1
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Gladysheva-Azgari M, Sharko F, Evteeva M, Kuvyrchenkova A, Boulygina E, Tsygankova S, Slobodova N, Pustovoit K, Melkina O, Nedoluzhko A, Korzhenkov A, Kudryavtseva A, Utkina A, Manukhov I, Rastorguev S, Zavilgelsky G. ArdA genes from pKM101 and from B. bifidum chromosome have a different range of regulated genes. Heliyon 2023; 9:e22986. [PMID: 38144267 PMCID: PMC10746416 DOI: 10.1016/j.heliyon.2023.e22986] [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: 04/17/2023] [Revised: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
The ardA genes are present in a wide variety of conjugative plasmids and play an important role in overcoming the restriction barrier. To date, there is no information on the chromosomal ardA genes. It is still unclear whether they keep their antirestriction activity and why bacterial chromosomes contain these genes. In the present study, we confirmed the antirestriction function of the ardA gene from the Bifidobacterium bifidum chromosome. Transcriptome analysis in Escherichia coli showed that the range of regulated genes varies significantly for ardA from conjugative plasmid pKM101 and from the B. bifidum chromosome. Moreover, if the targets for both ardA genes match, they often show an opposite effect on regulated gene expression. The results obtained indicate two seemingly mutually exclusive conclusions. On the one hand, the pleiotropic effect of ardA genes was shown not only on restriction-modification system, but also on expression of a number of other genes. On the other hand, the range of affected genes varies significally for ardA genes from different sources, which indicates the specificity of ardA to inhibited targets. Author Summary. Conjugative plasmids, bacteriophages, as well as transposons, are capable to transfer various genes, including antibiotic resistance genes, among bacterial cells. However, many of those genes pose a threat to the bacterial cells, therefore bacterial cells have special restriction systems that limit such transfer. Antirestriction genes have previously been described as a part of conjugative plasmids, and bacteriophages and transposons. Those plasmids are able to overcome bacterial cell protection in the presence of antirestriction genes, which inhibit bacterial restriction systems. This work unveils the antirestriction mechanisms, which play an important role in the bacterial life cycle. Here, we clearly show that antirestriction genes, which are able to inhibit cell protection, exist not only in plasmids but also in the bacterial chromosomes themselves. Moreover, antirestrictases have not only an inhibitory function but also participate in the regulation of other bacterial genes. The regulatory function of plasmid antirestriction genes also helps them to overcome the bacterial cell protection against gene transfer, whereas the regulatory function of genomic antirestrictases has no such effect.
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Affiliation(s)
| | - F.S. Sharko
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - M.A. Evteeva
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | | | - E.S. Boulygina
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - S.V. Tsygankova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - N.V. Slobodova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - K.S. Pustovoit
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - O.E. Melkina
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - A.V. Nedoluzhko
- European University at Saint Petersburg, 191187, Saint-Petersburg, Russia
| | - A.A. Korzhenkov
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - A.A. Kudryavtseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - A.A. Utkina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - I.V. Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
- Faculty of Physics, HSE University, 109028, Moscow, Russia
- Laboratory for Microbiology, BIOTECH University, 125080, Moscow, Russia
| | - S.M. Rastorguev
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova Str. 1, Moscow, 117997, Russia
| | - G.B. Zavilgelsky
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
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2
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Goojani HG, Besharati S, Chauhan P, Asseri AH, Lill H, Bald D. Cytochrome bd-I from Escherichia coli is catalytically active in the absence of the CydH subunit. FEBS Lett 2023; 597:547-556. [PMID: 36460943 DOI: 10.1002/1873-3468.14550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022]
Abstract
Cytochrome bd-I from Escherichia coli is a terminal oxidase in the respiratory chain that plays an important role under stress conditions. Cytochrome bd-I was thought to consist of the major subunits CydA and CydB plus the small CydX subunit. Recent high-resolution structures of cytochrome bd-I demonstrated the presence of an additional subunit, CydH/CydY (called CydH here), the function of which is unclear. In this report, we show that in the absence of CydH, cytochrome bd-I is catalytically active, can sustain bacterial growth and displays haem spectra and susceptibility for haem-binding inhibitors comparable to the wild-type enzyme. Removal of CydH did not elicit catalase activity of cytochrome bd-I in our experimental system. Taken together, in the absence of the CydH subunit cytochrome bd-I retained key enzymatic properties.
