The Gram-negative envelope is a complex structure that consists of the inner membrane, the periplasm, peptidoglycan and the outer membrane, and protects the bacterial cell from the environment. Changing environmental conditions can cause damage, which triggers the envelope stress responses to maintain cellular homeostasis. In this Review, we explore the causes, both environmental and intrinsic, of envelope stress, as well as the cellular stress response pathways that counter these stresses. Furthermore, we discuss the damage to the cell that occurs when these pathways are aberrantly activated either in the absence of stress or to an excessive degree. Finally, we review the mechanisms whereby the σE response constantly acts to prevent cell death caused by highly toxic unfolded outer membrane proteins. Together, the recent work that we discuss has provided insights that emphasize the necessity for proper levels of stress response activation and the detrimental consequences that can occur in the absence of proper regulation.
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Silhavy, T. J., Kahne, D. & Walker, S. The bacterial cell envelope. Cold Spring Harb. Perspect. Biol. 2, a000414 (2010). This work provides a comprehensive review of bacterial envelope structure.
Raetz, C. R. & Whitfield, C. Lipopolysaccharide endotoxins. Annu. Rev. Biochem. 71, 635–700 (2002).
Nikaido, H. Molecular basis of bacterial outer membrane permeability revisited. Microbiol. Mol. Biol. Rev. 67, 593–656 (2003).
Li, X.-Z., Plésiat, P. & Nikaido, H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin. Microbiol. Rev. 28, 337–418 (2015).
Navarro Llorens, J. M., Tormo, A. & Martinez-Garcia, E. Stationary phase in gram-negative bacteria. FEMS Microbiol. Rev. 34, 476–495 (2010).
Rojas, E. R. et al. The outer membrane is an essential load-bearing element in Gram-negative bacteria. Nature 559, 617–621 (2018). This study demonstrates that the outer membrane plays a large role in the physical integrity of the cell, a role traditionally believed to be held only by peptidoglycan.
Berry, J., Rajaure, M., Pang, T. & Young, R. The spanin complex is essential for lambda lysis. J. Bacteriol. 194, 5667–5674 (2012).
Flores-Kim, J. & Darwin, A. J. The phage shock protein response. Annu. Rev. Microbiol. 70, 83–101 (2016).
Wall, E., Majdalani, N. & Gottesman, S. The complex Rcs regulatory cascade. Annu. Rev. Microbiol. 72, 111–139 (2018).
Raivio, T. L. Everything old is new again: an update on current research on the Cpx envelope stress response. Biochim. Biophys. Acta 1843, 1529–1541 (2014).
Grabowicz, M. & Silhavy, T. J. Envelope stress responses: an interconnected safety net. Trends Biochem. Sci. 42, 232–242 (2017).
Raivio, T. L. Envelope stress responses and Gram-negative bacterial pathogenesis. Mol. Microbiol. 56, 1119–1128 (2005).
Pogliano, K. J. & Beckwith, J. The Cs sec mutants of Escherichia coli reflect the cold sensitivity of protein export itself. Genetics 133, 763–773 (1993).
Wang, J. The complex kinetics of protein folding in wide temperature ranges. Biophys. J. 87, 2164–2171 (2004).
Sinensky, M. Homeoviscous adaptation—a homeostatic process that regulates the viscosity of membrane lipids in Escherichia coli. Proc. Natl Acad. Sci. USA 71, 522–525 (1974).
Laminet, A. A., Ziegelhoffer, T., Georgopoulos, C. & Pluckthun, A. The Escherichia coli heat shock proteins GroEL and GroES modulate the folding of the beta-lactamase precursor. EMBO J. 9, 2315–2319 (1990).
Charlson, E. S., Werner, J. N. & Misra, R. Differential effects of yfgL mutation on Escherichia coli outer membrane proteins and lipopolysaccharide. J. Bacteriol. 188, 7186–7194 (2006).
Konovalova, A., Schwalm, J. A. & Silhavy, T. J. A. Suppressor mutation that creates a faster and more robust σE envelope stress response. J. Bacteriol. 198, 2345–2351 (2016). This study identifies a mutation in σ E that causes faster induction of the σ E response and suppresses OMP biogenesis defects.
Wood, J. M. Bacterial responses to osmotic challenges. J. Gen. Physiol. 145, 381–388 (2015).
Arts, I. S., Gennaris, A. & Collet, J.-F. Reducing systems protecting the bacterial cell envelope from oxidative damage. FEBS Lett. 589, 1559–1568 (2015).
Leonardi, R. & Jackowski, S. Biosynthesis of pantothenic acid & coenzyme A. EcoSal Plus https://doi.org/10.1128/ecosalplus.188.8.131.52 (2007).
Zientz, E., Dandekar, T. & Gross, R. Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol. Mol. Biol. Rev. 68, 745–770 (2004).
