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Soares R, Fonseca BM, Nash BW, Paquete CM, Louro RO. A survey of the Desulfuromonadia "cytochromome" provides a glimpse of the unexplored diversity of multiheme cytochromes in nature. BMC Genomics 2024; 25:982. [PMID: 39428470 PMCID: PMC11492766 DOI: 10.1186/s12864-024-10872-4] [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: 01/30/2024] [Accepted: 10/07/2024] [Indexed: 10/22/2024] Open
Abstract
BACKGROUND Multiheme cytochromes c (MHC) provide prokaryotes with a broad metabolic versatility that contributes to their role in the biogeochemical cycling of the elements and in energy production in bioelectrochemical systems. However, MHC have only been isolated and studied in detail from a limited number of species. Among these, Desulfuromonadia spp. are particularly MHC-rich. To obtain a broad view of the diversity of MHC, we employed bioinformatic tools to study the cytochromome encoded in the genomes of the Desulfuromonadia class. RESULTS We found that the distribution of the MHC families follows a different pattern between the two orders of the Desulfuromonadia class and that there is great diversity in the number of heme-binding motifs in MHC. However, the vast majority of MHC have up to 12 heme-binding motifs. MHC predicted to be extracellular are the least conserved and show high diversity, whereas inner membrane MHC are well conserved and show lower diversity. Although the most prevalent MHC have homologues already characterized, nearly half of the MHC families in the Desulforomonadia class have no known characterized homologues. AlphaFold2 was employed to predict their 3D structures. This provides an atlas of novel MHC, including examples with high beta-sheet content and nanowire MHC with unprecedented high numbers of putative heme cofactors per polypeptide. CONCLUSIONS This work illuminates for the first time the universe of experimentally uncharacterized cytochromes that are likely to contribute to the metabolic versatility and to the fitness of Desulfuromonadia in diverse environmental conditions and to drive biotechnological applications of these organisms.
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Affiliation(s)
- Ricardo Soares
- Av da República (EAN), Instituto de Tecnologia Química e Bioloógica António Xavier da Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
- Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
| | - Bruno M Fonseca
- Av da República (EAN), Instituto de Tecnologia Química e Bioloógica António Xavier da Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Benjamin W Nash
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Catarina M Paquete
- Av da República (EAN), Instituto de Tecnologia Química e Bioloógica António Xavier da Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Ricardo O Louro
- Av da República (EAN), Instituto de Tecnologia Química e Bioloógica António Xavier da Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal.
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2
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Li J, Han H, Chang Y, Wang B. The material-microorganism interface in microbial hybrid electrocatalysis systems. NANOSCALE 2023; 15:6009-6024. [PMID: 36912348 DOI: 10.1039/d3nr00742a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
This review presents a comprehensive summary of the material-microorganism interface in microbial hybrid electrocatalysis systems. Microbial hybrid electrocatalysis has been developed to combine the advantages of inorganic electrocatalysis and microbial catalysis. However, electron transfer at the interfaces between microorganisms and materials is a very critical issue that affects the efficiency of the system. Therefore, this review focuses on the electron transfer at the material-microorganism interface and the strategies for building efficient microorganism and material interfaces. We begin with a brief introduction of the electron transfer mechanism in both the bioanode and biocathode of bioelectrochemical systems to understand the material-microorganism interface. Next, we summarise the strategies for constructing efficient material-microorganism interfaces including material design and modification and bacterial engineering. We also discuss emerging studies on the bio-inorganic hybrid electrocatalysis system. Understanding the interface between electrode/active materials and the microorganisms, especially the electron transfer processes, could help to drive the evolution of material-microorganism hybrid electrocatalysis systems towards maturity.
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Affiliation(s)
- Jiyao Li
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China.
| | - Hexing Han
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China.
| | - Yanhong Chang
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Bin Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China.
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3
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Morgado L, Salgueiro CA. Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes. Metallomics 2022; 14:6539350. [DOI: 10.1093/mtomcs/mfac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Cytochromes are electron transfer proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electron outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and elucidate the stepwise electron transfer along the respiratory paths. However, investigating direct electron transfer events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. NMR spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor electron transfer within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of electron transfer between c-type cytochromes, using as model a triheme periplasmic cytochrome (PpcA) and a membrane associated monoheme cytochrome (OmcF) from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional electron transfer within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory electron transfer chains.
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Affiliation(s)
- Leonor Morgado
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carlos A Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
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4
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Jeuken LJC. Biodegradation of pollutants by exoelectrogenic bacteria is not always performed extracellularly. Environ Microbiol 2022; 24:1835-1837. [PMID: 35199430 PMCID: PMC9305215 DOI: 10.1111/1462-2920.15942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Lars J C Jeuken
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300RA, Leiden, the Netherlands
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5
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Yuan Q, Wang S, Wang X, Li N. Biosynthesis of vivianite from microbial extracellular electron transfer and environmental application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143076. [PMID: 33129535 DOI: 10.1016/j.scitotenv.2020.143076] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/01/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Vivianite (Fe3(PO4)2·8H2O) is a common hydrous ferrous phosphate mineral which often occurs in reductive conditions, especially anoxic non-sulfide environment containing high concentrations of ferrous iron (Fe2+) and orthophosphate (PO43-). Vivianite is an important product of dissimilatory iron reduction and a promising route for phosphorus recovery from wastewater. Its formation is closely related to the extracellular electron transfer (EET), a key mechanism for microbial respiration and a crucial explanation for the reduction of metal oxides in soil and sediments. Despite of the natural ubiquity, easy accessibility and attractive economic value, the application value of vivianite has not received much attention. This review introduces the characteristics, occurrence and biosynthesis of vivianite from microbial EET, and systematically analyzes the application value of vivianite in the environmental field, including immobilization of heavy metals (HMs), dechlorination of carbon tetrachloride (CT), sedimentary phosphorus sequestration and eutrophication alleviation. Additionally, its potential functions as a slow-release fertilizer are discussed as well. In general, vivianite is expected to make more contributions to the future scientific research, especially the solution of environmental problems. Overcoming the lack of understanding and some technical limitations will be beneficial to the further application of vivianite in environmental field.