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Affiliation(s)
- Hojjat Ghasemi Goojani
- Faculty of Science, Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Vrije Universiteit Amsterdam, The Netherlands
| | - Samira Besharati
- Faculty of Science, Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Vrije Universiteit Amsterdam, The Netherlands
| | - Priyanka Chauhan
- Faculty of Science, Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Vrije Universiteit Amsterdam, The Netherlands
| | - Amer H Asseri
- Faculty of Science, Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Vrije Universiteit Amsterdam, The Netherlands.,Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Holger Lill
- Faculty of Science, Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Vrije Universiteit Amsterdam, The Netherlands
| | - Dirk Bald
- Faculty of Science, Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Vrije Universiteit Amsterdam, The Netherlands
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3
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Friedrich T, Wohlwend D, Borisov VB. Recent Advances in Structural Studies of Cytochrome bd and Its Potential Application as a Drug Target. Int J Mol Sci 2022; 23:ijms23063166. [PMID: 35328590 PMCID: PMC8951039 DOI: 10.3390/ijms23063166] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Cytochrome bd is a triheme copper-free terminal oxidase in membrane respiratory chains of prokaryotes. This unique molecular machine couples electron transfer from quinol to O2 with the generation of a proton motive force without proton pumping. Apart from energy conservation, the bd enzyme plays an additional key role in the microbial cell, being involved in the response to different environmental stressors. Cytochrome bd promotes virulence in a number of pathogenic species that makes it a suitable molecular drug target candidate. This review focuses on recent advances in understanding the structure of cytochrome bd and the development of its selective inhibitors.
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Affiliation(s)
- Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany; (T.F.); (D.W.)
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany; (T.F.); (D.W.)
| | - Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
- Correspondence:
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4
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Yadavalli SS, Yuan J. Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer. J Bacteriol 2022; 204:e0034421. [PMID: 34516282 PMCID: PMC8765417 DOI: 10.1128/jb.00344-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small membrane proteins represent a subset of recently discovered small proteins (≤100 amino acids), which are a ubiquitous class of emerging regulators underlying bacterial adaptation to environmental stressors. Until relatively recently, small open reading frames encoding these proteins were not designated genes in genome annotations. Therefore, our understanding of small protein biology was primarily limited to a few candidates associated with previously characterized larger partner proteins. Following the first systematic analyses of small proteins in Escherichia coli over a decade ago, numerous small proteins across different bacteria have been uncovered. An estimated one-third of these newly discovered proteins in E. coli are localized to the cell membrane, where they may interact with distinct groups of membrane proteins, such as signal receptors, transporters, and enzymes, and affect their activities. Recently, there has been considerable progress in functionally characterizing small membrane protein regulators aided by innovative tools adapted specifically to study small proteins. Our review covers prototypical proteins that modulate a broad range of cellular processes, such as transport, signal transduction, stress response, respiration, cell division, sporulation, and membrane stability. Thus, small membrane proteins represent a versatile group of physiology regulators at the membrane and the whole cell. Additionally, small membrane proteins have the potential for clinical applications, where some of the proteins may act as antibacterial agents themselves while others serve as alternative drug targets for the development of novel antimicrobials.
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Affiliation(s)
- Srujana S. Yadavalli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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5
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Gelhausen R, Müller T, Svensson SL, Alkhnbashi OS, Sharma CM, Eggenhofer F, Backofen R. RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. Brief Bioinform 2022; 23:6509045. [PMID: 35037022 PMCID: PMC8921622 DOI: 10.1093/bib/bbab549] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
Small proteins encoded by short open reading frames (ORFs) with 50 codons or fewer are emerging as an important class of cellular macromolecules in diverse organisms. However, they often evade detection by proteomics or in silico methods. Ribosome profiling (Ribo-seq) has revealed widespread translation in genomic regions previously thought to be non-coding, driving the development of ORF detection tools using Ribo-seq data. However, only a handful of tools have been designed for bacteria, and these have not yet been systematically compared. Here, we aimed to identify tools that use Ribo-seq data to correctly determine the translational status of annotated bacterial ORFs and also discover novel translated regions with high sensitivity. To this end, we generated a large set of annotated ORFs from four diverse bacterial organisms, manually labeled for their translation status based on Ribo-seq data, which are available for future benchmarking studies. This set was used to investigate the predictive performance of seven Ribo-seq-based ORF detection tools (REPARATION_blast, DeepRibo, Ribo-TISH, PRICE, smORFer, ribotricer and SPECtre), as well as IRSOM, which uses coding potential and RNA-seq coverage only. DeepRibo and REPARATION_blast robustly predicted translated ORFs, including sORFs, with no significant difference for ORFs in close proximity to other genes versus stand-alone genes. However, no tool predicted a set of novel, experimentally verified sORFs with high sensitivity. Start codon predictions with smORFer show the value of initiation site profiling data to further improve the sensitivity of ORF prediction tools in bacteria. Overall, we find that bacterial tools perform well for sORF detection, although there is potential for improving their performance, applicability, usability and reproducibility.
