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(12) United States Patent (10) Patent No.: US 8,603,824 B2 Ramseier Et Al

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(12) United States Patent (10) Patent No.: US 8,603,824 B2 Ramseier Et Al USOO8603824B2 (12) United States Patent (10) Patent No.: US 8,603,824 B2 Ramseier et al. (45) Date of Patent: Dec. 10, 2013 (54) PROCESS FOR IMPROVED PROTEIN 5,399,684 A 3, 1995 Davie et al. EXPRESSION BY STRAIN ENGINEERING 5,418, 155 A 5/1995 Cormier et al. 5,441,934 A 8/1995 Krapcho et al. (75) Inventors: Thomas M. Ramseier, Poway, CA 5,508,192 A * 4/1996 Georgiou et al. .......... 435/252.3 (US); Hongfan Jin, San Diego, CA 5,527,883 A 6/1996 Thompson et al. (US); Charles H. Squires, Poway, CA 5,558,862 A 9, 1996 Corbinet al. 5,559,015 A 9/1996 Capage et al. (US) 5,571,694 A 11/1996 Makoff et al. (73) Assignee: Pfenex, Inc., San Diego, CA (US) 5,595,898 A 1/1997 Robinson et al. 5,610,044 A 3, 1997 Lam et al. (*) Notice: Subject to any disclaimer, the term of this 5,621,074 A 4/1997 Bjorn et al. patent is extended or adjusted under 35 5,622,846 A 4/1997 Kiener et al. 5,641,671 A 6/1997 Bos et al. U.S.C. 154(b) by 471 days. 5,641,870 A 6/1997 Rinderknecht et al. 5,643,774 A 7/1997 Ligon et al. (21) Appl. No.: 11/189,375 5,662,898 A 9/1997 Ligon et al. (22) Filed: Jul. 26, 2005 5,677,127 A 10/1997 Hogan et al. 5,683,888 A 1 1/1997 Campbell (65) Prior Publication Data 5,686,282 A 11/1997 Lam et al. US 2006/O110747 A1 May 25, 2006 5,686.283 A 1 1/1997 Gaffney et al. 5,698,425 A 12/1997 Ligon et al. Related U.S. Application Data 5,698,435 A 12/1997 Robinson et al. 5,710,031 A 1/1998 Gaffney et al. (60) Provisional application No. 60/591489, filed on Jul. 26, 2004. (Continued) FOREIGN PATENT DOCUMENTS (51) Int. Cl. CI2N 15/67 (2006.01) EP O121352 10, 1984 CI2N 15/63 (2006.01) EP O1551.89 9, 1985 CI2N 5/64 (2006.01) (Continued) CI2N 5/65 (2006.01) OTHER PUBLICATIONS CI2N 15/52 (2006.01) (52) U.S. Cl. Fathallah-Shaykh HM. Microarrays: applications and pitfalls. Arch USPC ............... 435/471; 435/69.1:435/6: 435/7.1; Neurol. Nov. 2005:62(11):1669-72.* Han etal, Engineering Escherichia coli for Increased Productivity of 435/287.2 Serine-Rich Proteins Based on Proteome Profiling, Applied and (58) Field of Classification Search Environmental Microbiology, Oct. 2003, vol. 69, No. 10, p. 5772 None 5781.* See application file for complete search history. Asai K., et al., “DNA microarray of Bacillus subtilis sigma factors of extraplasmic function family.” 2003, FEMS Microbiol. Lett 220(1), (56) References Cited pp. 155-160. Baneyx. F. “Recombinant Protein Expression in E. coli,' 1999, Curr. U.S. PATENT DOCUMENTS Opin. Biotech 10, pp. 411-421. Baneyx. F. 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The invention is a process of comparing two 5,169,772 A 12, 1992 Zimmerman et al. genetic profiles of a cell that expresses a recombinant protein 5,173,616 A 12/1992 Hinooka and modifying the cell to change the expression of a gene 5,232,840 A 8, 1993 Olins product that is upregulated in response to the recombinant 5,264,365 A 11/1993 Georgiou et al. protein expression. The process can improve protein produc 5,281,532 A 1/1994 Rammler et al. 5,292,507 A 3/1994 Charley tion or can improve protein quality, for example, by increas 5,292,658 A 3, 1994 Cormier et al. ing solubility of a recombinant protein. 5,348,867 A 9/1994 Georgiou et al. 35 Claims, 15 Drawing Sheets US 8,603,824 B2 Page 2 (56) References Cited 6,180.343 B1 1/2001 Anderson et al. 6,184,440 B1 2/2001 Shoseyov et al. 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