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Giuseppe PO, Von Atzingen M, Nascimento ALTO, Zanchin NIT, Guimarães BG. The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA. J Struct Biol 2010; 173:312-22. [PMID: 20970503 DOI: 10.1016/j.jsb.2010.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 10/11/2010] [Accepted: 10/18/2010] [Indexed: 12/22/2022]
Abstract
Leptospirosis is a world spread zoonosis caused by members of the genus Leptospira. Although leptospires were identified as the causal agent of leptospirosis almost 100 years ago, little is known about their biology, which hinders the development of new treatment and prevention strategies. One of the several aspects of the leptospiral biology not yet elucidated is the process by which outer membrane proteins (OMPs) traverse the periplasm and are inserted into the outer membrane. The crystal structure determination of the conserved hypothetical protein LIC12922 from Leptospira interrogans revealed a two domain protein homologous to the Escherichia coli periplasmic chaperone SurA. The LIC12922 NC-domain is structurally related to the chaperone modules of E. coli SurA and trigger factor, whereas the parvulin domain is devoid of peptidyl prolyl cis-trans isomerase activity. Phylogenetic analyses suggest a relationship between LIC12922 and the chaperones PrsA, PpiD and SurA. Based on our structural and evolutionary analyses, we postulate that LIC12922 is a periplasmic chaperone involved in OMPs biogenesis in Leptospira spp. Since LIC12922 homologs were identified in all spirochetal genomes sequenced to date, this assumption may have implications for the OMPs biogenesis studies not only in leptospires but in the entire Phylum Spirochaetes.
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Affiliation(s)
- Priscila O Giuseppe
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Giuseppe Máximo Scolfaro 10000, 13083-970 Campinas, SP, Brazil
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Weininger U, Jakob RP, Kovermann M, Balbach J, Schmid FX. The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity. Protein Sci 2010; 19:6-18. [PMID: 19866485 DOI: 10.1002/pro.277] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
PpiD is a periplasmic folding helper protein of Escherichia coli. It consists of an N-terminal helix that anchors PpiD in the inner membrane near the SecYEG translocon, followed by three periplasmic domains. The second domain (residues 264-357) shows homology to parvulin-like prolyl isomerases. This domain is a well folded, stable protein and follows a simple two-state folding mechanism. In its solution structure, as determined by NMR spectroscopy, it resembles most closely the first parvulin domain of the SurA protein, which resides in the periplasm of E. coli as well. A previously reported prolyl isomerase activity of PpiD could not be reproduced when using improved protease-free peptide assays or assays with refolding proteins as substrates. The parvulin domain of PpiD interacts, however, with a proline-containing tetrapeptide, and the binding site, as identified by NMR resonance shift analysis, colocalized with the catalytic sites of other parvulins. In its structure, the parvulin domain of PpiD resembles most closely the inactive first parvulin domain of SurA, which is part of the chaperone unit of this protein and presumably involved in substrate recognition.
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Affiliation(s)
- Ulrich Weininger
- Institut für Physik, Biophysik, and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle(Saale), Germany
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Gatsos X, Perry AJ, Anwari K, Dolezal P, Wolynec PP, Likić VA, Purcell AW, Buchanan SK, Lithgow T. Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev 2008; 32:995-1009. [PMID: 18759741 PMCID: PMC2635482 DOI: 10.1111/j.1574-6976.2008.00130.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/23/2008] [Accepted: 07/18/2008] [Indexed: 11/17/2022] Open
Abstract
The assembly of beta-barrel proteins into membranes is a fundamental process that is essential in Gram-negative bacteria, mitochondria and plastids. Our understanding of the mechanism of beta-barrel assembly is progressing from studies carried out in Escherichia coli and Neisseria meningitidis. Comparative sequence analysis suggests that while many components mediating beta-barrel protein assembly are conserved in all groups of bacteria with outer membranes, some components are notably absent. The Alphaproteobacteria in particular seem prone to gene loss and show the presence or absence of specific components mediating the assembly of beta-barrels: some components of the pathway appear to be missing from whole groups of bacteria (e.g. Skp, YfgL and NlpB), other proteins are conserved but are missing characteristic domains (e.g. SurA). This comparative analysis is also revealing important structural signatures that are vague unless multiple members from a protein family are considered as a group (e.g. tetratricopeptide repeat (TPR) motifs in YfiO, beta-propeller signatures in YfgL). Given that the process of the beta-barrel assembly is conserved, analysis of outer membrane biogenesis in Alphaproteobacteria, the bacterial group that gave rise to mitochondria, also promises insight into the assembly of beta-barrel proteins in eukaryotes.
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Affiliation(s)
- Xenia Gatsos
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Andrew J Perry
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Khatira Anwari
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Pavel Dolezal
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - P Peter Wolynec
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Vladimir A Likić
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
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Stymest KH, Klappa P. The periplasmic peptidyl prolyl cis-trans isomerases PpiD and SurA have partially overlapping substrate specificities. FEBS J 2008; 275:3470-9. [PMID: 18498364 DOI: 10.1111/j.1742-4658.2008.06493.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the rate-limiting steps in protein folding has been shown to be the cis-trans isomerization of proline residues, catalysed by a range of peptidyl prolyl cis-trans isomerases (PPIases). In the periplasmic space of Escherichia coli and other Gram-negative bacteria, two PPIases, SurA and PpiD, have been identified, which show high sequence similarity to the catalytic domain of the small PPIase parvulin. This observation raises a question regarding the biological significance of two apparently similar enzymes present in the same cellular compartment: do they interact with different substrates or do they catalyse different reactions? The substrate-binding motif of PpiD has not been characterized so far, and no biochemical data were available on how this folding catalyst recognizes and interacts with substrates. To characterize the interaction between model peptides and the periplasmic PPIase PpiD from E. coli, we employed a chemical crosslinking strategy that has been used previously to elucidate the interaction of substrates with SurA. We found that PpiD interacted with a range of model peptides independently of whether they contained proline residues or not. We further demonstrate here that PpiD and SurA interact with similar model peptides, and therefore must have partially overlapping substrate specificities. However, the binding motif of PpiD appears to be less specific than that of SurA, indicating that the two PPIases might interact with different substrates. We therefore propose that, although PpiD and SurA have partially overlapping substrate specificities, they fulfil different functions in the cell.