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Affiliation(s)
- Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany
| | - Teresa Müller
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany
| | - Sarah L Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2 / D15, 97080, Würzburg, Germany
| | - Omer S Alkhnbashi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany
| | - Cynthia M Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2 / D15, 97080, Würzburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, State, Germany
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6
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Abstract
Escherichia coli was one of the first species to have its genome sequenced and remains one of the best-characterized model organisms. Thus, it is perhaps surprising that recent studies have shown that a substantial number of genes have been overlooked. Genes encoding more than 140 small proteins, defined as those containing 50 or fewer amino acids, have been identified in E. coli in the past 10 years, and there is substantial evidence indicating that many more remain to be discovered. This review covers the methods that have been successful in identifying small proteins and the short open reading frames that encode them. The small proteins that have been functionally characterized to date in this model organism are also discussed. It is hoped that the review, along with the associated databases of known as well as predicted but undetected small proteins, will aid in and provide a roadmap for the continued identification and characterization of these proteins in E. coli as well as other bacteria.
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7
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Borisov VB, Siletsky SA, Paiardini A, Hoogewijs D, Forte E, Giuffrè A, Poole RK. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets. Antioxid Redox Signal 2021; 34:1280-1318. [PMID: 32924537 PMCID: PMC8112716 DOI: 10.1089/ars.2020.8039] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022]
Abstract
Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria formally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, peroxynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase. Since cytochrome bd is a uniquely bacterial enzyme, future research should focus on harnessing fundamental knowledge of its structure and function to the development of novel and effective antibacterial agents.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - David Hoogewijs
- Department of Medicine/Physiology, University of Fribourg, Fribourg, Switzerland
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
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8
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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9
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Garai P, Blanc‐Potard A. Uncovering small membrane proteins in pathogenic bacteria: Regulatory functions and therapeutic potential. Mol Microbiol 2020; 114:710-720. [DOI: 10.1111/mmi.14564] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Preeti Garai
- Laboratory of Pathogen‐Host Interactions Université de MontpellierCNRS‐UMR5235 Montpellier France
| | - Anne Blanc‐Potard
- Laboratory of Pathogen‐Host Interactions Université de MontpellierCNRS‐UMR5235 Montpellier France
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10
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Oxidative Phosphorylation—an Update on a New, Essential Target Space for Drug Discovery in Mycobacterium tuberculosis. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072339] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New drugs with new mechanisms of action are urgently required to tackle the global tuberculosis epidemic. Following the FDA-approval of the ATP synthase inhibitor bedaquiline (Sirturo®), energy metabolism has become the subject of intense focus as a novel pathway to exploit for tuberculosis drug development. This enthusiasm stems from the fact that oxidative phosphorylation (OxPhos) and the maintenance of the transmembrane electrochemical gradient are essential for the viability of replicating and non-replicating Mycobacterium tuberculosis (M. tb), the etiological agent of human tuberculosis (TB). Therefore, new drugs targeting this pathway have the potential to shorten TB treatment, which is one of the major goals of TB drug discovery. This review summarises the latest and key findings regarding the OxPhos pathway in M. tb and provides an overview of the inhibitors targeting various components. We also discuss the potential of new regimens containing these inhibitors, the flexibility of this pathway and, consequently, the complexity in targeting it. Lastly, we discuss opportunities and future directions of this drug target space.
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11
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Orr MW, Mao Y, Storz G, Qian SB. Alternative ORFs and small ORFs: shedding light on the dark proteome. Nucleic Acids Res 2020; 48:1029-1042. [PMID: 31504789 DOI: 10.1093/nar/gkz734] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/03/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Traditional annotation of protein-encoding genes relied on assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it is becoming clear that these initial assumptions are incorrect. The findings have led to the realization that genetic information is more densely coded and that the proteome is more complex than previously anticipated. As such, interest in the identification and characterization of the previously ignored 'dark proteome' is increasing, though we note that research in eukaryotes and bacteria has largely progressed in isolation. To bridge this gap and illustrate exciting findings emerging from studies of the dark proteome, we highlight recent advances in both eukaryotic and bacterial cells. We discuss progress in the detection of alternative ORFs as well as in the understanding of functions and the regulation of their expression and posit questions for future work.