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Affiliation(s)
- Qing Yuan
- Tianjin Key Lab of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Shu Wang
- Tianjin Key Lab of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- Tianjin Key Lab of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
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Zhao J, Li F, Cao Y, Zhang X, Chen T, Song H, Wang Z. Microbial extracellular electron transfer and strategies for engineering electroactive microorganisms. Biotechnol Adv 2020; 53:107682. [PMID: 33326817 DOI: 10.1016/j.biotechadv.2020.107682] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/04/2020] [Accepted: 12/09/2020] [Indexed: 11/27/2022]
Abstract
Electroactive microorganisms (EAMs) are ubiquitous in nature and have attracted considerable attention as they can be used for energy recovery and environmental remediation via their extracellular electron transfer (EET) capabilities. Although the EET mechanisms of Shewanella and Geobacter have been rigorously investigated and are well characterized, much less is known about the EET mechanisms of other microorganisms. For EAMs, efficient EET is crucial for the sustainable economic development of bioelectrochemical systems (BESs). Currently, the low efficiency of EET remains a key factor in limiting the development of BESs. In this review, we focus on the EET mechanisms of different microorganisms, (i.e., bacteria, fungi, and archaea). In addition, we describe in detail three engineering strategies for improving the EET ability of EAMs: (1) enhancing transmembrane electron transport via cytochrome protein channels; (2) accelerating electron transport via electron shuttle synthesis and transmission; and (3) promoting the microbe-electrode interface reaction via regulating biofilm formation. At the end of this review, we look to the future, with an emphasis on the cross-disciplinary integration of systems biology and synthetic biology to build high-performance EAM systems.
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Affiliation(s)
- Juntao Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBioResearch Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBioResearch Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBioResearch Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Xinbo Zhang
- Joint Research Centre for Protective Infrastructure Technology and Environmental Green Bioprocess, Department of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, People's Republic of China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBioResearch Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBioResearch Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBioResearch Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China.
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7
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Engineering S. oneidensis for Performance Improvement of Microbial Fuel Cell-a Mini Review. Appl Biochem Biotechnol 2020; 193:1170-1186. [PMID: 33200267 DOI: 10.1007/s12010-020-03469-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/09/2020] [Indexed: 02/02/2023]
Abstract
Microbial fuel cell (MFC) is a promising technology that utilizes exoelectrogens cultivated in the form of biofilm to generate power from various types of sources supplied. A metal-reducing pathway is utilized by these organisms to transfer electrons obtained from the metabolism of substrate from anaerobic respiration extracellularly. A widely established model organism that is capable of extracellular electron transfer (EET) is Shewanella oneidensis. This review highlights the strategies used in the transformation of S. oneidensis and the recent development of MFC in terms of intervention through genetic modifications. S. oneidensis was genetically engineered for several aims including the study on the underlying mechanisms of EET, and the enhancement of power generation and wastewater treating potential when used in an MFC. Through engineering S. oneidensis, genes responsible for EET are identified and strategies on enhancing the EET efficiency are studied. Overexpressing genes related to EET to enhance biofilm formation, mediator biosynthesis, and respiration appears as one of the common approaches.
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8
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Kong G, Song D, Guo J, Sun G, Zhu C, Chen F, Yang Y, Xu M. Lack of Periplasmic Non-heme Protein SorA Increases Shewanella decolorationis Current Generation. Front Microbiol 2020; 11:262. [PMID: 32158435 PMCID: PMC7052111 DOI: 10.3389/fmicb.2020.00262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 02/04/2020] [Indexed: 11/13/2022] Open
Abstract
Bacterial extracellular electron transport (EET) plays an important role in many natural and engineering processes. Some periplasmic non-heme redox proteins usually coexist with c-type cytochromes (CTCs) during the EET process. However, in contrast to CTCs, little is known about the roles of these non-heme redox proteins in EET. In this study, the transcriptome of Shewanella decolorationis S12 showed that the gene encoding a periplasmic sulfite dehydrogenase molybdenum-binding subunit SorA was significantly up-regulated during electrode respiration in microbial fuel cells (MFCs) compared with that during azo-dye reduction. The maximum current density of MFCs catalyzed by a mutant strain lacking SorA (ΔsorA) was 25% higher than that of wild strain S12 (20 vs. 16 μA/cm2). Both biofilm formation and the current generation of the anodic biofilms were increased by the disruption of sorA, which suggests that the existence of SorA in S. decolorationis S12 inhibits electrode respiration. In contrast, disruption of sorA had no effect on respiration by S. decolorationis S12 with oxygen, fumarate, azo dye, or ferric citrate as electron acceptors. This is the first report of the specific effect of a periplasmic non-heme redox protein on EET to electrode and provides novel information for enhancing bacterial current generation.
