1
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van der Velden TT, Kayastha K, Waterham CYJ, Brünle S, Jeuken LJC. Menaquinone-specific turnover by M. tuberculosis cytochrome bd is redox regulated by the Q-loop disulfide bond. J Biol Chem 2024:108094. [PMID: 39706268 DOI: 10.1016/j.jbc.2024.108094] [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: 10/09/2024] [Revised: 12/02/2024] [Accepted: 12/11/2024] [Indexed: 12/23/2024] Open
Abstract
Cytochrome bd from Mycobacterium tuberculosis (Mtbd) is a menaquinol oxidase that has gained interest as an antibiotic target due to its importance in survival under infectious conditions. Mtbd contains a characteristic disulfide bond that has been hypothesized to allow for Mtbd activity regulation at the enzymatic level, possibly helping M. tuberculosis to rapidly adapt to the hostile environment of the phagosome. Here, the role of the disulfide bond and quinone specificity have been determined by reconstitution of a minimal respiratory chain and the single-particle cryo-EM structure in the disulfide-reduced form. Mtbd was shown to be specific for menaquinone, while regulation by reduction of the Q-loop disulfide bond decreased oxidase activity up to 90%. Structural analysis shows that a salt bridge unique to Mtbd keeps the Q-loop partially structured in its disulfide-reduced form, which could facilitate the rapid activation of Mtbd upon exposure to reactive oxygen species. We signify Mtbd as the first redox sensory terminal oxidase and propose that this helps M. tuberculosis in the defence against reactive oxygen species encountered during infection.
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Affiliation(s)
- Tijn T van der Velden
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Kanwal Kayastha
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Caspar Y J Waterham
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Steffen Brünle
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Lars J C Jeuken
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands.
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2
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Ueki A, Harada S, Aoyagi M, Matsumoto H, Ueda R, Mizuguchi K, Méhes G, Nagamine K. Electric wiring of bacteria using redox polymers and selective measurement of metabolic activity in the presence of surrounding planktonic bacteria. Bioelectrochemistry 2024; 160:108779. [PMID: 39003947 DOI: 10.1016/j.bioelechem.2024.108779] [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: 05/28/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
Non-electroactive bacteria (n-EAB), constituting the majority of known bacteria to date, have been underutilized in electrochemical conversion technologies due to their lack of direct electron transfer to electrodes. In this study, we established an electric wiring between n-EAB (gram-positive Bacillus subtilis and gram-negative Escherichia coli) and an extracellular electrode via a ferrocene-polyethyleneimine-based redox polymer (Fc-PEI). Chronoamperometry recordings indicated that Fc-PEI can transfer intracellular electrons to the extracellular electrode regardless of the molecular organization of PEI (linear or branched) and the membrane structure of bacteria (gram-positive or -negative). As fluorescence staining suggested, Fc-PEI improves the permeability of the bacterial cell membrane, enabling electron carriers in the cell to react with Fc. In addition, experiments with Fc-immobilized electrodes without PEI suggested the existence of an alternative electron transfer pathway from B. subtilis to the extracellular Fc adsorbed onto the cell membrane. Furthermore, we proposed for the first time that the bacteria/Fc-linear PEI modified structure enables selective measurement of immobilized bacterial activity by physically blocking contact between the electrode surface and planktonic cells co-existing in the surrounding media. Such electrodes can be a powerful analytical tool for elucidating the metabolic activities of specific bacteria wired to the electrode even within complex bacterial communities.
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Affiliation(s)
- Aoba Ueki
- Graduate School of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Shoi Harada
- Faculty of Engineering, Department of Polymeric and Organic Materials Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Marika Aoyagi
- Graduate School of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Hirotaka Matsumoto
- Graduate School of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Riku Ueda
- Faculty of Engineering, Department of Polymeric and Organic Materials Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Kei Mizuguchi
- Graduate School of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Gábor Méhes
- Graduate School of Information, Production and Systems, Waseda University, 2-7 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Kuniaki Nagamine
- Graduate School of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan; Faculty of Engineering, Department of Polymeric and Organic Materials Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan.
