1
|
Zhang R, Wang Y. EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance. Appl Environ Microbiol 2023; 89:e0157723. [PMID: 38019025 PMCID: PMC10734491 DOI: 10.1128/aem.01577-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE EvgS/EvgA, one of the five unorthodox two-component systems in Escherichia coli, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.
Collapse
Affiliation(s)
- Ruizhen Zhang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yan Wang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
2
|
Mayer M, Winer L, Karniel A, Pinner E, Yardeni EH, Morgenstern D, Bibi E. Co-translational membrane targeting and holo-translocon docking of ribosomes translating the SRP receptor. J Mol Biol 2022; 434:167459. [DOI: 10.1016/j.jmb.2022.167459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 10/19/2022]
|
3
|
Genetic Evidence for SecY Translocon-Mediated Import of Two Contact-Dependent Growth Inhibition (CDI) Toxins. mBio 2021; 12:mBio.03367-20. [PMID: 33531386 PMCID: PMC7858069 DOI: 10.1128/mbio.03367-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Many bacterial species interact via direct cell-to-cell contact using CDI systems, which provide a mechanism to inject toxins that inhibit bacterial growth into one another. Here, we find that two CDI toxins, one that depolarizes membranes and another that degrades RNA, exploit the universally conserved SecY translocon machinery used to export proteins for target cell entry. The C-terminal (CT) toxin domains of contact-dependent growth inhibition (CDI) CdiA proteins target Gram-negative bacteria and must breach both the outer and inner membranes of target cells to exert growth inhibitory activity. Here, we examine two CdiA-CT toxins that exploit the bacterial general protein secretion machinery after delivery into the periplasm. A Ser281Phe amino acid substitution in transmembrane segment 7 of SecY, the universally conserved channel-forming subunit of the Sec translocon, decreases the cytotoxicity of the membrane depolarizing orphan10 toxin from enterohemorrhagic Escherichia coli EC869. Target cells expressing secYS281F and lacking either PpiD or YfgM, two SecY auxiliary factors, are fully protected from CDI-mediated inhibition either by CdiA-CTo10EC869 or by CdiA-CTGN05224, the latter being an EndoU RNase CdiA toxin from Klebsiella aerogenes GN05224 that has a related cytoplasm entry domain. RNase activity of CdiA-CTGN05224 was reduced in secYS281F target cells and absent in secYS281F ΔppiD or secYS281F ΔyfgM target cells during competition co-cultures. Importantly, an allele-specific mutation in secY (secYG313W) renders ΔppiD or ΔyfgM target cells specifically resistant to CdiA-CTGN05224 but not to CdiA-CTo10EC869, further suggesting a direct interaction between SecY and the CDI toxins. Our results provide genetic evidence of a unique confluence between the primary cellular export route for unfolded polypeptides and the import pathways of two CDI toxins.
Collapse
|
4
|
Escherichia coli CFT073 Fitness Factors during Urinary Tract Infection: Identification Using an Ordered Transposon Library. Appl Environ Microbiol 2020; 86:AEM.00691-20. [PMID: 32358013 DOI: 10.1128/aem.00691-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 12/15/2022] Open
Abstract
Urinary tract infections (UTI), the second most diagnosed infectious disease worldwide, are caused primarily by uropathogenic Escherichia coli (UPEC), placing a significant financial burden on the health care system. High-throughput transposon mutagenesis combined with genome-targeted sequencing is a powerful technique to interrogate genomes for fitness genes. Genome-wide analysis of E. coli requires random libraries of at least 50,000 mutants to achieve 99.99% saturation; however, the traditional murine model of ascending UTI does not permit testing of large mutant pools due to a bottleneck during infection. To address this, an E. coli CFT073 transposon mutant ordered library of 9,216 mutants was created and insertion sites were identified. A single transposon mutant was selected for each gene to assemble a condensed library consisting of 2,913 unique nonessential mutants. Using a modified UTI model in BALB/c mice, we identified 36 genes important for colonizing the bladder, including purB, yihE, and carB Screening of the condensed library in vitro identified yigP and ubiG to be essential for growth in human urine. Additionally, we developed a novel quantitative PCR (qPCR) technique to identify genes with fitness defects within defined subgroups of related genes (e.g., genes encoding fimbriae, toxins, etc.) following UTI. The number of mutants within these subgroups circumvents bottleneck restriction and facilitates validation of multiple mutants to generate individual competitive indices. Collectively, this study investigates the bottleneck effects during UTI, provides two techniques for evading those effects that can be applied to other disease models, and contributes a genetic tool in prototype strain CFT073 to the field.IMPORTANCE Uropathogenic Escherichia coli strains cause most uncomplicated urinary tract infections (UTI), one of the most common infectious diseases worldwide. Random transposon mutagenesis techniques have been utilized to identify essential bacterial genes during infection; however, this has been met with limitations when applied to the murine UTI model. Conventional high-throughput transposon mutagenesis screens are not feasible because of inoculum size restrictions due to a bottleneck during infection. Our study utilizes a condensed ordered transposon library, limiting the number of mutants while maintaining the largest possible genome coverage. Screening of this library in vivo, and in human urine in vitro, identified numerous candidate fitness factors. Additionally, we have developed a novel technique using qPCR to quantify bacterial outputs following infection with small subgroups of transposon mutants. Molecular approaches developed in this study will serve as useful tools to probe in vivo models that are restricted by anatomical, physiological, or genetic bottleneck limitations.
