References
- Archer, C. T., J. F. Kim, H. Jeong, J. H. Park, C. E. Vickers, S. Y. Lee, and L. K. Nielsen. 2011. The genome sequence of E. coli W (ATCC 9637): Comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics 12: 9. https://doi.org/10.1186/1471-2164-12-9
-
Bagos, P. G., T. D. Liakopoulos, I. C. Spyropoulos, and S. J. Hamodrakas. 2004. PRED-TMBB: A Web server for predicting the topology of
${\beta}$ -barrel outer membrane proteins. Nucleic Acids Res. 32: W400-W404. https://doi.org/10.1093/nar/gkh417 - Borgstrom, B. 1974. Bile salts - their physiological functions in the gastrointestinal tract. Acta Med. Scand. 196: 1-10.
- Bos, M. P., V. Robert, and J. Tommassen. 2007. Biogenesis of the Gram-negative bacterial outer membrane. Annu. Rev. Microbiol. 61: 191-214. https://doi.org/10.1146/annurev.micro.61.080706.093245
- Brown, J. L., T. Ross, T. A. McMeekin, and P. D. Nichols. 1997. Acid habituation of Escherichia coli and the potential role of cyclopropane fatty acids in low pH tolerance. Int. J. Food Microbiol. 37: 163-173. https://doi.org/10.1016/S0168-1605(97)00068-8
- Cronan, J. E. Jr. 1968. Phospholipid alterations during growth of Escherichia coli. J. Bacteriol. 95: 2054-2061.
- Doerrler, W. T. and C. R. Raetz. 2005. Loss of outer membrane proteins without inhibition of lipid export in an Escherichia coli YaeT mutant. J. Biol. Chem. 280: 27679-27687. https://doi.org/10.1074/jbc.M504796200
- Gardy, J. L., M. R. Laird, F. Chen, S. Rey, C. J. Walsh, M. Ester, and F. S. Brinkman. 2005. PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21: 617-623. https://doi.org/10.1093/bioinformatics/bti057
- Han, M. J., J. W. Lee, and S. Y. Lee. 2005. Enhanced proteome profiling by inhibiting proteolysis with small heat shock proteins. J. Proteome Res. 4: 2429-2434. https://doi.org/10.1021/pr050259m
- Han, M. J., H. Yun, J. W. Lee, Y. H. Lee, S. Y. Lee, J. S. Yoo, et al. 2011. Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods. Proteomics 11: 1213-1227. https://doi.org/10.1002/pmic.201000191
-
Harder, K. J., H. Nikaido, and M. Matsuhashi. 1981. Mutants of Escherichia coli that are resistant to certain
${\beta}$ -lactam compounds lack the ompF porin. Antimicrob. Agents Chemother. 20: 549-552. https://doi.org/10.1128/AAC.20.4.549 - Hasegawa, Y., H. Yamada, and S. Mizushima. 1976. Interactions of outer membrane proteins O-8 and O-9 with peptidoglycan sacculus of Escherichia coli K-12. J. Biochem. 80: 1401-1409. https://doi.org/10.1093/oxfordjournals.jbchem.a131413
- Hayes, E. T., J. C. Wilks, P. Sanfilippo, E. Yohannes, D. P. Tate, B. D. Jones, et al. 2006. Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12. BMC Microbiol. 6: 89. https://doi.org/10.1186/1471-2180-6-89
- Herrera, G., A. Martinez, M. Blanco, and J. E. O'Connor. 2002. Assessment of Escherichia coli B with enhanced permeability to fluorochromes for flow cytometric assays of bacterial cell function. Cytometry 49: 62-69. https://doi.org/10.1002/cyto.10148
- Ho, E. M., H. W. Chang, S. I. Kim, H. Y. Kahng, and K. H. Oh. 2004. Analysis of TNT (2,4,6-trinitrotoluene)-inducible cellular responses and stress shock proteome in Stenotrophomonas sp. OK-5. Curr. Microbiol. 49: 346-352. https://doi.org/10.1007/s00284-004-4322-7
- Huang, C. Z., X. M. Lin, L. N. Wu, D. F. Zhang, D. Liu, S. Y. Wang, and X. X. Peng. 2006. Systematic identification of the subproteome of Escherichia coli cell envelope reveals the interaction network of membrane proteins and membrane-associated peripheral proteins. J. Proteome Res. 5: 3268-3276. https://doi.org/10.1021/pr060257h
- Jeong, H., V. Barbe, C. H. Lee, D. Vallenet, D. S. Yu, S. H. Choi, et al. 2009. Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J. Mol. Biol. 394: 644-652. https://doi.org/10.1016/j.jmb.2009.09.052
- Jordan, K. N., L. Oxford, and C. P. O'Byrne. 1999. Survival of low-pH stress by Escherichia coli O157:H7: Correlation between alterations in the cell envelope and increased acid tolerance. Appl. Environ. Microbiol. 65: 3048-3055.