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3
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Janczak M, Vilhjálmsdóttir J, Ädelroth P. Proton transfer in cytochrome bd-I from E. coli involves Asp-105 in CydB. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149489. [PMID: 39009175 DOI: 10.1016/j.bbabio.2024.149489] [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: 04/30/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
Cytochrome bds are bacterial terminal oxidases expressed under low oxygen conditions, and they are important for the survival of many pathogens and hence potential drug targets. The largest subunit CydA contains the three redox-active cofactors heme b558, heme b595 and the active site heme d. One suggested proton transfer pathway is found at the interface between the CydA and the other major subunit CydB. Here we have studied the O2 reduction mechanism in E. coli cyt. bd-I using the flow-flash technique and focused on the mechanism, kinetics and pathway for proton transfer. Our results show that the peroxy (P) to ferryl (F) transition, coupled to the oxidation of the low-spin heme b558 is pH dependent, with a maximum rate constant (~104 s-1) that is slowed down at higher pH. We assign this behavior to rate-limitation by internal proton transfer from a titratable residue with pKa ~ 9.7. Proton uptake from solution occurs with the same P➔F rate constant. Site-directed mutagenesis shows significant effects on catalytic turnover in the CydB variants Asp58B➔Asn and Asp105B➔Asn variants consistent with them playing a role in proton transfer. Furthermore, in the Asp105B➔Asn variant, the reactions up to P formation occur essentially as in the wildtype bd-I, but the P➔F transition is specifically inhibited, supporting a direct and specific role for Asp105B in the functional proton transfer pathway in bd-I. We further discuss the possible identity of the high pKa proton donor, and the conservation pattern of the Asp-105B in the cyt. bd superfamily.
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Affiliation(s)
- M Janczak
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - J Vilhjálmsdóttir
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - P Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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4
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Burton AT, Zeinert R, Storz G. Large Roles of Small Proteins. Annu Rev Microbiol 2024; 78:1-22. [PMID: 38772630 DOI: 10.1146/annurev-micro-112723-083001] [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] [Indexed: 05/23/2024]
Abstract
Bacterial proteins of ≤50 amino acids, denoted small proteins or microproteins, have been traditionally understudied and overlooked, as standard computational, biochemical, and genetic approaches often do not detect proteins of this size. However, with the realization that small proteins are stably expressed and have important cellular roles, there has been increased identification of small proteins in bacteria and eukaryotes. Gradually, the functions of a few of these small proteins are being elucidated. Many interact with larger protein products to modulate their subcellular localization, stabilities, or activities. Here, we provide an overview of these diverse functions in bacteria, highlighting generalities among bacterial small proteins and similarly sized proteins in eukaryotic organisms and discussing questions for future research.
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Affiliation(s)
- Aisha T Burton
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, USA
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA;
| | - Rilee Zeinert
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, USA
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA;
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA;
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5
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Borisov VB, Arutyunyan AM. The fully reduced terminal oxidase bd-I isolated from Escherichia coli binds cyanide. J Inorg Biochem 2024; 259:112653. [PMID: 38943845 DOI: 10.1016/j.jinorgbio.2024.112653] [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: 06/03/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Cytochrome bd-I from Escherichia coli belongs to the superfamily of prokaryotic bd-type oxygen reductases. It contains three hemes, b558, b595 and d, and couples oxidation of quinol by dioxygen with the generation of a proton-motive force. The enzyme exhibits resistance to various stressors and is considered as a target protein for next-generation antimicrobials. By using electronic absorption and MCD spectroscopy, this work shows that cyanide binds to heme d2+ in the isolated fully reduced cytochrome bd-I. Cyanide-induced difference absorption spectra display changes near the heme d2+ α-band, a minimum at 633 nm and a maximum around 600 nm, and a W-shaped response in the Soret region. Apparent dissociation constant (Kd) of the cyanide complex of heme d2+ is ∼0.052 M. Kinetics of cyanide binding is monophasic, indicating the presence of a single ligand binding site in the enzyme. Consistently, MCD data show that cyanide binds to heme d2+ but not to b5582+ or b5952+. This agrees with the published structural data that the enzyme's active site is not a di-heme site. The observed rate of binding (kobs) increases as the concentration of cyanide is increased, giving a second-order rate constant (kon) of ∼0.1 M-1 s-1.
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Affiliation(s)
- Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia.
