Faculty & Research
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Molecular Biology Faculty

Thomas J. Silhavy

Warner-Lambert Parke-Davis Professor of Molecular Biology

Thomas J. Silhavy

phone (609) 258-5899
locationLewis Thomas Lab, 310
phone Lab (609) 258-5900
Faculty Assistant
Jennifer Munko
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phone (609) 258-5659

Research Focus

All cells have subcellular compartments that are bound by lipid bilayers, and this three-dimensional organization is essential for life. If we consider lipid bilayers themselves as compartments, then Gram-negative bacteria, such as Escherichia coli, have four distinct subcellular locations: the cytoplasm, inner membrane (IM), periplasm, and outer membrane (OM). The noncytoplasmic compartments are collectively termed the cell envelope. We wish to understand cellular assembly, in particular, the process of OM biogenesis. The OM is an asymmetric lipid bilayer containing phospholipids in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet. Membrane spanning outer membrane proteins (OMPs) typically assume a beta-barrel conformation. All OM components are synthesized in the cytoplasm or the IM and therefore, OM biogenesis requires the transport of these molecules across the cell envelope for assembly at their final cellular location. Strikingly, these transport and assembly processes occur in an environment that lacks an obvious energy source such as ATP. We have used a combination of genetics, biochemistry, and bioinformatics to identify the cellular machinery required for the assembly of OMPs and LPS in the OM. lpsBoth of these assembly machineries have protein components in every cellular compartment, and this spatial organization suggests the temporal order of component function (Figure 1). Current effort in the lab is directed towards understanding the how these machines function in molecular terms, and how their activities are coordinated.

Stationary phase

When E. coli deplete their environment of essential nutrients they enter a physiological state termed stationary phase in order to survive prolonged starvation and resist various toxic insults. Entry into stationary phase is accompanied by large changes in gene expression, most of which are mediated by sigma-S, the central regulator of the stationary phase response. Sigma-S regulation is complex and occurs at all levels, but regulated proteolysis is of primary importance for carbon starvation. In log phase cells, the two-component response regulator SprE directs sigma-S to the ClpP/ClpX protease, but as cells enter stationary phase this destruction ceases and sigma-S accumulates. SprE belongs to the response regulator family of two-component regulatory proteins. As such it was assumed that the activity of SprE was controlled by phosphorylation. We have shown that this model is not correct. Something else must control SprE activity upon carbon starvation. It was also assumed that starvation for any essential nutrient would increase RpoS levels by the same mechanism that causes RpoS accumulation under carbon starvation. We have shown that this is not the case either. The cellular response to nutrient limitation is much more complex than previously appreciated. We wish to understand the molecular events that signal starvation for various essential nutrients, and the mechanisms employed by the cell to insure survival under these stressful conditions.


Selected Publications

Zafar MA, Carabetta VJ, Mandel MJ, Silhavy TJ. (2014) Transcriptional occlusion caused by overlapping promoters. Proc Natl Acad Sci. 111: 1557-61. Pubmed

Silhavy TJ. (2014) 2013 Jack Kenney award for outstanding service. J Bacteriol. 196: 2. Pubmed

Ricci DP, Schwalm J, Gonzales-Cope M, Silhavy TJ. (2013) The activity and specificity of the outer membrane protein chaperone SurA are modulated by a proline isomerase domain. MBio. 4. pii: e00540-13. Pubmed

Dwyer RS, Ricci DP, Colwell LJ, Silhavy TJ, Wingreen NS. (2013) Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics. 195: 443-55. Pubmed

Schwalm J, Mahoney TF, Soltes GR, Silhavy TJ. (2013) A role for Skp in LptD assembly in Escherichia coli. J Bacteriol. 195: 3734-42. Pubmed

Rigel NW, Ricci DP, Silhavy TJ. (2013) Conformation-specific labeling of BamA and suppressor analysis suggest a cyclic mechanism for β-barrel assembly in Escherichia coli. Proc Natl Acad Sci110: 5151-6. Pubmed

Mahoney TF, Silhavy TJ. (2013) The Cpx stress response confers resistance to some, but not all bactericidal antibiotics. J Bacteriol. 195: 1869-74. Pubmed

Grabowicz M, Yeh J, Silhavy TJ. (2013) A dominant-negative lptE mutation that supports a role for LptE as a plug in the LptD barrel. J Bacteriol. 195: 1327-34. Pubmed

Silhavy TJ. (2013) 2012 Jack Kenney Award for Outstanding Service. J Bacteriol. 195: 2. Pubmed