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Affiliation(s)
- Guannan Kong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Da Song
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Jun Guo
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Guoping Sun
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chunjie Zhu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Fusheng Chen
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yonggang Yang
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, China
| | - Meiying Xu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
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9
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Ding D, Shu C, Sun X. Transcriptional regulatory module analysis reveals that bridge proteins reconcile multiple signals in extracellular electron transfer pathways. Proteins 2019; 88:196-205. [PMID: 31344265 DOI: 10.1002/prot.25789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 05/01/2019] [Accepted: 07/06/2019] [Indexed: 01/17/2023]
Abstract
Shewanella oneidensis MR-1 shows remarkable respiratory versatility with a large variety of extracellular electron acceptors (termed extracellular electron transfer, EET). To utilize the various electron acceptors, the bacterium must employ complex regulatory mechanisms to elicit the relevant EET pathways. To investigate the relevant mechanisms, we integrated EET genes and related transcriptional factors (TFs) into transcriptional regulatory modules (TRMs) and showed that many bridge proteins in these modules were signal proteins, which generally contained one or more signal processing domains (eg, GGDEF, EAL, PAS, etc.). Since Shewanella has to respond to diverse environmental conditions despite encoding few EET-relevant TFs, the overabundant signal proteins involved in the TRMs can help decipher the mechanism by which these microbes elicit a wide range of condition-specific responses. By combining proteomic data and protein bioinformatic analysis, we demonstrated that diverse signal proteins reconciled the different EET pathways, and we discussed the functional roles of signal proteins involved in the well-known MtrCAB pathway. Additionally, we showed that the signal proteins SO_2145 and SO_1417 played central roles in triggering EET pathways in anaerobic environments. Taken together, our results suggest that signal proteins have a profound impact on the transcriptional regulation of EET genes and thus have potential applications in microbial fuel cells.
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Affiliation(s)
- Dewu Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, PR China.,School of Mathematics and Computer Science, Yichun University, Yichun, PR China
| | - Chuanjun Shu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, PR China.,Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, PR China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, PR China
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10
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Zhong Y, Shi L. Genomic Analyses of the Quinol Oxidases and/or Quinone Reductases Involved in Bacterial Extracellular Electron Transfer. Front Microbiol 2018; 9:3029. [PMID: 30619124 PMCID: PMC6295460 DOI: 10.3389/fmicb.2018.03029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/23/2018] [Indexed: 11/18/2022] Open
Abstract
To exchange electrons with extracellular substrates, some microorganisms employ extracellular electron transfer (EET) pathways that physically connect extracellular redox reactions to intracellular metabolic activity. These pathways are made of redox and structural proteins that work cooperatively to transfer electrons between extracellular substrates and the cytoplasmic membrane. Crucial to the bacterial and archaeal EET pathways are the quinol oxidases and/or quinone reductases in the cytoplasmic membrane where they recycle the quinone/quinol pool in the cytoplasmic membrane during EET reaction. Up to date, three different families of quinol oxidases and/or quinone reductases involved in bacterial EET have been discovered. They are the CymA, CbcL/MtrH/MtoC, and ImcH families of quinol oxidases and/or quinone reductases that are all multiheme c-type cytochromes (c-Cyts). To investigate to what extent they are distributed among microorganisms, we search the bacterial as well as archaeal genomes for the homologs of these c-Cyts. Search results reveal that the homologs of these c-Cyts are only found in the Domain Bacteria. Moreover, the CymA homologs are only found in the phylum of Proteobacteria and most of them are in the Shewanella genus. In addition to Shewanella sp., CymA homologs are also found in other Fe(III)-reducing bacteria, such as of Vibrio parahaemolyticus. In contrast to CymA, CbcL/MtrH/MtoC, and ImcH homologs are much more widespread. CbcL/MtrH/MtoC homologs are found in 15 phyla, while ImcH homologs are found in 12 phyla. Furthermore, the heme-binding motifs of CbcL/MtrH/MtoC and ImcH homologs vary greatly, ranging from 3 to 23 and 6 to 10 heme-binding motifs for CbcL/MtrH/MtoC and ImcH homologs, respectively. Moreover, CymA and CbcL/MtrH/MtoC homologs are found in both Fe(III)-reducing and Fe(II)-oxidizing bacteria, suggesting that these families of c-Cyts catalyze both quinol-oxidizing and quinone-reducing reactions. ImcH homologs are only found in the Fe(III)-reducing bacteria, implying that they are only the quinol oxidases. Finally, some bacteria have the homologs of two different families of c-Cyts, which may improve the bacterial capability to exchange electrons with extracellular substrates.
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Affiliation(s)
- Yuhong Zhong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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11
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Lienemann M, TerAvest MA, Pitkänen J, Stuns I, Penttilä M, Ajo‐Franklin CM, Jäntti J. Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili. Microb Biotechnol 2018; 11:1184-1194. [PMID: 30296001 PMCID: PMC6196383 DOI: 10.1111/1751-7915.13309] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/02/2018] [Accepted: 08/07/2018] [Indexed: 12/01/2022] Open
Abstract
Biosensors detect signals using biological sensing components such as redox enzymes and biological cells. Although cellular versatility can be beneficial for different applications, limited stability and efficiency in signal transduction at electrode surfaces represent a challenge. Recent studies have shown that the Mtr electron conduit from Shewanella oneidensis MR-1 can be produced in Escherichia coli to generate an exoelectrogenic model system with well-characterized genetic tools. However, means to specifically immobilize this organism at solid substrates as electroactive biofilms have not been tested previously. Here, we show that mannose-binding Fim pili can be produced in exoelectrogenic E. coli and can be used to selectively attach cells to a mannose-coated material. Importantly, cells expressing fim genes retained current production by the heterologous Mtr electron conduit. Our results demonstrate the versatility of the exoelectrogenic E. coli system and motivate future work that aims to produce patterned biofilms for bioelectronic devices that can respond to various biochemical signals.