- Knowles, T. J., A. Scott-Tucker, M. Overduin, and I. R. Henderson. 2009. Membrane protein architects: The role of the BAM complex in outer membrane protein assembly. Nat. Rev. Microbiol. 7: 206-214. https://doi.org/10.1038/nrmicro2069
- Lee, J. W., S. Y. Lee, H. Song, and J. S. Yoo. 2006. The proteome of Mannheimia succiniciproducens, a capnophilic rumen bacterium. Proteomics 6: 3550-3566. https://doi.org/10.1002/pmic.200500837
- Leverrier, P., D. Vertommen, and J. F. Collet. 2010. Contribution of proteomics toward solving the fascinating mysteries of the biogenesis of the envelope of Escherichia coli. Proteomics 10: 771-784. https://doi.org/10.1002/pmic.200900461
- Madan Babu, M. and K. Sankaran. 2002. DOLOP - database of bacterial lipoproteins. Bioinformatics 18: 641-643. https://doi.org/10.1093/bioinformatics/18.4.641
- Malinverni, J. C., J. Werner, S. Kim, J. G. Sklar, D. Kahne, R. Misra, and T. J. Silhavy. 2006. YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli. Mol. Microbiol. 61: 151-164. https://doi.org/10.1111/j.1365-2958.2006.05211.x
- Masuda, K., S. Matsuyama, and H. Tokuda. 2002. Elucidation of the function of lipoprotein-sorting signals that determine membrane localization. Proc. Natl. Acad. Sci. USA 99: 7390-7395. https://doi.org/10.1073/pnas.112085599
- Maurer, L. M., E. Yohannes, S. S. Bondurant, M. Radmacher, and J. L. Slonczewski. 2005. pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12. J. Bacteriol. 187: 304-319. https://doi.org/10.1128/JB.187.1.304-319.2005
- Minamino, T., Y. Imae, F. Oosawa, Y. Kobayashi, and K. Oosawa. 2003. Effect of intracellular pH on rotational speed of bacterial flagellar motors. J. Bacteriol. 185: 1190-1194. https://doi.org/10.1128/JB.185.4.1190-1194.2003
- Molloy, M. P., B. R. Herbert, M. B. Slade, T. Rabilloud, A. S. Nouwens, K. L. Williams, and A. A. Gooley. 2000. Proteomic analysis of the Escherichia coli outer membrane. Eur. J. Biochem. 267: 2871-2881. https://doi.org/10.1046/j.1432-1327.2000.01296.x
- Nandi, B., R. K. Nandy, A. Sarkar, and A. C. Ghose. 2005. Structural features, properties and regulation of the outer-membrane protein W (OmpW) of Vibrio cholerae. Microbiology 151: 2975-2986. https://doi.org/10.1099/mic.0.27995-0
- Nikaido, H. 1996. Multidrug efflux pumps of Gram-negative bacteria. J. Bacteriol. 178: 5853-5859. https://doi.org/10.1128/jb.178.20.5853-5859.1996
- Nikaido, H. 2003. Molecular basis of bacterial outer membrane permeability revisited. Microbiol. Mol. Biol. Rev. 67: 593-656. https://doi.org/10.1128/MMBR.67.4.593-656.2003
- Nishino, K. and A. Yamaguchi. 2001. Analysis of a complete library of putative drug transporter genes in Escherichia coli. J. Bacteriol. 183: 5803-5812. https://doi.org/10.1128/JB.183.20.5803-5812.2001
-
Onufryk, C., M. L. Crouch, F. C. Fang, and C. A. Gross. 2005. Characterization of six lipoproteins in the
${\sigma}^E$ regulon. J. Bacteriol. 187: 4552-4561. https://doi.org/10.1128/JB.187.13.4552-4561.2005 - Pilsl, H., D. Smajs, and V. Braun. 1999. Characterization of colicin S4 and its receptor, OmpW, a minor protein of the Escherichia coli outer membrane. J. Bacteriol. 181: 3578-3581.
