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Chen Y, Mao R, Xu J, Huang Y, Xu J, Cui S, Zhu Z, Ji X, Huang S, Huang Y, Huang HY, Yen SC, Lin YCD, Huang HD. A Causal Regulation Modeling Algorithm for Temporal Events with Application to Escherichia coli's Aerobic to Anaerobic Transition. Int J Mol Sci 2024; 25:5654. [PMID: 38891842 PMCID: PMC11171773 DOI: 10.3390/ijms25115654] [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: 04/13/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Time-series experiments are crucial for understanding the transient and dynamic nature of biological phenomena. These experiments, leveraging advanced classification and clustering algorithms, allow for a deep dive into the cellular processes. However, while these approaches effectively identify patterns and trends within data, they often need to improve in elucidating the causal mechanisms behind these changes. Building on this foundation, our study introduces a novel algorithm for temporal causal signaling modeling, integrating established knowledge networks with sequential gene expression data to elucidate signal transduction pathways over time. Focusing on Escherichia coli's (E. coli) aerobic to anaerobic transition (AAT), this research marks a significant leap in understanding the organism's metabolic shifts. By applying our algorithm to a comprehensive E. coli regulatory network and a time-series microarray dataset, we constructed the cross-time point core signaling and regulatory processes of E. coli's AAT. Through gene expression analysis, we validated the primary regulatory interactions governing this process. We identified a novel regulatory scheme wherein environmentally responsive genes, soxR and oxyR, activate fur, modulating the nitrogen metabolism regulators fnr and nac. This regulatory cascade controls the stress regulators ompR and lrhA, ultimately affecting the cell motility gene flhD, unveiling a novel regulatory axis that elucidates the complex regulatory dynamics during the AAT process. Our approach, merging empirical data with prior knowledge, represents a significant advance in modeling cellular signaling processes, offering a deeper understanding of microbial physiology and its applications in biotechnology.
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Affiliation(s)
- Yigang Chen
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Runbo Mao
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
| | - Jiatong Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Yixian Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Jingyi Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
| | - Shidong Cui
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Zihao Zhu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Xiang Ji
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Shenghan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Yanzhe Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Shih-Chung Yen
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Yang-Chi-Duang Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.C.); (R.M.); (J.X.); (Y.H.); (J.X.); (S.C.); (Z.Z.); (X.J.); (S.H.); (Y.H.); (H.-Y.H.); (S.-C.Y.)
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China
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2
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Gu P, Li F, Huang Z. Engineering Escherichia coli for Isobutanol Production from Xylose or Glucose-Xylose Mixture. Microorganisms 2023; 11:2573. [PMID: 37894231 PMCID: PMC10609591 DOI: 10.3390/microorganisms11102573] [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: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Aiming to overcome the depletion of fossil fuels and serious environmental pollution, biofuels such as isobutanol have garnered increased attention. Among different synthesis methods, the microbial fermentation of isobutanol from raw substrate is a promising strategy due to its low cost and environmentally friendly and optically pure products. As an important component of lignocellulosics and the second most common sugar in nature, xylose has become a promising renewable resource for microbial production. However, bottlenecks in xylose utilization limit its wide application as substrates. In this work, an isobutanol synthetic pathway from xylose was first constructed in E. coli MG1655 through the combination of the Ehrlich and Dahms pathways. The engineering of xylose transport and electron transport chain complexes further improved xylose assimilation and isobutanol production. By optimizing xylose supplement concentration, the recombinant E. coli strain BWL4 could produce 485.35 mg/L isobutanol from 20 g/L of xylose. To our knowledge, this is the first report related to isobutanol production using xylose as a sole carbon source in E. coli. Additionally, a glucose-xylose mixture was utilized as the carbon source. The Entner-Doudorof pathway was used to assimilate glucose, and the Ehrlich pathway was applied for isobutanol production. After carefully engineering the recombinant E. coli, strain BWL9 could produce 528.72 mg/L isobutanol from a mixture of 20 g/L glucose and 10 g/L xylose. The engineering strategies applied in this work provide a useful reference for the microbial production of isobutanol from xylose or glucose-xylose mixture.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Fangfang Li
- Yantai Food and Drug Control and Test Center, Yantai 264003, China;
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
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3
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Droste J, Rückert C, Kalinowski J, Hamed MB, Anné J, Simoens K, Bernaerts K, Economou A, Busche T. Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Front Microbiol 2021; 12:604034. [PMID: 33935985 PMCID: PMC8079986 DOI: 10.3389/fmicb.2021.604034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/12/2021] [Indexed: 01/04/2023] Open
Abstract
