1
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Ito Y, Yoshidome D, Hidaka M, Araki Y, Ito K, Kosono S, Nishiyama M. Improvement of the nitrogenase activity in Escherichia coli that expresses the nitrogen fixation-related genes from Azotobacter vinelandii. Biochem Biophys Res Commun 2024; 728:150345. [PMID: 38971001 DOI: 10.1016/j.bbrc.2024.150345] [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: 04/09/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The transfer of nitrogen fixation (nif) genes from diazotrophs to non-diazotrophic hosts is of increasing interest for engineering biological nitrogen fixation. A recombinant Escherichia coli strain expressing Azotobacter vinelandii 18 nif genes (nifHDKBUSVQENXYWZMF, nifiscA, and nafU) were previously constructed and showed nitrogenase activity. In the present study, we constructed several E. coli strain derivatives in which all or some of the 18 nif genes were additionally integrated into the fliK locus of the chromosome in various combinations. E. coli derivatives with the chromosomal integration of nifiscA, nifU, and nifS, which are involved in the biosynthesis of the [4Fe-4S] cluster of dinitrogenase reductase, exhibited enhanced nitrogenase activity. We also revealed that overexpression of E. coli fldA and ydbK, which encode flavodoxin and flavodoxin-reducing enzyme, respectively, enhanced nitrogenase activity, likely by facilitating electron transfer to dinitrogenase reductase. The additional expression of nifM, putatively involved in maturation of dinitrogenase reductase, further enhanced nitrogenase activity and the amount of soluble NifH. By combining these factors, we successfully improved nitrogenase activity 10-fold.
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Affiliation(s)
- Yusuke Ito
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Daisuke Yoshidome
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Makoto Hidaka
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yasuko Araki
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Kotaro Ito
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Saori Kosono
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nishiyama
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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2
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Kim NK, Baek JE, Lee YJ, Oh Y, Oh JI. Rel-dependent decrease in the expression of ribosomal protein genes by inhibition of the respiratory electron transport chain in Mycobacterium smegmatis. Front Microbiol 2024; 15:1448277. [PMID: 39188315 PMCID: PMC11345224 DOI: 10.3389/fmicb.2024.1448277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
In this study, we demonstrated that both the expression of most ribosomal protein genes and the amount of ribosomes were decreased in the Δaa 3 mutant of Mycobacterium smegmatis, in which the major terminal oxidase (aa 3 cytochrome c oxidase) of the respiratory electron transport chain (ETC) is inactivated, compared to those in the wild-type strain. Deletion of the rel gene encoding the major (p)ppGpp synthetase in the background of the Δaa 3 mutant restored the reduced expression of ribosomal protein genes, suggesting that inhibition of the respiratory ETC leads to the Rel-dependent stringent response (SR) in this bacterium. Both a decrease in the expression of ribosomal protein genes by overexpression of rel and the increased expression of rel in the Δaa 3 mutant relative to the wild-type strain support the Rel-dependent induction of SR in the Δaa 3 mutant. We also demonstrated that the expression of ribosomal protein genes was decreased in M. smegmatis exposed to respiration-inhibitory conditions, such as KCN and bedaquiline treatment, null mutation of the cytochrome bcc 1 complex, and hypoxia. The MprBA-SigE-SigB regulatory pathway was implicated in both the increased expression of rel and the decreased expression of ribosomal protein genes in the Δaa 3 mutant of M. smegmatis.
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Affiliation(s)
- Na-Kyeong Kim
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Jong-Eun Baek
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Ye-Jin Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan, Republic of Korea
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3
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Borisov VB. Generation of Membrane Potential by Cytochrome bd. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1504-1512. [PMID: 38105020 DOI: 10.1134/s0006297923100073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 12/19/2023]
Abstract
An overview of current notions on the mechanism of generation of a transmembrane electric potential difference (Δψ) during the catalytic cycle of a bd-type triheme terminal quinol oxidase is presented in this work. It is suggested that the main contribution to Δψ formation is made by the movement of H+ across the membrane along the intra-protein hydrophilic proton-conducting pathway from the cytoplasm to the active site for oxygen reduction of this bacterial enzyme.
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Affiliation(s)
- Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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4
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Feregrino-Mondragón RD, Santiago-Martínez MG, Silva-Flores M, Encalada R, Reyes-Prieto A, Rodríguez-Zavala JS, Peña-Ocaña BA, Moreno-Sánchez R, Saavedra E, Jasso-Chávez R. Lactate oxidation is linked to energy conservation and to oxygen detoxification via a putative terminal cytochrome oxidase in Methanosarcina acetivorans. Arch Biochem Biophys 2023:109667. [PMID: 37327962 DOI: 10.1016/j.abb.2023.109667] [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: 12/27/2022] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
The marine archaeon Methanosarcina acetivorans contains a putative NAD + -independent d-lactate dehydrogenase (D-iLDH/glycolate oxidase) encoded by the MA4631 gene, belonging to the FAD-oxidase C superfamily. Nucleotide sequences similar to MA4631 gene, were identified in other methanogens and Firmicutes with >90 and 35-40% identity, respectively. Therefore, the lactate metabolism in M. acetivorans is reported here. Cells subjected to intermittent pulses of oxygen (air-adapted; AA-Ma cells) consumed lactate only in combination with acetate, increasing methane production and biomass yield. In AA-Ma cells incubated with d-lactate plus [14C]-l-lactate, the radioactive label was found in methane, CO2 and glycogen, indicating that lactate metabolism fed both methanogenesis and gluconeogenesis. Moreover, d-lactate oxidation was coupled to O2-consumption which was sensitive to HQNO; also, AA-Ma cells showed high transcript levels of gene dld and those encoding subunits A (MA1006) and B (MA1007) of a putative cytochrome bd quinol oxidase, compared to anaerobic control cells. An E. coli mutant deficient in dld complemented with the MA4631 gene, grew with d-lactate as carbon source and showed membrane-bound d-lactate:quinone oxidoreductase activity. The product of the MA4631 gene is a FAD-containing monomer showing activity of iLDH with preference to d-lactate. The results suggested that air adapted M. acetivorans is able to co-metabolize lactate and acetate with associated oxygen consumption by triggering the transcription and synthesis of the D-iLDH and a putative cytochrome bd: methanophenazine (quinol) oxidoreductase. Biomass generation and O2 consumption, suggest a potentially new oxygen detoxification mechanism coupled to energy conservation in this methanogen.
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Affiliation(s)
| | - Michel Geovanni Santiago-Martínez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico; Department of Molecular and Cell Biology, The University of Connecticut, Storrs, 06269, Connecticut, USA
| | - Mayel Silva-Flores
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Adrián Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - José S Rodríguez-Zavala
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Betsy Anaid Peña-Ocaña
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico.
