USOO8906636B2 (12) United States Patent (10) Patent No.: US 8,906,636 B2 Retallack et al. (45) Date of Patent: Dec. 9, 2014 (54) HIGH LEVEL EXPRESSION OF 5,169,760 A 12, 1992 Wilcox RECOMBINANT TOXIN PROTEINS 5,281,532 A 1/1994 Rammler et al. 5,389,540 A 2f1995 Makoff et al. 5,427,788 A 6/1995 Rappuoli et al. (71) Applicant: Pfenex Inc., San Diego, CA (US) 5,443,966 A 8, 1995 Fairweather et al. 5,571,694 A 11/1996 Makoff et al. (72) Inventors: Diane M. Retallack, Poway, CA (US); 5,614,382 A 3, 1997 Metcalf Lawrence Chew, San Diego, CA (US) 5,773,600 A 6/1998 Burnette, III 5,785,971 A 7/1998 Rappuoli et al. 5,792.458 A 8, 1998 Johnson et al. (73) Assignee: Pfenex Inc., San Diego, CA (US) 5,834,246 A 11/1998 Holmgren et al. 5,919,463 A 7/1999 Thomas, Jr. et al. (*) Notice: Subject to any disclaimer, the term of this 5,935,580 A 8, 1999 Ladant et al. patent is extended or adjusted under 35 6,010,871 A 1/2000 Takahara et al. U.S.C. 154(b) by 0 days. 6,043,057 A 3/2000 Holmgren et al. 6,140,082 A 10/2000 Loosmore et al. 6,733,760 B1 5, 2004 Wilkins et al. (21) Appl. No.: 13/952,484 6,939,548 B2 9, 2005 Wilkins et al. 7,169,399 B2 1/2007 Roberts (22) Filed: Jul. 26, 2013 7,226,597 B2 6/2007 Ballard et al. 7,232,671 B2 6/2007 Cieplak (65) Prior Publication Data 7,273,728 B2 9, 2007 Wolfe et al. 7.427.404 B1 9, 2008 Pizza et al. US 2014/OO51093 A1 Feb. 20, 2014 7,575,891 B2 8, 2009 Wolfe et al. 7,618,799 B2 11/2009 Coleman et al. Related U.S. Application Data 7,666.436 B1 2/2010 Pizza et al. 7,985,564 B2 7/2011 Retallack et al. (60) Division of application No. 13/073.955, and a 8,288,127 B2 10/2012 Schneider et al. continuation-in-part of application No. PCT/ 8,530,171 B2 9/2013 Retallack et al. US2010/030573, filed on Apr. 9, 2010, now Pat. No. (Continued) 8,530,171. (60) Provisional application No. 61/325,235, filed on Apr. FOREIGN PATENT DOCUMENTS 16, 2010, provisional application No. 61/319,152, EP 0207459 1, 1978 filed on Mar. 30, 2010. EP O478602 1, 1996 WO WO-90-09444 8, 1990 WO WO-90-15871 12/1990 (51) Int. Cl. WO WO-97-02836 1, 1997 CI2N 9/10 (2006.01) WO WO-2005-000346 1, 2005 CI2P 2L/00 (2006.01) WO WO-2005-0521.51 6, 2005 GOIN 33/573 (2006.01) WO WO-2005-056773 6, 2005 CI2N 15/78 (2006.01) WO WO-2005-0699.13 8, 2005 CI2P 21/02 (2006.01) WO WO-2005-089093 9, 2005 C07K (4/34 (2006.01) (Continued) (52) U.S. Cl. CPC .............. CI2N 9/1051 (2013.01); C12N 15/78 OTHER PUBLICATIONS (2013.01); CI2P21/00 (2013.01); C07K Yang et al., BMC Microbiology 8, article 192 (2008).* 2319/036 (2013.01); C12P21/02 (2013.01); Ellingsworth, L., Pseudomonas fluorescens: Expression System for C07K 14/34 (2013.01); G0IN33/573 (2013.01) Producing Recombinant Vaccines and Adjuvants (2006).* USPC ............... 435/7.4; 435/15; 435/23: 435/69.3: Allured et al., Structure of exotoxin A of Pseudomonas aeruginosa at 435/193:435/471 3.0-Angrstom resolution, PNAS USA 83:1320-1324 (1986). (58) Field of Classification Search CPC ...... C12N 15/78; C12N 9/1051; C12P 21/00; (Continued) GO1 N 33/573 USPC ...................... 435/7.4, 15, 23, 69.3, 193, 471 Primary Examiner — Chih-Min Kam See application file for complete search history. (74) Attorney, Agent, or Firm — Wilson Sonsini Goodrich & Rosati (56) References Cited U.S. PATENT DOCUMENTS (57) ABSTRACT 4,551,433 A 11, 1985 DeBoer The present invention relates to the field of recombinant toxin 4,695.455 A 9, 1987 Barnes et al. protein production in bacterial hosts. In particular, the present 4,709,017 A 11, 1987 Collier invention relates to production processes for obtaining high 4,755.465 A 7/1988 Gray et al. 4,830,962 A 5, 1989 Gelfand et al. levels of a recombinant CRM197, Diphtheria Toxin, Pertussis 4,861,595 A 8, 1989 Barnes et al. Toxin, Tetanus Toxoid Fragment C. Cholera Toxin B, Cholera 4,892,827 A 1/1990 Pastan et al. holotoxin, and Pseudomonas EXotoxin A, from a bacterial 4,925,792 A 5/1990 Rappuoli host. 5,055,294 A 10/1991 Gilroy 5,085,862 A 2f1992 Klein et al. 5,128,130 A 7/1992 Gilroy et al. 18 Claims, 59 Drawing Sheets US 8,906,636 B2 Page 2 (56) References Cited Frishman et al., Starts of Bacterial Genes: Estimating the Reliability of Computer Predictions, Gene 234(20): 257-265 (1999). U.S. PATENT DOCUMENTS Giannini et al., The amino acid sequence of two non-toxic mutants of diphtheria toxin: CRM45 and CRM 197, Nucl Acids Res 8,603,824 B2 12/2013 Ramseier et al. 2003,0224009 A1 12/2003 Terry et al. 12(10):4063-4069 (1984). 