Collapse
|
5
|
Jauss B, Petriman NA, Drepper F, Franz L, Sachelaru I, Welte T, Steinberg R, Warscheid B, Koch HG. Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli. J Biol Chem 2019; 294:19167-19183. [PMID: 31699901 DOI: 10.1074/jbc.ra119.010686] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
The SecYEG translocon constitutes the major protein transport channel in bacteria and transfers an enormous variety of different secretory and inner-membrane proteins. The minimal core of the SecYEG translocon consists of three inner-membrane proteins, SecY, SecE, and SecG, which, together with appropriate targeting factors, are sufficient for protein transport in vitro However, in vivo the SecYEG translocon has been shown to associate with multiple partner proteins, likely allowing the SecYEG translocon to process its diverse substrates. To obtain a global view on SecYEG plasticity in Escherichia coli, here we performed a quantitative interaction proteomic analysis, which identified several known SecYEG-interacting proteins, verified the interaction of SecYEG with quality-control proteins, and revealed several previously unknown putative SecYEG-interacting proteins. Surprisingly, we found that the chaperone complex PpiD/YfgM is the most prominent interaction partner of SecYEG. Detailed analyses of the PpiD-SecY interaction by site-directed cross-linking revealed that PpiD and the established SecY partner protein YidC use almost completely-overlapping binding sites on SecY. Both PpiD and YidC contacted the lateral gate, the plug domain, and the periplasmic cavity of SecY. However, quantitative MS and cross-linking analyses revealed that despite having almost identical binding sites, their binding to SecY is noncompetitive. This observation suggests that the SecYEG translocon forms different substrate-independent subassemblies in which SecYEG either associates with YidC or with the PpiD/YfgM complex. In summary, the results of this study indicate that the PpiD/YfgM chaperone complex is a primary interaction partner of the SecYEG translocon.
Collapse
Affiliation(s)
- Benjamin Jauss
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Lisa Franz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ilie Sachelaru
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Thomas Welte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
6
|
Lin A, Howbert JJ, Noble WS. Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data. J Proteome Res 2018; 17:3644-3656. [PMID: 30221945 DOI: 10.1021/acs.jproteome.8b00206] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
To achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very high-resolution information produced by state-of-the-art mass spectrometers. However, making use of this information while also ensuring that the search engine's scores are well calibrated, that is, that the score assigned to one spectrum can be meaningfully compared to the score assigned to a different spectrum, has proven to be challenging. Here we describe a database search score function, the "residue evidence" (res-ev) score, that achieves both of these goals simultaneously. We also demonstrate how to combine calibrated res-ev scores with calibrated XCorr scores to produce a "combined p value" score function. We provide a benchmark consisting of four mass spectrometry data sets, which we use to compare the combined p value to the score functions used by several existing search engines. Our results suggest that the combined p value achieves state-of-the-art performance, generally outperforming MS Amanda and Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of the Tide search engine in the Crux mass spectrometry toolkit ( http://crux.ms ).