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5
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Makarchuk I, Gerasimova T, Kägi J, Wohlwend D, Melin F, Friedrich T, Hellwig P. Mutating the environment of heme b 595 of E. coli cytochrome bd-I oxidase shifts its redox potential by 200 mV without inactivating the enzyme. Bioelectrochemistry 2023; 151:108379. [PMID: 36736178 DOI: 10.1016/j.bioelechem.2023.108379] [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: 09/08/2022] [Revised: 01/11/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023]
Abstract
Cytochrome bd-I catalyzes the reduction of oxygen to water with the aid of hemes b558, b595 and d. Here, effects of a mutation of E445, a ligand of heme b595 and of R448, hydrogen bonded to E445 are studied electrochemically in the E. coli enzyme. The equilibrium potential of the three hemes are shifted by up to 200 mV in these mutants. Strikingly the E445D and the R448N mutants show a turnover of 41 ± 2 % and 20 ± 4 %, respectively. Electrocatalytic studies confirm that the mutants react with oxygen and bind and release NO. These results point towards the ability of cytochrome bd to react even if the electron transfer is less favorable.
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Affiliation(s)
- Iryna Makarchuk
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Jan Kägi
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Daniel Wohlwend
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany.
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6
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Cao YC, Liao RZ. QM Calculations Revealed that Outer-Sphere Electron Transfer Boosted O-O Bond Cleavage in the Multiheme-Dependent Cytochrome bd Oxygen Reductase. Inorg Chem 2023; 62:4066-4075. [PMID: 36857027 DOI: 10.1021/acs.inorgchem.2c03742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The cytochrome bd oxygen reductase catalyzes the four-electron reduction of dioxygen to two water molecules. The structure of this enzyme reveals three heme molecules in the active site, which differs from that of heme-copper cytochrome c oxidase. The quantum chemical cluster approach was used to uncover the reaction mechanism of this intriguing metalloenzyme. The calculations suggested that a proton-coupled electron transfer reduction occurs first to generate a ferrous heme b595. This is followed by the dioxygen binding at the heme d center coupled with an outer-sphere electron transfer from the ferrous heme b595 to the dioxygen moiety, affording a ferric ion superoxide intermediate. A second proton-coupled electron transfer produces a heme d ferric hydroperoxide, which undergoes efficient O-O bond cleavage facilitated by an outer-sphere electron transfer from the ferrous heme b595 to the O-O σ* orbital and an inner-sphere proton transfer from the heme d hydroxyl group to the leaving hydroxide. The synergistic benefits of the two types of hemes rationalize the highly efficient oxygen reduction repertoire for the multi-heme-dependent cytochrome bd oxygen reductase family.
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Affiliation(s)
- Yu-Chen Cao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
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7
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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8
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Oh Y, Lee HN, Ko EM, Jeong JA, Park SW, Oh JI. Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions. J Microbiol 2023; 61:297-315. [PMID: 36847970 DOI: 10.1007/s12275-023-00026-8] [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: 12/29/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis. M. tuberculosis can survive in a dormant state within the granuloma, avoiding the host-mounting immune attack. M. tuberculosis bacilli in this state show increased tolerance to antibiotics and stress conditions, and thus the transition of M. tuberculosis to the nonreplicating dormant state acts as an obstacle to tuberculosis treatment. M. tuberculosis in the granuloma encounters hostile environments such as hypoxia, nitric oxide, reactive oxygen species, low pH, and nutrient deprivation, etc., which are expected to inhibit respiration of M. tuberculosis. To adapt to and survive in respiration-inhibitory conditions, it is required for M. tuberculosis to reprogram its metabolism and physiology. In order to get clues to the mechanism underlying the entry of M. tuberculosis to the dormant state, it is important to understand the mycobacterial regulatory systems that are involved in the regulation of gene expression in response to respiration inhibition. In this review, we briefly summarize the information regarding the regulatory systems implicated in upregulation of gene expression in mycobacteria exposed to respiration-inhibitory conditions. The regulatory systems covered in this review encompass the DosSR (DevSR) two-component system, SigF partner switching system, MprBA-SigE-SigB signaling pathway, cAMP receptor protein, and stringent response.
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Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Eon-Min Ko
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Ji-A Jeong
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea. .,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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9
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Discovery of 1-hydroxy-2-methylquinolin-4(1H)-one derivatives as new cytochrome bd oxidase inhibitors for tuberculosis therapy. Eur J Med Chem 2022; 245:114896. [DOI: 10.1016/j.ejmech.2022.114896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/19/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
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10
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Activation of the SigE-SigB signaling pathway by inhibition of the respiratory electron transport chain and its effect on rifampicin resistance in Mycobacterium smegmatis. J Microbiol 2022; 60:935-947. [DOI: 10.1007/s12275-022-2202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
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11
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Forte E, Nastasi MR, Borisov VB. Preparations of Terminal Oxidase Cytochrome bd-II Isolated from Escherichia coli Reveal Significant Hydrogen Peroxide Scavenging Activity. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:720-730. [PMID: 36171653 DOI: 10.1134/s0006297922080041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 06/16/2023]
Abstract
Cytochrome bd-II is one of the three terminal quinol oxidases of the aerobic respiratory chain of Escherichia coli. Preparations of the detergent-solubilized untagged bd-II oxidase isolated from the bacterium were shown to scavenge hydrogen peroxide (H2O2) with high rate producing molecular oxygen (O2). Addition of H2O2 to the same buffer that does not contain enzyme or contains thermally denatured cytochrome bd-II does not lead to any O2 production. The latter observation rules out involvement of adventitious transition metals bound to the protein. The H2O2-induced O2 production is not susceptible to inhibition by N-ethylmaleimide (the sulfhydryl binding compound), antimycin A (the compound that binds specifically to a quinol binding site), and CO (diatomic gas that binds specifically to the reduced heme d). However, O2 formation is inhibited by cyanide (IC50 = 4.5 ± 0.5 µM) and azide. Addition of H2O2 in the presence of dithiothreitol and ubiquinone-1 does not inactivate cytochrome bd-II and apparently does not affect the O2 reductase activity of the enzyme. The ability of cytochrome bd-II to detoxify H2O2 could play a role in bacterial physiology by conferring resistance to the peroxide-mediated stress.
