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Karbelkar AA, Font M, Smith TJ, Sondermann H, O’Toole GA. Reconstitution of a biofilm adhesin system from a sulfate-reducing bacterium in Pseudomonas fluorescens. Proc Natl Acad Sci U S A 2024; 121:e2320410121. [PMID: 38498718 PMCID: PMC10990149 DOI: 10.1073/pnas.2320410121] [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] [Received: 11/20/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Biofilms of sulfate-reducing bacterium (SRB) like Desulfovibrio vulgaris Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses. Although the mechanisms of biofilm formation by DvH are not yet well understood, recent studies indicate the large adhesin, DvhA, is a key determinant of biofilm formation. The dvhA gene neighborhood resembles the biofilm-regulating Lap system of Pseudomonas fluorescens but is curiously missing the c-di-GMP-binding regulator LapD. Instead, DvH encodes an evolutionarily unrelated c-di-GMP-binding protein (DVU1020) that we hypothesized is functionally analogous to LapD. To study this unusual Lap system and overcome experimental limitations with the slow-growing anaerobe DvH, we reconstituted its predicted SRB Lap system in a P. fluorescens strain lacking its native Lap regulatory components (ΔlapGΔlapD). Our data support the model that DvhA is a cell surface-associated LapA-like adhesin with a N-terminal "retention module" and that DvhA is released from the cell surface upon cleavage by the LapG-like protease DvhG. Further, we demonstrate DVU1020 (named here DvhD) represents a distinct class of c-di-GMP-binding, biofilm-regulating proteins that regulates DvhG activity in response to intracellular levels of this second messenger. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.
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Affiliation(s)
- Amruta A. Karbelkar
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
| | - Maria Font
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, D-22607Hamburg, Germany
| | - T. Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, D-22607Hamburg, Germany
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH03755
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Karbelkar AA, Font ME, Smith TJ, Sondermann H, O’Toole GA. Reconstitution of a Biofilm Adhesin System from a Sulfate-Reducing Bacterium in Pseudomonas fluorescens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568322. [PMID: 38045380 PMCID: PMC10690286 DOI: 10.1101/2023.11.22.568322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Biofilms of the sulfate reducing bacterium (SRB) Desulfovibrio vulgaris Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses; however, the mechanisms of biofilm formation by DvH are not yet well-understood. Evidence suggests that a large adhesin, DvhA, may be contributing to biofilm formation in DvH. The dvhA gene and its neighbors encode proteins that resemble the Lap system, which regulates biofilm formation by Pseudomonas fluorescens, including a LapG-like protease DvhG and effector protein DvhD, which has key differences from the previously described LapD. By expressing the Lap-like adhesion components of DvH in P. fluorescens, our data support the model that the N-terminal fragment of the large adhesin DvhA serves as an adhesin "retention module" and is the target of the DvhG/DvhD regulatory module, thereby controlling cell-surface location of the adhesin. By heterologously expressing the DvhG/DvhD-like proteins in a P. fluorescens background lacking native regulation (ΔlapGΔlapD) we also show that cell surface regulation of the adhesin is dependent upon the intracellular levels of c-di-GMP. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.
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Affiliation(s)
- Amruta A. Karbelkar
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Maria E. Font
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Germany
| | - T. Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Germany
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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3
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Singh SB, Carroll-Portillo A, Lin HC. Desulfovibrio in the Gut: The Enemy within? Microorganisms 2023; 11:1772. [PMID: 37512944 PMCID: PMC10383351 DOI: 10.3390/microorganisms11071772] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Desulfovibrio (DSV) are sulfate-reducing bacteria (SRB) that are ubiquitously present in the environment and as resident commensal bacteria within the human gastrointestinal tract. Though they are minor residents of the healthy gut, DSV are opportunistic pathobionts that may overgrow in the setting of various intestinal and extra-intestinal diseases. An increasing number of studies have demonstrated a positive correlation between DSV overgrowth (bloom) and various human diseases. While the relationship between DSV bloom and disease pathology has not been clearly established, mounting evidence suggests a causal role for these bacteria in disease development. As DSV are the most predominant genera of SRB in the gut, this review summarizes current knowledge regarding the relationship between DSV and a variety of diseases. In this study, we also discuss the mechanisms by which these bacteria may contribute to disease pathology.