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Affiliation(s)
| | - Michaela A. TerAvest
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMIUSA
- The Molecular FoundryLawrence Berkeley National LaboratoryMolecular Biophysics and Integrated Bioimaging DivisionSynthetic Biology InstituteBerkeleyCAUSA
| | - Juha‐Pekka Pitkänen
- VTT Technical Research Centre of Finland LtdEspooFinland
- Current affiliation: Solar Foods LtdHelsinkiFinland
| | - Ingmar Stuns
- VTT Technical Research Centre of Finland LtdEspooFinland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland LtdEspooFinland
| | - Caroline M. Ajo‐Franklin
- The Molecular FoundryLawrence Berkeley National LaboratoryMolecular Biophysics and Integrated Bioimaging DivisionSynthetic Biology InstituteBerkeleyCAUSA
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland LtdEspooFinland
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12
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Meibom KL, Cabello EM, Bernier-Latmani R. The Small RNA RyhB Is a Regulator of Cytochrome Expression in Shewanella oneidensis. Front Microbiol 2018. [PMID: 29515549 PMCID: PMC5826389 DOI: 10.3389/fmicb.2018.00268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Shewanella oneidensis produces an extensive electron transfer network that results in metabolic flexibility. A large number of c-type cytochromes are expressed by S. oneidensis and these function as the fundamental electron transport chain proteins. Although several S. oneidensis cytochromes have been well-characterized, little is known about how their expression is regulated. In this study, we investigate the role of the ferric uptake regulator (Fur) and the sRNA RyhB in regulation. Our results demonstrate that loss of Fur leads to diminished growth and an apparent decrease in heme-containing proteins. Remarkably, deleting the Fur-repressed ryhB gene almost completely reverses these physiological changes, indicating that the phenotypes resulting from loss of Fur are (at least partially) dependent on RyhB. RNA sequencing identified a number of possible RyhB repressed genes. A large fraction of these encode c-type cytochromes, among them two of the most abundant periplasmic cytochromes CctA (also known as STC) and ScyA. We show that RyhB destabilizes the mRNA of four of its target genes, cctA, scyA, omp35, and nrfA and this requires the presence of the RNA chaperone Hfq. Iron limitation decreases the expression of the RyhB target genes cctA and scyA and this regulation relies on the presence of both Fur and RyhB. Overall, this study suggests that controlling cytochrome expression is of importance to maintain iron homeostasis and that sRNAs molecules are important players in the regulation of fundamental processes in S. oneidensis MR-1.
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Affiliation(s)
- Karin L Meibom
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Elena M Cabello
- Bioinformatics and Biostatistics Core Facility, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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13
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Extracellular electron transfer mechanisms between microorganisms and minerals. Nat Rev Microbiol 2016; 14:651-62. [DOI: 10.1038/nrmicro.2016.93] [Citation(s) in RCA: 850] [Impact Index Per Article: 94.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Jensen HM, TerAvest MA, Kokish MG, Ajo-Franklin CM. CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli. ACS Synth Biol 2016; 5:679-88. [PMID: 27000939 DOI: 10.1021/acssynbio.5b00279] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Introducing extracellular electron transfer pathways into heterologous organisms offers the opportunity to explore fundamental biogeochemical processes and to biologically alter redox states of exogenous metals for various applications. While expression of the MtrCAB electron nanoconduit from Shewanella oneidensis MR-1 permits extracellular electron transfer in Escherichia coli, the low electron flux and absence of growth in these cells limits their practicality for such applications. Here we investigate how the rate of electron transfer to extracellular Fe(III) and cell survival in engineered E. coli are affected by mimicking different features of the S. oneidensis pathway: the number of electron nanoconduits, the link between the quinol pool and MtrA, and the presence of flavin-dependent electron transfer. While increasing the number of pathways does not significantly improve the extracellular electron transfer rate or cell survival, using the native inner membrane component, CymA, significantly improves the reduction rate of extracellular acceptors and increases cell viability. Strikingly, introducing both CymA and riboflavin to Mtr-expressing E. coli also allowed these cells to couple metal reduction to growth, which is the first time an increase in biomass of an engineered E. coli has been observed under Fe2O3 (s) reducing conditions. Overall, this work provides engineered E. coli strains for modulating extracellular metal reduction and elucidates critical factors for engineering extracellular electron transfer in heterologous organisms.
