1
|
Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3. Genet Res (Camb) 2021; 2021:9953783. [PMID: 34456634 PMCID: PMC8371737 DOI: 10.1155/2021/9953783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/28/2021] [Accepted: 07/20/2021] [Indexed: 12/01/2022] Open
Abstract
Because of the ability to metabolize a large number of electron acceptors such as nitrate, nitrite, fumarate, and metal oxides, Shewanella species have attracted much attention in recent years. Generally, the use of these electron acceptors is mainly achieved through electron transfer proteins and their interactions which will dynamically change across different environmental conditions in cells. Therefore, functional analysis of condition-specific molecular networks can reveal biological information on electron transfer processes. By integrating expression data and molecular networks, we constructed condition-specific molecular networks for Shewanella piezotolerans WP3. We then identified condition-specific key genes and studied their potential functions with an emphasis on their roles in electron transfer processes. Functional module analysis showed that different flagellar assembly modules appeared under these conditions and suggested that flagellar proteins are important for these conditions. We also identified the electron transfer modules underlying these various environmental conditions. The present results could help with screening electron transfer genes and understanding electron transfer processes under various environmental conditions for the Shewanella species.
Collapse
|
2
|
Abstract
Respiration of perchlorate and chlorate [collectively, (per)chlorate] was only recognized in the last 20 years, yet substantial advances have been made in our understanding of the underlying metabolisms. Although it was once considered solely anthropogenic, pervasive natural sources, both terrestrial and extraterrestrial, indicate an ancient (per)chlorate presence across our solar system. These discoveries stimulated interest in (per)chlorate microbiology, and the application of advanced approaches highlights exciting new facets. Forward and reverse genetics revealed new information regarding underlying molecular biology and associated regulatory mechanisms. Structural and functional analysis characterized core enzymes and identified novel reaction sequences. Comparative genomics elucidated evolutionary aspects, and stress analysis identified novel response mechanisms to reactive chlorine species. Finally, systems biology identified unique metabolic versatility and novel mechanisms of (per)chlorate respiration, including symbiosis and a hybrid enzymatic-abiotic metabolism. While many published studies focus on (per)chlorate and their basic metabolism, this review highlights seminal advances made over the last decade and identifies new directions and potential novel applications.
Collapse
Affiliation(s)
- Matthew D Youngblut
- Energy Biosciences Institute, University of California, Berkeley, California 94704;
| | - Ouwei Wang
- Energy Biosciences Institute, University of California, Berkeley, California 94704; .,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Tyler P Barnum
- Energy Biosciences Institute, University of California, Berkeley, California 94704; .,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - John D Coates
- Energy Biosciences Institute, University of California, Berkeley, California 94704; .,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| |
Collapse
|
3
|
Clark IC, Youngblut M, Jacobsen G, Wetmore KM, Deutschbauer A, Lucas L, Coates JD. Genetic dissection of chlorate respiration in Pseudomonas stutzeri PDA reveals syntrophic (per)chlorate reduction. Environ Microbiol 2015; 18:3342-3354. [PMID: 26411776 DOI: 10.1111/1462-2920.13068] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/02/2015] [Accepted: 09/23/2015] [Indexed: 12/22/2022]
Abstract
Genes important for growth of Pseudomonas stutzeri PDA on chlorate were identified using a randomly DNA bar-coded transposon mutant library. During chlorate reduction, mutations in genes encoding the chlorate reductase clrABC, predicted molybdopterin cofactor chaperon clrD, molybdopterin biosynthesis and two genes of unknown function (clrE, clrF) had fitness defects in pooled mutant assays (Bar-seq). Markerless in-frame deletions confirmed that clrA, clrB and clrC were essential for chlorate reduction, while clrD, clrE and clrF had less severe growth defects. Interestingly, the key detoxification gene cld was essential for chlorate reduction in isogenic pure culture experiments, but showed only minor fitness defects in Bar-seq experiments. We hypothesized this was enabled through chlorite dismutation by the community, as most strains in the Bar-seq library contained an intact cld. In support of this, Δcld grew with wild-type PDA or ΔclrA, and purified Cld also restored growth to the Δcld mutant. Expanding on this, wild-type PDA and a Δcld mutant of the perchlorate reducer Azospira suillum PS grew on perchlorate in co-culture, but not individually. These results demonstrate that co-occurrence of cld and a chloroxyanion reductase within a single organism is not necessary and raises the possibility of syntrophic (per)chlorate respiration in the environment.
Collapse
Affiliation(s)
- Iain C Clark
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720, USA
| | - Matt Youngblut
- Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Gillian Jacobsen
- Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Kelly M Wetmore
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lauren Lucas
- Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John D Coates
- Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
4
|
Paulo TDF, de Sousa TP, de Abreu DS, Felício NH, Bernhardt PV, Lopes LGDF, Sousa EHS, Diógenes ICN. Electrochemistry, surface plasmon resonance, and quartz crystal microbalance: an associative study on cytochrome c adsorption on pyridine tail-group monolayers on gold. J Phys Chem B 2013; 117:8673-80. [PMID: 23819458 DOI: 10.1021/jp400694k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and electrochemistry techniques were used to study the electron-transfer (ET) reaction of cytochrome c (Cyt c) on gold surfaces modified with thionicotinamide, thioisonicotinamide, 4-mercaptopyridine, 5-(4-pyridyl)-1,3,4-oxadiazole-2-thiol, 5-phenyl-1,3,4-oxadiazole-2-thiol, 4,4'-bipyridine, and 4,4'-dithiopyridine. The electrochemical results showed that the ET process is complex, being chiefly diffusional with steps depending on the orientation of the pyridine or phenyl tail group of the modifiers. The correlation between the electrochemical results and those acquired by SPR and QCM indicated the presence of an adlayer of Cyt c adsorbed on the thiolate SAMs. This adlayer, although being not electroactive, is essential to assess the ET reaction of Cyt c in solution. The results presented in this work are consistent with the statement (Feng, Z. Q.; Imabayashi, S.; Kakiuchi, T.; Niki, K. J. Electroanal. Chem. 1995, 394, 149-154) that the ET reaction of Cyt c can be explained in terms of the through-bond tunneling mechanism.
