Genomes and Genes
Summary: Proteins found in the PERIPLASM of organisms with cell walls.
- Baker L, Poole L. Catalytic mechanism of thiol peroxidase from Escherichia coli. Sulfenic acid formation and overoxidation of essential CYS61. J Biol Chem. 2003;278:9203-11 pubmed..Unlike most other 2-Cys peroxiredoxins, which operate by an intersubunit disulfide mechanism, Tpx contains a redox-active intrasubunit disulfide bond yet is homodimeric in solution. ..
- Rajasekaran M, Mitchell S, Gibson T, Hussain R, Siligardi G, Andrews S, et al. Isolation and characterisation of EfeM, a periplasmic component of the putative EfeUOBM iron transporter of Pseudomonas syringae pv. syringae. Biochem Biophys Res Commun. 2010;398:366-71 pubmed publisher..Purified EfeM was crystallised by hanging-drop vapor diffusion to give needle-shaped crystals that diffracted to a resolution of 1.6A. This is the first molecular study of a peptidase M75 domain with a presumed iron transport role. ..
- Humphreys S, Rowley G, Stevenson A, Kenyon W, Spector M, Roberts M. Role of periplasmic peptidylprolyl isomerases in Salmonella enterica serovar Typhimurium virulence. Infect Immun. 2003;71:5386-8 pubmed
- Agudo D, Mendoza M, Castañares C, Nombela C, Rotger R. A proteomic approach to study Salmonella typhi periplasmic proteins altered by a lack of the DsbA thiol: disulfide isomerase. Proteomics. 2004;4:355-63 pubmed..The AI-2 autoinducer-producing protein LuxS, which is involved in quorum-sensing signalling was also absent. ..
- Ng T, Akman L, Osisami M, Thanassi D. The usher N terminus is the initial targeting site for chaperone-subunit complexes and participates in subsequent pilus biogenesis events. J Bacteriol. 2004;186:5321-31 pubmed..Thus, the usher N terminus does not function simply as a static binding site for chaperone-subunit complexes but also participates in subsequent pilus assembly events. ..
- Mogensen J, Otzen D. Interactions between folding factors and bacterial outer membrane proteins. Mol Microbiol. 2005;57:326-46 pubmed..Recently, a number of periplasmic proteins and one OMP have been shown to play a role in OMP biogenesis...
- Jin L, Pandey P, Babine R, Gorga J, Seidl K, Gelfand E, et al. Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions. J Biol Chem. 2005;280:4704-12 pubmed..These structures provide us with an understanding of substrate binding interactions of FXIa, the structural information essential for the structure-based design of FXIa-selective inhibitors. ..
- Brøndsted L, Andersen M, Parker M, Jørgensen K, Ingmer H. The HtrA protease of Campylobacter jejuni is required for heat and oxygen tolerance and for optimal interaction with human epithelial cells. Appl Environ Microbiol. 2005;71:3205-12 pubmed..This defect may be a consequence of the observed altered morphology of the htrA mutant. Thus, our results suggest that in C. jejuni, HtrA is important for growth during stressful conditions and has an impact on virulence. ..
- Stoop A, Craik C. Engineering of a macromolecular scaffold to develop specific protease inhibitors. Nat Biotechnol. 2003;21:1063-8 pubmed..The adaptability of the scaffold was demonstrated by the isolation of inhibitors to two additional serine proteases, MT-SP1/matriptase and Factor XIIa. ..
- Shen Q, Bai X, Chang L, Wu Y, Wang H, Sui S. Bowl-shaped oligomeric structures on membranes as DegP's new functional forms in protein quality control. Proc Natl Acad Sci U S A. 2009;106:4858-63 pubmed publisher..Our findings imply that DegP might regulate its dual roles during protein quality control, depending on its assembly state in the narrow bacterial envelope. ..
- Lin D, Kim B, Slauch J. DsbL and DsbI contribute to periplasmic disulfide bond formation in Salmonella enterica serovar Typhimurium. Microbiology. 2009;155:4014-24 pubmed publisherDisulfide bond formation in periplasmic proteins is catalysed by the DsbA/DsbB system in most Gram-negative bacteria...