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Affiliation(s)
- Mona Wu Orr
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
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12
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Theßeling A, Burschel S, Wohlwend D, Friedrich T. The long Q‐loop ofEscherichia colicytochromebdoxidase is required for assembly and structural integrity. FEBS Lett 2020; 594:1577-1585. [DOI: 10.1002/1873-3468.13749] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 11/08/2022]
Affiliation(s)
| | - Sabrina Burschel
- Institut für Biochemie Albert‐Ludwigs‐Universität Freiburg Germany
| | - Daniel Wohlwend
- Institut für Biochemie Albert‐Ludwigs‐Universität Freiburg Germany
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13
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Goojani HG, Konings J, Hakvoort H, Hong S, Gennis RB, Sakamoto J, Lill H, Bald D. The carboxy-terminal insert in the Q-loop is needed for functionality of Escherichia coli cytochrome bd-I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148175. [PMID: 32061652 DOI: 10.1016/j.bbabio.2020.148175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/24/2020] [Accepted: 02/10/2020] [Indexed: 12/27/2022]
Abstract
Cytochrome bd, a component of the prokaryotic respiratory chain, is important under physiological stress and during pathogenicity. Electrons from quinol substrates are passed on via heme groups in the CydA subunit and used to reduce molecular oxygen. Close to the quinol binding site, CydA displays a periplasmic hydrophilic loop called Q-loop that is essential for quinol oxidation. In the carboxy-terminal part of this loop, CydA from Escherichia coli and other proteobacteria harbors an insert of ~60 residues with unknown function. In the current work, we demonstrate that growth of the multiple-deletion strain E. coli MB43∆cydA (∆cydA∆cydB∆appB∆cyoB∆nuoB) can be enhanced by transformation with E. coli cytochrome bd-I and we utilize this system for assessment of Q-loop mutants. Deletion of the cytochrome bd-I Q-loop insert abolished MB43∆cydA growth recovery. Swapping the cytochrome bd-I Q-loop for the Q-loop from Geobacillus thermodenitrificans or Mycobacterium tuberculosis CydA, which lack the insert, did not enhance the growth of MB43∆cydA, whereas swapping for the Q-loop from E. coli cytochrome bd-II recovered growth. Alanine scanning experiments identified the cytochrome bd-I Q-loop insert regions Ile318-Met322, Gln338-Asp342, Tyr353-Leu357, and Thr368-Ile372 as important for enzyme functionality. Those mutants that completely failed to recover growth of MB43∆cydA also lacked oxygen consumption activity and heme absorption peaks. Moreover, we were not able to isolate cytochrome bd-I from these inactive mutants. The results indicate that the cytochrome bd Q-loop exhibits low plasticity and that the Q-loop insert in E. coli is needed for complete, stable, assembly of cytochrome bd-I.
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Affiliation(s)
- Hojjat Ghasemi Goojani
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Julia Konings
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Henk Hakvoort
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Sangjin Hong
- Department of Biochemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801, United States
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801, United States
| | - Junshi Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - Holger Lill
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Dirk Bald
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.
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14
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Mascolo L, Bald D. Cytochrome bd in Mycobacterium tuberculosis: A respiratory chain protein involved in the defense against antibacterials. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 152:55-63. [PMID: 31738981 DOI: 10.1016/j.pbiomolbio.2019.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/12/2019] [Indexed: 12/27/2022]
Abstract
The branched respiratory chain of Mycobacterium tuberculosis has attracted attention as a highly promising target for next-generation antibacterials. This system includes two terminal oxidases of which the exclusively bacterial cytochrome bd represents the less energy-efficient one. Albeit dispensable for growth under standard laboratory conditions, cytochrome bd is important during environmental stress. In this review, we discuss the role of cytochrome bd during infection of the mammalian host and in the defense against antibacterials. Deeper insight into the biochemistry of mycobacterial cytochrome bd is needed to understand the physiological role of this bacteria-specific defense factor. Conversely, cytochrome bd may be utilized to gain information on mycobacterial physiology in vitro and during host infection. Knowledge-based manipulation of cytochrome bd function may assist in designing the next-generation tuberculosis combination chemotherapy.
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Affiliation(s)
- Ludovica Mascolo
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Dirk Bald
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
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15
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In the respiratory chain of Escherichia coli cytochromes bd-I and bd-II are more sensitive to carbon monoxide inhibition than cytochrome bo 3. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148088. [PMID: 31669488 DOI: 10.1016/j.bbabio.2019.148088] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/27/2019] [Accepted: 10/18/2019] [Indexed: 11/23/2022]
Abstract
Bacteria can not only encounter carbon monoxide (CO) in their habitats but also produce the gas endogenously. Bacterial respiratory oxidases, thus, represent possible targets for CO. Accordingly, host macrophages were proposed to produce CO and release it into the surrounding microenvironment to sense viable bacteria through a mechanism that in Escherichia (E.) coli was suggested to involve the targeting of a bd-type respiratory oxidase by CO. The aerobic respiratory chain of E. coli possesses three terminal quinol:O2-oxidoreductases: the heme-copper oxidase bo3 and two copper-lacking bd-type oxidases, bd-I and bd-II. Heme-copper and bd-type oxidases differ in the mechanism and efficiency of proton motive force generation and in resistance to oxidative and nitrosative stress, cyanide and hydrogen sulfide. Here, we investigated at varied O2 concentrations the effect of CO gas on the O2 reductase activity of the purified cytochromes bo3, bd-I and bd-II of E. coli. We found that CO, in competition with O2, reversibly inhibits the three enzymes. The inhibition constants Ki for the bo3, bd-I and bd-II oxidases are 2.4 ± 0.3, 0.04 ± 0.01 and 0.2 ± 0.1 μM CO, respectively. Thus, in E. coli, bd-type oxidases are more sensitive to CO inhibition than the heme-copper cytochrome bo3. The possible physiological consequences of this finding are discussed.