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
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6
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Carlson RP, Beck AE, Benitez MG, Harcombe WR, Mahadevan R, Gedeon T. Cell Geometry and Membrane Protein Crowding Constrain Growth Rate, Overflow Metabolism, Respiration, and Maintenance Energy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609071. [PMID: 39229203 PMCID: PMC11370460 DOI: 10.1101/2024.08.21.609071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
A metabolic theory is presented for predicting maximum growth rate, overflow metabolism, respiration efficiency, and maintenance energy flux based on the intersection of cell geometry, membrane protein crowding, and metabolism. The importance of cytosolic macromolecular crowding on phenotype has been established in the literature but the importance of surface area has been largely overlooked due to incomplete knowledge of membrane properties. We demonstrate that the capacity of the membrane to host proteins increases with growth rate offsetting decreases in surface area-to-volume ratios (SA:V). This increase in membrane protein is hypothesized to be essential to competitive Escherichia coli phenotypes. The presented membrane-centric theory uses biophysical properties and metabolic systems analysis to successfully predict the phenotypes of E. coli K-12 strains, MG1655 and NCM3722, which are genetically similar but have SA:V ratios that differ up to 30%, maximum growth rates on glucose media that differ by 40%, and overflow phenotypes that start at growth rates that differ by 80%. These analyses did not consider cytosolic macromolecular crowding, highlighting the distinct properties of the presented theory. Cell geometry and membrane protein crowding are significant biophysical constraints on phenotype and provide a theoretical framework for improved understanding and control of cell biology.
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Affiliation(s)
- Ross P. Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT USA
| | - Ashley E. Beck
- Department of Biological and Environmental Sciences, Carroll College, Helena, MT USA
| | | | - William R. Harcombe
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN USA
| | | | - Tomáš Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, MT USA
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7
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Spari D, Schmid A, Sanchez-Taltavull D, Murugan S, Keller K, Ennaciri N, Salm L, Stroka D, Beldi G. Released bacterial ATP shapes local and systemic inflammation during abdominal sepsis. eLife 2024; 13:RP96678. [PMID: 39163101 PMCID: PMC11335348 DOI: 10.7554/elife.96678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024] Open
Abstract
Sepsis causes millions of deaths per year worldwide and is a current global health priority declared by the WHO. Sepsis-related deaths are a result of dysregulated inflammatory immune responses indicating the need to develop strategies to target inflammation. An important mediator of inflammation is extracellular adenosine triphosphate (ATP) that is released by inflamed host cells and tissues, and also by bacteria in a strain-specific and growth-dependent manner. Here, we investigated the mechanisms by which bacteria release ATP. Using genetic mutant strains of Escherichia coli (E. coli), we demonstrate that ATP release is dependent on ATP synthase within the inner bacterial membrane. In addition, impaired integrity of the outer bacterial membrane notably contributes to ATP release and is associated with bacterial death. In a mouse model of abdominal sepsis, local effects of bacterial ATP were analyzed using a transformed E. coli bearing an arabinose-inducible periplasmic apyrase hydrolyzing ATP to be released. Abrogating bacterial ATP release shows that bacterial ATP suppresses local immune responses, resulting in reduced neutrophil counts and impaired survival. In addition, bacterial ATP has systemic effects via its transport in outer membrane vesicles (OMV). ATP-loaded OMV are quickly distributed throughout the body and upregulated expression of genes activating degranulation in neutrophils, potentially contributing to the exacerbation of sepsis severity. This study reveals mechanisms of bacterial ATP release and its local and systemic roles in sepsis pathogenesis.
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Affiliation(s)
- Daniel Spari
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Annina Schmid
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Daniel Sanchez-Taltavull
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Shaira Murugan
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Keely Keller
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Nadia Ennaciri
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Lilian Salm
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
| | - Guido Beldi
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University Hospital of BernBernSwitzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University Hospital of BernBernSwitzerland
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8
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Henry SA, Webster CM, Shaw LN, Torres NJ, Jobson ME, Totzke BC, Jackson JK, McGreig JE, Wass MN, Robinson GK, Shepherd M. Steroid Drugs Inhibit Bacterial Respiratory Oxidases and Are Lethal Toward Methicillin-Resistant Staphylococcus aureus. J Infect Dis 2024; 230:e149-e158. [PMID: 39052707 PMCID: PMC11272085 DOI: 10.1093/infdis/jiad540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/28/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Cytochrome bd complexes are respiratory oxidases found exclusively in prokaryotes that are important during infection for numerous bacterial pathogens. METHODS In silico docking was employed to screen approved drugs for their ability to bind to the quinol site of Escherichia coli cytochrome bd-I. Respiratory inhibition was assessed with oxygen electrodes using membranes isolated from E. coli and methicillin-resistant Staphylococcus aureus strains expressing single respiratory oxidases (ie, cytochromes bd, bo', or aa3). Growth/viability assays were used to measure bacteriostatic and bactericidal effects. RESULTS The steroid drugs ethinylestradiol and quinestrol inhibited E. coli bd-I activity with median inhibitory concentration (IC50) values of 47 ± 28.9 µg/mL (158 ± 97.2 µM) and 0.2 ± 0.04 µg/mL (0.5 ± 0.1 µM), respectively. Quinestrol inhibited growth of an E. coli "bd-I only" strain with an IC50 of 0.06 ± 0.02 µg/mL (0.2 ± 0.07 µM). Growth of an S. aureus "bd only" strain was inhibited by quinestrol with an IC50 of 2.2 ± 0.43 µg/mL (6.0 ± 1.2 µM). Quinestrol exhibited potent bactericidal effects against S. aureus but not E. coli. CONCLUSIONS Quinestrol inhibits cytochrome bd in E. coli and S. aureus membranes and inhibits the growth of both species, yet is only bactericidal toward S. aureus.