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Affiliation(s)
- Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, I-00185, Italy
| | - Martina R Nastasi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, I-00185, Italy
| | - Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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12
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Borisov VB, Forte E. Bioenergetics and Reactive Nitrogen Species in Bacteria. Int J Mol Sci 2022; 23:7321. [PMID: 35806323 PMCID: PMC9266656 DOI: 10.3390/ijms23137321] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
The production of reactive nitrogen species (RNS) by the innate immune system is part of the host's defense against invading pathogenic bacteria. In this review, we summarize recent studies on the molecular basis of the effects of nitric oxide and peroxynitrite on microbial respiration and energy conservation. We discuss possible molecular mechanisms underlying RNS resistance in bacteria mediated by unique respiratory oxygen reductases, the mycobacterial bcc-aa3 supercomplex, and bd-type cytochromes. A complete picture of the impact of RNS on microbial bioenergetics is not yet available. However, this research area is developing very rapidly, and the knowledge gained should help us develop new methods of treating infectious diseases.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
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13
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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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14
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Mechanistic and structural diversity between cytochrome bd isoforms of Escherichia coli. Proc Natl Acad Sci U S A 2021; 118:2114013118. [PMID: 34873041 DOI: 10.1073/pnas.2114013118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
The treatment of infectious diseases caused by multidrug-resistant pathogens is a major clinical challenge of the 21st century. The membrane-embedded respiratory cytochrome bd-type oxygen reductase is a critical survival factor utilized by pathogenic bacteria during infection, proliferation and the transition from acute to chronic states. Escherichia coli encodes for two cytochrome bd isoforms that are both involved in respiration under oxygen limited conditions. Mechanistic and structural differences between cydABX (Ecbd-I) and appCBX (Ecbd-II) operon encoded cytochrome bd variants have remained elusive in the past. Here, we demonstrate that cytochrome bd-II catalyzes oxidation of benzoquinols while possessing additional specificity for naphthoquinones. Our data show that although menaquinol-1 (MK1) is not able to directly transfer electrons onto cytochrome bd-II from E. coli, it has a stimulatory effect on its oxygen reduction rate in the presence of ubiquinol-1. We further determined cryo-EM structures of cytochrome bd-II to high resolution of 2.1 Å. Our structural insights confirm that the general architecture and substrate accessible pathways are conserved between the two bd oxidase isoforms, but two notable differences are apparent upon inspection: (i) Ecbd-II does not contain a CydH-like subunit, thereby exposing heme b 595 to the membrane environment and (ii) the AppB subunit harbors a structural demethylmenaquinone-8 molecule instead of ubiquinone-8 as found in CydB of Ecbd-I Our work completes the structural landscape of terminal respiratory oxygen reductases of E. coli and suggests that structural and functional properties of the respective oxidases are linked to quinol-pool dependent metabolic adaptations in E. coli.
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15
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Borisov VB, Forte E. Impact of Hydrogen Sulfide on Mitochondrial and Bacterial Bioenergetics. Int J Mol Sci 2021; 22:12688. [PMID: 34884491 PMCID: PMC8657789 DOI: 10.3390/ijms222312688] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
This review focuses on the effects of hydrogen sulfide (H2S) on the unique bioenergetic molecular machines in mitochondria and bacteria-the protein complexes of electron transport chains and associated enzymes. H2S, along with nitric oxide and carbon monoxide, belongs to the class of endogenous gaseous signaling molecules. This compound plays critical roles in physiology and pathophysiology. Enzymes implicated in H2S metabolism and physiological actions are promising targets for novel pharmaceutical agents. The biological effects of H2S are biphasic, changing from cytoprotection to cytotoxicity through increasing the compound concentration. In mammals, H2S enhances the activity of FoF1-ATP (adenosine triphosphate) synthase and lactate dehydrogenase via their S-sulfhydration, thereby stimulating mitochondrial electron transport. H2S serves as an electron donor for the mitochondrial respiratory chain via sulfide quinone oxidoreductase and cytochrome c oxidase at low H2S levels. The latter enzyme is inhibited by high H2S concentrations, resulting in the reversible inhibition of electron transport and ATP production in mitochondria. In the branched respiratory chain of Escherichia coli, H2S inhibits the bo3 terminal oxidase but does not affect the alternative bd-type oxidases. Thus, in E. coli and presumably other bacteria, cytochrome bd permits respiration and cell growth in H2S-rich environments. A complete picture of the impact of H2S on bioenergetics is lacking, but this field is fast-moving, and active ongoing research on this topic will likely shed light on additional, yet unknown biological effects.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
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16
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Siletsky SA, Borisov VB. Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives. Int J Mol Sci 2021; 22:10852. [PMID: 34639193 PMCID: PMC8509429 DOI: 10.3390/ijms221910852] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.
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Affiliation(s)
- Sergey A. Siletsky
- Department of Bioenergetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Vitaliy B. Borisov
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia;
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17
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Safarian S, Opel-Reading HK, Wu D, Mehdipour AR, Hards K, Harold LK, Radloff M, Stewart I, Welsch S, Hummer G, Cook GM, Krause KL, Michel H. The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB. Nat Commun 2021; 12:5236. [PMID: 34475399 PMCID: PMC8413341 DOI: 10.1038/s41467-021-25537-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
New drugs are urgently needed to combat the global TB epidemic. Targeting simultaneously multiple respiratory enzyme complexes of Mycobacterium tuberculosis is regarded as one of the most effective treatment options to shorten drug administration regimes, and reduce the opportunity for the emergence of drug resistance. During infection and proliferation, the cytochrome bd oxidase plays a crucial role for mycobacterial pathophysiology by maintaining aerobic respiration at limited oxygen concentrations. Here, we present the cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 Å. In conjunction with atomistic molecular dynamics (MD) simulation studies we discovered a previously unknown MK-9-binding site, as well as a unique disulfide bond within the Q-loop domain that defines an inactive conformation of the canonical quinol oxidation site in Actinobacteria. Our detailed insights into the long-sought atomic framework of the cytochrome bd oxidase from M. tuberculosis will form the basis for the design of highly specific drugs to act on this enzyme.
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Affiliation(s)
- Schara Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany.
| | | | - Di Wu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Ahmad R Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Melanie Radloff
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Ian Stewart
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Kurt L Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany.
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18
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Cryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels. Nat Commun 2021; 12:4621. [PMID: 34330928 PMCID: PMC8324918 DOI: 10.1038/s41467-021-24924-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 07/14/2021] [Indexed: 12/21/2022] Open
Abstract
Cytochromes bd are ubiquitous amongst prokaryotes including many human-pathogenic bacteria. Such complexes are targets for the development of antimicrobial drugs. However, an understanding of the relationship between the structure and functional mechanisms of these oxidases is incomplete. Here, we have determined the 2.8 Å structure of Mycobacterium smegmatis cytochrome bd by single-particle cryo-electron microscopy. This bd oxidase consists of two subunits CydA and CydB, that adopt a pseudo two-fold symmetrical arrangement. The structural topology of its Q-loop domain, whose function is to bind the substrate, quinol, is significantly different compared to the C-terminal region reported for cytochromes bd from Geobacillus thermodenitrificans (G. th) and Escherichia coli (E. coli). In addition, we have identified two potential oxygen access channels in the structure and shown that similar tunnels also exist in G. th and E. coli cytochromes bd. This study provides insights to develop a framework for the rational design of antituberculosis compounds that block the oxygen access channels of this oxidase. Cytochromes bd oxidase (Cyt-bd) catalyzes the reduction of oxygen to water and is the terminal oxidase in the respiratory chain of prokaryotes. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Cyt-bd and identify two potential oxygen access channels in the structure, which is of interest for the development of novel antituberculosis drugs.