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Affiliation(s)
- Sudha B Singh
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, USA
| | - Amanda Carroll-Portillo
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Henry C Lin
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM 87131, USA
- Medicine Service, New Mexico VA Health Care System, Albuquerque, NM 87108, USA
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4
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Scherhag A, Räschle M, Unbehend N, Venn B, Glueck D, Mühlhaus T, Keller S, Pérez Patallo E, Zehner S, Frankenberg-Dinkel N. Characterization of a soluble library of the Pseudomonas aeruginosa PAO1 membrane proteome with emphasis on c-di-GMP turnover enzymes. MICROLIFE 2023; 4:uqad028. [PMID: 37441524 PMCID: PMC10335732 DOI: 10.1093/femsml/uqad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/30/2023] [Indexed: 07/15/2023]
Abstract
Studies of protein-protein interactions in membranes are very important to fully understand the biological function of a cell. The extraction of proteins from the native membrane environment is a critical step in the preparation of membrane proteins that might affect the stability of protein complexes. In this work, we used the amphiphilic diisobutylene/maleic acid copolymer to extract the membrane proteome of the opportunistic pathogen Pseudomonas aeruginosa, thereby creating a soluble membrane-protein library within a native-like lipid-bilayer environment. Size fractionation of nanodisc-embedded proteins and subsequent mass spectrometry enabled the identification of 3358 proteins. The native membrane-protein library showed a very good overall coverage compared to previous proteome data. The pattern of size fractionation indicated that protein complexes were preserved in the library. More than 20 previously described complexes, e.g. the SecYEG and Pili complexes, were identified and analyzed for coelution. Although the mass-spectrometric dataset alone did not reveal new protein complexes, combining pulldown assays with mass spectrometry was successful in identifying new protein interactions in the native membrane-protein library. Thus, we identified several candidate proteins for interactions with the membrane phosphodiesterase NbdA, a member of the c-di-GMP network. We confirmed the candidate proteins CzcR, PA4200, SadC, and PilB as novel interaction partners of NbdA using the bacterial adenylate cyclase two-hybrid assay. Taken together, this work demonstrates the usefulness of the native membrane-protein library of P. aeruginosa for the investigation of protein interactions and membrane-protein complexes. Data are available via ProteomeXchange with identifiers PXD039702 and PXD039700.
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Affiliation(s)
- Anna Scherhag
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Markus Räschle
- Department of Molecular Genetics, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Niklas Unbehend
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Benedikt Venn
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - David Glueck
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Timo Mühlhaus
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Sandro Keller
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Eugenio Pérez Patallo
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | | | - Nicole Frankenberg-Dinkel
- Corresponding author. RPTU Kaiserslautern-Landau, Microbiology, Kaiserslautern 67655, Germany. E-mail:
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5
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Barton LL, Duarte AG, Staicu LC. Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments. Biometals 2023; 36:339-350. [PMID: 35767096 DOI: 10.1007/s10534-022-00410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.
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Affiliation(s)
- Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM, 87131, USA
| | - Americo G Duarte
- Instituto de Tecnologia Química E Biológica António Xavier/Universidade NOVA de Lisboa, Av. República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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6
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Young JW, Zhao Z, Wason IS, Duong van Hoa F. A Dual Detergent Strategy to Capture a Bacterial Outer Membrane Proteome in Peptidiscs for Characterization by Mass Spectrometry and Binding Assays. J Proteome Res 2022; 22:1537-1545. [PMID: 36516475 DOI: 10.1021/acs.jproteome.2c00560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outer membrane of Gram-negative bacteria plays a critical role in protecting the cell against external stressors, including antibiotics, and therefore is a prime target for antimicrobial discovery. To facilitate the discovery efforts, a precise knowledge of the outer membrane proteome, and possible variations during pathogenesis, is important. Characterization of the bacterial outer membrane remain challenging, however, and low throughput, due to the high hydrophobicity and relatively low abundance of this cell compartment. Here we adapt our peptidisc-based method to selectively isolate the outer membrane proteome before analysis by mass spectrometry. Using a dual detergent membrane solubilization approach, followed by protein purification in peptidiscs, we capture over 70 outer membrane proteins, including 26 integral β-barrels and 26 lipoproteins. Many of these proteins are present at high peptide intensities, indicative of a high abundance in the library sample. We further show that the isolated outer membrane proteome can be employed in downstream ligand-binding assays. This peptidisc library made of outer membrane proteins may therefore be useful to systematically survey other bacterial outer membrane proteomes, but also as a nanoparticle format able to support the discovery of next-generation antimicrobials. Data are available via ProteomeXchange identifier PXD036749.
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Affiliation(s)
- John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Irvinder Singh Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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7
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Rahman MA, Heme UH, Parvez MAK. In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments. PLoS One 2022; 17:e0276085. [PMID: 36228026 PMCID: PMC9560612 DOI: 10.1371/journal.pone.0276085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2022] Open
Abstract
Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins' potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.