- Mealman T, Bagai I, Singh P, Goodlett D, Rensing C, Zhou H, et al. Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Biochemistry. 2011;50:2559-66 pubmed publisherThe Escherichia coli periplasmic proteins CusF and CusB, as part of the CusCFBA efflux system, aid in the resistance of elevated levels of copper and silver by direct metal transfer between the metallochaperone CusF and the membrane ..
- Sharma O, Cramer W. Minimum length requirement of the flexible N-terminal translocation subdomain of colicin E3. J Bacteriol. 2007;189:363-8 pubmed
- Meltzer M, Hasenbein S, Mamant N, Merdanovic M, Poepsel S, Hauske P, et al. Structure, function and regulation of the conserved serine proteases DegP and DegS of Escherichia coli. Res Microbiol. 2009;160:660-6 pubmed publisher..The underlying mechanisms of their main functions in stress sensing, regulation and protection during the unfolded protein response are discussed. ..
- Goemans C, Denoncin K, Collet J. Folding mechanisms of periplasmic proteins. Biochim Biophys Acta. 2014;1843:1517-28 pubmed publisher..coli and highlight the questions that remain unsolved. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey. ..
- Tripathi L, Sowdhamini R. Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genomics. 2006;7:200 pubmed..Further investigation of these aspects may prove beneficial in our understanding of similar processes in commercially significant crop plant species. ..
- Pan K, Hsiao H, Weng C, Wu M, Chou C. Roles of DegP in prevention of protein misfolding in the periplasm upon overexpression of penicillin acylase in Escherichia coli. J Bacteriol. 2003;185:3020-30 pubmed..The chaperone activity of DegP is proposed to be another possible factor contributing to the suppression...
- Hunke S, Betton J. Temperature effect on inclusion body formation and stress response in the periplasm of Escherichia coli. Mol Microbiol. 2003;50:1579-89 pubmed
- Raffa R, Raivio T. A third envelope stress signal transduction pathway in Escherichia coli. Mol Microbiol. 2002;45:1599-611 pubmed..We propose that the Bae signal transduction pathway controls a third envelope stress response in E. coli that induces expression of a distinct set of adaptive genes. ..
- Penfold C, Healy B, Housden N, Boetzel R, Vankemmelbeke M, Moore G, et al. Flexibility in the receptor-binding domain of the enzymatic colicin E9 is required for toxicity against Escherichia coli cells. J Bacteriol. 2004;186:4520-7 pubmed..The data are consistent with a requirement for the flexibility of the coiled-coil R domain after binding to BtuB. ..
- Loftus S, Walker D, Mat M, Bonsor D, James R, Moore G, et al. Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9. Proc Natl Acad Sci U S A. 2006;103:12353-8 pubmed publisher..Our study demonstrates that natively disordered proteins can compete with globular proteins for binding to folded scaffolds but that this can require cofactors such as metal ions to offset unfavorable interactions...
- Bagai I, Rensing C, Blackburn N, McEvoy M. Direct metal transfer between periplasmic proteins identifies a bacterial copper chaperone. Biochemistry. 2008;47:11408-14 pubmed publisher..Using isothermal titration calorimetry, we have demonstrated that two periplasmic proteins, CusF and CusB, of the Escherichia coli Cu(I)/Ag(I) efflux system undergo a metal-dependent interaction...
- Jomaa A, Iwanczyk J, Tran J, Ortega J. Characterization of the autocleavage process of the Escherichia coli HtrA protein: implications for its physiological role. J Bacteriol. 2009;191:1924-32 pubmed publisher..Our data support a model in which the physiological role of the self-cleavage process is to eliminate the excess of HtrA once the stress conditions cease. ..
- Choi J, Choi S, Choi J, Cha M, Kim I, Shin W. Crystal structure of Escherichia coli thiol peroxidase in the oxidized state: insights into intramolecular disulfide formation and substrate binding in atypical 2-Cys peroxiredoxins. J Biol Chem. 2003;278:49478-86 pubmed
- Ingmer H, Brøndsted L. Proteases in bacterial pathogenesis. Res Microbiol. 2009;160:704-10 pubmed publisher..We have focused on the contribution of the conserved Lon, Clp, HtrA and FtsH proteases to pathogenesis and have highlighted common biological processes for which their activities are important for virulence. ..
- CastilloKeller M, Misra R. Protease-deficient DegP suppresses lethal effects of a mutant OmpC protein by its capture. J Bacteriol. 2003;185:148-54 pubmed..Displacement of OmpC(2Cys) by DegP(S210A) also alleviates the negative effect that the mutant OmpC protein has on wild-type OmpF. ..