Collapse
Affiliation(s)
- Andy Lin
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - J Jeffry Howbert
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - William Stafford Noble
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.,Department of Computer Science and Engineering , University of Washington , Seattle , Washington 98195 , United States
| |
Collapse
|
7
|
Gagné-Thivierge C, Kukavica-Ibrulj I, Filion G, Dekimpe V, Tan SGE, Vincent AT, Déziel É, Levesque RC, Charette SJ. A multi-host approach to identify a transposon mutant of Pseudomonas aeruginosa LESB58 lacking full virulence. BMC Res Notes 2018; 11:198. [PMID: 29580289 PMCID: PMC5870910 DOI: 10.1186/s13104-018-3308-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/20/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Pseudomonas aeruginosa is an opportunistic bacterial pathogen well known to cause chronic lung infections in individuals with cystic fibrosis (CF). Some strains adapted to this particular niche show distinct phenotypes, such as biofilm hyperproduction. It is necessary to study CF clinical P. aeruginosa isolates, such as Liverpool Epidemic Strains (LES), to acquire a better understanding of the key genes essential for in vivo maintenance and the major virulence mechanisms involved in CF lung infections. Previously, a library of 9216 mutants of the LESB58 strain were generated by signature-tagged mutagenesis (STM) and screened in the rat model of chronic lung infection, allowing the identification of 163 STM mutants showing defects in in vivo maintenance. RESULTS In the present study, these 163 mutants were successively screened in two additional surrogate host models (the amoeba and the fruit fly). The STM PALES_11731 mutant was the unique non-virulent in the three hosts. A competitive index study in rat lungs confirmed that the mutant was 20-fold less virulent than the wild-type strain. This study demonstrated the pertinence to use a multi-host approach to study the genetic determinants of P. aeruginosa strains infecting CF patients.
Collapse
Affiliation(s)
- Cynthia Gagné-Thivierge
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, Canada
| | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Département de microbiologie, infectiologie et immunologie, Faculté de Médecine, Université Laval, Quebec City, QC, Canada
| | - Geneviève Filion
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, Canada
| | | | - Sok Gheck E Tan
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, Canada
| | - Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, Canada
| | - Éric Déziel
- INRS-Institut Armand Frappier, Laval, QC, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Département de microbiologie, infectiologie et immunologie, Faculté de Médecine, Université Laval, Quebec City, QC, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada. .,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada. .,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, Canada.
| |
Collapse
|
8
|
Bittner LM, Arends J, Narberhaus F. When, how and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli. Biol Chem 2017; 398:625-635. [PMID: 28085670 DOI: 10.1515/hsz-2016-0302] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/09/2017] [Indexed: 11/15/2022]
Abstract
Cellular proteomes are dynamic and adjusted to permanently changing conditions by ATP-fueled proteolytic machineries. Among the five AAA+ proteases in Escherichia coli FtsH is the only essential and membrane-anchored metalloprotease. FtsH is a homohexamer that uses its ATPase domain to unfold and translocate substrates that are subsequently degraded without the need of ATP in the proteolytic chamber of the protease domain. FtsH eliminates misfolded proteins in the context of general quality control and properly folded proteins for regulatory reasons. Recent trapping approaches have revealed a number of novel FtsH substrates. This review summarizes the substrate diversity of FtsH and presents details on the surprisingly diverse recognition principles of three well-characterized substrates: LpxC, the key enzyme of lipopolysaccharide biosynthesis; RpoH, the alternative heat-shock sigma factor and YfgM, a bifunctional membrane protein implicated in periplasmic chaperone functions and cytoplasmic stress adaptation.