Price, C. E. & Driessen, A. J. M. Biogenesis of membrane bound respiratory complexes in Escherichia coli. Biochim. Biophys. Acta 1803, 748–766 (2010).
Marvin, H. J., ter Beest, M. B. & Witholt, B. Release of outer membrane fragments from wild-type Escherichia coli and from several E. coli lipopolysaccharide mutants by EDTA and heat shock treatments. J. Bacteriol. 171, 5262–5267 (1989).
Kershaw, C. J., Brown, N. L., Constantinidou, C., Patel, M. D. & Hobman, J. L. The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations. Microbiology 151, 1187–1198 (2005).
Wang, D. & Fierke, C. A. The BaeSR regulon is involved in defense against zinc toxicity in E. coli. Metallomics 5, 372–383 (2013).
Laubacher, M. E. & Ades, S. E. The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance. J. Bacteriol. 190, 2065–2074 (2008).
Farris, C., Sanowar, S., Bader, M. W., Pfuetzner, R. & Miller, S. I. Antimicrobial peptides activate the Rcs regulon through the outer membrane lipoprotein RcsF. J. Bacteriol. 192, 4894–4903 (2010).
van Stelten, J., Silva, F., Belin, D. & Silhavy, T. J. Effects of antibiotics and a proto-oncogene homolog on destruction of protein translocator SecY. Science 325, 753–756 (2009).
Hibbing, M. E., Fuqua, C., Parsek, M. R. & Peterson, S. B. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15–25 (2010).
Hancock, R. E. W. & Diamond, G. The role of cationic antimicrobial peptides in innate host defences. Trends Microbiol. 8, 402–410 (2000).
Merritt, M. E. & Donaldson, J. R. Effect of bile salts on the DNA and membrane integrity of enteric bacteria. J. Med. Microbiol. 58, 1533–1541 (2009).
Guest, R. L. & Raivio, T. L. Role of the Gram-negative envelope stress response in the presence of antimicrobial agents. Trends Microbiol. 24, 377–390 (2016).
Mohler, K. & Ibba, M. Translational fidelity and mistranslation in the cellular response to stress. Nat. Microbiol. 2, 17117 (2017).
Morra, R. et al. Translation stress positively regulates MscL-dependent excretion of cytoplasmic proteins. mBio 9, e02118–17 (2018). This study demonstrates that either protein overexpression or antibiotics inhibiting translation elongation cause aberrant protein secretion in a manner dependent on a large mechanosensitive protein channel involved in protection from osmotic shock.
Grabowicz, M. & Silhavy, T. J. Redefining the essential trafficking pathway for outer membrane lipoproteins. Proc. Natl Acad. Sci. USA 114, 4769–4774 (2017).
Konovalova, A., Mitchell, A. M. & Silhavy, T. J. A lipoprotein/beta-barrel complex monitors lipopolysaccharide integrity transducing information across the outer membrane. eLife 5, e15276 (2016).
Danese, P. N. et al. Accumulation of the enterobacterial common antigen lipid II biosynthetic intermediate stimulates degP transcription in Escherichia coli. J. Bacteriol. 180, 5875–5884 (1998).
Girgis, H. S., Liu, Y., Ryu, W. S. & Tavazoie, S. A. Comprehensive genetic characterization of bacterial motility. PLOS Genet. 3, e154 (2007).
Walsh, N. P., Alba, B. M., Bose, B., Gross, C. A. & Sauer, R. T. 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 (2003).
Mecsas, J., Rouviere, P. E., Erickson, J. W., Donohue, T. J. & Gross, C. A. The activity of sigma E, an Escherichia coli heat-inducible sigma-factor, is modulated by expression of outer membrane proteins. Genes Dev. 7, 2618–2628 (1993).
Lima, S., Guo, M. S., Chaba, R., Gross, C. A. & Sauer, R. T. Dual molecular signals mediate the bacterial response to outer-membrane stress. Science 340, 837–841 (2013).
Klein, G. et al. Multiple transcriptional factors regulate transcription of the rpoE gene in Escherichia coli under different growth conditions and when the lipopolysaccharide biosynthesis is defective. J. Biol. Chem. 291, 22999–23019 (2016).
Amar, A., Pezzoni, M., Pizarro, R. A. & Costa, C. S. New envelope stress factors involved in σE activation and conditional lethality of rpoE mutations in Salmonella enterica. Microbiology 164, 1293–1307 (2018). This study defines new inducing signals for the σ E response in Salmonella and determines that the σ E response in Salmonella becomes essential in the absence of O antigen.
Wang, Q. P. & Kaguni, J. M. A novel sigma factor is involved in expression of the rpoH gene of Escherichia coli. J. Bacteriol. 171, 4248–4253 (1989).