- Sobiecka Szkatula A, Polit A, Scire A, Gieldon A, Tanfani F, Szkarlat Z, et al. Temperature-induced conformational changes within the regulatory loops L1-L2-LA of the HtrA heat-shock protease from Escherichia coli. Biochim Biophys Acta. 2009;1794:1573-82 pubmed publisher..Summing up, the HtrA structure appears to open gradually, parallel to the gradual increase of its proteolytic activity. ..
- Collet J, Riemer J, Bader M, Bardwell J. Reconstitution of a disulfide isomerization system. J Biol Chem. 2002;277:26886-92 pubmed..We also determined the redox potential of the gamma domain to be -241 mV, and that of the alpha domain was found to be -229 mV. This shows that the direction of electron flow within DsbD is thermodynamically driven. ..
- Spiers A, Lamb H, Cocklin S, Wheeler K, Budworth J, Dodds A, et al. PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptide. J Biol Chem. 2002;277:39443-9 pubmed
- Depuydt M, Leonard S, Vertommen D, Denoncin K, Morsomme P, Wahni K, et al. A periplasmic reducing system protects single cysteine residues from oxidation. Science. 2009;326:1109-11 pubmed publisher..However, many periplasmic proteins contain single cysteine residues, which are vulnerable to oxidation to sulfenic acids and then irreversibly ..
- Marrero K, S nchez A, Gonz lez L, Led n T, Rodr guez Ulloa A, Castellanos Serra L, et al. Periplasmic proteins encoded by VCA0261-0260 and VC2216 genes together with copA and cueR products are required for copper tolerance but not for virulence in Vibrio cholerae. Microbiology. 2012;158:2005-16 pubmed publisher..cholerae, which lacks orthologues of the periplasmic copper tolerance proteins CueO, CusCFBA and CueP, involves CopA and CueR proteins along with the periplasmic Cot (VCA0261-0260) and CopG (VC2216) V. cholerae homologues...
- Boigegrain R, Salhi I, Alvarez Martinez M, Machold J, Fedon Y, Arpagaus M, et al. Release of periplasmic proteins of Brucella suis upon acidic shock involves the outer membrane protein Omp25. Infect Immun. 2004;72:5693-703 pubmed..Together, these results suggest that Omp25 is involved in the membrane permeability of Brucella in acidic medium...
- Hands S, Holland L, Vankemmelbeke M, Fraser L, Macdonald C, Moore G, et al. Interactions of TolB with the translocation domain of colicin E9 require an extended TolB box. J Bacteriol. 2005;187:6733-41 pubmed..All active variants had AABUF profiles that were similar to the wild-type residues at those positions and provided information on the size, stereochemistry, and potential folding pattern of the residues of the TolB Box. ..
- Bonsor D, Grishkovskaya I, Dodson E, Kleanthous C. Molecular mimicry enables competitive recruitment by a natively disordered protein. J Am Chem Soc. 2007;129:4800-7 pubmed..The study therefore explains how colicins recruit TolB in the bacterial periplasm and highlights a novel binding mechanism for a natively disordered protein. ..
- Eggers C, Murray I, Delmar V, Day A, Craik C. The periplasmic serine protease inhibitor ecotin protects bacteria against neutrophil elastase. Biochem J. 2004;379:107-18 pubmed..This suggests that an important part of the antimicrobial mechanism of neutrophil elastase may be a periplasmic bacteriostatic effect of protease that has translocated across the damaged outer membrane. ..
- Groll M, Bochtler M, Brandstetter H, Clausen T, Huber R. Molecular machines for protein degradation. Chembiochem. 2005;6:222-56 pubmed..Some of these compounds may find therapeutic applications in contemporary medicine. ..
- Hernández Montes G, ARGUELLO J, Valderrama B. Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria. BMC Microbiol. 2012;12:249 pubmed publisher..These observations suggest complex evolutionary dynamics and still unexplored interactions to achieve copper homeostasis, challenging some of the molecular transport mechanism proposed for these systems. ..
- Motaleb M, Pitzer J, Sultan S, Liu J. A novel gene inactivation system reveals altered periplasmic flagellar orientation in a Borrelia burgdorferi fliL mutant. J Bacteriol. 2011;193:3324-31 pubmed publisher..Our results suggest that FliL is likely involved in coordinating or regulating the orientation of periplasmic flagella in B. burgdorferi. ..