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Affiliation(s)
- Md. Atikur Rahman
- Institute of Microbiology, Friedrich Schiller University Jena, Thuringia, Germany
| | - Uzma Habiba Heme
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Thuringia, Germany
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8
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Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris. ISME JOURNAL 2020; 14:2862-2876. [PMID: 32934357 DOI: 10.1038/s41396-020-00753-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 11/08/2022]
Abstract
Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.
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Salas D, Stacey RG, Akinlaja M, Foster LJ. Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks. Mol Cell Proteomics 2020; 19:1-10. [PMID: 31792070 PMCID: PMC6944233 DOI: 10.1074/mcp.r119.001803] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/26/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding how proteins interact is crucial to understanding cellular processes. Among the available interactome mapping methods, co-elution stands out as a method that is simultaneous in nature and capable of identifying interactions between all the proteins detected in a sample. The general workflow in co-elution methods involves the mild extraction of protein complexes and their separation into several fractions, across which proteins bound together in the same complex will show similar co-elution profiles when analyzed appropriately. In this review we discuss the different separation, quantification and bioinformatic strategies used in co-elution studies, and the important considerations in designing these studies. The benefits of co-elution versus other methods makes it a valuable starting point when asking questions that involve the perturbation of the interactome.
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Affiliation(s)
- Daniela Salas
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | - R Greg Stacey
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Mopelola Akinlaja
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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da Costa WLO, Araújo CLDA, Dias LM, Pereira LCDS, Alves JTC, Araújo FA, Folador EL, Henriques I, Silva A, Folador ARC. Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PLoS One 2018; 13:e0198965. [PMID: 29940001 PMCID: PMC6016940 DOI: 10.1371/journal.pone.0198965] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023] Open
Abstract
Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of this bacterium, and the use of bioinformatics tools can assist in the biological understanding of this organism through functional annotation analysis. Thus, our study aimed to assign functions to proteins previously described as HPs, present in the genome of E. antarcticum B7. We used an extensive in silico workflow combining several bioinformatics tools for function annotation, sub-cellular localization and physicochemical characterization, three-dimensional structure determination, and protein-protein interactions. This genome contains 2772 genes, of which 765 CDS were annotated as HPs. The amino acid sequences of all HPs were submitted to our workflow and we successfully attributed function to 132 HPs. We identified 11 proteins that play important roles in the mechanisms of adaptation to adverse environments, such as flagellar biosynthesis, biofilm formation, carotenoids biosynthesis, and others. In addition, three predicted HPs are possibly related to arsenic tolerance. Through an in vitro assay, we verified that E. antarcticum B7 can grow at high concentrations of this metal. The approach used was important to precisely assign function to proteins from diverse classes and to infer relationships with proteins with functions already described in the literature. This approach aims to produce a better understanding of the mechanism by which this bacterium adapts to extreme environments and to the finding of targets with biotechnological interest.
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Affiliation(s)
- Wana Lailan Oliveira da Costa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Carlos Leonardo de Aragão Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Larissa Maranhão Dias
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Lino César de Sousa Pereira
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Jorianne Thyeska Castro Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Fabrício Almeida Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraiba, João Pessoa, Paraíba, Brazil
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
- * E-mail: ,
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12
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Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. J Bacteriol 2017; 199:JB.00286-17. [PMID: 28874410 PMCID: PMC5686591 DOI: 10.1128/jb.00286-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
Due in large part to their ability to facilitate the diffusion of a diverse range of solutes across the outer membrane (OM) of Gram-negative bacteria, the porins represent one of the most prominent and important bacterial membrane protein superfamilies. Notably, for the Gram-negative bacterium Desulfovibrio vulgaris Hildenborough, a model organism for studies of sulfate-reducing bacteria, no genes for porins have been identified or proposed in its annotated genome. Results from initial biochemical studies suggested that the product of the DVU0799 gene, which is one of the most abundant proteins of the D. vulgaris Hildenborough OM and purified as a homotrimeric complex, was a strong porin candidate. To investigate this possibility, this protein was further characterized biochemically and biophysically. Structural analyses via electron microscopy of negatively stained protein identified trimeric particles with stain-filled depressions and structural modeling suggested a β-barrel structure for the monomer, motifs common among the known porins. Functional studies were performed in which crude OM preparations or purified DVU0799 was reconstituted into proteoliposomes and the proteoliposomes were examined for permeability against a series of test solutes. The results obtained establish DVU0799 to be a pore-forming protein with permeability properties similar to those observed for classical bacterial porins, such as those of Escherichia coli. Taken together, these findings identify this highly abundant OM protein to be the major porin of D. vulgaris Hildenborough. Classification of DVU0799 in this model organism expands the database of functionally characterized porins and may also extend the range over which sequence analysis strategies can be used to identify porins in other bacterial genomes. IMPORTANCE Porins are membrane proteins that form transmembrane pores for the passive transport of small molecules across the outer membranes of Gram-negative bacteria. The present study identified and characterized the major porin of the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, observing its preference for anionic sugars over neutral ones. Its predicted architecture appears to be novel for a classical porin, as its core β-barrel structure is of a type typically found in solute-specific channels. Broader use of the methods employed here, such as assays for channel permeability and electron microscopy of purified samples, is expected to help expand the database of confirmed porin sequences and improve the range over which sequence analysis-based strategies can be used to identify porins in other Gram-negative bacteria. Functional characterization of these critical gatekeeping proteins from divergent Desulfovibrio species should offer an improved understanding of the physiological features that determine their habitat range and supporting activities.