Streptomyces lividans TK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genus Streptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products. S. lividans TK24 is the plasmid-free derivative of S. lividans 66 and a close genetic relative of the strain Streptomyces coelicolor A3(2). In this study, we used transcriptome and proteome data to improve the annotation of the S. lividans TK24 genome. The RNA-seq data of primary 5'-ends of transcripts were used to determine transcription start sites (TSS) in the genome. We identified 5,424 TSS, of which 4,664 were assigned to annotated CDS and ncRNAs, 687 to antisense transcripts distributed between 606 CDS and their UTRs, 67 to tRNAs, and 108 to novel transcripts and CDS. Using the TSS data, the promoter regions and their motifs were analyzed in detail, revealing a conserved -10 (TAnnnT) and a weakly conserved -35 region (nTGACn). The analysis of the 5' untranslated region (UTRs) of S. lividans TK24 revealed 17% leaderless transcripts. Several cis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5'-UTRs. The S. lividans TK24 transcriptome contains at least 929 operons. The genome harbors 27 secondary metabolite gene clusters of which 26 could be shown to be transcribed under at least one of the applied conditions. Comparison of the reannotated genome with that of the strain Streptomyces coelicolor A3(2) revealed a high degree of similarity. This study presents an extensive reannotation of the S. lividans TK24 genome based on transcriptome and proteome analyses. The analysis of TSS data revealed insights into the promoter structure, 5'-UTRs, cis-regulatory elements, attenuator structures and novel transcripts, like small RNAs. Finally, the repertoire of secondary metabolite gene clusters was examined. These data provide a basis for future studies regarding gene characterization, transcriptional regulatory networks, and usage as a secondary metabolite producing strain.
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Affiliation(s)
- Julian Droste
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Mohamed Belal Hamed
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium.,Molecular Biology Department, National Research Centre, Dokii, Egypt
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium
| | - Kenneth Simoens
- Bio- and Chemical Systems Technology, Reactor Engineering, and Safety (CREaS) Section, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Kristel Bernaerts
- Bio- and Chemical Systems Technology, Reactor Engineering, and Safety (CREaS) Section, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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4
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Liu TT, Xiao H, Xiao JH, Zhong JJ. Impact of oxygen supply on production of terpenoids by microorganisms: State of the art. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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5
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Jung H, Han J, Oh M. Improved production of 2,3-butanediol and isobutanol by engineering electron transport chain in Escherichia coli. Microb Biotechnol 2021; 14:213-226. [PMID: 32954676 PMCID: PMC7888471 DOI: 10.1111/1751-7915.13669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
The electron transport chain (ETC) is one of the major energy generation pathways in microorganisms under aerobic condition. Higher yield of ATP can be achieved through oxidative phosphorylation with consumption of NADH than with substrate level phosphorylation. However, most value-added metabolites are in an electrochemically reduced state, which requires reducing equivalent NADH as a cofactor. Therefore, optimal production of value-added metabolites should be balanced with ETC in terms of energy production. In this study, we attempted to reduce the activity of ETC to secure availability of NADH. The ETC mutants exhibited poor growth rate and production of fermentative metabolites compared to parental strain. Introduction of heterologous pathways for synthesis of 2,3-butanediol and isobutanol to ETC mutants resulted in increased titres and yields of the metabolites. ETC mutants yielded higher NADH/NAD+ ratio but similar ATP content than that by the parental strain. Furthermore, ETC mutants operated fermentative metabolism pathways independent of oxygen supply in large-scale fermenter, resulting in increased yield and titre of 2,3-butanediol. Thus, engineering of ETC is a useful metabolic engineering approach for production of reduced metabolites.
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Affiliation(s)
- Hwi‐Min Jung
- Department of Chemical and Biological EngineeringKorea University145 Anam‐ro, Seongbuk‐guSeoul02841Korea
| | - Jae‐Ho Han
- Department of Chemical and Biological EngineeringKorea University145 Anam‐ro, Seongbuk‐guSeoul02841Korea
| | - Min‐Kyu Oh
- Department of Chemical and Biological EngineeringKorea University145 Anam‐ro, Seongbuk‐guSeoul02841Korea
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6
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Chanin RB, Winter MG, Spiga L, Hughes ER, Zhu W, Taylor SJ, Arenales A, Gillis CC, Büttner L, Jimenez AG, Smoot MP, Santos RL, Winter SE. Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation. Cell Host Microbe 2020; 28:780-788.e5. [PMID: 33053375 DOI: 10.1016/j.chom.2020.09.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/06/2020] [Accepted: 09/03/2020] [Indexed: 12/19/2022]
Abstract
The intestinal epithelium separates host tissue and gut-associated microbial communities. During inflammation, the host releases reactive oxygen and nitrogen species as an antimicrobial response. The impact of these radicals on gut microbes is incompletely understood. We discovered that the cryptic appBCX genes, predicted to encode a cytochrome bd-II oxidase, conferred a fitness advantage for E. coli in chemical and genetic models of non-infectious colitis. This fitness advantage was absent in mice that lacked epithelial NADPH oxidase 1 (NOX1) activity. In laboratory growth experiments, supplementation with exogenous hydrogen peroxide enhanced E. coli growth through AppBCX-mediated respiration in a catalase-dependent manner. We conclude that epithelial-derived reactive oxygen species are degraded in the gut lumen, which gives rise to molecular oxygen that supports the aerobic respiration of E. coli. This work illustrates how epithelial host responses intersect with gut microbial metabolism in the context of gut inflammation.