Ades, S. E., Connolly, L. E., Alba, B. M. & Gross, C. A. The Escherichia coli σE-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-σ factor. Genes Dev. 13, 2449–2461 (1999).
Campbell, E. A. et al. Crystal structure of Escherichia coli σE with the cytoplasmic domain of its anti-σE RseA. Mol. Cell 11, 1067–1078 (2003).
Chaba, R. et al. Signal integration by DegS and RseB governs the σE-mediated envelope stress response in Escherichia coli. Proc. Natl Acad. Sci. USA 108, 2106–2111 (2011). This study demonstrates that both activation of DegS and inactivation of RseB are necessary to activate the σ E response and suggests that unfolded OMPs may be sufficient for both signals.
Akiyama, Y., Kanehara, K. & Ito, K. RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences. EMBO J. 23, 4434–4442 (2004).
Akiyama, K. et al. Roles of the membrane-reentrant β-hairpin-like loop of RseP protease in selective substrate cleavage. eLife 4, e08928 (2015).
Flynn, J. M., Levchenko, I., Sauer, R. T. & Baker, T. A. Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation. Genes Dev. 18, 2292–2301 (2004).
Rhodius, V. A., Suh, W. C., Nonaka, G., West, J. & Gross, C. A. Conserved and variable functions of the σE stress response in related genomes. PLOS Biol. 4, e2 (2006).
Dartigalongue, C., Missiakas, D. & Raina, S. Characterization of the Escherichia coli σEregulon. J. Biol. Chem. 276, 20866–20875 (2001).
Guillier, M., Gottesman, S. & Storz, G. Modulating the outer membrane with small RNAs. Genes Dev. 20, 2338–2348 (2006).
Guo, M. S. et al. MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Genes Dev. 28, 1620–1634 (2014).
McEwen, J. & Silverman, P. Chromosomal mutations of Escherichia coli that alter expression of conjugative plasmid functions. Proc. Natl Acad. Sci. USA 77, 513–517 (1980).
Danese, P. N. & Silhavy, T. J. CpxP, a stress-combative member of the Cpx regulon. J. Bacteriol. 180, 831–839 (1998).
Jubelin, G. et al. CpxR/OmpR interplay regulates Curli gene expression in response to osmolarity in Escherichia coli. J. Bacteriol. 187, 2038–2049 (2005).
Otto, K. & Silhavy, T. J. Surface sensing and adhesion of Escherichia coli controlled by the Cpx-signaling pathway. Proc. Natl Acad. Sci. USA 99, 2287–2292 (2002).
Evans, K. L., Kannan, S., Li, G., de Pedro, M. A. & Young, K. D. Eliminating a set of four penicillin binding proteins triggers the Rcs phosphorelay and Cpx stress responses in Escherichia coli. J. Bacteriol. 195, 4415–4424 (2013).
Bury-Moné, S. et al. Global analysis of extracytoplasmic stress signaling in Escherichia coli. PLOS Genet. 5, e1000651 (2009).
Yamamoto, K. & Ishihama, A. Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli. Biosci. Biotechnol. Biochem. 70, 1688–1695 (2006).
Mileykovskaya, E. & Dowhan, W. The Cpx two-component signal transduction pathway is activated in Escherichia coli mutant strains lacking phosphatidylethanolamine. J. Bacteriol. 179, 1029–1034 (1997).
Kwon, E. et al. The crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA. Protein Sci. 21, 1334–1343 (2012).
Cosma, C. L., Danese, P. N., Carlson, J. H., Silhavy, T. J. & Snyder, W. B. Mutational activation of the Cpx signal transduction pathway of Escherichia coli suppresses the toxicity conferred by certain envelope-associated stresses. Mol. Microbiol. 18, 491–505 (1995).
Danese, P. N., Snyder, W. B., Cosma, C. L., Davis, L. J. & Silhavy, T. J. The Cpx two-component signal transduction pathway of Escherichia coli regulates transcription of the gene specifying the stress-inducible periplasmic protease, DegP. Genes Dev. 9, 387–398 (1995).
Raivio, T. L. & Silhavy, T. J. Transduction of envelope stress in Escherichia coli by the Cpx two-component system. J. Bacteriol. 179, 7724–7733 (1997).
Price, N. L. & Raivio, T. L. Characterization of the Cpx regulon in Escherichia coli strain MC4100. J. Bacteriol. 191, 1798–1815 (2009). This study provides the first comprehensive analysis of the Cpx regulon.
Raivio, T. L., Popkin, D. L. & Silhavy, T. J. The Cpx envelope stress response is controlled by amplification and feedback inhibition. J. Bacteriol. 181, 5263–5272 (1999).