Collapse
Affiliation(s)
- Tércio de F Paulo
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, Fortaleza, Ceará, Brasil 60455-970
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Peng S, Liang DW, Diao P, Liu Y, Lan F, Yang Y, Lu S, Xiang Y. Nernst-ping-pong model for evaluating the effects of the substrate concentration and anode potential on the kinetic characteristics of bioanode. BIORESOURCE TECHNOLOGY 2013; 136:610-616. [PMID: 23567738 DOI: 10.1016/j.biortech.2013.03.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/06/2013] [Accepted: 03/09/2013] [Indexed: 06/02/2023]
Abstract
Understanding the electron-transfer mechanism and kinetic characteristics of bioanodes is greatly significant to enhance the electron-generating efficiencies in bioelectrochemical systems (BESs). A Nernst-ping-pong model is proposed here to investigate the kinetics and biochemical processes of bioanodes in a microbial electrolysis cell. This model can accurately describe the effects of the substrate (including substrate inhibition) and the anode potential on the current of bioanodes. Results show that the half-wave potential positively shifts as the substrate concentration increases, indicating that the rate-determining steps of anodic processes change from substrate oxidation to intracellular electron transport reaction. The anode potential has negligible effects on the enzymatic catalysis of anodic microbes in the range of -0.25 V to +0.1 V vs. a saturated calomel electrode. It turns out that to reduce the anodic energy loss caused by overpotential, higher substrate concentrations are preferred, if the substrate do not significantly and adversely affect the output current.
Collapse
Affiliation(s)
- Sikan Peng
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry & Environment, Beihang University, Beijing 100191, PR China
| | | | | | | | | | | | | | | |
Collapse
|
6
|
The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
Collapse
|
7
|
Kalimuthu P, Leimkühler S, Bernhardt PV. Catalytic Electrochemistry of Xanthine Dehydrogenase. J Phys Chem B 2012; 116:11600-7. [DOI: 10.1021/jp307374z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular
Biosciences, University of Queensland,
Brisbane 4072, Australia
| | - Silke Leimkühler
- Institut für Biochemie
und Biologie, Universität Potsdam, 14476 Potsdam, Germany
| | - Paul V. Bernhardt
- School of Chemistry and Molecular
Biosciences, University of Queensland,
Brisbane 4072, Australia
| |
Collapse
|
8
|
Nilsson T, Rova M, Smedja Bäcklund A. Microbial metabolism of oxochlorates: a bioenergetic perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:189-97. [PMID: 22735192 DOI: 10.1016/j.bbabio.2012.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 06/05/2012] [Accepted: 06/15/2012] [Indexed: 11/28/2022]
Abstract
The microbial metabolism of oxochlorates is part of the biogeochemical cycle of chlorine. Organisms capable of growth using perchlorate or chlorate as respiratory electron acceptors are also interesting for applications in biotreatment of oxochlorate-containing effluents or bioremediation of contaminated areas. In this review, we discuss the reactions of oxochlorate respiration, the corresponding enzymes, and the relation to respiratory electron transport that can contribute to a proton gradient across the cell membrane. Enzymes specific for oxochlorate respiration are oxochlorate reductases and chlorite dismutase. The former belong to DMSO reductase family of molybdenum-containing enzymes. The heme protein chlorite dismutase, which decomposes chlorite into chloride and molecular oxygen, is only distantly related to other proteins with known functions. Pathways for electron transport may be different in perchlorate and chlorate reducers, but appear in both cases to be similar to pathways found in other respiratory systems. This article is part of a Special Issue entitled: Evolutionary aspects bioenergetic systems.
Collapse
Affiliation(s)
- Thomas Nilsson
- Karlstad University, Dept. Chemistry and Biomedical Sciences, SE-651 88 Karlstad, Sweden.
| | | | | |
Collapse
|
9
|
Bäcklund AS, Nilsson T. Purification and characterization of a soluble cytochrome c capable of delivering electrons to chlorate reductase in Ideonella dechloratans. FEMS Microbiol Lett 2011; 321:115-20. [DOI: 10.1111/j.1574-6968.2011.02321.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
10
|
Bernhardt PV. Exploiting the versatility and selectivity of Mo enzymes with electrochemistry. Chem Commun (Camb) 2011; 47:1663-73. [DOI: 10.1039/c0cc03681a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Chen KI, McEwan AG, Bernhardt PV. Mediated electrochemistry of dimethyl sulfoxide reductase from Rhodobacter capsulatus. J Biol Inorg Chem 2008; 14:409-19. [DOI: 10.1007/s00775-008-0458-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 11/26/2008] [Indexed: 11/29/2022]
|