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Affiliation(s)
- Samantha A Henry
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Calum M Webster
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Lindsey N Shaw
- Department of Molecular Biosciences, University of South Florida, Tampa
| | | | | | - Brendan C Totzke
- Department of Molecular Biosciences, University of South Florida, Tampa
| | - Jessica K Jackson
- Department of Molecular Biosciences, University of South Florida, Tampa
| | - Jake E McGreig
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Gary K Robinson
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Mark Shepherd
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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9
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Seitz C, Ahn SH, Wei H, Kyte M, Cook GM, Krause KL, McCammon JA. Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase. J Chem Inf Model 2024; 64:5232-5241. [PMID: 38874541 DOI: 10.1021/acs.jcim.4c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Discovered in the 1920s, cytochrome bd is a terminal oxidase that has received renewed attention as a drug target since its atomic structure was first determined in 2016. Only found in prokaryotes, we study it here as a drug target for Mycobacterium tuberculosis (Mtb). Most previous drug discovery efforts toward cytochrome bd have involved analogues of the canonical substrate quinone, known as Aurachin D. Here, we report six new cytochrome bd inhibitor scaffolds determined from a computational screen and confirmed on target activity through in vitro testing. These scaffolds provide new avenues for lead optimization toward Mtb therapeutics.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Haixin Wei
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Matson Kyte
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Kurt L Krause
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
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10
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Sun G, DeFelice MM, Gillies TE, Ahn-Horst TA, Andrews CJ, Krummenacker M, Karp PD, Morrison JH, Covert MW. Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons. Cell Syst 2024; 15:227-245.e7. [PMID: 38417437 PMCID: PMC10957310 DOI: 10.1016/j.cels.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/12/2023] [Accepted: 02/08/2024] [Indexed: 03/01/2024]
Abstract
Many bacteria use operons to coregulate genes, but it remains unclear how operons benefit bacteria. We integrated E. coli's 788 polycistronic operons and 1,231 transcription units into an existing whole-cell model and found inconsistencies between the proposed operon structures and the RNA-seq read counts that the model was parameterized from. We resolved these inconsistencies through iterative, model-guided corrections to both datasets, including the correction of RNA-seq counts of short genes that were misreported as zero by existing alignment algorithms. The resulting model suggested two main modes by which operons benefit bacteria. For 86% of low-expression operons, adding operons increased the co-expression probabilities of their constituent proteins, whereas for 92% of high-expression operons, adding operons resulted in more stable expression ratios between the proteins. These simulations underscored the need for further experimental work on how operons reduce noise and synchronize both the expression timing and the quantity of constituent genes. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Taryn E Gillies
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Travis A Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Cecelia J Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Jerry H Morrison
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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11
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Nastasi MR, Borisov VB, Forte E. Membrane-Bound Redox Enzyme Cytochrome bd-I Promotes Carbon Monoxide-Resistant Escherichia coli Growth and Respiration. Int J Mol Sci 2024; 25:1277. [PMID: 38279276 PMCID: PMC10815991 DOI: 10.3390/ijms25021277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/23/2023] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
The terminal oxidases of bacterial aerobic respiratory chains are redox-active electrogenic enzymes that catalyze the four-electron reduction of O2 to 2H2O taking out electrons from quinol or cytochrome c. Living bacteria often deal with carbon monoxide (CO) which can act as both a signaling molecule and a poison. Bacterial terminal oxidases contain hemes; therefore, they are potential targets for CO. However, our knowledge of this issue is limited and contradictory. Here, we investigated the effect of CO on the cell growth and aerobic respiration of three different Escherichia coli mutants, each expressing only one terminal quinol oxidase: cytochrome bd-I, cytochrome bd-II, or cytochrome bo3. We found that following the addition of CO to bd-I-only cells, a minimal effect on growth was observed, whereas the growth of both bd-II-only and bo3-only strains was severely impaired. Consistently, the degree of resistance of aerobic respiration of bd-I-only cells to CO is high, as opposed to high CO sensitivity displayed by bd-II-only and bo3-only cells consuming O2. Such a difference between the oxidases in sensitivity to CO was also observed with isolated membranes of the mutants. Accordingly, O2 consumption of wild-type cells showed relatively low CO sensitivity under conditions favoring the expression of a bd-type oxidase.