Silhavy TJ. (2013) Editorial and policy changes for 2013. J Bacteriol. 195:1. Pubmed

Ricci DP, Silhavy TJ. (2012) The Bam machine: a molecular cooper. Biochim Biophys Acta. 1818: 1067-84. Pubmed

Rigel NW, Silhavy TJ. (2012) Making a beta-barrel: assembly of outer membrane proteins in Gram-negative bacteria. Curr Opin Microbiol. 15: 189-193. Pubmed

Peterson CN, Levchenko I, Rabinowitz JD, Baker TA, Silhavy TJ. (2012) RpoS proteolysis is controlled directly by ATP levels in Escherichia coli. Genes Dev. 26: 548-553. PubMed

Rigel NW, Schwalm J, Ricci DP, Silhavy TJ. (2012) BamE modulates the Escherichia coli beta-barrel assembly machine component BamA. J Bacteriol. 194: 1002-1008. PubMed

Ricci DP, Hagan CL, Kahne D, Silhavy TJ. (2012) Activation of the Escherichia coli β-barrel assembly machine (Bam) is required for essential components to interact properly with substrate. Proc Natl Acad Sci. 109: 3487-3491. PubMed

Chimalakonda G, Ruiz N, Chng SS, Garner RA, Kahne D, Silhavy TJ. (2011) Lipoprotein LptE is required for the assembly of LptD by the {beta}-barrel assembly machine in the outer membrane of Escherichia coli. Proc Natl Acad Sci. 108: 2492-2497. PubMed

Cowles CE, Li Y, Semmelhack MF, Cristea IM, Silhavy TJ. (2011) The free and bound forms of Lpp occupy distinct subcellular locations in Escherichia coli. Mol Microbiol. 79: 1168-1181. PubMed

Ruiz N, Chng SS, Hiniker A, Kahne D, Silhavy TJ. (2010) Nonconsecutive disulfide bond formation in an essential integral outer membrane protein. Proc Natl Acad Sci. 107: 12245-12250. PubMed

Carabetta VJ, Silhavy TJ, Cristea IM. (2010) The response regulator SprE (RssB) is required for maintaining PAP I-degradosome association during stationary phase. J Bacteriol. 192: 3713-3721. PubMed

Silhavy TJ, Kahne D, Walker S. (2010) The bacterial cell envelope. Cold Spring Harb Perspect Biol. 2: a000414. PubMed

Carabetta VJ, Mohanty BK, Kushner SR, Silhavy TJ. (2009) The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli. J Bacteriol. 191: 6812-6821. PubMed

van Stelten J, Silva F, Belin D, Silhavy TJ. (2009) Effects of antibiotics and a proto-oncogene homolog on destruction of protein translocator SecY. Science. 325: 753-756. PubMed

Ruiz N, Kahne D, Silhavy TJ. (2009) Transport of lipopolysaccharide across the cell envelope: the long road of discovery. Nat Rev Microbiol 7: 677-683. PubMed

Malinverni JC, Silhavy TJ. (2009) An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane. Proc Natl Acad Sci. 106: 8009-8014. PubMed

Silhavy TJ, Gitai Z. (2008) Sex to the rescue. Nat Methods. 5: 759-760. PubMed

Ruiz N, Gronenberg LS, Kahne D, Silhavy TJ. (2008) Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli. Proc Natl Acad Sci.105: 5537-5542. PubMed

Sklar JG, Wu T, Kahne D, Silhavy TJ. (2007) Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli. Genes Dev 21: 2473-2484. PubMed

Sklar JG, Wu T, Gronenberg LS, Malinverni JC, Kahne D, Silhavy TJ (2007). Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli. Proc Natl Acad Sci USA 104: 6400-6405. PubMed

Button JE, Silhavy TJ, Ruiz N (2006). A suppressor of cell death caused by the loss of {sigma}E downregulates extracytoplasmic stress responses and outer membrane vesicle production in Escherichia coli. J Bacteriol 189: 1523-1530. PubMed

Ruiz N, Wu T, Kahne D, Silhavy TJ (2006). Probing the barrier function of the outer membrane with chemical conditionality. ACS Chem Biol 1: 385-395. PubMed

Ureta AR, Endres RG, Wingreen NS, Silhavy TJ (2006). Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment. J Bacteriol 189: 446-454. PubMed

Gaal T, Mandel MJ, Silhavy TJ, Gourse RL (2006). Crl facilitates RNA polymerase holoenzyme formation. J Bacteriol 188: 7966-7970. PubMed