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Affiliation(s)
- Rachael B Chanin
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Savannah J Taylor
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alexandre Arenales
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270, Brazil
| | - Caroline C Gillis
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa Büttner
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Angel G Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Madeline P Smoot
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Renato L Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270, Brazil
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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7
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Integral caa 3-Cytochrome c Oxidase from Thermus thermophilus: Purification and Crystallization. Methods Mol Biol 2020. [PMID: 31342419 DOI: 10.1007/978-1-4939-9678-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cytochrome c oxidase is a respiratory enzyme catalyzing the energy-conserving reduction of molecular oxygen to water-a fundamental biological process of cell respiration. The first crystal structures of the type A cytochrome c oxidases, bovine heart and Paracoccus denitrificans cytochrome c oxidases, were published in 1995 and contributed immensely to the understanding of the enzyme's mechanism of action. The senior author's research focus was directed toward understanding the structure and function of the type B cytochrome c oxidases, ba3-oxidase and type A2 caa3-oxidase, both from the extreme thermophilic bacterium Thermus thermophilus. While the ba3-oxidase structure was published in 2000 and functional characterization is well-documented in the literature, we recently successfully solved the structure of the caa3-nature made enzyme-substrate complex. This chapter is dedicated to the purification and crystallization process of caa3-cytochrome c oxidase.
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8
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Kashyap DR, Kowalczyk DA, Shan Y, Yang CK, Gupta D, Dziarski R. Formate dehydrogenase, ubiquinone, and cytochrome bd-I are required for peptidoglycan recognition protein-induced oxidative stress and killing in Escherichia coli. Sci Rep 2020; 10:1993. [PMID: 32029761 PMCID: PMC7005000 DOI: 10.1038/s41598-020-58302-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 01/14/2020] [Indexed: 11/09/2022] Open
Abstract
Mammalian Peptidoglycan Recognition Proteins (PGRPs) kill bacteria through induction of synergistic oxidative, thiol, and metal stress. PGRPs induce oxidative stress in bacteria through a block in the respiratory chain, which results in decreased respiration and incomplete reduction of oxygen (O2) to hydrogen peroxide (H2O2). In this study we identify the site of PGRP-induced generation of H2O2 in Escherichia coli. Tn-seq screening of E. coli Tn10 insertion library revealed that mutants in formate dehydrogenase (FDH) genes had the highest survival following PGRP treatment. Mutants lacking functional FDH-O had abolished PGRP-induced H2O2 production and the highest resistance to PGRP-induced killing, and formate enhanced PGRP-induced killing and H2O2 production in an FDH-dependent manner. Mutants in ubiquinone synthesis (but not menaquinone and demethylmenaquinone) and cytochrome bd-I (but not cytochromes bo3 and bd-II) also had completely abolished PGRP-induced H2O2 production and high resistance to PGRP-induced killing. Because electrons in the respiratory chain flow from dehydrogenases' substrates through quinones and then cytochromes to O2, these results imply that the site of PGRP-induced incomplete reduction of O2 to H2O2 is downstream from dehydrogenases and ubiquinone at the level of cytochrome bd-I, which results in oxidative stress. These results reveal several essential steps in PGRP-induced bacterial killing.
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Affiliation(s)
- Des R Kashyap
- Indiana University School of Medicine-Northwest, Gary, IN, 46408, USA
| | | | - Yue Shan
- Antimicrobial Discovery Center, Northeastern University, Boston, MA, 02115, USA.,Department of Medicine, The University of Chicago, Chicago, 60637, USA
| | - Chun-Kai Yang
- Indiana University School of Medicine-Northwest, Gary, IN, 46408, USA
| | - Dipika Gupta
- Indiana University School of Medicine-Northwest, Gary, IN, 46408, USA
| | - Roman Dziarski
- Indiana University School of Medicine-Northwest, Gary, IN, 46408, USA.