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19
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Borisov VB. Effect of Membrane Environment on the Ligand-Binding Properties of the Terminal Oxidase Cytochrome bd-I from Escherichia coli. BIOCHEMISTRY (MOSCOW) 2021; 85:1603-1612. [PMID: 33705298 DOI: 10.1134/s0006297920120123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytochrome bd-I is a terminal oxidase of the Escherichia coli respiratory chain. This integral membrane protein contains three redox-active prosthetic groups (hemes b558, b595, and d) and couples the electron transfer from quinol to molecular oxygen to the generation of proton motive force, as one of its important physiological functions. The study was aimed at examining the effect of the membrane environment on the ligand-binding properties of cytochrome bd-I by absorption spectroscopy. The membrane environment was found to modulate the ligand-binding characteristics of the hemoprotein in both oxidized and reduced states. Absorption changes upon the addition of exogenous ligands, such as cyanide or carbon monoxide (CO), to the detergent-solubilized enzyme were much more significant and heterogeneous than those observed with the membrane-bound enzyme. In the native membranes, both cyanide and CO interacted mainly with heme d. An additional ligand-binding site (heme b558) appeared in the isolated enzyme, as was evidenced by more pronounced changes in the absorption in the Soret band. This additional reactivity could also be detected after treatment of E. coli membranes with a detergent. The observed effect did not result from the enzyme denaturation, since reconstitution of the isolated enzyme into azolectin liposomes restored the ligand-binding pattern close to that observed for the intact membranes.
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Affiliation(s)
- V B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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20
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Identification and optimization of quinolone-based inhibitors against cytochrome bd oxidase using an electrochemical assay. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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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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22
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Borisov VB, Siletsky SA, Nastasi MR, Forte E. ROS Defense Systems and Terminal Oxidases in Bacteria. Antioxidants (Basel) 2021; 10:antiox10060839. [PMID: 34073980 PMCID: PMC8225038 DOI: 10.3390/antiox10060839] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) comprise the superoxide anion (O2•−), hydrogen peroxide (H2O2), hydroxyl radical (•OH), and singlet oxygen (1O2). ROS can damage a variety of macromolecules, including DNA, RNA, proteins, and lipids, and compromise cell viability. To prevent or reduce ROS-induced oxidative stress, bacteria utilize different ROS defense mechanisms, of which ROS scavenging enzymes, such as superoxide dismutases, catalases, and peroxidases, are the best characterized. Recently, evidence has been accumulating that some of the terminal oxidases in bacterial respiratory chains may also play a protective role against ROS. The present review covers this role of terminal oxidases in light of recent findings.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia;
- Correspondence: (V.B.B.); (E.F.)
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia;
| | - Martina R. Nastasi
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy;
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy;
- Correspondence: (V.B.B.); (E.F.)
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23
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Borisov VB, Forte E. Terminal Oxidase Cytochrome bd Protects Bacteria Against Hydrogen Sulfide Toxicity. BIOCHEMISTRY (MOSCOW) 2021; 86:22-32. [PMID: 33705279 DOI: 10.1134/s000629792101003x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hydrogen sulfide (H2S) is often called the third gasotransmitter (after nitric oxide and carbon monoxide), or endogenous gaseous signaling molecule. This compound plays important roles in organisms from different taxonomic groups, from bacteria to animals and humans. In mammalian cells, H2S has a cytoprotective effect at nanomolar concentrations, but becomes cytotoxic at higher concentrations. The primary target of H2S is mitochondria. At submicromolar concentrations, H2S inhibits mitochondrial heme-copper cytochrome c oxidase, thereby blocking aerobic respiration and oxidative phosphorylation and eventually leading to cell death. Since the concentration of H2S in the gut is extremely high, the question arises - how can gut bacteria maintain the functioning of their oxygen-dependent respiratory electron transport chains under such conditions? This review provides an answer to this question and discusses the key role of non-canonical bd-type terminal oxidases of the enterobacterium Escherichia coli, a component of the gut microbiota, in maintaining aerobic respiration and growth in the presence of toxic concentrations of H2S in the light of recent experimental data.
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Affiliation(s)
- Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, I-00185 Rome, Italy
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24
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Nikolaev A, Safarian S, Thesseling A, Wohlwend D, Friedrich T, Michel H, Kusumoto T, Sakamoto J, Melin F, Hellwig P. Electrocatalytic evidence of the diversity of the oxygen reaction in the bacterial bd oxidase from different organisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148436. [PMID: 33940039 DOI: 10.1016/j.bbabio.2021.148436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022]
Abstract
Cytochrome bd oxidase is a bacterial terminal oxygen reductase that was suggested to enable adaptation to different environments and to confer resistance to stress conditions. An electrocatalytic study of the cyt bd oxidases from Escherichia coli, Corynebacterium glutamicum and Geobacillus thermodenitrificans gives evidence for a different reactivity towards oxygen. An inversion of the redox potential values of the three hemes is found when comparing the enzymes from different bacteria. This inversion can be correlated with different protonated glutamic acids as evidenced by reaction induced FTIR spectroscopy. The influence of the microenvironment of the hemes on the reactivity towards oxygen is discussed.
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Affiliation(s)
- Anton Nikolaev
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg - CNRS 4, rue Blaise Pascal, 67081 Strasborg, France
| | - Schara Safarian
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hartmut Michel
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Tomoichirou Kusumoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Fukuoka, Japan
| | - Junshi Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Fukuoka, Japan
| | - Frederic Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg - CNRS 4, rue Blaise Pascal, 67081 Strasborg, France.
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg - CNRS 4, rue Blaise Pascal, 67081 Strasborg, France; USIAS, University of Strasbourg Institute for Advanced Studies, Strasbourg, France.