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Alcock FH, Grossmann JG, Gentle IE, Likić VA, Lithgow T, Tokatlidis K. Conserved substrate binding by chaperones in the bacterial periplasm and the mitochondrial intermembrane space. Biochem J 2007; 409:377-87. [PMID: 17894549 DOI: 10.1042/bj20070877] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mitochondria were derived from intracellular bacteria and the mitochondrial intermembrane space is topologically equivalent to the bacterial periplasm. Both compartments contain ATP-independent chaperones involved in the transport of hydrophobic membrane proteins. The mitochondrial TIM (translocase of the mitochondrial inner membrane) 10 complex and the periplasmic chaperone SurA were examined in terms of evolutionary relation, structural similarity, substrate binding specificity and their function in transporting polypeptides for insertion into membranes. The two chaperones are evolutionarily unrelated; structurally, they are also distinct both in their characteristics, as determined by SAXS (small-angle X-ray scattering), and in pairwise structural comparison using the distance matrix alignment (DALILite server). Despite their structural differences, SurA and the TIM10 complex share a common binding specificity in Pepscan assays of substrate proteins. Comprehensive analysis of the binding on a total of 1407 immobilized 13-mer peptides revealed that the TIM10 complex, like SurA, does not bind hydrophobic peptides generally, but that both chaperones display selectivity for peptides rich in aromatic residues and with net positive charge. This common binding specificity was not sufficient for SurA to completely replace TIM10 in yeast cells in vivo. In yeast cells lacking TIM10, when SurA is targeted to the intermembrane space of mitochondria, it binds translocating substrate proteins, but fails to completely transfer the substrate to the translocase in the mitochondrial inner membrane. We suggest that SurA was incapable of presenting substrates effectively to the primitive TOM (translocase of the mitochondrial outer membrane) and TIM complexes in early mitochondria, and was replaced by the more effective small Tim chaperone.
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Affiliation(s)
- Felicity H Alcock
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas, PO Box 1385, 71110 Heraklion, Crete, Greece
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Castanié-Cornet MP, Cam K, Jacq A. RcsF is an outer membrane lipoprotein involved in the RcsCDB phosphorelay signaling pathway in Escherichia coli. J Bacteriol 2006; 188:4264-70. [PMID: 16740933 PMCID: PMC1482940 DOI: 10.1128/jb.00004-06] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RcsCDB signal transduction system is an atypical His-Asp phosphorelay conserved in gamma-proteobacteria. Besides the three proteins directly involved in the phosphorelay, two proteins modulate the activity of the system. One is RcsA, which can stimulate the activity of the response regulator RcsB independently of the phosphorelay to regulate a subset of RcsB targets. The other is RcsF, a putative outer membrane lipoprotein mediating the signaling to the sensor RcsC. How RcsF transduces the signal to RcsC is unknown. Although the molecular and physiological signals remain to be identified, the common feature among the reported Rcs-activating conditions is perturbation of the envelope. As an initial step to explore the RcsF-RcsC functional relationship, we demonstrate that RcsF is an outer membrane lipoprotein oriented towards the periplasm. We also report that a null mutation in surA, a gene required for correct folding of periplasmic proteins, activates the Rcs pathway through RcsF. In contrast, activation of this pathway by overproduction of the membrane chaperone-like protein DjlA does not require RcsF. Conversely, activation of the pathway by RcsF overproduction does not require DjlA either, indicating the existence of two independent signaling pathways toward RcsC.
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Affiliation(s)
- Marie-Pierre Castanié-Cornet
- Institut de Génétique et de Microbiologie, UMR 8621, Centre National de la Recherche Scientifique and Université Paris-Sud, Bâtiment 400, 91 405 Orsay cedex, France
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Eggenhofer E, Haslbeck M, Scharf B. MotE serves as a new chaperone specific for the periplasmic motility protein, MotC, in Sinorhizobium meliloti. Mol Microbiol 2004; 52:701-12. [PMID: 15101977 DOI: 10.1111/j.1365-2958.2004.04022.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The flagella of Sinorhizobium meliloti rotate solely clockwise and vary their rotary speed to provoke changes in the swimming path. This mode of motility control has its molecular corollary in two novel motility proteins, MotC and MotD, present in addition to the ubiquitous MotA/MotB energizing proton channel. MotC binds to the periplasmic portion of MotB, whereas MotD interacts with FliM at the cytoplasmic face of the rotor. We report here the assignment and analysis of a fifth motility protein, MotE. Deletion of motE resulted in aggregation and decay of the periplasmic MotC protein and, as a consequence, in paralysis of the cell. The 179-residue MotE protein bears an N-terminal signal peptide and is rapidly secreted to the periplasm, where it forms stable dimers that are linked by a disulphide bridge between the cysteine 53 residues. Both, the monomeric and the dimeric MotE bind to MotC, and dimerization is essential for MotE stability in the periplasm. We conclude that MotE is a periplasmic chaperone specific for MotC being responsible for its proper folding and stability. We also propose that the MotE dimer serves as a shuttle to target MotC to its binding site at MotB.
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Affiliation(s)
- Elke Eggenhofer
- Lehrstuhl für Genetik, Universität Regensburg, D-93040 Regensburg, Germany
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