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9
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Tempelhagen L, Ayer A, Culham DE, Stocker R, Wood JM. Cultivation at high osmotic pressure confers ubiquinone 8–independent protection of respiration on Escherichia coli. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49909-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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10
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Tempelhagen L, Ayer A, Culham DE, Stocker R, Wood JM. Cultivation at high osmotic pressure confers ubiquinone 8-independent protection of respiration on Escherichia coli. J Biol Chem 2019; 295:981-993. [PMID: 31826918 DOI: 10.1074/jbc.ra119.011549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/11/2019] [Indexed: 11/06/2022] Open
Abstract
Ubiquinone 8 (coenzyme Q8 or Q8) mediates electron transfer within the aerobic respiratory chain, mitigates oxidative stress, and contributes to gene expression in Escherichia coli In addition, Q8 was proposed to confer bacterial osmotolerance by accumulating during growth at high osmotic pressure and altering membrane stability. The osmolyte trehalose and membrane lipid cardiolipin accumulate in E. coli cells cultivated at high osmotic pressure. Here, Q8 deficiency impaired E. coli growth at low osmotic pressure and rendered growth osmotically sensitive. The Q8 deficiency impeded cellular O2 uptake and also inhibited the activities of two proton symporters, the osmosensing transporter ProP and the lactose transporter LacY. Q8 supplementation decreased membrane fluidity in liposomes, but did not affect ProP activity in proteoliposomes, which is respiration-independent. Liposomes and proteoliposomes prepared with E. coli lipids were used for these experiments. Similar oxygen uptake rates were observed for bacteria cultivated at low and high osmotic pressures. In contrast, respiration was dramatically inhibited when bacteria grown at the same low osmotic pressure were shifted to high osmotic pressure. Thus, respiration was restored during prolonged growth of E. coli at high osmotic pressure. Of note, bacteria cultivated at low and high osmotic pressures had similar Q8 concentrations. The protection of respiration was neither diminished by cardiolipin deficiency nor conferred by trehalose overproduction during growth at low osmotic pressure, but rather might be achieved by Q8-independent respiratory chain remodeling. We conclude that osmotolerance is conferred through Q8-independent protection of respiration, not by altering physical properties of the membrane.
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Affiliation(s)
- Laura Tempelhagen
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Anita Ayer
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2050, Australia
| | - Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Roland Stocker
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2050, Australia
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
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11
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Speijer D. Can All Major ROS Forming Sites of the Respiratory Chain Be Activated By High FADH 2 /NADH Ratios?: Ancient evolutionary constraints determine mitochondrial ROS formation. Bioessays 2018; 41:e1800180. [PMID: 30512221 DOI: 10.1002/bies.201800180] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/30/2018] [Indexed: 01/20/2023]
Abstract
Aspects of peroxisome evolution, uncoupling, carnitine shuttles, supercomplex formation, and missing neuronal fatty acid oxidation (FAO) are linked to reactive oxygen species (ROS) formation in respiratory chains. Oxidation of substrates with high FADH2 /NADH (F/N) ratios (e.g., FAs) initiate ROS formation in Complex I due to insufficient availability of its electron acceptor (Q) and reverse electron transport from QH2 , e.g., during FAO or glycerol-3-phosphate shuttle use. Here it is proposed that the Q-cycle of Complex III contributes to enhanced ROS formation going from low F/N ratio substrates (glucose) to high F/N substrates. This contribution is twofold: 1) Complex III uses Q as substrate, thus also competing with Complex I; 2) Complex III itself will produce more ROS under these conditions. I link this scenario to the universally observed Complex III dimerization. The Q-cycle of Complex III thus again illustrates the tension between efficient ATP generation and endogenous ROS formation. This model can explain recent findings concerning succinate and ROS-induced uncoupling.
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Affiliation(s)
- Dave Speijer
- Academic Medical Center (AMC), University of Amsterdam, Medical Biochemistry, Room K1-257, 1105, AZ Amsterdam, The Netherlands
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12
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Zhang L, Bao W, Wei R, Fu S, Gong H. Inactivating NADH:quinone oxidoreductases affects the growth and metabolism of Klebsiella pneumoniae. Biotechnol Appl Biochem 2018; 65:857-864. [PMID: 30063071 DOI: 10.1002/bab.1684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/22/2018] [Indexed: 11/10/2022]
Abstract
NADH:quinone oxidoreductases (NQOs) act as the electron entry sites in bacterial respiration and oxidize intracellular NADH that is essential for the synthesis of numerous molecules. Klebsiella pneumoniae contains three NQOs (NDH-1, NDH-2, and NQR). The effects of inactivating these NQOs, separately and together, on cell metabolism were investigated under different culture conditions. Defective growth was evident in NDH-1-NDH-2 double and NDH-1-NDH-2-NQR triple deficient mutants, which was probably due to damage to the respiratory chain. The results also showed that K. pneumoniae can flexibly use NQOs to maintain normal growth in single NQO-deficient mutants. And more interestingly, under aerobic conditions, inactivating NDH-1 resulted in a high intracellular NADH:NAD+ ratio, which was proven to be beneficial for 2,3-butanediol production. Compared with the parent strain, 2,3-butanediol production by the NDH-1-deficient mutant was increased by 46% and 62% in glycerol- and glucose-based media, respectively. Thus, our findings provide a practical strategy for metabolic engineering of respiratory chains to promote the biosynthesis of 2,3-butanediol in K. pneumoniae.
