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Liu S, Hu R, Peng N, Zhou Z, Chen R, He Z, Wang C. Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments. THE ISME JOURNAL 2023; 17:2313-2325. [PMID: 37880540 PMCID: PMC10689504 DOI: 10.1038/s41396-023-01544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Nenglong Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruihan Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf. Appl Environ Microbiol 2022; 88:e0021622. [PMID: 35404072 PMCID: PMC9088280 DOI: 10.1128/aem.00216-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using 13C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. 13C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated 13C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated 13C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated 13C-bicarbonate under sediment anoxic conditions also assimilated 13C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches. IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using 13C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.
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Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. THE ISME JOURNAL 2021; 15:1810-1825. [PMID: 33504941 DOI: 10.1101/2020.06.03.132969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 05/21/2023]
Abstract
Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.
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Affiliation(s)
- Heyu Lin
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC, 3004, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC, 3004, Australia
| | - Carl H Lamborg
- Department of Ocean Sciences, University of California, Santa Cruz, CA, 95064, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN, 37831, USA
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Monash, VIC, 3800, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Currently at School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. THE ISME JOURNAL 2021; 15:1810-1825. [PMID: 33504941 PMCID: PMC8163782 DOI: 10.1038/s41396-020-00889-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023]
Abstract
Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.
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Affiliation(s)
- Heyu Lin
- grid.1008.90000 0001 2179 088XSchool of Earth Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - David B. Ascher
- grid.1008.90000 0001 2179 088XStructural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1051.50000 0000 9760 5620Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC 3004 Australia
| | - Yoochan Myung
- grid.1008.90000 0001 2179 088XStructural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1051.50000 0000 9760 5620Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC 3004 Australia
| | - Carl H. Lamborg
- grid.205975.c0000 0001 0740 6917Department of Ocean Sciences, University of California, Santa Cruz, CA 95064 USA
| | - Steven J. Hallam
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z1 Canada ,grid.17091.3e0000 0001 2288 9830Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Caitlin M. Gionfriddo
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831 USA ,grid.419533.90000 0000 8612 0361Present Address: Smithsonian Environmental Research Center, Edgewater, MD 21037 USA
| | - Kathryn E. Holt
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Monash, VIC 3800 Australia ,grid.8991.90000 0004 0425 469XDepartment of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - John W. Moreau
- grid.1008.90000 0001 2179 088XSchool of Earth Sciences, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.8756.c0000 0001 2193 314XPresent Address: Currently at School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ UK
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Boden R. Reclassification of Halothiobacillus hydrothermalis and Halothiobacillus halophilus to Guyparkeria gen. nov. in the Thioalkalibacteraceae fam. nov., with emended descriptions of the genus Halothiobacillus and family Halothiobacillaceae. Int J Syst Evol Microbiol 2017; 67:3919-3928. [PMID: 28884673 DOI: 10.1099/ijsem.0.002222] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Halothiobacillus contains four species of obligate autotrophs with validly published names, of which Halothiobacillus halophilus and Halothiobacillus hydrothermalis are very distant from the type species - on the basis of the 16S rRNA gene, they have 90.7 % and 90.9 % identity to that of the type species, Halothiobacillus neapolitanus. As these values fall below the Yarza cut-off for the rank of genus, and these two species also show no clear affiliation to the closely related genus Thioalkalibacter, a polyphasic study was undertaken to determine if they represent a separate genus. Unlike Halothiobacillus spp. sensu stricto, H. halophilus and H. hydrothermalis are halophilic (rather than halotolerant) and moderately alkaliphilic (rather than neutrophilic) and additionally do not produce tetrathionate as a detectable intermediate of thiosulfate metabolism, indicating some significant metabolic differences. On the basis of these data and of functional gene examination, it is proposed that they be circumscribed as a new genus Guyparkeria gen.nov, for which the type species is Guyparkeria halophila gen. nov., comb. nov. Additionally, Thioalkalibacter and Guyparkeria gen. nov. fall distant from the Halothiobacillaceae so the Thioalkalibacteraceae fam. nov. is proposed, for which Thioalkalibacter is the type genus. Emended descriptions of Halothiobacillus, Halothiobacillus neapolitanus and the Halothiobacillaceae are provided.