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Affiliation(s)
- Heather M. Jensen
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Michaela A. TerAvest
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Mark G. Kokish
- Materials
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Caroline M. Ajo-Franklin
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Synthetic Biology Institute, Berkeley, California 94720, United States
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15
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Oram J, Jeuken LJC. A Re-evaluation of Electron-Transfer Mechanisms in Microbial Electrochemistry: Shewanella Releases Iron that Mediates Extracellular Electron Transfer. ChemElectroChem 2016; 3:829-835. [PMID: 27668145 PMCID: PMC5021177 DOI: 10.1002/celc.201500505] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 12/11/2022]
Abstract
Exoelectrogenic bacteria can couple their metabolism to extracellular electron acceptors, including macroscopic electrodes, and this has applications in energy production, bioremediation and biosensing. Optimisation of these technologies relies on a detailed molecular understanding of extracellular electron‐transfer (EET) mechanisms, and Shewanella oneidensis MR‐1 (MR‐1) has become a model organism for such fundamental studies. Here, cyclic voltammetry was used to determine the relationship between the surface chemistry of electrodes (modified gold, ITO and carbon electrodes) and the EET mechanism. On ultra‐smooth gold electrodes modified with self‐assembled monolayers containing carboxylic‐acid‐terminated thiols, an EET pathway dominates with an oxidative catalytic onset at 0.1 V versus SHE. Addition of iron(II)chloride enhances the catalytic current, whereas the siderophore deferoxamine abolishes this signal, leading us to conclude that this pathway proceeds via an iron mediated electron transfer mechanism. The same EET pathway is observed at other electrodes, but the onset potential is dependent on the electrolyte composition and electrode surface chemistry. EET pathways with onset potentials above −0.1 V versus SHE have previously been ascribed to direct electron‐transfer (DET) mechanisms through the surface exposed decaheme cytochromes (MtrC/OmcA) of MR‐1. In light of the results reported here, we propose that the previously identified DET mechanism of MR‐1 needs to be re‐evaluated.
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Affiliation(s)
- Joseph Oram
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT UK
| | - Lars J C Jeuken
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT UK
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16
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Shi L, Tien M, Fredrickson J, Zachara J, Rosso K. Microbial Redox Proteins and Protein Complexes for Extracellular Respiration. REDOX PROTEINS IN SUPERCOMPLEXES AND SIGNALOSOMES 2015:187-216. [DOI: 10.1201/b19087-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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17
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Breuer M, Rosso KM, Blumberger J, Butt JN. Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. J R Soc Interface 2015; 12:20141117. [PMID: 25411412 DOI: 10.1098/rsif.2014.1117] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.
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Affiliation(s)
- Marian Breuer
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Julea N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
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18
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Alves MN, Neto SE, Alves AS, Fonseca BM, Carrêlo A, Pacheco I, Paquete CM, Soares CM, Louro RO. Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1. Front Microbiol 2015; 6:665. [PMID: 26175726 PMCID: PMC4484225 DOI: 10.3389/fmicb.2015.00665] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/17/2015] [Indexed: 01/14/2023] Open
Abstract
The versatile anaerobic metabolism of the Gram-negative bacterium Shewanella oneidensis MR-1 (SOMR-1) relies on a multitude of redox proteins found in its periplasm. Most are multiheme cytochromes that carry electrons to terminal reductases of insoluble electron acceptors located at the cell surface, or bona fide terminal reductases of soluble electron acceptors. In this study, the interaction network of several multiheme cytochromes was explored by a combination of NMR spectroscopy, activity assays followed by UV-visible spectroscopy and comparison of surface electrostatic potentials. From these data the small tetraheme cytochrome (STC) emerges as the main periplasmic redox shuttle in SOMR-1. It accepts electrons from CymA and distributes them to a number of terminal oxidoreductases involved in the respiration of various compounds. STC is also involved in the electron transfer pathway to reduce nitrite by interaction with the octaheme tetrathionate reductase (OTR), but not with cytochrome c nitrite reductase (ccNiR). In the main pathway leading the metal respiration STC pairs with flavocytochrome c (FccA), the other major periplasmic cytochrome, which provides redundancy in this important pathway. The data reveals that the two proteins compete for the binding site at the surface of MtrA, the decaheme cytochrome inserted on the periplasmic side of the MtrCAB-OmcA outer-membrane complex. However, this is not observed for the MtrA homologues. Indeed, neither STC nor FccA interact with MtrD, the best replacement for MtrA, and only STC is able to interact with the decaheme cytochrome DmsE of the outer-membrane complex DmsEFABGH. Overall, these results shown that STC plays a central role in the anaerobic respiratory metabolism of SOMR-1. Nonetheless, the trans-periplasmic electron transfer chain is functionally resilient as a consequence of redundancies that arise from the presence of alternative pathways that bypass/compete with STC.
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Affiliation(s)
- Mónica N Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Sónia E Neto
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Alexandra S Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Bruno M Fonseca
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Afonso Carrêlo
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Isabel Pacheco
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Catarina M Paquete
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cláudio M Soares
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Ricardo O Louro
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
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19
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Ding DW, Xu J, Li L, Xie JM, Sun X. Identifying the potential extracellular electron transfer pathways from a c-type cytochrome network. MOLECULAR BIOSYSTEMS 2014; 10:3138-46. [PMID: 25227320 DOI: 10.1039/c4mb00386a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Extracellular electron transfer (EET) is the key feature of some bacteria, such as Geobacter sulfurreducens and Shewanella oneidensis. Via EET processes, these bacteria can grow on electrode surfaces and make current output of microbial fuel cells. c-Type cytochromes can be used as carriers to transfer electrons, which play an important role in EET processes. Typically, from the inner (cytoplasmic) membrane through the periplasm to the outer membrane, they could form EET pathways. Recent studies suggest that a group of c-type cytochromes could form a network which extended the well-known EET pathways. We obtained the protein interaction information for all 41 c-type cytochromes in Shewanella oneidensis MR-1, constructed a large-scale protein interaction network, and studied its structural characteristics and functional significance. Centrality analysis has identified the top 10 key proteins of the network, and 7 of them are associated with electricity production in the bacteria, which suggests that the ability of Shewanella oneidensis MR-1 to produce electricity might be derived from the unique structure of the c-type cytochrome network. By modularity analysis, we obtained 5 modules from the network. The subcellular localization study has shown that the proteins in these modules all have diversiform cellular compartments, which reflects their potential to form EET pathways. In particular, combination of protein subcellular localization and operon analysis, the well-known and new candidate EET pathways are obtained from the Mtr-like module, indicating that potential EET pathways could be obtained from such a c-type cytochrome network.