Chao, Y. & Vogel, J. A. 3΄ UTR-derived small RNA provides the regulatory noncoding arm of the inner membrane stress response. Mol. Cell 61, 352–363 (2016). This study identifies the CpxQ sRNA, which is transcribed with CpxP and downregulates inner membrane proteins that tend to misfold, as well as Skp, a periplasmic chaperone.
Grabowicz, M., Koren, D. & Silhavy, T. J. The CpxQ sRNA negatively regulates Skp to prevent mistargeting of β-barrel outer membrane proteins into the cytoplasmic membrane. mBio 7, e00312–16 (2016). This study determines that CpxQ downregulates Skp to prevent the insertion of OMPs into the inner membrane, which would lead to the dissipation of the PMF.
Snyder, W. B., Davis, L. J., Danese, P. N., Cosma, C. L. & Silhavy, T. J. Overproduction of NlpE, a new outer membrane lipoprotein, suppresses the toxicity of periplasmic LacZ by activation of the Cpx signal transduction pathway. J. Bacteriol. 177, 4216–4223 (1995).
May, K. L., Lehman, K. M., Mitchell, A. M. & Grabowicz, M. Identification of a stress response monitoring lipoprotein trafficking to the outer membrane. mBio https://doi.org/10.1128/mBio.00618-19 (2019).
Guest, R. L., Wang, J., Wong, J. L. & Raivio, T. L. A. Bacterial stress response regulates respiratory protein complexes to control envelope stress adaptation. J. Bacteriol. 199, e00153–17 (2017).
López, C., Checa, S. K. & Soncini, F. C. CpxR/CpxA controls scsABCD transcription to counteract copper and oxidative stress in Salmonella enterica serovar Typhimurium. J. Bacteriol. 200, e00126–18 (2018).
Gottesman, S., Trisler, P. & Torres-Cabassa, A. Regulation of capsular polysaccharide synthesis in Escherichia coli K-12: characterization of three regulatory genes. J. Bacteriol. 162, 1111–1119 (1985).
Shiba, Y. et al. Exploring the relationship between lipoprotein mislocalization and activation of the Rcs signal transduction system in Escherichia coli. Microbiology 158, 1238–1248 (2012). This study determines that the temperature sensitivity of a psgA mutant is due to the inner membrane localization of RcsF, caused by inefficiency in lipoprotein processing.
Ebel, W., Vaughn, G. J., Peters, H. K. 3rd & Trempy, J. E. Inactivation of mdoH leads to increased expression of colanic acid capsular polysaccharide in Escherichia coli. J. Bacteriol. 179, 6858–6861 (1997).
Konovalova, A., Perlman, D. H., Cowles, C. E. & Silhavy, T. J. Transmembrane domain of surface-exposed outer membrane lipoprotein RcsF is threaded through the lumen of beta-barrel proteins. Proc. Natl Acad. Sci. USA 111, E4350–E4358 (2014).
Cho, S.-H. et al. Detecting envelope stress by monitoring β-barrel assembly. Cell 159, 1652–1664 (2014).
Hussein, N. A., Cho, S.-H., Laloux, G., Siam, R. & Collet, J.-F. Distinct domains of Escherichia coli IgaA connect envelope stress sensing and down-regulation of the Rcs phosphorelay across subcellular compartments. PLOS Genet. 14, e1007398 (2018).
Takeda, S., Fujisawa, Y., Matsubara, M., Aiba, H. & Mizuno, T. A novel feature of the multistep phosphorelay in Escherichia coli: a revised model of the RcsC -→ YojN -→ RcsB signalling pathway implicated in capsular synthesis and swarming behaviour. Mol. Microbiol. 40, 440–450 (2001).
Torres-Cabassa, A. S. & Gottesman, S. Capsule synthesis in Escherichia coli K-12 is regulated by proteolysis. J. Bacteriol. 169, 981–989 (1987).
Jubete, Y., Maurizi, M. R. & Gottesman, S. Role of the heat shock protein DnaJ in the Lon-dependent degradation of naturally unstable proteins. J. Biol. Chem. 271, 30798–30803 (1996).
Ebel, W. & Trempy, J. E. Escherichia coli RcsA, a positive activator of colanic acid capsular polysaccharide synthesis, functions to activate its own expression. J. Bacteriol. 181, 577–584 (1999).
Majdalani, N., Hernandez, D. & Gottesman, S. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol. Microbiol. 46, 813–826 (2002).
Majdalani, N., Chen, S., Murrow, J., St John, K. & Gottesman, S. Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol. Microbiol. 39, 1382–1394 (2001).
Ferrieres, L., Aslam, S. N., Cooper, R. M. & Clarke, D. J. The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production. Microbiology 153, 1070–1080 (2007).
Wehland, M. & Bernhard, F. The RcsAB box. Characterization of a new operator essential for the regulation of exopolysaccharide biosynthesis in enteric bacteria. J. Biol. Chem. 275, 7013–7020 (2000).