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16
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Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kühlbrandt W, Michel H. Active site rearrangement and structural divergence in prokaryotic respiratory oxidases. Science 2019; 366:100-104. [DOI: 10.1126/science.aay0967] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/04/2019] [Indexed: 12/30/2022]
Abstract
Cytochrome bd–type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of theEscherichia colicytochrome bd-I oxidase by single-particle cryo–electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily–specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.
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Affiliation(s)
- S. Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - A. Hahn
- Department of Structural Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - D. J. Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - M. Radloff
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - M. L. Eisinger
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - A. Nikolaev
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - J. Meier-Credo
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - F. Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - H. Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - R. B. Gennis
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - J. Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - J. D. Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - P. Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
- University of Strasbourg Institute for Advanced Study, Strasbourg, France
| | - W. Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - H. Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
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17
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Taylor AJ, Kelly DJ. The function, biogenesis and regulation of the electron transport chains in Campylobacter jejuni: New insights into the bioenergetics of a major food-borne pathogen. Adv Microb Physiol 2019; 74:239-329. [PMID: 31126532 DOI: 10.1016/bs.ampbs.2019.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Despite its small genome size, C. jejuni is a versatile and metabolically active pathogen, with a complex and highly branched set of respiratory chains allowing the use of a wide range of electron donors and alternative electron acceptors in addition to oxygen, including fumarate, nitrate, nitrite, tetrathionate and N- or S-oxides. Several novel enzymes participate in these electron transport chains, including a tungsten containing formate dehydrogenase, a Complex I that uses flavodoxin and not NADH, a periplasmic facing fumarate reductase and a cytochrome c tetrathionate reductase. This review presents an updated description of the composition and bioenergetics of these various respiratory chains as they are currently understood, including recent work that gives new insights into energy conservation during electron transport to various alternative electron acceptors. The regulation of synthesis and assembly of the electron transport chains is also discussed. A deeper appreciation of the unique features of the respiratory systems of C. jejuni may be helpful in informing strategies to control this important pathogen.
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Affiliation(s)
- Aidan J Taylor
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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18
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Lemaire ON, Infossi P, Ali Chaouche A, Espinosa L, Leimkühler S, Giudici-Orticoni MT, Méjean V, Iobbi-Nivol C. Small membranous proteins of the TorE/NapE family, crutches for cognate respiratory systems in Proteobacteria. Sci Rep 2018; 8:13576. [PMID: 30206249 PMCID: PMC6134056 DOI: 10.1038/s41598-018-31851-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/23/2018] [Indexed: 01/18/2023] Open
Abstract
In this report, we investigate small proteins involved in bacterial alternative respiratory systems that improve the enzymatic efficiency through better anchorage and multimerization of membrane components. Using the small protein TorE of the respiratory TMAO reductase system as a model, we discovered that TorE is part of a subfamily of small proteins that are present in proteobacteria in which they play a similar role for bacterial respiratory systems. We reveal by microscopy that, in Shewanella oneidensis MR1, alternative respiratory systems are evenly distributed in the membrane contrary to what has been described for Escherichia coli. Thus, the better efficiency of the respiratory systems observed in the presence of the small proteins is not due to a specific localization in the membrane, but rather to the formation of membranous complexes formed by TorE homologs with their c-type cytochrome partner protein. By an in vivo approach combining Clear Native electrophoresis and fluorescent translational fusions, we determined the 4:4 stoichiometry of the complexes. In addition, mild solubilization of the cytochrome indicates that the presence of the small protein reinforces its anchoring to the membrane. Therefore, assembly of the complex induced by this small protein improves the efficiency of the respiratory system.
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Affiliation(s)
- Olivier N Lemaire
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Pascale Infossi
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Amine Ali Chaouche
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Leon Espinosa
- Aix-Marseille Université, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476, Potsdam, Germany
| | - Marie-Thérèse Giudici-Orticoni
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Vincent Méjean
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402, Marseille, France.
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19
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Investigation of amino acid specificity in the CydX small protein shows sequence plasticity at the functional level. PLoS One 2018; 13:e0198699. [PMID: 29912917 PMCID: PMC6005532 DOI: 10.1371/journal.pone.0198699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022] Open
Abstract
Small proteins are a new and expanding area of research. Many characterized small proteins are composed of a single hydrophobic α-helix, and the functional requirements of their limited amino acid sequence are not well understood. One hydrophobic small protein, CydX, has been shown to be a component of the cytochrome bd oxidase complex in Escherichia coli, and is required for enzyme function. To investigate small protein sequence specificity, an alanine scanning mutagenesis on the small protein CydX was conducted using mutant alleles expressed from the E. coli chromosome at the wild-type locus. The resulting mutant strains were assayed for CydX function. No single amino acid was required to maintain wild-type resistance to β-mercaptoethanol. However, substitutions of 10-amino acid blocks indicated that the N-terminus of the protein was required for wild-type CydX activity. A series of double mutants showed that multiple mutations at the N-terminus led to β-mercaptoethanol sensitivity in vivo. Triple mutants showed both in vivo and in vitro phenotypes. Together, these data provide evidence suggesting a high level of functional plasticity in CydX, in which multiple amino acids may work cooperatively to facilitate CydX function.