Collapse
Affiliation(s)
- Lisa-Marie Bittner
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| |
Collapse
|
9
|
Vazquez-Albacete D, Cavaleiro AM, Christensen U, Seppälä S, Møller BL, Nørholm MHH. An expression tag toolbox for microbial production of membrane bound plant cytochromes P450. Biotechnol Bioeng 2016; 114:751-760. [PMID: 27748524 DOI: 10.1002/bit.26203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 11/11/2022]
Abstract
Membrane-associated Cytochromes P450 (P450s) are one of the most important enzyme families for biosynthesis of plant-derived medicinal compounds. However, the hydrophobic nature of P450s makes their use in robust cell factories a challenge. Here, we explore a small library of N-terminal expression tag chimeras of the model plant P450 CYP79A1 in different Escherichia coli strains. Using a high-throughput screening platform based on C-terminal GFP fusions, we identify several highly expressing and robustly performing chimeric designs. Analysis of long-term cultures by flow cytometry showed homogeneous populations for some of the conditions. Three chimeric designs were chosen for a more complex combinatorial assembly of a multigene pathway consisting of two P450s and a redox partner. Cells expressing these recombinant enzymes catalyzed the conversion of the substrate to highly different ratios of the intermediate and the final product of the pathway. Finally, the effect of a robustly performing expression tag was explored with a library of 49 different P450s from medicinal plants and nearly half of these were improved in expression by more than twofold. The developed toolbox serves as a platform to tune P450 performance in microbial cells, thereby facilitating recombinant production of complex plant P450-derived biochemicals. Biotechnol. Bioeng. 2017;114: 751-760. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Dario Vazquez-Albacete
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Ana Mafalda Cavaleiro
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Ulla Christensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Susanna Seppälä
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.,Center for Synthetic Biology: bioSYNergy, University of Copenhagen, Copenhagen, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark.,Center for Synthetic Biology: bioSYNergy, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
10
|
De Geyter J, Tsirigotaki A, Orfanoudaki G, Zorzini V, Economou A, Karamanou S. Protein folding in the cell envelope of Escherichia coli. Nat Microbiol 2016; 1:16107. [PMID: 27573113 DOI: 10.1038/nmicrobiol.2016.107] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]
Abstract
While the entire proteome is synthesized on cytoplasmic ribosomes, almost half associates with, localizes in or crosses the bacterial cell envelope. In Escherichia coli a variety of mechanisms are important for taking these polypeptides into or across the plasma membrane, maintaining them in soluble form, trafficking them to their correct cell envelope locations and then folding them into the right structures. The fidelity of these processes must be maintained under various environmental conditions including during stress; if this fails, proteases are called in to degrade mislocalized or aggregated proteins. Various soluble, diffusible chaperones (acting as holdases, foldases or pilotins) and folding catalysts are also utilized to restore proteostasis. These responses can be general, dealing with multiple polypeptides, with functional overlaps and operating within redundant networks. Other chaperones are specialized factors, dealing only with a few exported proteins. Several complex machineries have evolved to deal with binding to, integration in and crossing of the outer membrane. This complex protein network is responsible for fundamental cellular processes such as cell wall biogenesis; cell division; the export, uptake and degradation of molecules; and resistance against exogenous toxic factors. The underlying processes, contributing to our fundamental understanding of proteostasis, are a treasure trove for the development of novel antibiotics, biopharmaceuticals and vaccines.
Collapse
Affiliation(s)
- Jozefien De Geyter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Alexandra Tsirigotaki
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Valentina Zorzini
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Spyridoula Karamanou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| |
Collapse
|
11
|
Cleary SP, Thompson AM, Prell JS. Fourier Analysis Method for Analyzing Highly Congested Mass Spectra of Ion Populations with Repeated Subunits. Anal Chem 2016; 88:6205-13. [DOI: 10.1021/acs.analchem.6b01088] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sean P. Cleary
- Department
of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Avery M. Thompson
- Department
of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S. Prell
- Department
of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| |
Collapse
|
12
|
Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
Collapse
Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
| |
Collapse
|
13
|
Bittner LM, Westphal K, Narberhaus F. Conditional Proteolysis of the Membrane Protein YfgM by the FtsH Protease Depends on a Novel N-terminal Degron. J Biol Chem 2015; 290:19367-78. [PMID: 26092727 DOI: 10.1074/jbc.m115.648550] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/16/2023] Open
Abstract
Regulated proteolysis efficiently and rapidly adapts the bacterial proteome to changing environmental conditions. Many protease substrates contain recognition motifs, so-called degrons, that direct them to the appropriate protease. Here we describe an entirely new degron identified in the cytoplasmic N-terminal end of the membrane-anchored protein YfgM of Escherichia coli. YfgM is stable during exponential growth and degraded in stationary phase by the essential FtsH protease. The alarmone (p)ppGpp, but not the previously described YfgM interactors RcsB and PpiD, influence YfgM degradation. By scanning mutagenesis, we define individual amino acids responsible for turnover of YfgM and find that the degron does not at all comply with the known N-end rule pathway. The YfgM degron is a distinct module that facilitates FtsH-mediated degradation when fused to the N terminus of another monotopic membrane protein but not to that of a cytoplasmic protein. Several lines of evidence suggest that stress-induced degradation of YfgM relieves the response regulator RcsB and thereby permits cellular protection by the Rcs phosphorelay system. On the basis of these and other results in the literature, we propose a model for how the membrane-spanning YfgM protein serves as connector between the stress responses in the periplasm and cytoplasm.
Collapse
Affiliation(s)
| | - Kai Westphal
- From Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Franz Narberhaus
- From Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
| |
Collapse
|