein is fused to a secretion signal coding sequence that when expressed directs transfer of the toxin protein to the periplasm.

24. The method of claim 23, wherein the recombinant toxin protein is CRM197 and wherein the recombinant toxin protein is fused to the secretion leader Azu, Pbp, IbpS31A, CupA2, or PbpA20V.

25. The method of claim 21, wherein the host cell is defective in the expression of at least one protease or wherein the host cell overexpresses at least one folding modulator, or a combination thereof.

26. The method of claim 21, wherein the recombinant toxin protein is CRM197 and the host cell is defective in the expression of the proteases Hs1U, Hs1V, Prcl, DegPl, DegP2, and AprA.

27. The method of claim 21, wherein the recombinant toxin protein is fused to a secretion leader that is Azu, IbpS31A, CupA2, PbpA20V, or Pbp.

28. The method of claim 21, wherein the recombinant toxin protein is CRM197 and the host cell is defective in the expression of a protease that is Serralysin, Hs1U, Hs1V, Prcl, DegPl, DegP2, or AprA, or a combination thereof, or wherein the host cell overexpresses folding modulators DsbA, DsbB, DsbC, and DsbD, and further wherein the recombinant toxin protein is fused to the Azu, Pbp, or native secretion leader.

29. The method of claim 21, wherein the recombinant toxin protein is CRM197, the host cell is wild-type and wherein the recombinant toxin protein is fused to the secretion leader Pbp or Azu.

30. The method of claim 21, wherein the expression vector comprises a lac promoter operatively linked to the protein coding sequence, and wherein the culturing comprises induction of the promoter using IPTG at a concentration of about 0.02 to about 1.0 mM, the cell density at induction is an optical density of about 40 to about 200 absorbance units (AU), the pH of the culture is from about 6 to about 7.5, and the growth temperature is about 20 to about 35° C.

31. The method of claim 30, wherein the lac promoter is selected from the following promoters: tac, trc, Ptacl6, Ptacl7, PtacII, PlacUV5 and T7lac.

32. The method of claim 21, wherein the host cell is a Pseudomonas cell.

33. The method of claim 21, wherein the host cell is Pseudomonas fluorescens.

34. The method of claim 21, wherein the nucleotide sequence has been optimized for expression in the Pseudomonad host cell.

35. The method of claim 34, wherein the nucleotide sequence has been optimized for expression in the Pseudomonas host cell.

36. The method of claim 35, wherein the nucleotide sequence has been optimized for expression in the Pseudomonas fluorescens host cell.