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Affiliation(s)
- De-Wu Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P.R. China.
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20
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Electroactive bacteria—molecular mechanisms and genetic tools. Appl Microbiol Biotechnol 2014; 98:8481-95. [DOI: 10.1007/s00253-014-6005-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022]
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21
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Wee SK, Burns JL, DiChristina TJ. Identification of a molecular signature unique to metal-reducingGammaproteobacteria. FEMS Microbiol Lett 2013; 350:90-9. [DOI: 10.1111/1574-6968.12304] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Seng K. Wee
- School of Biology; Georgia Institute of Technology; Atlanta GA USA
| | - Justin L. Burns
- School of Biology; Georgia Institute of Technology; Atlanta GA USA
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22
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Mind the gap: diversity and reactivity relationships among multihaem cytochromes of the MtrA/DmsE family. Biochem Soc Trans 2013; 40:1268-73. [PMID: 23176466 DOI: 10.1042/bst20120106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Shewanella oneidensis MR-1 has the ability to use many external terminal electron acceptors during anaerobic respiration, such as DMSO. The pathway that facilitates this electron transfer includes the decahaem cytochrome DmsE, a paralogue of the MtrA family of decahaem cytochromes. Although both DmsE and MtrA are decahaem cytochromes implicated in the long-range electron transfer across a ~300 Å (1 Å=0.1 nm) wide periplasmic 'gap', MtrA has been shown to be only 105 Å in maximal length. In the present paper, DmsE is further characterized via protein film voltammetry, revealing that the electrochemistry of the DmsE haem cofactors display macroscopic potentials lower than those of MtrA by 100 mV. It is possible this tuning of the redox potential of DmsE is required to shuttle electrons to the outer-membrane proteins specific to DMSO reduction. Other decahaem cytochromes found in S. oneidensis, such as the outer-membrane proteins MtrC, MtrF and OmcA, have been shown to have electrochemical properties similar to those of MtrA, yet possess a different evolutionary relationship.
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23
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The roles of CymA in support of the respiratory flexibility of Shewanella oneidensis MR-1. Biochem Soc Trans 2013; 40:1217-21. [PMID: 23176457 DOI: 10.1042/bst20120150] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Shewanella species are isolated from the oxic/anoxic regions of seawater and aquatic sediments where redox conditions fluctuate in time and space. Colonization of these environments is by virtue of flexible respiratory chains, many of which are notable for the ability to reduce extracellular substrates including the Fe(III) and Mn(IV) contained in oxide and phyllosilicate minerals. Shewanella oneidensis MR-1 serves as a model organism to consider the biochemical basis of this flexibility. In the present paper, we summarize the various systems that serve to branch the respiratory chain of S. oneidensis MR-1 in order that electrons from quinol oxidation can be delivered the various terminal electron acceptors able to support aerobic and anaerobic growth. This serves to highlight several unanswered questions relating to the regulation of respiratory electron transport in Shewanella and the central role(s) of the tetrahaem-containing quinol dehydrogenase CymA in that process.
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24
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Bewley KD, Ellis KE, Firer-Sherwood MA, Elliott SJ. Multi-heme proteins: nature's electronic multi-purpose tool. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:938-48. [PMID: 23558243 DOI: 10.1016/j.bbabio.2013.03.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 02/06/2023]
Abstract
While iron is often a limiting nutrient to Biology, when the element is found in the form of heme cofactors (iron protoporphyrin IX), living systems have excelled at modifying and tailoring the chemistry of the metal. In the context of proteins and enzymes, heme cofactors are increasingly found in stoichiometries greater than one, where a single protein macromolecule contains more than one heme unit. When paired or coupled together, these protein associated heme groups perform a wide variety of tasks, such as redox communication, long range electron transfer and storage of reducing/oxidizing equivalents. Here, we review recent advances in the field of multi-heme proteins, focusing on emergent properties of these complex redox proteins, and strategies found in Nature where such proteins appear to be modular and essential components of larger biochemical pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Kathryn D Bewley
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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25
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Goldbeck CP, Jensen HM, TerAvest MA, Beedle N, Appling Y, Hepler M, Cambray G, Mutalik V, Angenent LT, Ajo-Franklin CM. Tuning promoter strengths for improved synthesis and function of electron conduits in Escherichia coli. ACS Synth Biol 2013; 2:150-9. [PMID: 23656438 DOI: 10.1021/sb300119v] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Introduction of the electron transfer complex MtrCAB from Shewanella oneidensis MR-1 into a heterologous host provides a modular and molecularly defined route for electrons to be transferred to an extracellular inorganic solid. However, an Escherichia coli strain expressing this pathway displayed limited control of MtrCAB expression and impaired cell growth. To overcome these limitations and to improve heterologous extracellular electron transfer, we used an E. coli host with a more tunable induction system and a panel of constitutive promoters to generate a library of strains that separately transcribe the mtr and cytochrome c maturation (ccm) operons over 3 orders of magnitude. From this library, we identified strains that show 2.2 times higher levels of MtrC and MtrA and that have improved cell growth. We find that a ~300-fold decrease in the efficiency of MtrC and MtrA synthesis with increasing mtr promoter activity critically limits the maximum expression level of MtrC and MtrA. We also tested the extracellular electron transfer capabilities of a subset of the strains using a three-electrode microbial electrochemical system. Interestingly, the strain with improved cell growth and fewer morphological changes generated the largest maximal current per cfu, rather than the strain with more MtrC and MtrA. This strain also showed ~30-fold greater maximal current per cfu than its ccm-only control strain. Thus, the conditions for optimal MtrCAB expression and anode reduction are distinct, and minimal perturbations to cell morphology are correlated with improved extracellular electron transfer in E. coli.