- Collins E, Whittaker S, Tozawa K, MacDonald C, Boetzel R, Penfold C, et al. Structural dynamics of the membrane translocation domain of colicin E9 and its interaction with TolB. J Mol Biol. 2002;318:787-804 pubmed..The flexibility of the translocation domain of colicin E9 may be connected with its need to recognise protein partners that assist it in crossing the outer membrane and in the translocation event itself. ..
- Merdanovic M, Mamant N, Meltzer M, Poepsel S, Auckenthaler A, Melgaard R, et al. Determinants of structural and functional plasticity of a widely conserved protease chaperone complex. Nat Struct Mol Biol. 2010;17:837-43 pubmed publisher..The implications of these data for the mechanism of protein quality control are discussed. ..
- Jiang J, Zhang X, Chen Y, Wu Y, Zhou Z, Chang Z, et al. Activation of DegP chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins. Proc Natl Acad Sci U S A. 2008;105:11939-44 pubmed publisher..Such interactions simultaneously eliminate the inhibitory effects of the PDZ2 domain. Additionally, both DegP oligomers were also observed in extracts of E. coli cells, strongly implicating their physiological importance. ..
- Charlson E, Werner J, Misra R. Differential effects of yfgL mutation on Escherichia coli outer membrane proteins and lipopolysaccharide. J Bacteriol. 2006;188:7186-94 pubmed..The results support the hypothesis that TolC and major outer membrane proteins compete for the YaeT/YfiO complex, since mutations that adversely affect synthesis or assembly of major outer membrane proteins lead to elevated TolC levels. ..
- Sklar J, Wu T, Kahne D, Silhavy T. Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli. Genes Dev. 2007;21:2473-84 pubmed..The seemingly redundant periplasmic chaperones do function in parallel, but the relative importance of the primary function of each pathway depends on whether or not cells are under stress. ..
- Skorko Glonek J, Zurawa D, Tanfani F, Scire A, Wawrzynów A, Narkiewicz J, et al. The N-terminal region of HtrA heat shock protease from Escherichia coli is essential for stabilization of HtrA primary structure and maintaining of its oligomeric structure. Biochim Biophys Acta. 2003;1649:171-82 pubmed..Autocleavage caused the native, hexameric HtrA molecules dissociate into monomers that were still proteolytically active. This shows that the N-terminal part of HtrA is essential for maintaining quaternary structure of HtrA. ..
- Wang S, Hur E, Sousa C, Brinen L, Slivka E, Fletterick R. The extended interactions and Gla domain of blood coagulation factor Xa. Biochemistry. 2003;42:7959-66 pubmed..The first 11 residues of the domain assume a novel conformation and likely represent an intermediate folding state of the domain. ..
- Dubuisson J, Vianney A, Lazzaroni J. Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB. J Bacteriol. 2002;184:4620-5 pubmed..The isolation of suppressor mutants of tolA mutations in the tolB gene confirmed an interaction between TolAIII and the N-terminal domain of TolB. ..
- Iwanczyk J, Damjanovic D, Kooistra J, Leong V, Jomaa A, Ghirlando R, et al. Role of the PDZ domains in Escherichia coli DegP protein. J Bacteriol. 2007;189:3176-86 pubmed
- Purdy G, Fisher C, Payne S. IcsA surface presentation in Shigella flexneri requires the periplasmic chaperones DegP, Skp, and SurA. J Bacteriol. 2007;189:5566-73 pubmed..Therefore, the three periplasmic folding factors DegP, Skp, and SurA were all required for IcsA localization and plaque formation by S. flexneri. ..
- Iwanczyk J, Leong V, Ortega J. Factors defining the functional oligomeric state of Escherichia coli DegP protease. PLoS ONE. 2011;6:e18944 pubmed publisher..However, small substrate molecules (peptides) always triggered the same oligomeric state regardless of their concentration. These results clarify important aspects of the regulation of the oligomeric state of DegP. ..
- Krojer T, Sawa J, Schäfer E, Saibil H, Ehrmann M, Clausen T. Structural basis for the regulated protease and chaperone function of DegP. Nature. 2008;453:885-90 pubmed publisher..Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases. ..