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25
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Reed CJ, Lam QN, Mirts EN, Lu Y. Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chem Soc Rev 2021; 50:2486-2539. [PMID: 33475096 PMCID: PMC7920998 DOI: 10.1039/d0cs01297a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
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Affiliation(s)
- Christopher J Reed
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA.
| | - Quan N Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA
| | - Evan N Mirts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA. and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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26
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Ko EM, Oh JI. Induction of the cydAB Operon Encoding the bd Quinol Oxidase Under Respiration-Inhibitory Conditions by the Major cAMP Receptor Protein MSMEG_6189 in Mycobacterium smegmatis. Front Microbiol 2020; 11:608624. [PMID: 33343552 PMCID: PMC7739888 DOI: 10.3389/fmicb.2020.608624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/06/2020] [Indexed: 12/29/2022] Open
Abstract
The respiratory electron transport chain (ETC) of Mycobacterium smegmatis is terminated with two terminal oxidases, the aa 3 cytochrome c oxidase and the cytochrome bd quinol oxidase. The bd quinol oxidase with a higher binding affinity for O2 than the aa 3 oxidase is known to play an important role in aerobic respiration under oxygen-limiting conditions. Using relevant crp1 (MSMEG_6189) and crp2 (MSMEG_0539) mutant strains of M. smegmatis, we demonstrated that Crp1 plays a predominant role in induction of the cydAB operon under ETC-inhibitory conditions. Two Crp-binding sequences were identified upstream of the cydA gene, both of which are necessary for induction of cydAB expression under ETC-inhibitory conditions. The intracellular level of cAMP in M. smegmatis was found to be increased under ETC-inhibitory conditions. The crp2 gene was found to be negatively regulated by Crp1 and Crp2, which appears to lead to significantly low cellular abundance of Crp2 relative to Crp1 in M. smegmatis. Our RNA sequencing analyses suggest that in addition to the SigF partner switching system, Crp1 is involved in induction of gene expression in M. smegmatis exposed to ETC-inhibitory conditions.
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Affiliation(s)
- Eon-Min Ko
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
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27
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Zhang Z, Sun J, Guo H, Wang C, Fang T, Rogers MJ, He J, Wang H. Anaerobic biodegradation of phenanthrene by a newly isolated nitrate-dependent Achromobacter denitrificans strain PheN1 and exploration of the biotransformation processes by metabolite and genome analyses. Environ Microbiol 2020; 23:908-923. [PMID: 32812321 DOI: 10.1111/1462-2920.15201] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/15/2020] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread and harmful contaminants and are more persistent under anaerobic conditions. The bioremediation of PAHs in anaerobic zones has been enhanced by treating the contamination with nitrate, which is thermodynamically favourable, cost-effective, and highly soluble. However, anaerobic PAHs biotransformation processes that employ nitrate as an electron acceptor have not been fully explored. In this study, we investigated the anaerobic biotransformation of PAHs by strain PheN1, a newly isolated phenanthrene-degrading denitrifier, using phenanthrene as a model compound. PheN1 is phylogenetically closely related to Achromobacter denitrificans and reduces nitrate to nitrite (not N2 ) during the anaerobic phenanthrene degradation process. Phenanthrene biotransformation processes were detected using gas chromatography-mass spectrometry and were further examined by reverse transcription-quantitative PCR and genome analyses. Carboxylation and methylation were both found to be the initial steps in the phenanthrene degradation process. Downstream biotransformation processed benzene compounds and cyclohexane derivatives. This study describes the isolation of an anaerobic phenanthrene-degrading bacterium along with the pure-culture evidence of phenanthrene biotransformation processes with nitrate as an electron acceptor. The findings in this study can improve our understanding of anaerobic PAHs biodegradation processes and guide PAHs bioremediation by adding nitrate to anaerobic environments.
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Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Tingting Fang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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Borisov VB, Siletsky SA. Features of Organization and Mechanism of Catalysis of Two Families of Terminal Oxidases: Heme-Copper and bd-Type. BIOCHEMISTRY (MOSCOW) 2019; 84:1390-1402. [DOI: 10.1134/s0006297919110130] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Murali R, Gennis RB. Functional importance of Glutamate-445 and Glutamate-99 in proton-coupled electron transfer during oxygen reduction by cytochrome bd from Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:577-590. [PMID: 29719208 DOI: 10.1016/j.bbabio.2018.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/27/2022]
Abstract
The recent X-ray structure of the cytochrome bd respiratory oxygen reductase showed that two of the three heme components, heme d and heme b595, have glutamic acid as an axial ligand. No other native heme proteins are known to have glutamic acid axial ligands. In this work, site-directed mutagenesis is used to probe the roles of these glutamic acids, E445 and E99 in the E. coli enzyme. It is concluded that neither glutamate is a strong ligand to the heme Fe and they are not the major determinates of heme binding to the protein. Although very important, neither glutamate is absolutely essential for catalytic function. The close interactions between the three hemes in cyt bd result in highly cooperative properties. For example, mutation of E445, which is near heme d, has its greatest effects on the properties of heme b595 and heme b558. It is concluded that 1) O2 binds to the hydrophilic side of heme d and displaces E445; 2) E445 forms a salt bridge with R448 within the O2 binding pocket, and both residues play a role to stabilize oxygenated states of heme d during catalysis; 3) E445 and E99 are each protonated accompanying electron transfer to heme d and heme b595, respectively; 4) All protons used to generate water within the heme d active site come from the cytoplasm and are delivered through a channel that must include internal water molecules to assist proton transfer: [cytoplasm] → E107 → E99 (heme b595) → E445 (heme d) → oxygenated heme d.
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Affiliation(s)
- Ranjani Murali
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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Siletsky SA, Dyuba AV, Elkina DA, Monakhova MV, Borisov VB. Spectral-Kinetic Analysis of Recombination Reaction of Heme Centers of bd-Type Quinol Oxidase from Escherichia coli with Carbon Monoxide. BIOCHEMISTRY (MOSCOW) 2018; 82:1354-1366. [PMID: 29223162 DOI: 10.1134/s000629791711013x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recombination of the isolated, fully reduced bd-type quinol oxidase from Escherichia coli with carbon monoxide was studied by pulsed absorption spectrophotometry with microsecond time resolution. Analysis of the kinetic phases of recombination was carried out using the global analysis of multiwavelength kinetic data ("Global fitting"). It was found that the unresolved photodissociation of CO is followed by a stepwise (with four phases) recombination with characteristic times (τ) of about 20 µs, 250 µs, 1.1 ms, and 24 ms. The 20-µs phase most likely reflects bimolecular recombination of CO with heme d. Two subsequent kinetic transitions, with τ ~ 250 µs and 1.1 ms, were resolved for the first time. It is assumed that the 250-µs phase is heterogeneous and includes two different processes: recombination of CO with ~7% of heme b595 and transition of heme d from a pentacoordinate to a transient hexacoordinate state in this enzyme population. The 24-ms transition probably reflects a return of heme d to the pentacoordinate state in the same protein fraction. The 1.1-ms phase can be explained by recombination of CO with ~15% of heme b558. Possible models of interaction of CO with different heme centers are discussed.