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Affiliation(s)
| | - Heather M. Jensen
- Department
of Chemistry, University of California,
Berkeley, California 94720,
United States
| | - Michaela A. TerAvest
- Department
of Biological and
Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | | | | | - Matt Hepler
- Department
of Chemistry, University of California,
Berkeley, California 94720,
United States
| | - Guillaume Cambray
- BIOFAB International Open Facility Advancing Biotechnology (BIOFAB), Emeryville,
California 94608, United States
- California Institute for Quantitative
Biosciences, University of California,
Berkeley, California, 94720, United States
| | - Vivek Mutalik
- BIOFAB International Open Facility Advancing Biotechnology (BIOFAB), Emeryville,
California 94608, United States
| | - Largus T. Angenent
- Department
of Biological and
Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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26
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Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1. Biochem J 2012; 449:101-8. [DOI: 10.1042/bj20121467] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Extracellular electron transfer is the key metabolic trait that enables some bacteria to play a significant role in the biogeochemical cycling of metals and in bioelectrochemical devices such as microbial fuel cells. In Shewanella oneidensis MR-1, electrons generated in the cytoplasm by catabolic processes must cross the periplasmic space to reach terminal oxidoreductases found at the cell surface. Lack of knowledge on how these electrons flow across the periplasmic space is one of the unresolved issues related with extracellular electron transfer. Using NMR to probe protein–protein interactions, kinetic measurements of electron transfer and electrostatic calculations, we were able to identify protein partners and their docking sites, and determine the dissociation constants. The results showed that both STC (small tetrahaem cytochrome c) and FccA (flavocytochrome c) interact with their redox partners, CymA and MtrA, through a single haem, avoiding the establishment of stable redox complexes capable of spanning the periplasmic space. Furthermore, we verified that the most abundant periplasmic cytochromes STC, FccA and ScyA (monohaem cytochrome c5) do not interact with each other and this is likely to be the consequence of negative surface charges in these proteins. This reveals the co-existence of two non-mixing redox pathways that lead to extracellular electron transfer in S. oneidensis MR-1 established through transient protein interactions.
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27
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Patil SA, Hägerhäll C, Gorton L. Electron transfer mechanisms between microorganisms and electrodes in bioelectrochemical systems. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12566-012-0033-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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29
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Marritt SJ, Lowe TG, Bye J, McMillan DGG, Shi L, Fredrickson J, Zachara J, Richardson DJ, Cheesman MR, Jeuken LJC, Butt JN. A functional description of CymA, an electron-transfer hub supporting anaerobic respiratory flexibility in Shewanella. Biochem J 2012; 444:465-74. [PMID: 22458729 DOI: 10.1042/bj20120197] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
CymA (tetrahaem cytochrome c) is a member of the NapC/NirT family of quinol dehydrogenases. Essential for the anaerobic respiratory flexibility of shewanellae, CymA transfers electrons from menaquinol to various dedicated systems for the reduction of terminal electron acceptors including fumarate and insoluble minerals of Fe(III). Spectroscopic characterization of CymA from Shewanella oneidensis strain MR-1 identifies three low-spin His/His co-ordinated c-haems and a single high-spin c-haem with His/H(2)O co-ordination lying adjacent to the quinol-binding site. At pH 7, binding of the menaquinol analogue, 2-heptyl-4-hydroxyquinoline-N-oxide, does not alter the mid-point potentials of the high-spin (approximately -240 mV) and low-spin (approximately -110, -190 and -265 mV) haems that appear biased to transfer electrons from the high- to low-spin centres following quinol oxidation. CymA is reduced with menadiol (E(m) = -80 mV) in the presence of NADH (E(m) = -320 mV) and an NADH-menadione (2-methyl-1,4-naphthoquinone) oxidoreductase, but not by menadiol alone. In cytoplasmic membranes reduction of CymA may then require the thermodynamic driving force from NADH, formate or H2 oxidation as the redox poise of the menaquinol pool in isolation is insufficient. Spectroscopic studies suggest that CymA requires a non-haem co-factor for quinol oxidation and that the reduced enzyme forms a 1:1 complex with its redox partner Fcc3 (flavocytochrome c3 fumarate reductase). The implications for CymA supporting the respiratory flexibility of shewanellae are discussed.