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Affiliation(s)
- Lijuan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Wenjing Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Renquan Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Shuilin Fu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Heng Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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13
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Structural basis for energy transduction by respiratory alternative complex III. Nat Commun 2018; 9:1728. [PMID: 29712914 PMCID: PMC5928083 DOI: 10.1038/s41467-018-04141-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/02/2018] [Indexed: 01/30/2023] Open
Abstract
Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may have alternative complexes performing the same catalytic reactions as the mitochondrial complexes. This is the case for the alternative complex III (ACIII), a quinol:cytochrome c/HiPIP oxidoreductase. In order to understand the catalytic mechanism of this respiratory enzyme, we determined the structure of ACIII from Rhodothermus marinus at 3.9 Å resolution by single-particle cryo-electron microscopy. ACIII presents a so-far unique structure, for which we establish the arrangement of the cofactors (four iron–sulfur clusters and six c-type hemes) and propose the location of the quinol-binding site and the presence of two putative proton pathways in the membrane. Altogether, this structure provides insights into a mechanism for energy transduction and introduces ACIII as a redox-driven proton pump. Some prokaryotes use alternative respiratory chain complexes, such as the alternative complex III (ACIII), to generate energy. Here authors provide the cryoEM structure of ACIII from Rhodothermus marinus which shows the arrangement of cofactors and provides insights into the mechanism for energy transduction.
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14
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Long YM, Hu LG, Yan XT, Zhao XC, Zhou QF, Cai Y, Jiang GB. Surface ligand controls silver ion release of nanosilver and its antibacterial activity against Escherichia coli. Int J Nanomedicine 2017; 12:3193-3206. [PMID: 28458540 PMCID: PMC5402892 DOI: 10.2147/ijn.s132327] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Understanding the mechanism of nanosilver-dependent antibacterial activity against microorganisms helps optimize the design and usage of the related nanomaterials. In this study, we prepared four kinds of 10 nm-sized silver nanoparticles (AgNPs) with dictated surface chemistry by capping different ligands, including citrate, mercaptopropionic acid, mercaptohexanoic acid, and mercaptopropionic sulfonic acid. Their surface-dependent chemistry and antibacterial activities were investigated. Owing to the weak bond to surface Ag, short carbon chain, and low silver ion attraction, citrate-coated AgNPs caused the highest silver ion release and the strongest antibacterial activity against Escherichia coli, when compared to the other tested AgNPs. The study on the underlying antibacterial mechanisms indicated that cellular membrane uptake of Ag, NAD+/NADH ratio increase, and intracellular reactive oxygen species (ROS) generation were significantly induced in both AgNP and silver ion exposure groups. The released silver ions from AgNPs inside cells through a Trojan-horse-type mechanism were suggested to interact with respiratory chain proteins on the membrane, interrupt intracellular O2 reduction, and induce ROS production. The further oxidative damages of lipid peroxidation and membrane breakdown caused the lethal effect on E. coli. Altogether, this study demonstrated that AgNPs exerted antibacterial activity through the release of silver ions and the subsequent induction of intracellular ROS generation by interacting with the cell membrane. The findings are helpful in guiding the controllable synthesis through the regulation of surface coating for medical care purpose.