Francez-Charlot, A. et al. RcsCDB His-Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli. Mol. Microbiol. 49, 823–832 (2003).
Venkatesh, G. R. et al. BglJ–RcsB heterodimers relieve repression of the Escherichia coli bgl operon by H-NS. J. Bacteriol. 192, 6456–6464 (2010).
Castanie-Cornet, M. P., Treffandier, H., Francez-Charlot, A., Gutierrez, C. & Cam, K. The glutamate-dependent acid resistance system in Escherichia coli: essential and dual role of the His-Asp phosphorelay RcsCDB/AF. Microbiology 153, 238–246 (2007).
Pannen, D., Fabisch, M., Gausling, L. & Schnetz, K. Interaction of the RcsB response regulator with auxiliary transcription regulators in Escherichia coli. J. Biol. Chem. 291, 2357–2370 (2016).
Nagasawa, S., Ishige, K. & Mizuno, T. Novel members of the two-component signal transduction genes in Escherichia coli. J. Biochem. 114, 350–357 (1993).
Raffa, R. G. & Raivio, T. L. A third envelope stress signal transduction pathway in Escherichia coli. Mol. Microbiol. 45, 1599–1611 (2002). This study identifies the BaeSR two-component system as an envelope stress response that induces spy expression in response to envelope damage.
Zhou, L., Lei, X.-H., Bochner, B. R. & Wanner, B. L. Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems. J. Bacteriol. 185, 4956–4972 (2003).
Leblanc, S. K. D., Oates, C. W. & Raivio, T. L. Characterization of the induction and cellular role of the BaeSR two-component envelope stress response of Escherichia coli. J. Bacteriol. 193, 3367–3375 (2011).
Nishino, K., Honda, T. & Yamaguchi, A. Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system. J. Bacteriol. 187, 1763–1772 (2005).
Nagakubo, S., Nishino, K., Hirata, T. & Yamaguchi, A. The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC. J. Bacteriol. 184, 4161–4167 (2002).
Brissette, J. L., Russel, M., Weiner, L. & Model, P. Phage shock protein, a stress protein of Escherichia coli. Proc. Natl Acad. Sci. USA 87, 862–866 (1990).
van der Laan, M. et al. A conserved function of YidC in the biogenesis of respiratory chain complexes. Proc. Natl Acad. Sci. USA 100, 5801–5806 (2003).
Maxson, M. E. & Darwin, A. J. Identification of Inducers of the Yersinia enterocolitica phage shock protein system and comparison to the regulation of the RpoE and Cpx extracytoplasmic stress responses. J. Bacteriol. 186, 4199–4208 (2004).
Becker, L. A., Bang, I. S., Crouch, M. L. & Fang, F. C. Compensatory role of PspA, a member of the phage shock protein operon, in rpoE mutant Salmonella enterica serovar Typhimurium. Mol. Microbiol. 56, 1004–1016 (2005).
Kobayashi, H., Yamamoto, M. & Aono, R. Appearance of a stress-response protein, phage-shock protein A, in Escherichia coli exposed to hydrophobic organic solvents. Microbiology 144, 353–359 (1998).
Jones, S. E., Lloyd, L. J., Tan, K. K. & Buck, M. Secretion defects that activate the phage shock response of Escherichia coli. J. Bacteriol. 185, 6707–6711 (2003).
Carlson, J. H. & Silhavy, T. J. Signal sequence processing is required for the assembly of LamB trimers in the outer membrane of Escherichia coli. J. Bacteriol. 175, 3327–3334 (1993).
Weiner, L. & Model, P. Role of an Escherichia coli stress-response operon in stationary-phase survival. Proc. Natl Acad. Sci. USA 91, 2191–2195 (1994).
Engl, C. et al. Dissipation of proton motive force is not sufficient to induce the phage shock protein response in Escherichia coli. Curr. Microbiol. 62, 1374–1385 (2011).
Wang, P., Kuhn, A. & Dalbey, R. E. Global change of gene expression and cell physiology in YidC-depleted Escherichia coli. J. Bacteriol. 192, 2193–2209 (2010).
McDonald, C., Jovanovic, G., Ces, O. & Buck, M. Membrane stored curvature elastic stress modulates recruitment of maintenance proteins PspA and Vipp1. mBio 6, e01188–15 (2015). This study identifies stored curvature elastic stress of the inner membrane as the direct cause of PspA binding to the inner membrane rather than dissipation of the PMF.
Dworkin, J., Jovanovic, G. & Model, P. The PspA protein of Escherichia coli is a negative regulator of σ54-dependent transcription. J. Bacteriol. 182, 311–319 (2000).
Elderkin, S., Bordes, P., Jones, S., Rappas, M. & Buck, M. Molecular determinants for PspA-mediated repression of the AAA transcriptional activator PspF. J. Bacteriol. 187, 3238–3248 (2005).