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Affiliation(s)
- Martina R. Nastasi
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
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12
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Nastasi MR, Borisov VB, Forte E. The terminal oxidase cytochrome bd-I confers carbon monoxide resistance to Escherichia coli cells. J Inorg Biochem 2023; 247:112341. [PMID: 37515940 DOI: 10.1016/j.jinorgbio.2023.112341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/12/2023] [Accepted: 07/22/2023] [Indexed: 07/31/2023]
Abstract
Carbon monoxide (CO) plays a multifaceted role in the physiology of organisms, from poison to signaling molecule. Heme proteins, including terminal oxidases, are plausible CO targets. Three quinol oxidases terminate the branched aerobic respiratory chain of Escherichia coli. These are the heme‑copper cytochrome bo3 and two copper-lacking bd-type cytochromes, bd-I and bd-II. All three enzymes generate a proton motive force during the four-electron oxygen reduction reaction that is used for ATP production. The bd-type oxidases also contribute to mechanisms of bacterial defense against various types of stresses. Here we report that in E. coli cells, at the enzyme concentrations tested, cytochrome bd-I is much more resistant to inhibition by CO than cytochrome bd-II and cytochrome bo3. The apparent half-maximal inhibitory concentration values, IC50, for inhibition of O2 consumption of the membrane-bound bd-II and bo3 oxidases by CO at ~150 μM O2 were estimated to be 187.1 ± 11.1 and 183.3 ± 13.5 μM CO, respectively. Under the same conditions, the maximum inhibition observed with the membrane-bound cytochrome bd-I was 20 ± 10% at ~200 μM CO.
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Affiliation(s)
- Martina R Nastasi
- Department of Biochemical Sciences, Sapienza University of Rome, I-00185 Rome, Italy
| | - Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, I-00185 Rome, Italy.
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13
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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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14
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Kägi J, Sloan W, Schimpf J, Nasiri HR, Lashley D, Friedrich T. Exploring ND-011992, a quinazoline-type inhibitor targeting quinone reductases and quinol oxidases. Sci Rep 2023; 13:12226. [PMID: 37507428 PMCID: PMC10382516 DOI: 10.1038/s41598-023-39430-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial energy metabolism has become a promising target for next-generation tuberculosis chemotherapy. One strategy to hamper ATP production is to inhibit the respiratory oxidases. The respiratory chain of Mycobacterium tuberculosis comprises a cytochrome bcc:aa3 and a cytochrome bd ubiquinol oxidase that require a combined approach to block their activity. A quinazoline-type compound called ND-011992 has previously been reported to ineffectively inhibit bd oxidases, but to act bactericidal in combination with inhibitors of cytochrome bcc:aa3 oxidase. Due to the structural similarity of ND-011992 to quinazoline-type inhibitors of respiratory complex I, we suspected that this compound is also capable of blocking other respiratory chain complexes. Here, we synthesized ND-011992 and a bromine derivative to study their effect on the respiratory chain complexes of Escherichia coli. And indeed, ND-011992 was found to inhibit respiratory complex I and bo3 oxidase in addition to bd-I and bd-II oxidases. The IC50 values are all in the low micromolar range, with inhibition of complex I providing the lowest value with an IC50 of 0.12 µM. Thus, ND-011992 acts on both, quinone reductases and quinol oxidases and could be very well suited to regulate the activity of the entire respiratory chain.
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Affiliation(s)
- Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willough Sloan
- Department of Chemistry, William & Mary, Williamsburg, VA, USA
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hamid R Nasiri
- Department of Cellular Microbiology, University Hohenheim, Stuttgart, Germany
| | - Dana Lashley
- Department of Chemistry, William & Mary, Williamsburg, VA, USA.