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Affiliation(s)
- Yan-Min Long
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Beijing, China
- Institute of Environment and Health, Jianghan University, Wuhan, Hubei, China
| | - Li-Gang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xue-Ting Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Chen Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qun-Fang Zhou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Cai
- Institute of Environment and Health, Jianghan University, Wuhan, Hubei, China
- Department of Chemistry and Biochemistry, Southeast Environmental Research Center, Florida International University, Miami, FL, USA
| | - Gui-Bin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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15
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Development of a commercial scale process for production of 1,4-butanediol from sugar. Curr Opin Biotechnol 2016; 42:118-125. [DOI: 10.1016/j.copbio.2016.04.016] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/22/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022]
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16
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Cardiolipin deficiency causes a dissociation of the b 6 c:caa 3 megacomplex in B. subtilis membranes. J Bioenerg Biomembr 2016; 48:451-67. [PMID: 27503613 DOI: 10.1007/s10863-016-9671-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/21/2016] [Indexed: 10/21/2022]
Abstract
The associations among respiratory complexes in energy-transducing membranes have been established. In fact, it is known that the Gram-negative bacteria Paracoccus denitrificans and Escherichia coli have respiratory supercomplexes in their membranes. These supercomplexes are important for channeling substrates between enzymes in a metabolic pathway, and the assembly of these supercomplexes depends on the protein subunits and membrane lipids, mainly cardiolipin, which is present in both the mitochondrial inner membrane and bacterial membranes. The Gram-positive bacterium Bacillus subtilis has a branched respiratory chain, in which some complexes generate proton motive force whereas others constitute an escape valve of excess reducing power. Some peculiarities of this respiratory chain are the following: a type II NADH dehydrogenase, a unique b 6 c complex that has a b 6 type cytochrome with a covalently bound heme, and a c-type heme attached to the third subunit, which is similar to subunit IV of the photosynthetic b 6 f complex. Cytochrome c oxygen reductase (caa 3 ) contains a c-type cytochrome on subunit I. We previously showed that the b 6 c and the caa 3 complexes form a supercomplex. Both the b 6 c and the caa 3 together with the quinol oxygen reductase aa 3 generate the proton motive force in B. subtilis. In order to seek proof that this supercomplex is important for bacterial growth in aerobic conditions we compared the b 6 c: caa 3 supercomplex from wild type membranes with membranes from two mutants lacking cardiolipin. Both mutant complexes were found to have similar activity and heme content as the wild type. Clear native electrophoresis showed that mutants lacking cardiolipin had b 6 c:caa 3 supercomplexes of lower mass or even individual complexes after membrane solubilization with digitonin. The use of dodecyl maltoside revealed a more evident difference between wild-type and mutant supercomplexes. Here we provide evidence showing that cardiolipin plays a role in the stability of the b 6 c:caa 3 supercomplex in B. subtilis.
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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18
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Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes. J Bacteriol 2016; 198:1268-80. [PMID: 26833419 PMCID: PMC4859585 DOI: 10.1128/jb.01025-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to bacterial electron transport chains has been tested in only a few species. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides, an alphaproteobacterium that contains well-characterized electron transport chains. We found that R. sphaeroides complex I activity is important for aerobic respiration and required for anaerobic dimethyl sulfoxide (DMSO) respiration (in the absence of light), photoautotrophic growth, and photoheterotrophic growth (in the absence of an external electron acceptor). Our data also provide insight into the functions of the phylogenetically distinct R. sphaeroidescomplex I enzymes (complex IA and complex IE) in maintaining a cellular redox state during photoheterotrophic growth. We propose that the function of each isozyme during photoheterotrophic growth is either NADH synthesis (complex IA) or NADH oxidation (complex IE). The canonical alphaproteobacterial complex I isozyme (complex IA) was also shown to be important for routing electrons to nitrogenase-mediated H2 production, while the horizontally acquired enzyme (complex IE) was dispensable in this process. Unlike the singular role of complex I in mitochondria, we predict that the phylogenetically distinct complex I enzymes found across bacterial species have evolved to enhance the functions of their respective electron transport chains. IMPORTANCE Cells use a proton motive force (PMF), NADH, and ATP to support numerous processes. In mitochondria, complex I uses NADH oxidation to generate a PMF, which can drive ATP synthesis. This study analyzed the function of complex I in bacteria, which contain more-diverse and more-flexible electron transport chains than mitochondria. We tested complex I function in Rhodobacter sphaeroides, a bacterium predicted to encode two phylogenetically distinct complex I isozymes. R. sphaeroides cells lacking both isozymes had growth defects during all tested modes of growth, illustrating the important function of this enzyme under diverse conditions. We conclude that the two isozymes are not functionally redundant and predict that phylogenetically distinct complex I enzymes have evolved to support the diverse lifestyles of bacteria.
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19
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Sawers RG, Falke D, Fischer M. Oxygen and Nitrate Respiration in Streptomyces coelicolor A3(2). Adv Microb Physiol 2016; 68:1-40. [PMID: 27134020 DOI: 10.1016/bs.ampbs.2016.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Streptomyces species belong to the phylum Actinobacteria and can only grow with oxygen as a terminal electron acceptor. Like other members of this phylum, such as corynebacteria and mycobacteria, the aerobic respiratory chain lacks a soluble cytochrome c. It is therefore implicit that direct electron transfer between the cytochrome bc1 and the cytochrome aa3 oxidase complexes occurs. The complex developmental cycle of streptomycetes manifests itself in the production of spores, which germinate in the presence of oxygen into a substrate mycelium that greatly facilitates acquisition of nutrients necessary to support their saprophytic lifestyle in soils. Due to the highly variable oxygen levels in soils, streptomycetes have developed means of surviving long periods of hypoxia or even anaerobiosis but they fail to grow under these conditions. Little to nothing is understood about how they maintain viability under conditions of oxygen limitation. It is assumed that they can utilise a number of different electron acceptors to help them maintain a membrane potential, one of which is nitrate. The model streptomycete remains Streptomyces coelicolor A3(2), and it synthesises three nonredundant respiratory nitrate reductases (Nar). These Nar enzymes are synthesised during different phases of the developmental cycle and they are functional only under oxygen-limiting (<5% oxygen in air) conditions. Nevertheless, the regulation of their synthesis does not appear to be responsive to nitrate and in the case of Nar1, it appears to be developmentally regulated. This review highlights some of the novel aspects of our current, but somewhat limited, knowledge of respiration in these fascinating bacteria.