Yamaguchi, S., Reid, D. A., Rothenberg, E. & Darwin, A. J. Changes in Psp protein binding partners, localization and behaviour upon activation of the Yersinia enterocolitica phage shock protein response. Mol. Microbiol. 87, 656–671 (2013).
Weiner, L., Brissette, J. L., Ramani, N. & Model, P. Analysis of the proteins and cis-acting elements regulating the stress-induced phage shock protein operon. Nucleic Acids Res. 23, 2030–2036 (1995).
Weiner, L., Brissette, J. L. & Model, P. Stress-induced expression of the Escherichia coli phage shock protein operon is dependent on σ54 and modulated by positive and negative feedback mechanisms. Genes Dev. 5, 1912–1923 (1991).
Jovanovic, G., Engl, C. & Buck, M. Physical, functional and conditional interactions between ArcAB and phage shock proteins upon secretin-induced stress in Escherichia coli. Mol. Microbiol. 74, 16–28 (2009).
Jovanovic, G., Weiner, L. & Model, P. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J. Bacteriol. 178, 1936–1945 (1996).
Lloyd, L. J. et al. Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein G (PspG). J. Biol. Chem. 279, 55707–55714 (2004).
Kobayashi, R., Suzuki, T. & Yoshida, M. Escherichia coli phage-shock protein A (PspA) binds to membrane phospholipids and repairs proton leakage of the damaged membranes. Mol. Microbiol. 66, 100–109 (2007).
Kleerebezem, M., Crielaard, W. & Tommassen, J. Involvement of stress protein PspA (phage shock protein A) of Escherichia coli in maintenance of the protonmotive force under stress conditions. EMBO J. 15, 162–171 (1996).
Jovanovic, G., Lloyd, L. J., Stumpf, M. P. H., Mayhew, A. J. & Buck, M. Induction and function of the phage shock protein extracytoplasmic stress response in Escherichia coli. J. Biol. Chem. 281, 21147–21161 (2006).
De Las Peñas, A., Connolly, L. & Gross, C. A. σE is an essential sigma factor in Escherichia coli. J. Bacteriol. 179, 6862–6864 (1997).
Missiakas, D., Mayer, M. P., Lemaire, M., Georgopoulos, C. & Raina, S. Modulation of the Escherichia coli σE (RpoE) heat-shock transcription-factor activity by the RseA, RseB, and RseC proteins. Mol. Microbiol. 24, 355–371 (1997).
De Las Peñas, A., Connolly, L. & Gross, C. A. The σE-mediated response to extracytoplasmic stress in Escherichia coli is transduced by RseA, and RseB, two negative regulators of σE. Mol. Microbiol. 24, 373–385 (1997).
Nicoloff, H., Gopalkrishnan, S. & Ades, S. E. Appropriate regulation of the σE-dependent envelope stress response is necessary to maintain cell envelope integrity and stationary-phase survival in Escherichia coli. J. Bacteriol. 199, e00089–17 (2017). This study demonstrates that high-level σ E activity leads to membrane permeability and is lethal during stationary phase due to the expression of sRNAs targeting OMP translation.
Price, M. N. et al. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 557, 503–509 (2018).
Liu, A. et al. Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code. Antimicrob. Agents Chemother. 54, 1393–1403 (2010).
Hart, E. M. et al. Fine tuning of σE activation suppresses multiple assembly-defective mutations in Escherichia coli. J. Bacteriol. https://doi.org/10.1128/JB.00745-18 (2019).
Nitta, T., Nagamitsu, H., Murata, M., Izu, H. & Yamada, M. Function of the σE regulon in dead-cell lysis in stationary-phase Escherichia coli. J. Bacteriol. 182, 5231–5237 (2000).
Pogliano, J. et al. Aberrant cell division and random FtsZ ring positioning in Escherichia coli cpxA* mutants. J. Bacteriol. 180, 3486–3490 (1998).
Delhaye, A., Collet, J.-F. & Laloux, G. Fine-tuning of the Cpx envelope stress response is required for cell wall homeostasis in Escherichia coli. mBio 7, e00047–16 (2016). This study demonstrates that many of the cell growth and division phenotypes caused by aberrant Cpx activation are due to overexpression of ldtD and increased peptidoglycan crosslinking.
Bernal-Cabas, M., Ayala, J. A. & Raivio, T. L. The Cpx envelope stress response modifies peptidoglycan cross-linking via the l,d-transpeptidase LdtD and the novel protein YgaU. J. Bacteriol. 197, 603–614 (2015).
Shiba, Y. et al. Activation of the Rcs signal transduction system is responsible for the thermosensitive growth defect of an Escherichia coli mutant lacking phosphatidylglycerol and cardiolipin. J. Bacteriol. 186, 6526–6535 (2004).