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De León KB, Zane GM, Trotter VV, Krantz GP, Arkin AP, Butland GP, Walian PJ, Fields MW, Wall JD. Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough. mBio 2017; 8:e01696-17. [PMID: 29042504 PMCID: PMC5646257 DOI: 10.1128/mbio.01696-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 12/28/2022] Open
Abstract
Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D. vulgaris Hildenborough. Two T1SS cargo proteins were identified as likely biofilm structural proteins, and the presence of at least one (with either being sufficient) was shown to be required for biofilm formation. Antibodies specific to these biofilm structural proteins confirmed that DVU1017, and thus the T1SS, is essential for localization of these adhesion proteins on the cell surface. We propose that DVU1017 is a member of the lapB category of microbial surface proteins because of its phenotypic similarity to the adhesin export system described for biofilm formation in the environmental pseudomonads. These findings have led to the identification of two functions required for biofilm formation in D. vulgaris Hildenborough and focus attention on the importance of monitoring laboratory-driven evolution, as phenotypes as fundamental as biofilm formation can be altered.IMPORTANCE The growth of bacteria attached to a surface (i.e., biofilm), specifically biofilms of sulfate-reducing bacteria, has a profound impact on the economy of developed nations due to steel and concrete corrosion in industrial pipelines and processing facilities. Furthermore, the presence of sulfate-reducing bacteria in oil wells causes oil souring from sulfide production, resulting in product loss, a health hazard to workers, and ultimately abandonment of wells. Identification of the required genes is a critical step for determining the mechanism of biofilm formation by sulfate reducers. Here, the transporter by which putative biofilm structural proteins are exported from sulfate-reducing Desulfovibrio vulgaris Hildenborough cells was discovered, and a single nucleotide change within the gene coding for this transporter was found to be sufficient to completely stop formation of biofilm.
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Affiliation(s)
- Kara B De León
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Valentine V Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Gregory P Krantz
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Gareth P Butland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Peter J Walian
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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Gagarinova A, Phanse S, Cygler M, Babu M. Insights from protein-protein interaction studies on bacterial pathogenesis. Expert Rev Proteomics 2017; 14:779-797. [DOI: 10.1080/14789450.2017.1365603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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15
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Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics 2016; 15:2186-202. [PMID: 27099342 PMCID: PMC5083090 DOI: 10.1074/mcp.m115.057117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/18/2023] Open
Abstract
Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.
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Affiliation(s)
- Maxim Shatsky
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Ming Dong
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Haichuan Liu
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Lee Lisheng Yang
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Megan Choi
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mary E Singer
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jil T Geller
- **Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Susan J Fisher
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Steven C Hall
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - Terry C Hazen
- ‡‡Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996; §§Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Steven E Brenner
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; ¶¶Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Gareth Butland
- ‖‖Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian Jin
- ‖Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - H Ewa Witkowska
- ¶OB/GYN Department, University of California San Francisco-Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, California 94143
| | - John-Marc Chandonia
- From the ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Mark D Biggin
- §Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
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16
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Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics 2016; 15:1539-55. [PMID: 26873250 DOI: 10.1074/mcp.m115.054692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/31/2023] Open
Abstract
Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates. In addition, our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.