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Affiliation(s)
- S A Siletsky
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119991, Russia.
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Yassin AF, Langenberg S, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Mukherjee S, Reddy TBK, Daum C, Shapiro N, Ivanova N, Woyke T, Kyrpides NC. Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence. PLoS One 2017; 12:e0188914. [PMID: 29216246 PMCID: PMC5720513 DOI: 10.1371/journal.pone.0188914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022] Open
Abstract
The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.
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Affiliation(s)
- Atteyet F. Yassin
- Institut für medizinische Mikrobiologie und Immunologie der Universität Bonn, Bonn, Germany
- * E-mail:
| | - Stefan Langenberg
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Manoj Pillay
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Krishnaveni Palaniappan
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Neha Varghese
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Natalia Mikhailova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - T. B. K. Reddy
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Chris Daum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
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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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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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Borisov VB, Forte E, Siletsky SA, Arese M, Davletshin AI, Sarti P, Giuffrè A. Cytochrome bd protects bacteria against oxidative and nitrosative stress: A potential target for next-generation antimicrobial agents. BIOCHEMISTRY (MOSCOW) 2015; 80:565-75. [DOI: 10.1134/s0006297915050077] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ramel F, Brasseur G, Pieulle L, Valette O, Hirschler-Réa A, Fardeau ML, Dolla A. Growth of the obligate anaerobe Desulfovibrio vulgaris Hildenborough under continuous low oxygen concentration sparging: impact of the membrane-bound oxygen reductases. PLoS One 2015; 10:e0123455. [PMID: 25837676 PMCID: PMC4383621 DOI: 10.1371/journal.pone.0123455] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
Although obligate anaerobe, the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) exhibits high aerotolerance that involves several enzymatic systems, including two membrane-bound oxygen reductases, a bd-quinol oxidase and a cc(b/o)o3 cytochrome oxidase. Effect of constant low oxygen concentration on growth and morphology of the wild-type, single (Δbd, Δcox) and double deletion (Δcoxbd) mutant strains of the genes encoding these oxygen reductases was studied. When both wild-type and deletion mutant strains were cultured in lactate/sulfate medium under constant 0.02% O2 sparging, they were able to grow but the final biomasses and the growth yield were lower than that obtained under anaerobic conditions. At the end of the growth, lactate was not completely consumed and when conditions were then switched to anaerobic, growth resumed. Time-lapse microscopy revealed that a large majority of the cells were then able to divide (over 97%) but the time to recover a complete division event was longer for single deletion mutant Δbd than for the three other strains. Determination of the molar growth yields on lactate suggested that a part of the energy gained from lactate oxidation was derived toward cells protection/repairing against oxidative conditions rather than biosynthesis, and that this part was higher in the single deletion mutant Δbd and, to a lesser extent, Δcox strains. Our data show that when DvH encounters oxidative conditions, it is able to stop growing and to rapidly resume growing when conditions are switched to anaerobic, suggesting that it enters active dormancy sate under oxidative conditions. We propose that the pyruvate-ferredoxin oxidoreductase (PFOR) plays a central role in this phenomenon by reversibly switching from an oxidative-sensitive fully active state to an oxidative-insensitive inactive state. The oxygen reductases, and especially the bd-quinol oxidase, would have a crucial function by maintaining reducing conditions that permit PFOR to stay in its active state.
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Affiliation(s)
- Fanny Ramel
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Gael Brasseur
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | | | - Odile Valette
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Agnès Hirschler-Réa
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, UM110, 13288 Marseille, Cedex 09, France
| | - Marie Laure Fardeau
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, UM110, 13288 Marseille, Cedex 09, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
- * E-mail:
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Chen H, Luo Q, Yin J, Gao T, Gao H. Evidence for the requirement of CydX in function but not assembly of the cytochrome bd oxidase in Shewanella oneidensis. Biochim Biophys Acta Gen Subj 2014; 1850:318-28. [PMID: 25316290 DOI: 10.1016/j.bbagen.2014.10.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/25/2014] [Accepted: 10/06/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cytochrome bd oxidase, existing widely in bacteria, produces a proton motive force by the vectorial charge transfer of protons and more importantly, endows bacteria with a number of vitally important physiological functions, such as enhancing tolerance to various stresses. Although extensively studied as a CydA-CydB two-subunit complex for decades, the complex in certain groups of bacteria is recently found to in fact consist of an additional subunit, which is functionally essential. METHODS We investigated the assembly of the CydA-CydB complex using BiFC. We investigated the function of CydX using mutational analysis. RESULTS CydX, a 38-amino-acid inner-membrane protein, is associated with the CydA-CydB complex in Shewanella oneidensis, a facultative anaerobe renowned for its respiratory versatility. It is clear that CydX is neither required for the in vivo assembly of the CydA-CydB complex nor relies on the complex for its translocation and integration into the membrane. The N-terminal segment (1-25 amino acid residues) and short periplasmic overhang of CydX, with respect to functionality, are important whereas the remaining C-terminal segment is rather flexible. CONCLUSION Based on these findings, we postulate that CydX may function by positioning and stabilizing the prosthetic hemes, especially heme d in the CydA-CydB complex although a role of participating in catalytic reaction is not excluded. GENERAL SIGNIFICANCE The work provides novel insights into our understanding of the small subunit of the cytochrome bd oxidase.
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Affiliation(s)
- Haijiang Chen
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qixia Luo
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jianhua Yin
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tong Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Siletsky SA, Zaspa AA, Poole RK, Borisov VB. Microsecond time-resolved absorption spectroscopy used to study CO compounds of cytochrome bd from Escherichia coli. PLoS One 2014; 9:e95617. [PMID: 24755641 PMCID: PMC3995794 DOI: 10.1371/journal.pone.0095617] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 03/28/2014] [Indexed: 11/18/2022] Open
Abstract
Cytochrome bd is a tri-heme (b558, b595, d) respiratory oxygen reductase that is found in many bacteria including pathogenic species. It couples the electron transfer from quinol to O2 with generation of an electrochemical proton gradient. We examined photolysis and subsequent recombination of CO with isolated cytochrome bd from Escherichia coli in one-electron reduced (MV) and fully reduced (R) states by microsecond time-resolved absorption spectroscopy at 532-nm excitation. Both Soret and visible band regions were examined. CO photodissociation from MV enzyme possibly causes fast (τ<1.5 µs) electron transfer from heme d to heme b595 in a small fraction of the protein, not reported earlier. Then the electron migrates to heme b558 (τ∼16 µs). It returns from the b-hemes to heme d with τ∼180 µs. Unlike cytochrome bd in the R state, in MV enzyme the apparent contribution of absorbance changes associated with CO dissociation from heme d is small, if any. Photodissociation of CO from heme d in MV enzyme is suggested to be accompanied by the binding of an internal ligand (L) at the opposite side of the heme. CO recombines with heme d (τ∼16 µs) yielding a transient hexacoordinate state (CO-Fe2+-L). Then the ligand slowly (τ∼30 ms) dissociates from heme d. Recombination of CO with a reduced heme b in a fraction of the MV sample may also contribute to the 30-ms phase. In R enzyme, CO recombines to heme d (τ∼20 µs), some heme b558 (τ∼0.2-3 ms), and finally migrates from heme d to heme b595 (τ∼24 ms) in ∼5% of the enzyme population. Data are consistent with the recent nanosecond study of Rappaport et al. conducted on the membranes at 640-nm excitation but limited to the Soret band. The additional phases were revealed due to differences in excitation and other experimental conditions.