Tao, K., Narita, S. & Tokuda, H. Defective lipoprotein sorting induces lolA expression through the Rcs stress response phosphorelay system. J. Bacteriol. 194, 3643–3650 (2012).
Boulanger, A. et al. Multistress regulation in Escherichia coli: expression of osmB involves two independent promoters responding either to σS or to the RcsCDB His-Asp phosphorelay. J. Bacteriol. 187, 3282–3286 (2005).
Umekawa, M. et al. Importance of the proline-rich region for the regulatory function of RcsF, an outer membrane lipoprotein component of the Escherichia coli Rcs signal transduction system. Microbiology 159, 1818–1827 (2013).
Heacock, P. N. & Dowhan, W. Construction of a lethal mutation in the synthesis of the major acidic phospholipids of Escherichia coli. J. Biol. Chem. 262, 13044–13049 (1987).
Kikuchi, S., Shibuya, I. & Matsumoto, K. Viability of an Escherichia coli pgsA null mutant lacking detectable phosphatidylglycerol and cardiolipin. J. Bacteriol. 182, 371–376 (2000).
Costa, C. S., Pettinari, M. J., Mendez, B. S. & Anton, D. N. Null mutations in the essential gene yrfF (mucM) are not lethal in rcsB, yojN or rcsC strains of Salmonella enterica serovar Typhimurium. FEMS Microbiol. Lett. 222, 25–32 (2003).
Wu, T. et al. Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli. Cell 121, 235–245 (2005).
Ruiz, N., Falcone, B., Kahne, D. & Silhavy, T. J. Chemical conditionality: a genetic strategy to probe organelle assembly. Cell 121, 307–317 (2005).
Strauch, K. L. & Beckwith, J. An Escherichia coli mutation preventing degradation of abnormal periplasmic proteins. Proc. Natl Acad. Sci. USA 85, 1576–1580 (1988).
Gerken, H., Charlson, E. S., Cicirelli, E. M., Kenney, L. J. & Misra, R. MzrA: a novel modulator of the EnvZ/OmpR two-component regulon. Mol. Microbiol. 72, 1408–1422 (2009).
Leiser, O. P., Charlson, E. S., Gerken, H. & Misra, R. Reversal of the ΔdegP phenotypes by a novel rpoE allele of Escherichia coli. PLOS ONE 7, e33979 (2012).
Rouvière, P. E. & Gross, C. A. SurA, a periplasmic protein with peptidyl-prolyl isomerase activity, participates in the assembly of outer membrane porins. Genes Dev. 10, 3170–3182 (1996).
Heusipp, G., Schmidt, M. A. & Miller, V. L. Identification of rpoE and nadB as host responsive elements of Yersinia enterocolitica. FEMS Microbiol. Lett. 226, 291–298 (2003).
Davis, B. M. & Waldor, M. K. High-throughput sequencing reveals suppressors of Vibrio cholerae rpoE mutations: one fewer porin is enough. Nucleic Acids Res. 37, 5757–5767 (2009).
Humphreys, S., Stevenson, A., Bacon, A., Weinhardt, A. B. & Roberts, M. The alternative sigma factor, σE, is critically important for the virulence of Salmonella typhimurium. Infect. Immun. 67, 1560–1568 (1999).
Craig, J. E., Nobbs, A. & High, N. J. The extracytoplasmic sigma factor, σE, is required for intracellular survival of nontypeable Haemophilus influenzae in J774 macrophages. Infect. Immun. 70, 708–715 (2002).
Martin, D. W., Holloway, B. W. & Deretic, V. Characterization of a locus determining the mucoid status of Pseudomonas aeruginosa: AlgU shows sequence similarities with a Bacillus sigma factor. J. Bacteriol. 175, 1153–1164 (1993).
Davies, B., Brown, P. D., East, N., Crimmin, M. J. & Balkwill, F. R. A. Synthetic matrix metalloproteinase inhibitor decreases tumor burden and prolongs survival of mice bearing human ovarian carcinoma xenografts. Cancer Res. 53, 2087–2091 (1993).
Konovalova, A. et al. Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins. Proc. Natl Acad. Sci. USA 115, E6614–E6621 (2018). This study identifies a small-molecule inhibitor of RseP and demonstrates that unfolded OMPs accumulate with σ E inhibition even in the absence of stress.
Bulieris, P. V., Behrens, S., Holst, O. & Kleinschmidt, J. H. Folding and insertion of the outer membrane protein OmpA is assisted by the chaperone Skp and by lipopolysaccharide. J. Biol. Chem. 278, 9092–9099 (2003).
Payne, J. W. & Gilvarg, C. Size restriction on peptide utilization in Escherichia coli. J. Biol. Chem. 243, 6291–6299 (1968).