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20
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VanOrsdel CE, Kelly JP, Burke BN, Lein CD, Oufiero CE, Sanchez JF, Wimmers LE, Hearn DJ, Abuikhdair FJ, Barnhart KR, Duley ML, Ernst SEG, Kenerson BA, Serafin AJ, Hemm MR. Identifying New Small Proteins in Escherichia coli. Proteomics 2018; 18:e1700064. [PMID: 29645342 PMCID: PMC6001520 DOI: 10.1002/pmic.201700064] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 03/05/2018] [Indexed: 12/11/2022]
Abstract
The number of small proteins (SPs) encoded in the Escherichia coli genome is unknown, as current bioinformatics and biochemical techniques make short gene and small protein identification challenging. One method of small protein identification involves adding an epitope tag to the 3′ end of a short open reading frame (sORF) on the chromosome, with synthesis confirmed by immunoblot assays. In this study, this strategy was used to identify new E. coli small proteins, tagging 80 sORFs in the E. coli genome, and assayed for protein synthesis. The selected sORFs represent diverse sequence characteristics, including degrees of sORF conservation, predicted transmembrane domains, sORF direction with respect to flanking genes, ribosome binding site (RBS) prediction, and ribosome profiling results. Of 80 sORFs, 36 resulted in encoded synthesized proteins—a 45% success rate. Modeling of detected versus non‐detected small proteins analysis showed predictions based on RBS prediction, transcription data, and ribosome profiling had statistically‐significant correlation with protein synthesis; however, there was no correlation between current sORF annotation and protein synthesis. These results suggest substantial numbers of small proteins remain undiscovered in E. coli, and existing bioinformatics techniques must continue to improve to facilitate identification.
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Affiliation(s)
- Caitlin E VanOrsdel
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - John P Kelly
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Brittany N Burke
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Christina D Lein
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | | | - Joseph F Sanchez
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Larry E Wimmers
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - David J Hearn
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Fatimeh J Abuikhdair
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Kathryn R Barnhart
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Michelle L Duley
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Sarah E G Ernst
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Briana A Kenerson
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Aubrey J Serafin
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
| | - Matthew R Hemm
- Department of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA
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21
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Abstract
Cytochrome bd is a unique prokaryotic respiratory terminal oxidase that does not belong to the extensively investigated family of haem-copper oxidases (HCOs). The enzyme catalyses the four-electron reduction of O2 to 2H2O, using quinols as physiological reducing substrates. The reaction is electrogenic and cytochrome bd therefore sustains bacterial energy metabolism by contributing to maintain the transmembrane proton motive force required for ATP synthesis. As compared to HCOs, cytochrome bd displays several distinctive features in terms of (i) metal composition (it lacks Cu and harbours a d-type haem in addition to two haems b), (ii) overall three-dimensional structure, that only recently has been solved, and arrangement of the redox cofactors, (iii) lesser energetic efficiency (it is not a proton pump), (iv) higher O2 affinity, (v) higher resistance to inhibitors such as cyanide, nitric oxide (NO) and hydrogen sulphide (H2S) and (vi) ability to efficiently metabolize potentially toxic reactive oxygen and nitrogen species like hydrogen peroxide (H2O2) and peroxynitrite (ONOO-). Compelling evidence suggests that, beyond its bioenergetic role, cytochrome bd plays multiple functions in bacterial physiology and affords protection against oxidative and nitrosative stress. Relevant to human pathophysiology, thanks to its peculiar properties, the enzyme has been shown to promote virulence in several bacterial pathogens, being currently recognized as a target for the development of new antibiotics. This review aims to give an update on our current understanding of bd-type oxidases with a focus on their reactivity with gaseous ligands and its potential impact on bacterial physiology and human pathophysiology.
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22
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Yang X, Jensen SI, Wulff T, Harrison SJ, Long KS. Identification and validation of novel small proteins in Pseudomonas putida. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:966-974. [PMID: 27717237 DOI: 10.1111/1758-2229.12473] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/06/2016] [Accepted: 09/10/2016] [Indexed: 06/06/2023]
Abstract
Small proteins of 50 amino acids or less have been understudied due to difficulties that impede their annotation and detection. In order to obtain information on small open reading frames (sORFs) in Pseudomonas putida, bioinformatic and proteomic approaches were used to identify putative sORFs in the well-characterized strain KT2440. A plasmid-based system was established for sORF validation, enabling expression of C-terminal sequential peptide affinity tagged variants and their detection via protein immunoblotting. Out of 22 tested putative sORFs, the expression of 14 sORFs was confirmed, where all except one are novel. All of the validated sORFs except one are located adjacent to annotated genes on the same strand and three are in close proximity to genes with known functions. These include an ABC transporter operon and the two transcriptional regulators Fis and CysB involved in biofilm formation and cysteine biosynthesis respectively. The work sheds light on the P. putida small proteome and small protein identification, a necessary first step towards gaining insights into their functions and possible evolutionary implications.