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Affiliation(s)
- R G Sawers
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.
| | - D Falke
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - M Fischer
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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20
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The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics. EcoSal Plus 2015; 6. [PMID: 26442941 DOI: 10.1128/ecosalplus.esp-0005-2013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli contains a versatile respiratory chain that oxidizes 10 different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. Salmonella is able to use two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. A large number of respiratory pathways can be established by combining different electron donors and acceptors. The respiratory dehydrogenases use quinones as the electron acceptors that are oxidized by the terminal reductase and oxidases. The enzymes vary largely with respect to their composition, architecture, membrane topology, and the mode of energy conservation. Most of the energy-conserving dehydrogenases (FdnGHI, HyaABC, HybCOAB, and others) and the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δp) by a redox-loop mechanism. Two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases and terminal reductases do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known or can be predicted. The H+/2e- ratios for most respiratory chains are in the range from 2 to 6 H+/2e-. The energetics of the individual redox reactions and the respiratory chains is described and related to the H+/2e- ratios.
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21
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Single-molecule studies of the dynamics and interactions of bacterial OXPHOS complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:224-31. [PMID: 26498189 DOI: 10.1016/j.bbabio.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 12/29/2022]
Abstract
Although significant insight has been gained into biochemical, genetic and structural features of oxidative phosphorylation (OXPHOS) at the single-enzyme level, relatively little was known of how the component complexes function together in time and space until recently. Several pioneering single-molecule studies have emerged over the last decade in particular, which have illuminated our knowledge of OXPHOS, most especially on model bacterial systems. Here, we discuss these recent findings of bacterial OXPHOS, many of which generate time-resolved information of the OXPHOS machinery with the native physiological context intact. These new investigations are transforming our knowledge not only of the molecular arrangement of OXPHOS components in live bacteria, but also of the way components dynamically interact with each other in a functional state. These new discoveries have important implications towards putative supercomplex formation in bacterial OXPHOS in particular. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
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22
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Duarte M, Tomás AM. The mitochondrial complex I of trypanosomatids--an overview of current knowledge. J Bioenerg Biomembr 2014; 46:299-311. [PMID: 24961227 DOI: 10.1007/s10863-014-9556-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/17/2014] [Indexed: 01/23/2023]
Abstract
The contribution of trypanosomatid mitochondrial complex I for energy transduction has long been debated. Herein, we summarize current knowledge on the composition and relevance of this enzyme. Bioinformatic and proteomic analyses allowed the identification of many conserved and trypanosomatid-specific subunits of NADH:ubiquinone oxidoreductase, revealing a multifunctional enzyme capable of performing bioenergetic activities and possibly, also of functioning in fatty acid metabolism. A multimeric structure organized in 5 domains of more than 2 MDa is predicted, in contrast to the 1 MDa described for mammalian complex I. The relevance of mitochondrial complex I within the Trypanosomatidae family is quite diverse with its NADH oxidation activity being dispensable for both procyclic and bloodstream Trypanosoma brucei, whereas in Phytomonas serpens the enzyme is the only respiratory complex able to sustain membrane potential. Aside from complex I, trypanosomatid mitochondria contain a type II NADH dehydrogenase and a NADH-dependent fumarate reductase as alternative electron entry points into the respiratory chain and thus, some trypanosomatids may have bypassed the need for complex I. The involvement of each of these enzymes in the maintenance of the mitochondrial redox balance in trypanosomatids is still an open question and requires further investigation.