2006, OOO8877 A1 1/2006 Retallack et al. Greenfield et al., Nucleotide sequence of the structural gene for 2006,0040352 A1 2/2006 Retallack et al. diphtheria toxin carried by corynebacteriophage B, PNAS USA 2006, O110747 A1 5, 2006 Ramseier et al. 80:6853-6857 (1983). 2006/0234346 A1 10, 2006 Retallack et al. Gurkin and Ellar, Recombinant production of bacterial toxins and 2006, O246036 A1 11/2006 Francis et al. their derivatives in the methylotrophic yeast Pichia pastoris, Micro 2007/0292918 A1 12/2007 Stelman et al. 2008/O193974 A1 8/2008 Coleman et al. bial Cell Factories 4:33 (2005). 2008/0269070 A1 10/2008 Ramseier et al. Haemophilus b Conjugate Vaccine (Diphtheria CRM197 Protein 2009,0081184 A1 3/2009 Margolin et al. Conjugate (HibTiter) Package Insert, 17 pages dated Jan. 2007. 2009/0325230 A1 12/2009 Schneider et al. Harakunietal. Heteropentameric Cholera Toxin B Subunit Chimeric 2010.0048864 A1 2/2010 Coleman et al. Molecules Genetically Fused to a Vaccine Antigen Induce Systemic 2010.0137162 A1 6, 2010 Retallack and Mucosal Immune Responses: a Potential New Strategy to Target 2011/0287443 A1 11/2011 Retallack et al. Recombinant Vaccine Antigens to Mucosal Immune Systems, Infec 2012,02896.88 A1 11/2012 Blais et al. tion and Immunity 73(9): 5654-5665 (2005). 2014/0051093 A1 2/2014 Retallack et al. Ikehata et al., Primary structure of nitrile hydratase deduced from the nucleotide sequence of a Rhodococcus species and its expression in FOREIGN PATENT DOCUMENTS Escherichia coli, EurJ Biochem 181(3):563-570 (1989). WO WO-2006-014899 2, 2006 Jank and Aktories, Structure and mode of action of clostridial WO WO-2007-146139 12/2007 glucosylating toxins: the ABCD model, Trends in Microbiol. WO WO-2008-094986 8, 2008 16(5):222-229 (2008). WO WO-2008-134461 11, 2008 Kaslow et al., Structure-Activity Analysis of the Activation of Pertus WO WO-2010-008764 1, 2010 sis Toxin, Biochem 26(1): 123-127 (1987). WO WO-2011-042516 4/2011 Kinket al. Antibodies to Recombinant Clostridium dificile Toxins A and B Arean Effective Treatment and Prevent Relapse of C. difficile OTHER PUBLICATIONS Associates Disease in a Hamster Model of Infection, Infection and Immunity, 66(5):2018-2025 (May 1998). Anderson et al., Safety and Immunogenicity of Meningococcal A and Kulich et al., Expression of Recombinant Exoenzyme S of C Polysaccharide Conjugate Vaccine in Adults, Infection and Immu Pseudomonas aeruginosa, Infection and Immunity 63(1): 1-8 nity 62(8):3391-3395 (1994). (1995). AU App No. 2010201410 Examination Report dated Jun. 6, 2014. Lee et al., Characterization of a Cloned Temperature-Sensitive Con Barth et al., Binary Bacterial Toxins: Biochemistry, Biology, and struct of the Diphtheria Toxin A Domain, Biochem 44(7):2555-2565 Applications of Common Clostridium and Bacillus Proteins, (2005) (Abstract). Microbiol Mol Biol Rev 68(3):373-402 (2004). Linet al., The Efficacy of a Salmonella typhi ViConjugate Vaccine in Bergey’s Manual of Determinative Bacteriology, R.E. Buchanan and Two-to-Five Year-Old Children, New England J Med 344(17): 1263 1269 (2001). N.E. Gibbons eds., pp. 217-289, 8th ed., The Williams & Wilkins Co., Lukac et al., Toxoid of Pseudomonas aeruginosa Exotoxin A Gen Baltimore, MD, 1974. erated by Deletion of an Active-Site Residue, Infection and Immunity Bishai et al., High-Level Expression of a Proteolytically Sensitive 56(12):3095-3098 (1988). Diphtheria Toxin Fragment in Escherichia coli, J Bacteriology Maunsell et al., Complex regulation of AprA metalloprotease in 169(11):5140-5151 (1987). Pseudomonas fluorescens M114: evidence for the involvement of Burnette et al., Properties of Pertussis Toxin B Oligomer Assembled iron, the ECF sigma factor, PbrA and pseudobactin M114 In Vitro from Recombinant Polypeptides Produced by Escherichia siderophore, Microbiol 152(Pt 1):29-42 (2006). coli, Infection and Immunity 60(6):2252-2256 (1992). McCoy et al., PAR1 and PAR2 couple to overlapping and distinct sets Carbonetti et al., Proteolytic cleavage of pertussis toxin S1 subunit is of G proteins and linked signaling pathways to differentially regulate not essential for its activity in mammalian cells, BMC Microbiology cell physiology, Molecular Pharmacology Fast Forward. Published 5:7 (2005). on Mar. 9, 2010 as doi:10.1124/mol. 109.062018. CN201080066026.6 Office Action dated May 12, 2014.