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Affiliation(s)
- Xiaochen Yang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Sheila I Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Scott J Harrison
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Katherine S Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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23
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Abstract
Like most bacteria, Escherichia coli has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate-specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophosphate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and dimethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O₂ is served by two major oxidoreductases (oxidases), cytochrome bo₃ encoded by cyoABCDE and cytochrome bd encoded by cydABX. Terminal oxidases of aerobic respiratory chains of bacteria, which use O₂ as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome c or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome bo₃ and cytochrome bd in E. coli. It also presents a discussion on the genetics and the prosthetic groups of cytochrome bo₃ and cytochrome bd. The E. coli membrane contains three types of quinones that all have an octaprenyl side chain (C₄₀). It has been proposed that the bo₃ oxidase can have two ubiquinone-binding sites with different affinities. "WHAT'S NEW" IN THE REVISED ARTICLE: The revised article comprises additional information about subunit composition of cytochrome bd and its role in bacterial resistance to nitrosative and oxidative stresses. Also, we present the novel data on the electrogenic function of appBCX-encoded cytochrome bd-II, a second bd-type oxidase that had been thought not to contribute to generation of a proton motive force in E. coli, although its spectral properties closely resemble those of cydABX-encoded cytochrome bd.
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24
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Safarian S, Rajendran C, Müller H, Preu J, Langer JD, Ovchinnikov S, Hirose T, Kusumoto T, Sakamoto J, Michel H. Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. Science 2016; 352:583-6. [PMID: 27126043 DOI: 10.1126/science.aaf2477] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/28/2016] [Indexed: 12/29/2022]
Abstract
The cytochrome bd oxidases are terminal oxidases that are present in bacteria and archaea. They reduce molecular oxygen (dioxygen) to water, avoiding the production of reactive oxygen species. In addition to their contribution to the proton motive force, they mediate viability under oxygen-related stress conditions and confer tolerance to nitric oxide, thus contributing to the virulence of pathogenic bacteria. Here we present the atomic structure of the bd oxidase from Geobacillus thermodenitrificans, revealing a pseudosymmetrical subunit fold. The arrangement and order of the heme cofactors support the conclusions from spectroscopic measurements that the cleavage of the dioxygen bond may be mechanistically similar to that in the heme-copper-containing oxidases, even though the structures are completely different.
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Affiliation(s)
- Schara Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany
| | - Chitra Rajendran
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany. Present address: Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstrasse 31, D-93051 Regensburg, Germany
| | - Hannelore Müller
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany
| | - Julia Preu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany. Present address: Department of Molecular Membrane Biology, Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, D-60438 Frankfurt/Main, Germany
| | | | - Taichiro Hirose
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - Tomoichirou Kusumoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - Junshi Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany.
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25
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Siletsky SA, Rappaport F, Poole RK, Borisov VB. Evidence for Fast Electron Transfer between the High-Spin Haems in Cytochrome bd-I from Escherichia coli. PLoS One 2016; 11:e0155186. [PMID: 27152644 PMCID: PMC4859518 DOI: 10.1371/journal.pone.0155186] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/25/2016] [Indexed: 12/21/2022] Open
Abstract
Cytochrome bd-I is one of the three proton motive force-generating quinol oxidases in the O2-dependent respiratory chain of Escherichia coli. It contains one low-spin haem (b558) and the two high-spin haems (b595 and d) as the redox-active cofactors. In order to examine the flash-induced intraprotein reverse electron transfer (the so-called ''electron backflow''), CO was photolyzed from the ferrous haem d in one-electron reduced (b5583+b5953+d2+-CO) cytochrome bd-I, and the fully reduced (b5582+b5952+d2+-CO) oxidase as a control. In contrast to the fully reduced cytochrome bd-I, the transient spectrum of one-electron reduced oxidase at a delay time of 1.5 μs is clearly different from that at a delay time of 200 ns. The difference between the two spectra can be modeled as the electron transfer from haem d to haem b595 in 3–4% of the cytochrome bd-I population. Thus, the interhaem electron backflow reaction induced by photodissociation of CO from haem d in one-electron reduced cytochrome bd-I comprises two kinetically different phases: the previously unnoticed fast electron transfer from haem d to haem b595 within 0.2–1.5 μs and the slower well-defined electron equilibration with τ ~16 μs. The major new finding of this work is the lack of electron transfer at 200 ns.