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Affiliation(s)
- Margarida Duarte
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180, Porto, Portugal,
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23
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Llorente-Garcia I, Lenn T, Erhardt H, Harriman OL, Liu LN, Robson A, Chiu SW, Matthews S, Willis NJ, Bray CD, Lee SH, Shin JY, Bustamante C, Liphardt J, Friedrich T, Mullineaux CW, Leake MC. Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:811-24. [DOI: 10.1016/j.bbabio.2014.01.020] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/22/2014] [Accepted: 01/30/2014] [Indexed: 02/04/2023]
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Erhardt H, Dempwolff F, Pfreundschuh M, Riehle M, Schäfer C, Pohl T, Graumann P, Friedrich T. Organization of the Escherichia coli aerobic enzyme complexes of oxidative phosphorylation in dynamic domains within the cytoplasmic membrane. Microbiologyopen 2014; 3:316-26. [PMID: 24729508 PMCID: PMC4082705 DOI: 10.1002/mbo3.163] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/20/2013] [Accepted: 01/07/2014] [Indexed: 12/25/2022] Open
Abstract
The Escherichia coli cytoplasmic membrane contains the enzyme complexes of oxidative phosphorylation (OXPHOS). Not much is known about their supramolecular organization and their dynamics within the membrane in this model organism. In mitochondria and other bacteria, it was demonstrated by nondenaturing electrophoretic methods and electron microscopy that the OXPHOS complexes are organized in so-called supercomplexes, stable assemblies with a defined number of the individual enzyme complexes. To investigate the organization of the E. coli enzyme complexes of aerobic OXPHOS in vivo, we established fluorescent protein fusions of the NADH:ubiquinone oxidoreductase, the succinate:ubiquinone oxidoreductase, the cytochrome bd-I, and the cytochrome bo3 terminal oxidases, and the FoF1 ATP-synthase. The fusions were integrated in the chromosome to prevent artifacts caused by protein overproduction. Biochemical analysis revealed that all modified complexes were fully assembled, active, and stable. The distribution of the OXPHOS complexes in living cells was determined using total internal reflection fluorescence microscopy. The dynamics within the membrane were detected by fluorescence recovery after photobleaching. All aerobic OXPHOS complexes showed an uneven distribution in large mobile patches within the E. coli cytoplasmic membrane. It is discussed whether the individual OXPHOS complexes are organized as clustered individual complexes, here called “segrazones.”
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Affiliation(s)
- Heiko Erhardt
- Institut für Biochemie, Albert-Ludwigs-Universität, Albertstraße 21, Freiburg, 79104, Germany
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25
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Cation transport by the respiratory NADH:quinone oxidoreductase (complex I): facts and hypotheses. Biochem Soc Trans 2014; 41:1280-7. [PMID: 24059520 DOI: 10.1042/bst20130024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The respiratory complex I (electrogenic NADH:quinone oxidoreductase) has been considered to act exclusively as a H+ pump. This was questioned when the search for the NADH-driven respiratory Na+ pump in Klebsiella pneumoniae initiated by Peter Dimroth led to the discovery of a Na+-translocating complex in this enterobacterium. The 3D structures of complex I from different organisms support the idea that the mechanism of cation transport by complex I involves conformational changes of the membrane-bound NuoL, NuoM and NuoN subunits. In vitro methods to follow Na+ transport were compared with in vivo approaches to test whether complex I, or its individual NuoL, NuoM or NuoN subunits, extrude Na+ from the cytoplasm to the periplasm of bacterial host cells. The truncated NuoL subunit of the Escherichia coli complex I which comprises amino acids 1-369 exhibits Na+ transport activity in vitro. This observation, together with an analysis of putative cation channels in NuoL, suggests that there exists in NuoL at least one continuous pathway for cations lined by amino acid residues from transmembrane segments 3, 4, 5, 7 and 8. Finally, we discuss recent studies on Na+ transport by mitochondrial complex I with respect to its putative role in the cycling of Na+ ions across the inner mitochondrial membrane.
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26
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Suenobu T, Shibata S, Fukuzumi S. Catalytic oxidation of formic acid by dioxygen with an organoiridium complex. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00957f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic oxidation of formic acid by dioxygen occurred efficiently using an organoiridium complex as a catalyst in a water-containing organic solvent as well as in water at ambient temperature.
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Affiliation(s)
- Tomoyoshi Suenobu
- Department of Material and Life Science
- Graduate School of Engineering
- Osaka University and ALCA
- Japan Science and Technology Agency (JST)
- Suita, Japan
| | - Satoshi Shibata
- Department of Material and Life Science
- Graduate School of Engineering
- Osaka University and ALCA
- Japan Science and Technology Agency (JST)
- Suita, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science
- Graduate School of Engineering
- Osaka University and ALCA
- Japan Science and Technology Agency (JST)
- Suita, Japan
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27
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The bc:caa3 supercomplexes from the Gram positive bacterium Bacillus subtilis respiratory chain: A megacomplex organization? Arch Biochem Biophys 2013; 537:153-60. [DOI: 10.1016/j.abb.2013.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/08/2013] [Accepted: 07/12/2013] [Indexed: 11/19/2022]
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28
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Sousa PM, Videira MA, Melo AM. The formate:oxygen oxidoreductase supercomplex of Escherichia coli
aerobic respiratory chain. FEBS Lett 2013; 587:2559-64. [DOI: 10.1016/j.febslet.2013.06.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 01/20/2023]
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