- Prasadarao, N. V., A. M. Blom, B. O. Villoutreix, and L. C. Linsangan. 2002. A novel interaction of outer membrane protein A with C4b binding protein mediates serum resistance of Escherichia coli K1. J. Immunol. 169: 6352-6360. https://doi.org/10.4049/jimmunol.169.11.6352
-
Rhodius, V. A., W. C. Suh, G. Nonaka, J. West, and C. A. Gross, 2006. Conserved and variable functions of the
${\sigma}^E$ stress response in related genomes. PLoS Biol. 4: e2. https://doi.org/10.1371/journal.pbio.0040002 - Schneider, D., E. Duperchy, J. Depeyrot, E. Coursange, R. Lenski, and M. Blot. 2002. Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers. BMC Microbiol. 2: 18. https://doi.org/10.1186/1471-2180-2-18
- Sonntag, I., H. Schwarz, Y. Hirota, and U. Henning. 1978. Cell envelope and shape of Escherichia coli: Multiple mutants missing the outer membrane lipoprotein and other major outer membrane proteins. J. Bacteriol. 136: 280-285.
- Stancik, L. M., D. M. Stancik, B. Schmidt, D. M. Barnhart, Y. N. Yoncheva, and J. L. Slonczewski. 2002. pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J. Bacteriol. 184: 4246-4258. https://doi.org/10.1128/JB.184.15.4246-4258.2002
- Stenberg, F., P. Chovanec, S. L. Maslen, C. V. Robinson, L. L. Ilag, G. von Heijne, and D. O. Daley. 2005. Protein complexes of the Escherichia coli cell envelope. J. Biol. Chem. 280: 34409-34419. https://doi.org/10.1074/jbc.M506479200
- Studier, F. W., P. Daegelen, R. E. Lenski, S. Maslov, and J. F. Kim. 2009. Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J. Mol. Biol. 394: 653-680. https://doi.org/10.1016/j.jmb.2009.09.021
- Sugawara, E. and H. Nikaido. 1992. Pore-forming activity of OmpA protein of Escherichia coli. J. Biol. Chem. 267: 2507-2511.
- Sulavik, M. C., C. Houseweart, C. Cramer, N. Jiwani, N. Murgolo, J. Greene, et al. 2001. Antibiotic susceptibility profiles of Escherichia coli strains lacking multidrug efflux pump genes. Antimicrob. Agents Chemother. 45: 1126-1136. https://doi.org/10.1128/AAC.45.4.1126-1136.2001
- Tokuda, H. and S. Matsuyama. 2004. Sorting of lipoproteins to the outer membrane in E. coli. Biochim. Biophys. Acta 1694: IN1-9. https://doi.org/10.1016/j.bbamcr.2004.07.002
- van Beilen, J. B., S. Panke, S. Lucchini, A. G. Franchini, M. Rothlisberger, and B. Witholt. 2001. Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: Evolution and regulation of the alk genes. Microbiology 147: 1621-1630. https://doi.org/10.1099/00221287-147-6-1621
- Walsh, N. P., B. M. Alba, B. Bose, C. A. Gross, and R. T. Sauer. 2003. OMP peptide signals initiate the envelope-stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain. Cell 113: 61-71. https://doi.org/10.1016/S0092-8674(03)00203-4
- Wang, Y. 2002. The function of OmpA in Escherichia coli. Biochem. Biophys. Res. Commun. 292: 396-401. https://doi.org/10.1006/bbrc.2002.6657
- Wu, H. C. 1996. Biosynthesis of lipoproteins in Escherichia coli and Salmonella, pp. 262-282. In F. C. Neidhardt, R. Curtiss III, J. L.Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (eds.). Escherichia coli and Salmonella Typhimurium: Cellular and Molecular Biology, 2nd Ed. ASM Press, Washington, DC.
- Wu, T., J. Malinverni, N. Ruiz, S. Kim, T. J. Silhavy, and D. Kahne. 2005. Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli. Cell 121: 235-245. https://doi.org/10.1016/j.cell.2005.02.015
- Xia, X. X., M. J. Han, S. Y. Lee, and J. S. Yoo. 2008. Comparison of the extracellular proteomes of Escherichia coli B and K-12 strains during high cell density cultivation. Proteomics 8: 2089-2103. https://doi.org/10.1002/pmic.200700826
- Xu, C., H. Ren, S. Wang, and X. Peng. 2004. Proteomic analysis of salt-sensitive outer membrane proteins of Vibrio parahaemolyticus. Res. Microbiol. 155: 835-842. https://doi.org/10.1016/j.resmic.2004.07.001
- Xu, C., S. Wang, H. Ren, X. Lin, L. Wu, and X. Peng. 2005. Proteomic analysis on the expression of outer membrane proteins of Vibrio alginolyticus at different sodium concentrations. Proteomics 5: 3142-3152. https://doi.org/10.1002/pmic.200401128
- Zhang, Y. M. and C. O. Rock. 2008. Membrane lipid homeostasis in bacteria. Nat. Rev. Microbiol. 6: 222-233. https://doi.org/10.1038/nrmicro1839
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