Malinverni JC, Werner J, Kim S, Sklar JG, Kahne D, Misra R, Silhavy TJ (2006). YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli. Mol Microbiol 61: 151-164. PubMed

Peterson CN, Carabetta VJ, Chowdhury T, Silhavy TJ (2006). LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli. J Bacteriol 188: 3175-3181. PubMed

Ruiz N, Kahne D, Silhavy TJ (2006). Advances in understanding bacterial outer-membrane biogenesis. Nat Rev Microbiol 4: 57-66. PubMed

Isaac DD, Pinkner JS, Hultgren SJ, Silhavy TJ (2006). The extracytoplasmic adaptor protein CpxP is degraded with substrate by DegP. Proc Natl Acad Sci USA 102: 17775-17779. PubMed

Justice SS, Hunstad DA, Harper JR, Duguay AR, Pinkner JS, Bann J, Frieden C, Silhavy TJ, Hultgren SJ (2005). Periplasmic peptidyl prolyl cis-trans isomerases are not essential for viability, but SurA is required for pilus biogenesis in Escherichia coli. J Bacteriol 187: 7680-7686. PubMed

Peterson CN, Mandel MJ, Silhavy TJ (2005). Escherichia coli starvation diets: essential nutrients weigh in distinctly. J Bacteriol 187: 7549-7553. PubMed

Ruiz N, Falcone B, Kahne D and Silhavy TJ (2005). Chemical conditionality: a genetic strategy to probe organelle assembly. Cell 121: 307-317. PubMed

Wu T, Malinverni J, Ruiz N, Kim S, Silhavy TJ and Kahne D (2005). Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli. Cell 121: 235-245. PubMed

Ruiz N, Silhavy TJ (2005). Sensing external stress: watchdogs of the Escherichia coli cell envelope. Curr Opin Microbiol 8: 122-126. PubMed

Mandel MJ and Silhavy TJ (2005). Starvation for different nutrients in Escherichia coli results in differential modulation of RpoS levels and stability. J Bacteriol 187: 434-442. PubMed

Duguay AR, Silhavy TJ (2004). Quality control in the bacterial periplasm. Biochim Biophys Acta 1694: 121-134. PubMed

Batchelor E, Silhavy TJ, Goulian M (2004). Continuous control in bacterial regulatory circuits. J Bacteriol 186: 7618-7625. PubMed

Peterson CN, Ruiz N and Silhavy TJ (2004). RpoS proteolysis is regulated by a mechanism that does not require the SprE (RssB) response regulator phosphorylation site. J Bacteriol 186: 7403-7410. PubMed

Gibbs KA, Isaac DD, Xu J, Hendrix RW, Silhavy TJ, Theriot JA (2004). Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB. Mol Microbiol 53: 1771-1783. PubMed

Lee YM, DiGiuseppe PA, Silhavy TJ, Hultgren SJ (2004). P pilus assembly motif necessary for activation of the CpxRA pathway by PapE in Escherichia coli. J Bacteriol 186: 4326-4337. PubMed

Hand NJ and Silhavy TJ (2004). Null mutations in a Nudix gene, ygdP, implicate an alarmone response in a novel suppression of hybrid jamming. J Bacteriol 185: 6530-6539. PubMed

Ruiz N and Silhavy TJ (2003). Constitutive activation of the Escherichia coli Pho regulon upregulates rpoS translation in an Hfq-dependent fashion. J Bacteriol 185: 5984-5992. PubMed

Bowers CW, Lau F and Silhavy TJ (2003). Secretion of LamB-LacZ by the signal recognition particle pathway of Escherichia coli. J Bacteriol 185: 5697-5705. PubMed

Shuman HA and Silhavy TJ (2003). The art and design of genetic screens: Escherichia coli. Nat Rev Genet 4: 419-431. PubMed

DiGiuseppe PA and Silhavy TJ (2003). Signal detection and target gene induction by the CpxRA two-component system. J Bacteriol 185: 2432-2440. PubMed

Duguay AR, Silhavy TJ (2002). Signal sequence mutations as tools for the characterization of LamB folding intermediates. J Bacteriol 184: 6918-6928. PubMed

Braun M and Silhavy TJ (2002). Imp/OstA is required for cell envelope biogenesis in Escherichia coli. Mol Microbiol 45: 1289-1302. PubMed

Otto K and Silhavy TJ (2002). Surface sensing and adhesion of Escherichia coli controlled by the Cpx-signaling pathway. Proc Natl Acad Sci USA 99: 2287-2292. PubMed

 

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