Kato, A., Tanabe, H. & Utsumi, R. Molecular characterization of the PhoP-PhoQ two-component system in Escherichia coli K-12: identification of extracellular Mg2+-responsive promoters. J. Bacteriol. 181, 5516–5520 (1999).
Véscovi, E. G., Soncini, F. C. & Groisman, E. A. Mg2+ as an extracellular signal: environmental regulation of Salmonella virulence. Cell 84, 165–174 (1996).
Prost, L. R. et al. Activation of the bacterial sensor kinase PhoQ by acidic pH. Mol. Cell 26, 165–174 (2007).
Bader, M. W. et al. Recognition of antimicrobial peptides by a bacterial sensor kinase. Cell 122, 461–472 (2005).
Lippa, A. M. & Goulian, M. Perturbation of the oxidizing environment of the periplasm stimulates the PhoQ/PhoP system in Escherichia coli. J. Bacteriol. 194, 1457–1463 (2012).
Zwir, I. et al. Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica. Proc. Natl Acad. Sci. USA 102, 2862–2867 (2005).
Minagawa, S. et al. Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli. J. Bacteriol. 185, 3696–3702 (2003).
Gunn, J. S. et al. PmrA–PmrB-regulated genes necessary for 4-aminoarabinose lipid A modification and polymyxin resistance. Mol. Microbiol. 27, 1171–1182 (1998).
Pratt, L. A., Hsing, W., Gibson, K. E. & Silhavy, T. J. From acids to osmZ: multiple factors influence synthesis of the OmpF and OmpC porins in Escherichia coli. Mol. Microbiol. 20, 911–917 (1996).
Mitchell, A. M., Wang, W. & Silhavy, T. J. Novel RpoS-dependent mechanisms strengthen the envelope permeability barrier during stationary phase. J. Bacteriol. 199, e00708–16 (2017).
Hirschman, J., Wong, P. K., Sei, K., Keener, J. & Kustu, S. Products of nitrogen regulatory genes ntrA and ntrC of enteric bacteria activate glnA transcription in vitro: evidence that the ntrA product is a sigma factor. Proc. Natl Acad. Sci. USA 82, 7525–7529 (1985).
The authors thank members of the Silhavy laboratory for productive discussions. In addition, they thank the National Institute of General Medical Sciences for funding (grant R32-GM118024 to T.J.S.).
Nature Reviews Microbiology thanks S. Ades, A. Darwin and the other anonymous reviewer(s) for their contribution to the peer review of this work.
The authors declare no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- Outer membrane ß-barrel proteins
(OMPs). Integral membrane proteins of the outer membrane with a β-barrel structure.
- Efflux pumps
Proton-motive-force-driven or ATP-driven transporters that transport toxic molecules out of the cell.
- Bile salts
Molecules that are produced as part of bile that function as detergents and help the nutritional absorption of lipids.
A set of genes that are transcriptionally regulated by a regulator.
- β-Barrel assembly machinery
(BAM). An outer membrane protein complex that inserts outer membrane proteins into the outer membrane.
A small RNA that decreases the translation of some outer membrane β-barrel proteins as well as other targets.
A small RNA that decreases the translation of some outer membrane proteins as well as other targets.
A highly abundant outer membrane lipoprotein that crosslinks the outer membrane to the peptidoglycan layer.
- Two-component system
A signalling system comprising an inner membrane sensor histidine kinase that phosphorylates a response regulator that functions as a transcriptional control factor.
A periplasmic chaperone that helps prevent the misfolding and aggregation of newly synthesized outer membrane β-barrel proteins.
A transcriptional regulator that is possibly involved in the utilization of β-glucosides.
A transcriptional regulator that controls genes related to pH homeostasis and efflux.
A transcription factor involved in the switch between a planktonic and an adhered lifestyle.
A transcriptional regulator with poorly defined function.
- Proton motive force
(PMF). The build-up of protons in the periplasm generated by the electron transport chain used to generate ATP as well as directly drive some transport processes.
A sigma factor involved in controlling the expression of nitrogen-regulated and nitrogen-related genes.
An outer membrane protein involved in the secretion of substrates through the outer membrane.
An antibiotic that targets peptidoglycan biosynthesis by preventing recycling of the isoprenoid lipid carrier used to assemble peptidoglycan monomers.
An antibiotic that targets transcriptional elongation.
- FtsZ ring
An assembly of a ring of FtsZ proteins that represents the earliest characterized step in cell division and determines the location of the septum.
An L,D-transpeptidase that catalyses meso-diaminopimelyl → meso-diaminopimelyl peptide bond crosslinks in peptidoglycan.
A phosphatidylglycerophosphate synthase that catalyses the first committed step in the biosynthesis of acidic phospholipids.
A metalloproteinase inhibitor that can inhibit the activity of the protease RseP.