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Affiliation(s)
- Sophie J Marritt
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
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30
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Seidel J, Hoffmann M, Ellis KE, Seidel A, Spatzal T, Gerhardt S, Elliott SJ, Einsle O. MacA is a second cytochrome c peroxidase of Geobacter sulfurreducens. Biochemistry 2012; 51:2747-56. [PMID: 22417533 DOI: 10.1021/bi300249u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS(-2) as an electron donor. The observed K(M) was 38.5 ± 3.7 μM H(2)O(2) and v(max) was 0.78 ± 0.03 μmol of H(2)O(2)·min(-1)·mg(-1), resulting in a turnover number k(cat) = 0.46 · s(-1). In contrast, no Fe(III) reductase activity was observed. MacA was found to display electrochemical properties similar to other bacterial diheme peroxidases, in addition to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergoes conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein, the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation.
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Affiliation(s)
- Julian Seidel
- Lehrstuhl für Biochemie, Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
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31
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Shi L, Rosso KM, Clarke TA, Richardson DJ, Zachara JM, Fredrickson JK. Molecular Underpinnings of Fe(III) Oxide Reduction by Shewanella Oneidensis MR-1. Front Microbiol 2012; 3:50. [PMID: 22363328 PMCID: PMC3279761 DOI: 10.3389/fmicb.2012.00050] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 01/30/2012] [Indexed: 11/25/2022] Open
Abstract
In the absence of O2 and other electron acceptors, the Gram-negative bacterium Shewanella oneidensis MR-1 can use ferric [Fe(III)] (oxy)(hydr)oxide minerals as the terminal electron acceptors for anaerobic respiration. At circumneutral pH and in the absence of strong complexing ligands, Fe(III) oxides are relatively insoluble and thus are external to the bacterial cells. S. oneidensis MR-1 and related strains of metal-reducing Shewanella have evolved machinery (i.e., metal-reducing or Mtr pathway) for transferring electrons from the inner-membrane, through the periplasm and across the outer-membrane to the surface of extracellular Fe(III) oxides. The protein components identified to date for the Mtr pathway include CymA, MtrA, MtrB, MtrC, and OmcA. CymA is an inner-membrane tetraheme c-type cytochrome (c-Cyt) that belongs to the NapC/NrfH family of quinol dehydrogenases. It is proposed that CymA oxidizes the quinol in the inner-membrane and transfers the released electrons to MtrA either directly or indirectly through other periplasmic proteins. A decaheme c-Cyt, MtrA is thought to be embedded in the trans outer-membrane and porin-like protein MtrB. Together, MtrAB deliver the electrons through the outer-membrane to the MtrC and OmcA on the outmost bacterial surface. MtrC and OmcA are the outer-membrane decaheme c-Cyts that are translocated across the outer-membrane by the bacterial type II secretion system. Functioning as terminal reductases, MtrC and OmcA can bind the surface of Fe(III) oxides and transfer electrons directly to these minerals via their solvent-exposed hemes. To increase their reaction rates, MtrC and OmcA can use the flavins secreted by S. oneidensis MR-1 cells as diffusible co-factors for reduction of Fe(III) oxides. Because of their extracellular location and broad redox potentials, MtrC and OmcA can also serve as the terminal reductases for soluble forms of Fe(III). In addition to Fe(III) oxides, Mtr pathway is also involved in reduction of manganese oxides and other metals. Although our understanding of the Mtr pathway is still far from complete, it is the best characterized microbial pathway used for extracellular electron exchange. Characterizations of the Mtr pathway have made significant contributions to the molecular understanding of microbial reduction of Fe(III) oxides.
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Affiliation(s)
- Liang Shi
- Pacific Northwest National Laboratory Richland, WA, USA
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Firer-Sherwood MA, Ando N, Drennan CL, Elliott SJ. Solution-based structural analysis of the decaheme cytochrome, MtrA, by small-angle X-ray scattering and analytical ultracentrifugation. J Phys Chem B 2011; 115:11208-14. [PMID: 21838277 PMCID: PMC3178274 DOI: 10.1021/jp203603r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/12/2011] [Indexed: 01/05/2023]
Abstract
The potential exploitation of metal-reducing bacteria as a means for environmental cleanup or alternative fuel is an exciting prospect; however, the cellular processes that would allow for these applications need to be better understood. MtrA is a periplasmic decaheme c-type cytochrome from Shewanella oneidensis involved in the reduction of extracellular iron oxides and therefore is a critical element in Shewanella ability to engage in extracellular charge transfer. As a relatively small 333-residue protein, the heme content is surprisingly high. MtrA is believed to obtain electrons from the inner membrane-bound quinol oxidoreductase, CymA, and shuttle them across the outer membrane to MtrC, another decaheme cytochrome that directly interacts with insoluble metal oxides. How MtrA is able to perform this task is a question of interest. Here through the use of two solution-based techniques, small-angle X-ray scattering (SAXS) and analytical ultracentrifugation (AUC), we present the first structural analysis of MtrA. Our results establish that between 0.5 and 4 mg/mL, MtrA exists as a monomeric protein that is shaped like an extended molecular "wire" with a maximum protein dimension (D(max)) of 104 Å and a rod-like aspect ratio of 2.2 to 2.5. This study contributes to a greater understanding of how MtrA fulfills its role in the redox processes that must occur before electrons reach the outside of the cell.
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Affiliation(s)
- Mackenzie A. Firer-Sherwood
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Nozomi Ando
- Howard Hughes Medical Institute, Departments of Biology and Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Howard Hughes Medical Institute, Departments of Biology and Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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