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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15
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Kruth S, Nett M. Aurachins, Bacterial Antibiotics Interfering with Electron Transport Processes. Antibiotics (Basel) 2023; 12:1067. [PMID: 37370386 DOI: 10.3390/antibiotics12061067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Aurachins are farnesylated quinolone alkaloids of bacterial origin and excellent inhibitors of the respiratory chain in pro- and eukaryotes. Therefore, they have become important tool compounds for the investigation of electron transport processes and they also serve as lead structures for the development of antibacterial and antiprotozoal drugs. Especially aurachin D proved to be a valuable starting point for structure-activity relationship studies. Aurachin D is a selective inhibitor of the cytochrome bd oxidase, which has received increasing attention as a target for the treatment of infectious diseases caused by mycobacteria. Moreover, aurachin D possesses remarkable activities against Leishmania donovani, the causative agent of leishmaniasis. Aurachins are naturally produced by myxobacteria of the genus Stigmatella as well as by some Streptomyces and Rhodococcus strains. The recombinant production of these antibiotics turned out to be challenging due to their complex biosynthesis and their inherent toxicity. Recently, the biotechnological production of aurachin D was established in E. coli with a titer which is higher than previously reported from natural producer organisms.
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Affiliation(s)
- Sebastian Kruth
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Markus Nett
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
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16
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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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17
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Wu D, Mehdipour AR, Finke F, Goojani HG, Groh RR, Grund TN, Reichhart TMB, Zimmermann R, Welsch S, Bald D, Shepherd M, Hummer G, Safarian S. Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nat Chem Biol 2023:10.1038/s41589-023-01314-5. [PMID: 37095238 PMCID: PMC10374445 DOI: 10.1038/s41589-023-01314-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.
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Affiliation(s)
- 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
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | - Franziska Finke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Hojjat G Goojani
- Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Faculty of Science, Vrije University of Amsterdam, Amsterdam, the Netherlands
| | - Roan R Groh
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Tamara N Grund
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Thomas M B Reichhart
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Rita Zimmermann
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Dirk Bald
- Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Faculty of Science, Vrije University of Amsterdam, Amsterdam, the Netherlands
| | - Mark Shepherd
- School of Biosciences, RAPID Group, University of Kent, Canterbury, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Schara Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt/Main, Germany.
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18
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Makarchuk I, Kägi J, Gerasimova T, Wohlwend D, Friedrich T, Melin F, Hellwig P. pH-dependent kinetics of NO release from E. coli bd-I and bd-II oxidase reveals involvement of Asp/Glu58 B. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148952. [PMID: 36535430 DOI: 10.1016/j.bbabio.2022.148952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Escherichia coli contains two cytochrome bd oxidases, bd-I and bd-II. The structure of both enzymes is highly similar, but they exhibit subtle differences such as the accessibility of the active site through a putative proton channel. Here, we demonstrate that the duroquinol:dioxygen oxidoreductase activity of bd-I increased with alkaline pH, whereas bd-II showed a broad activity maximum around pH 7. Likewise, the pH dependence of NO release from the reduced active site, an essential property of bd oxidases, differed between the two oxidases as detected by UV/vis spectroscopy. Both findings may be attributed to differences in the proton channel leading to the active site heme d. The channel comprises a titratable residue (Asp58B in bd-I and Glu58B in bd-II). Conservative mutations at this position drastically altered NO release demonstrating its contribution to the process.
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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
| | - Jan Kägi
- 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
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- 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
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France.