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Affiliation(s)
- Maxim Shatsky
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Simon Allen
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Barbara L Gold
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Nancy L Liu
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Thomas R Juba
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - Sonia A Reveco
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Dwayne A Elias
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Ramadevi Prathapam
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jennifer He
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Wenhong Yang
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Evelin D Szakal
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Haichuan Liu
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mary E Singer
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jil T Geller
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Bonita R Lam
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Avneesh Saini
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Valentine V Trotter
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Steven C Hall
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Susan J Fisher
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Steven E Brenner
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; the Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, 94720
| | - Swapnil R Chhabra
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Terry C Hazen
- the Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, 37996; and
| | - Judy D Wall
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - H Ewa Witkowska
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mark D Biggin
- the Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - John-Marc Chandonia
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
| | - Gareth Butland
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
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17
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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18
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Alfonso-Garrido J, Garcia-Calvo E, Luque-Garcia JL. Sample preparation strategies for improving the identification of membrane proteins by mass spectrometry. Anal Bioanal Chem 2015; 407:4893-905. [PMID: 25967148 DOI: 10.1007/s00216-015-8732-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/15/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]
Abstract
Despite enormous advances in the mass spectrometry and proteomics fields during the last two decades, the analysis of membrane proteins still remains a challenge for the proteomic community. Membrane proteins play a wide number of key roles in several cellular events, making them relevant target molecules to study in a significant variety of investigations (e.g., cellular signaling, immune surveillance, drug targets, vaccine candidates, etc.). Here, we critically review the several attempts that have been carried out on the different steps of the sample preparation procedure to improve and modify existing conventional proteomic strategies in order to make them suitable for the study of membrane proteins. We also revise novel techniques that have been designed to tackle the difficult but relevant task of identifying and characterizing membrane proteins.
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Affiliation(s)
- Javier Alfonso-Garrido
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28004, Madrid, Spain
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19
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Korte HL, Fels SR, Christensen GA, Price MN, Kuehl JV, Zane GM, Deutschbauer AM, Arkin AP, Wall JD. Genetic basis for nitrate resistance in Desulfovibrio strains. Front Microbiol 2014; 5:153. [PMID: 24795702 PMCID: PMC4001038 DOI: 10.3389/fmicb.2014.00153] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/21/2014] [Indexed: 12/31/2022] Open
Abstract
Nitrate is an inhibitor of sulfate-reducing bacteria (SRB). In petroleum production sites, amendments of nitrate and nitrite are used to prevent SRB production of sulfide that causes souring of oil wells. A better understanding of nitrate stress responses in the model SRB, Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, will strengthen predictions of environmental outcomes of nitrate application. Nitrate inhibition of SRB has historically been considered to result from the generation of small amounts of nitrite, to which SRB are quite sensitive. Here we explored the possibility that nitrate might inhibit SRB by a mechanism other than through nitrite inhibition. We found that nitrate-stressed D. vulgaris cultures grown in lactate-sulfate conditions eventually grew in the presence of high concentrations of nitrate, and their resistance continued through several subcultures. Nitrate consumption was not detected over the course of the experiment, suggesting adaptation to nitrate. With high-throughput genetic approaches employing TnLE-seq for D. vulgaris and a pooled mutant library of D. alaskensis, we determined the fitness of many transposon mutants of both organisms in nitrate stress conditions. We found that several mutants, including homologs present in both strains, had a greatly increased ability to grow in the presence of nitrate but not nitrite. The mutated genes conferring nitrate resistance included the gene encoding the putative Rex transcriptional regulator (DVU0916/Dde_2702), as well as a cluster of genes (DVU0251-DVU0245/Dde_0597-Dde_0605) that is poorly annotated. Follow-up studies with individual D. vulgaris transposon and deletion mutants confirmed high-throughput results. We conclude that, in D. vulgaris and D. alaskensis, nitrate resistance in wild-type cultures is likely conferred by spontaneous mutations. Furthermore, the mechanisms that confer nitrate resistance may be different from those that confer nitrite resistance.
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Affiliation(s)
- Hannah L Korte
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Samuel R Fels
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA
| | - Geoff A Christensen
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Morgan N Price
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jennifer V Kuehl
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Adam M Deutschbauer
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Adam P Arkin
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA
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Carlson HK, Iavarone AT, Coates JD. Surfaceomics and surface-enhanced Raman spectroscopy of environmental microbes: Matching cofactors with redox-active surface proteins. Proteomics 2013; 13:2761-5. [DOI: 10.1002/pmic.201300010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/12/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Hans K. Carlson
- Department of Plant and Microbial Biology; University of California; Berkeley CA USA
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility; University of California; Berkeley CA USA
| | - John D. Coates
- Department of Plant and Microbial Biology; University of California; Berkeley CA USA
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