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Affiliation(s)
- Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- * E-mail: (VBB); (SAS); (RKP)
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, Unite Mixte de Recherche 7141 CNRS, Universite Paris 6, Paris, France
| | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
- * E-mail: (VBB); (SAS); (RKP)
| | - Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- * E-mail: (VBB); (SAS); (RKP)
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Leclerc J, Rosenfeld E, Trainini M, Martin B, Meuric V, Bonnaure-Mallet M, Baysse C. The Cytochrome bd Oxidase of Porphyromonas gingivalis Contributes to Oxidative Stress Resistance and Dioxygen Tolerance. PLoS One 2015; 10:e0143808. [PMID: 26629705 PMCID: PMC4668044 DOI: 10.1371/journal.pone.0143808] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/10/2015] [Indexed: 11/18/2022] Open
Abstract
Porphyromonas gingivalis is an etiologic agent of periodontal disease in humans. The disease is associated with the formation of a mixed oral biofilm which is exposed to oxygen and environmental stress, such as oxidative stress. To investigate possible roles for cytochrome bd oxidase in the growth and persistence of this anaerobic bacterium inside the oral biofilm, mutant strains deficient in cytochrome bd oxidase activity were characterized. This study demonstrated that the cytochrome bd oxidase of Porphyromonas gingivalis, encoded by cydAB, was able to catalyse O2 consumption and was involved in peroxide and superoxide resistance, and dioxygen tolerance.
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Affiliation(s)
- Julia Leclerc
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
| | - Eric Rosenfeld
- UMR CNRS 7266 LIENSs, University of La Rochelle, La Rochelle, France
| | - Mathieu Trainini
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
| | - Bénédicte Martin
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
| | - Vincent Meuric
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
- UMR CNRS 7266 LIENSs, University of La Rochelle, La Rochelle, France
- CHU Rennes, Rennes, France
| | - Martine Bonnaure-Mallet
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
- UMR CNRS 7266 LIENSs, University of La Rochelle, La Rochelle, France
- CHU Rennes, Rennes, France
| | - Christine Baysse
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
- * E-mail:
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Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B. Extensive identification and analysis of conserved small ORFs in animals. Genome Biol 2015; 16:179. [PMID: 26364619 PMCID: PMC4568590 DOI: 10.1186/s13059-015-0742-x] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/05/2015] [Indexed: 02/06/2023] Open
Abstract
Background There is increasing evidence that transcripts or transcript regions annotated as non-coding can harbor functional short open reading frames (sORFs). Loss-of-function experiments have identified essential developmental or physiological roles for a few of the encoded peptides (micropeptides), but genome-wide experimental or computational identification of functional sORFs remains challenging. Results Here, we expand our previously developed method and present results of an integrated computational pipeline for the identification of conserved sORFs in human, mouse, zebrafish, fruit fly, and the nematode C. elegans. Isolating specific conservation signatures indicative of purifying selection on amino acid (rather than nucleotide) sequence, we identify about 2,000 novel small ORFs located in the untranslated regions of canonical mRNAs or on transcripts annotated as non-coding. Predicted sORFs show stronger conservation signatures than those identified in previous studies and are sometimes conserved over large evolutionary distances. The encoded peptides have little homology to known proteins and are enriched in disordered regions and short linear interaction motifs. Published ribosome profiling data indicate translation of more than 100 novel sORFs, and mass spectrometry data provide evidence for more than 70 novel candidates. Conclusions Taken together, we identify hundreds of previously unknown conserved sORFs in major model organisms. Our computational analyses and integration with experimental data show that these sORFs are expressed, often translated, and sometimes widely conserved, in some cases even between vertebrates and invertebrates. We thus provide an integrated resource of putatively functional micropeptides for functional validation in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0742-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian D Mackowiak
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Henrik Zauber
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Chris Bielow
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany. .,Berlin Institute of Health, Kapelle-Ufer 2, 10117, Berlin, Germany.
| | - Denise Thiel
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Kamila Kutz
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Lorenzo Calviello
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Guido Mastrobuoni
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Stefan Kempa
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Matthias Selbach
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Benedikt Obermayer
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
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Liu YW, Kelly DJ. Cytochromecbiogenesis inCampylobacter jejunirequires cytochromec6(CccA; Cj1153) to maintain apocytochrome cysteine thiols in a reduced state for haem attachment. Mol Microbiol 2015; 96:1298-317. [DOI: 10.1111/mmi.13008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Yang-Wei Liu
- Department of Molecular Biology and Biotechnology; The University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology; The University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
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Abstract
Aside from a few serendipitous discoveries, small proteins of less than 50 amino acids in bacteria and 100 amino acids in eukaryotes were largely ignored due to challenges in their genetic and biochemical detection. However, with the ever-increasing availability of completed genome sequences and deep sequencing, which allows analysis of genome-wide ribosome occupancy, hundreds of small proteins are now being identified. This brings to the forefront the challenges and opportunities associated with the characterization of these proteins. See research article: http://www.biomedcentral.com/1471-2164/15/946.
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