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19
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Li J, Xiao X, Zhou M, Zhang Y. Strategy for the Adaptation to Stressful Conditions of the Novel Isolated Conditional Piezophilic Strain Halomonas titanicae ANRCS81. Appl Environ Microbiol 2023; 89:e0130422. [PMID: 36912687 PMCID: PMC10057041 DOI: 10.1128/aem.01304-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
Microorganisms have successfully predominated deep-sea ecosystems, while we know little about their adaptation strategy to multiple environmental stresses therein, including high hydrostatic pressure (HHP). Here, we focused on the genus Halomonas, one of the most widely distributed halophilic bacterial genera in marine ecosystems and isolated a piezophilic strain Halomonas titanicae ANRCS81 from Antarctic deep-sea sediment. The strain grew under a broad range of temperatures (2 to 45°C), pressures (0.1 to 55 MPa), salinities (NaCl, 0.5 to 17.5%, wt/vol), and chaotropic agent (Mg2+, 0 to 0.9 M) with either oxygen or nitrate as an electron acceptor. Genome annotation revealed that strain ANRCS81 expressed potential antioxidant genes/proteins and possessed versatile energy generation pathways. Based on the transcriptomic analysis, when the strain was incubated at 40 MPa, genes related to antioxidant defenses, anaerobic respiration, and fermentation were upregulated, indicating that HHP induced intracellular oxidative stress. Under HHP, superoxide dismutase (SOD) activity increased, glucose consumption increased with less CO2 generation, and nitrate/nitrite consumption increased with more ammonium generation. The cellular response to HHP represents the common adaptation developed by Halomonas to inhabit and drive geochemical cycling in deep-sea environments. IMPORTANCE Microbial growth and metabolic responses to environmental changes are core aspects of adaptation strategies developed during evolution. In particular, high hydrostatic pressure (HHP) is the most common but least examined environmental factor driving microbial adaptation in the deep sea. According to recent studies, microorganisms developed a common adaptation strategy to multiple stresses, including HHP, with antioxidant defenses and energy regulation as key components, but experimental data are lacking. Meanwhile, cellular SOD activity is elevated under HHP. The significance of this research lies in identifying the HHP adaptation strategy of a Halomonas strain at the genomic, transcriptomic, and metabolic activity levels, which will allow researchers to bridge environmental factors with the ecological function of marine microorganisms.
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Affiliation(s)
- Jiakang Li
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Meng Zhou
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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20
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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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21
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Grund TN, Kabashima Y, Kusumoto T, Wu D, Welsch S, Sakamoto J, Michel H, Safarian S. The cryoEM structure of cytochrome bd from C. glutamicum provides novel insights into structural properties of actinobacterial terminal oxidases. Front Chem 2023; 10:1085463. [PMID: 36688035 PMCID: PMC9846854 DOI: 10.3389/fchem.2022.1085463] [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: 11/01/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Cytochromes bd are essential for microaerobic respiration of many prokaryotes including a number of human pathogens. These enzymes catalyze the reduction of molecular oxygen to water using quinols as electron donors. Their importance for prokaryotic survival and the absence of eukaryotic homologs make these enzyme ideal targets for antimicrobial drugs. Here, we determined the cryoEM structure of the menaquinol-oxidizing cytochrome bd-type oxygen reductase of the facultative anaerobic Actinobacterium Corynebacterium glutamicum at a resolution of 2.7 Å. The obtained structure adopts the signature pseudosymmetrical heterodimeric architecture of canonical cytochrome bd oxidases formed by the core subunits CydA and CydB. No accessory subunits were identified for this cytochrome bd homolog. The two b-type hemes and the oxygen binding heme d are organized in a triangular geometry with a protein environment around these redox cofactors similar to that of the closely related cytochrome bd from M. tuberculosis. We identified oxygen and a proton conducting channels emerging from the membrane space and the cytoplasm, respectively. Compared to the prototypical enzyme homolog from the E. coli, the most apparent difference is found in the location and size of the proton channel entry site. In canonical cytochrome bd oxidases quinol oxidation occurs at the highly flexible periplasmic Q-loop located in the loop region between TMHs six and seven. An alternative quinol-binding site near heme b 595 was previously identified for cytochrome bd from M. tuberculosis. We discuss the relevance of the two quinol oxidation sites in actinobacterial bd-type oxidases and highlight important differences that may explain functional and electrochemical differences between C. glutamicum and M. tuberculosis. This study expands our current understanding of the structural diversity of actinobacterial and proteobacterial cytochrome bd oxygen reductases and provides deeper insights into the unique structural and functional properties of various cytochrome bd variants from different phylae.
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Affiliation(s)
- Tamara N. Grund
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Yoshiki Kabashima
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
| | - Tomoichirou Kusumoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
| | - Di Wu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Junshi Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Schara Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP Frankfurt, Frankfurt, Germany,*Correspondence: Schara Safarian,
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22
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Huang H, Lin L, Bu F, Su Y, Zheng X, Chen Y. Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15594-15606. [PMID: 36322896 DOI: 10.1021/acs.est.2c04276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The dissemination of plasmid-borne antibiotic resistance genes (ARGs) among bacteria is becoming a global challenge to the "One Health" concept. During conjugation, the donor/recipient usually encounter diverse stresses induced by the surrounding environment. Previous studies mainly focused on the effects of oxidative stress on plasmid conjugation, but ignored the potential contribution of reductive stress (RS), the other side of the intracellular redox spectrum. Herein, we demonstrated for the first time that RS induced by dithiothreitol could significantly boost the horizontal transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella Typhimurium, and Pseudomonas putida KT2440). Phenotypic and genotypic tests confirmed that RS upregulated genes encoding the transfer apparatus of plasmid RP4, which was attributed to the promoted consumption of intracellular glutamine in the donor rather than the widely reported SOS response. Moreover, RS was verified to benefit ATP supply by activating glycolysis (e.g., GAPDH) and the respiratory chain (e.g., appBC), triggering the deficiency of intracellular free Mg2+ by promoting its binding, and reducing membrane permeability by stimulating cardiolipin biosynthesis, all of which were beneficial to the functioning of transfer apparatus. Overall, our findings uncovered the neglected risks of RS in ARG spreading and updated the regulatory mechanism of plasmid conjugation.