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Affiliation(s)
- Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Andrey A. Zaspa
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
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Cytochrome bd oxidase and bacterial tolerance to oxidative and nitrosative stress. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1178-87. [PMID: 24486503 DOI: 10.1016/j.bbabio.2014.01.016] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/25/2014] [Accepted: 01/27/2014] [Indexed: 12/28/2022]
Abstract
Cytochrome bd is a prokaryotic respiratory quinol:O2 oxidoreductase, phylogenetically unrelated to the extensively studied heme-copper oxidases (HCOs). The enzyme contributes to energy conservation by generating a proton motive force, though working with a lower energetic efficiency as compared to HCOs. Relevant to patho-physiology, members of the bd-family were shown to promote virulence in some pathogenic bacteria, which makes these enzymes of interest also as potential drug targets. Beyond its role in cell bioenergetics, cytochrome bd accomplishes several additional physiological functions, being apparently implicated in the response of the bacterial cell to a number of stress conditions. Compelling experimental evidence suggests that the enzyme enhances bacterial tolerance to oxidative and nitrosative stress conditions, owing to its unusually high nitric oxide (NO) dissociation rate and a notable catalase activity; the latter has been recently documented in one of the two bd-type oxidases of Escherichia coli. Current knowledge on cytochrome bd and its reactivity with O2, NO and H2O2 is summarized in this review in the light of the hypothesis that the preferential (over HCOs) expression of cytochrome bd in pathogenic bacteria may represent a strategy to evade the host immune attack based on production of NO and reactive oxygen species (ROS). This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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41
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Le Laz S, Kpebe A, Bauzan M, Lignon S, Rousset M, Brugna M. A biochemical approach to study the role of the terminal oxidases in aerobic respiration in Shewanella oneidensis MR-1. PLoS One 2014; 9:e86343. [PMID: 24466040 PMCID: PMC3899249 DOI: 10.1371/journal.pone.0086343] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/11/2013] [Indexed: 11/19/2022] Open
Abstract
The genome of the facultative anaerobic γ-proteobacterium Shewanella oneidensis MR-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a A-type cytochrome c oxidase and a cbb3-type oxidase. In this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. Our data revealed that the cbb3-type oxidase is the major terminal oxidase under aerobic conditions while both cbb3-type and bd-type oxidases are involved in respiration at low-O2 tensions. On the contrary, the low O2-affinity A-type cytochrome c oxidase was not detected in our experimental conditions even under aerobic conditions and would therefore not be required for aerobic respiration in S. oneidensis MR-1. In addition, the deduced amino acid sequence suggests that the A-type cytochrome c oxidase is a ccaa3-type oxidase since an uncommon extra-C terminal domain contains two c-type heme binding motifs. The particularity of the aerobic respiratory pathway and the physiological implication of the presence of a ccaa3-type oxidase in S. oneidensis MR-1 are discussed.
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Affiliation(s)
- Sébastien Le Laz
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, Marseille, France
| | - Arlette Kpebe
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, Marseille, France
| | - Marielle Bauzan
- CNRS, Aix-Marseille Université, Unité de fermentation, FR3479, IMM, Marseille, France
| | - Sabrina Lignon
- CNRS, Aix-Marseille Université, Plate-forme Protéomique, FR3479, IMM, MaP IBiSA, Marseille, France
| | - Marc Rousset
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, Marseille, France
| | - Myriam Brugna
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, Marseille, France
- * E-mail:
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Miura H, Mogi T, Ano Y, Migita CT, Matsutani M, Yakushi T, Kita K, Matsushita K. Cyanide-insensitive quinol oxidase (CIO) from Gluconobacter oxydans is a unique terminal oxidase subfamily of cytochrome bd. ACTA ACUST UNITED AC 2013; 153:535-45. [DOI: 10.1093/jb/mvt019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Arutyunyan AM, Sakamoto J, Inadome M, Kabashima Y, Borisov VB. Optical and magneto-optical activity of cytochrome bd from Geobacillus thermodenitrificans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:2087-94. [DOI: 10.1016/j.bbabio.2012.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 06/13/2012] [Accepted: 06/15/2012] [Indexed: 10/28/2022]
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Borisov VB, Gennis RB, Hemp J, Verkhovsky MI. The cytochrome bd respiratory oxygen reductases. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1807:1398-413. [PMID: 21756872 PMCID: PMC3171616 DOI: 10.1016/j.bbabio.2011.06.016] [Citation(s) in RCA: 374] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 06/23/2011] [Accepted: 06/24/2011] [Indexed: 01/03/2023]
Abstract
Cytochrome bd is a respiratory quinol: O₂ oxidoreductase found in many prokaryotes, including a number of pathogens. The main bioenergetic function of the enzyme is the production of a proton motive force by the vectorial charge transfer of protons. The sequences of cytochromes bd are not homologous to those of the other respiratory oxygen reductases, i.e., the heme-copper oxygen reductases or alternative oxidases (AOX). Generally, cytochromes bd are noteworthy for their high affinity for O₂ and resistance to inhibition by cyanide. In E. coli, for example, cytochrome bd (specifically, cytochrome bd-I) is expressed under O₂-limited conditions. Among the members of the bd-family are the so-called cyanide-insensitive quinol oxidases (CIO) which often have a low content of the eponymous heme d but, instead, have heme b in place of heme d in at least a majority of the enzyme population. However, at this point, no sequence motif has been identified to distinguish cytochrome bd (with a stoichiometric complement of heme d) from an enzyme designated as CIO. Members of the bd-family can be subdivided into those which contain either a long or a short hydrophilic connection between transmembrane helices 6 and 7 in subunit I, designated as the Q-loop. However, it is not clear whether there is a functional consequence of this difference. This review summarizes current knowledge on the physiological functions, genetics, structural and catalytic properties of cytochromes bd. Included in this review are descriptions of the intermediates of the catalytic cycle, the proposed site for the reduction of O₂, evidence for a proton channel connecting this active site to the bacterial cytoplasm, and the molecular mechanism by which a membrane potential is generated.
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Affiliation(s)
- Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russian Federation.
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Giuffrè A, Borisov VB, Mastronicola D, Sarti P, Forte E. Cytochromebdoxidase and nitric oxide: From reaction mechanisms to bacterial physiology. FEBS Lett 2011; 586:622-9. [DOI: 10.1016/j.febslet.2011.07.035] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 07/20/2011] [Accepted: 07/26/2011] [Indexed: 11/27/2022]
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Catalytic intermediates of cytochrome bd terminal oxidase at steady-state: Ferryl and oxy-ferrous species dominate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:503-9. [DOI: 10.1016/j.bbabio.2011.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 02/15/2011] [Indexed: 11/22/2022]
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47
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Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb(3). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:813-8. [PMID: 21315685 DOI: 10.1016/j.bbabio.2011.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 11/21/2022]
Abstract
The proton-pumping cbb(3)-type cytochrome c oxidases catalyze cell respiration in many pathogenic bacteria. For reasons not yet understood, the apparent dioxygen (O(2)) affinity in these enzymes is very high relative to other members of the heme-copper oxidase (HCO) superfamily. Based on density functional theory (DFT) calculations on intermediates of the oxygen scission reaction in active-site models of cbb(3)- and aa(3)-type oxidases, we find that a transient peroxy intermediate (I(P), Fe[III]-OOH(-)) is ~6kcal/mol more stable in the former case, resulting in more efficient kinetic trapping of dioxygen and hence in a higher apparent oxygen affinity. The major molecular basis for this stabilization is a glutamate residue, polarizing the proximal histidine ligand of heme b(3) in the active site.
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Bergmann F, Selesi D, Weinmaier T, Tischler P, Rattei T, Meckenstock RU. Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47. Environ Microbiol 2010; 13:1125-37. [PMID: 21176053 DOI: 10.1111/j.1462-2920.2010.02391.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobic degradation of polycyclic aromatic hydrocarbons (PAHs) is an important process during natural attenuation of aromatic hydrocarbon spills. However, knowledge about metabolic potential and physiology of organisms involved in anaerobic degradation of PAHs is scarce. Therefore, we introduce the first genome of the sulfate-reducing Deltaproteobacterium N47 able to catabolize naphthalene, 2-methylnaphthalene, or 2-naphthoic acid as sole carbon source. Based on proteomics, we analysed metabolic pathways during growth on PAHs to gain physiological insights on anaerobic PAH degradation. The genomic assembly and taxonomic binning resulted in 17 contigs covering most of the sulfate reducer N47 genome according to general cluster of orthologous groups (COGs) analyses. According to the genes present, the Deltaproteobacterium N47 can potentially grow with the following sugars including d-mannose, d-fructose, d-galactose, α-d-glucose-1P, starch, glycogen, peptidoglycan and possesses the prerequisites for butanoic acid fermentation. Despite the inability for culture N47 to utilize NO(3) (-) as terminal electron acceptor, genes for nitrate ammonification are present. Furthermore, it is the first sequenced genome containing a complete TCA cycle along with the carbon monoxide dehydrogenase pathway. The genome contained a significant percentage of repetitive sequences and transposase-related protein domains enhancing the ability of genome evolution. Likewise, the sulfate reducer N47 genome contained many unique putative genes with unknown function, which are candidates for yet-unknown metabolic pathways.
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Affiliation(s)
- Franz Bergmann
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, Germany
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Borisov VB, Davletshin AI, Konstantinov AA. Peroxidase activity of cytochrome bd from Escherichia coli. BIOCHEMISTRY (MOSCOW) 2010; 75:428-36. [PMID: 20618131 DOI: 10.1134/s000629791004005x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cytochrome bd from Escherichia coli is able to oxidize such substrates as guaiacol, ferrocene, benzohydroquinone, and potassium ferrocyanide through the peroxidase mechanism, while none of these donors is oxidized in the oxidase reaction (i.e. in the reaction that involves molecular oxygen as the electron acceptor). Peroxidation of guaiacol has been studied in detail. The dependence of the rate of the reaction on the concentration of the enzyme and substrates as well as the effect of various inhibitors of the oxidase reaction on the peroxidase activity have been tested. The dependence of the guaiacol-peroxidase activity on the H2O2 concentration is linear up to the concentration of 8 mM. At higher concentrations of H2O2, inactivation of the enzyme is observed. Guaiacol markedly protects the enzyme from inactivation induced by peroxide. The peroxidase activity of cytochrome bd increases with increasing guaiacol concentration, reaching saturation in the range from 0.5 to 2.5 mM, but then starts falling. Such inhibitors of the ubiquinol-oxidase activity of cytochrome bd as cyanide, pentachlorophenol, and 2-n-heptyl 4-hydroxyquinoline-N-oxide also suppress its guaiacol-peroxidase activity; in contrast, zinc ions have no influence on the enzyme-catalyzed peroxidation of guaiacol. These data suggest that guaiacol interacts with the enzyme in the center of ubiquinol binding and donates electrons into the di-heme center of oxygen reduction via heme b(558), and H2O2 is reduced by heme d. Although the peroxidase activity of cytochrome bd from E. coli is low compared to peroxidases, it might be of physiological significance for the bacterium itself and plays a pathophysiological role for humans and animals.
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Affiliation(s)
- V B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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50
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Meuric V, Rouillon A, Chandad F, Bonnaure-Mallet M. Putative respiratory chain of Porphyromonas gingivalis. Future Microbiol 2010; 5:717-34. [PMID: 20441545 DOI: 10.2217/fmb.10.32] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The electron transfer chain in Porphyromonas gingivalis, or periodontopathogens, has not yet been characterized. P. gingivalis, a strict anaerobic bacteria and the second colonizer of the oral cavity, is considered to be a major causal agent involved in periodontal diseases. Primary colonizers create a favorable environment for P. gingivalis growth by decreasing oxygen pressure. Oxygen does not appear to be the final electron acceptor of the respiratory chain. Fumarate and cytochrome b have been implicated as major components of the respiratory activity. However, the P. gingivalis genome shows many other enzymes that could be implicated in aerobic or nitrite respiration. Using bioinformatic tools and literature studies of respiratory pathways, the ATP synthesis mechanism from the sodium cycle and nutrients metabolism, the putative respirasome of P. gingivalis has been proposed.
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Affiliation(s)
- Vincent Meuric
- Equipe de Microbiologie, UPRES-EA 1254, Université Européenne de Bretagne, Université de Rennes I, UFR Odontologie, Bâtiment 15, 2 Avenue du Professeur Léon Bernard, 35043 Rennes Cedex, France
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