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Affiliation(s)
- Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Lin Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Fan Bu
- Shanghai Electric Environmental Protection Group, Shanghai Electric Group Co. Ltd, Shanghai 200092, China
| | - Yinglong Su
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200092, China
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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23
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Kruth S, Schibajew L, Nett M. Biocatalytic production of the antibiotic aurachin D in Escherichia coli. AMB Express 2022; 12:138. [DOI: 10.1186/s13568-022-01478-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Abstract
Aurachin D is a potent inhibitor of cytochrome bd oxidases, which are potential targets in the treatment of infectious diseases. In this study, our aim was to improve the biocatalytic production of aurachin D from a quinolone precursor molecule with recombinant Escherichia coli cells expressing the biosynthesis enzyme AuaA. In order to achieve a high-level production of this membrane-bound farnesyltransferase in E. coli, the expression of the auaA gene was translationally coupled to an upstream cistron in accordance with a bicistronic design (BCD) strategy. Screening of various BCD elements led to the identification of optimized auaA expression cassettes, which increased the aurachin D titer in E. coli up to 29-fold in comparison to T7-mediated expression. This titer could be further raised by codon optimization of auaA and by introducing the mevalonate pathway into the production strain. The latter measure was intended to improve the availability of farnesyl pyrophosphate, which is needed as a cosubstrate for the AuaA-catalyzed reaction. In sum, the described efforts resulted in a strain producing aurachin D with a titer that is 424 times higher than that obtained with the original, non-optimized expression host.
Graphical Abstract
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24
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Response of Mycobacterium smegmatis to the Cytochrome bcc Inhibitor Q203. Int J Mol Sci 2022; 23:ijms231810331. [PMID: 36142240 PMCID: PMC9498996 DOI: 10.3390/ijms231810331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
For the design of next-generation tuberculosis chemotherapy, insight into bacterial defence against drugs is required. Currently, targeting respiration has attracted strong attention for combatting drug-resistant mycobacteria. Q203 (telacebec), an inhibitor of the cytochrome bcc complex in the mycobacterial respiratory chain, is currently evaluated in phase-2 clinical trials. Q203 has bacteriostatic activity against M. tuberculosis, which can be converted to bactericidal activity by concurrently inhibiting an alternative branch of the mycobacterial respiratory chain, cytochrome bd. In contrast, non-tuberculous mycobacteria, such as Mycobacterium smegmatis, show only very little sensitivity to Q203. In this report, we investigated factors that M. smegmatis employs to adapt to Q203 in the presence or absence of a functional cytochrome bd, especially regarding its terminal oxidases. In the presence of a functional cytochrome bd, M. smegmatis responds to Q203 by increasing the expression of cytochrome bcc as well as of cytochrome bd, whereas a M. smegmatisbd-KO strain adapted to Q203 by increasing the expression of cytochrome bcc. Interestingly, single-cell studies revealed cell-to-cell variability in drug adaptation. We also investigated the role of a putative second cytochrome bd isoform postulated for M. smegmatis. Although this putative isoform showed differential expression in response to Q203 in the M. smegmatisbd-KO strain, it did not display functional features similar to the characterised cytochrome bd variant.
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Design, synthesis and biological evaluation of (Quinazoline 4-yloxy)acetamide and (4-oxoquinazoline-3(4H)-yl)acetamide derivatives as inhibitors of Mycobacterium tuberculosis bd oxidase. Eur J Med Chem 2022; 242:114639. [DOI: 10.1016/j.ejmech.2022.114639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022]
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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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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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Quinones: More Than Electron Shuttles. Res Microbiol 2022; 173:103953. [DOI: 10.1016/j.resmic.2022.103953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 11/21/2022]
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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: 24] [Impact Index Per Article: 12.0] [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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