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Affiliation(s)
- Rich Boden
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonopoulos D, Kemner KM, Meyer F. The complete genome sequence for putative H2- and S-oxidizerCandidatusSulfuricurvum sp., assembledde novofrom an aquifer-derived metagenome. Environ Microbiol 2014; 16:3443-62. [DOI: 10.1111/1462-2920.12453] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/04/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Kim M. Handley
- Department of Ecology and Evolution; University of Chicago; Chicago IL 60637 USA
- Institute for Genomics and Systems Biology; Argonne National Laboratory; Lemont IL 60439 USA
| | - Daniela Bartels
- Institute for Genomics and Systems Biology; Argonne National Laboratory; Lemont IL 60439 USA
- Computation Institute; University of Chicago; Chicago IL 60637 USA
| | | | - Kenneth H. Williams
- Earth Science Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - William L. Trimble
- Mathematics and Computer Science Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Kelly Skinner
- Biosciences Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Jack A. Gilbert
- Department of Ecology and Evolution; University of Chicago; Chicago IL 60637 USA
- Institute for Genomics and Systems Biology; Argonne National Laboratory; Lemont IL 60439 USA
- Biosciences Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Narayan Desai
- Mathematics and Computer Science Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Elizabeth M. Glass
- Computation Institute; University of Chicago; Chicago IL 60637 USA
- Mathematics and Computer Science Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Tobias Paczian
- Computation Institute; University of Chicago; Chicago IL 60637 USA
- Mathematics and Computer Science Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Andreas Wilke
- Computation Institute; University of Chicago; Chicago IL 60637 USA
- Mathematics and Computer Science Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Dionysios Antonopoulos
- Institute for Genomics and Systems Biology; Argonne National Laboratory; Lemont IL 60439 USA
- Biosciences Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Kenneth M. Kemner
- Biosciences Division; Argonne National Laboratory; Lemont IL 60439 USA
| | - Folker Meyer
- Institute for Genomics and Systems Biology; Argonne National Laboratory; Lemont IL 60439 USA
- Computation Institute; University of Chicago; Chicago IL 60637 USA
- Mathematics and Computer Science Division; Argonne National Laboratory; Lemont IL 60439 USA
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7
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Handley KM, VerBerkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, Frischkorn KR, Chourey K, Thomas BC, Shah MB, Long PE, Hettich RL, Banfield JF. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. THE ISME JOURNAL 2013; 7:800-16. [PMID: 23190730 PMCID: PMC3603403 DOI: 10.1038/ismej.2012.148] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/28/2012] [Accepted: 10/08/2012] [Indexed: 11/09/2022]
Abstract
Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used proteogenomics to test the hypothesis that excess input of acetate activates complex community functioning and syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer and recovered during microbial sulfate reduction. De novo reconstruction of community sequences yielded near-complete genomes of Desulfobacter (Deltaproteobacteria), Sulfurovum- and Sulfurimonas-like Epsilonproteobacteria and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen fixation and acetate oxidation to CO2 during amendment. Results indicate less abundant Desulfuromonadales, and possibly Bacteroidetes, also actively contributed to CO2 production via the tricarboxylic acid (TCA) cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. We infer that high acetate concentrations, aimed at stimulating anaerobic heterotrophy, led to the co-enrichment of, and carbon fixation in Epsilonproteobacteria. Results give an insight into ecosystem behavior following addition of simple organic carbon to the subsurface, and demonstrate a range of biological processes and community interactions were stimulated.
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Affiliation(s)
- Kim M Handley
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Nathan C VerBerkmoes
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Carl I Steefel
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
| | - Kenneth H Williams
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
| | - Itai Sharon
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Christopher S Miller
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Kyle R Frischkorn
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Karuna Chourey
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Brian C Thomas
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Manesh B Shah
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Philip E Long
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
| | - Robert L Hettich
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
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8
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Li Y, Hopper A, Overton T, Squire DJP, Cole J, Tovell N. Organization of the electron transfer chain to oxygen in the obligate human pathogen Neisseria gonorrhoeae: roles for cytochromes c4 and c5, but not cytochrome c2, in oxygen reduction. J Bacteriol 2010; 192:2395-406. [PMID: 20154126 PMCID: PMC2863483 DOI: 10.1128/jb.00002-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Accepted: 02/09/2010] [Indexed: 02/07/2023] Open
Abstract
Although Neisseria gonorrhoeae is a prolific source of eight c-type cytochromes, little is known about how its electron transfer pathways to oxygen are organized. In this study, the roles in the respiratory chain to oxygen of cytochromes c(2), c(4), and c(5), encoded by the genes cccA, cycA, and cycB, respectively, have been investigated. Single mutations in genes for either cytochrome c(4) or c(5) resulted in an increased sensitivity to growth inhibition by excess oxygen and small decreases in the respiratory capacity of the parent, which were complemented by the chromosomal integration of an ectopic, isopropyl-beta-d-thiogalactopyranoside (IPTG)-inducible copy of the cycA or cycB gene. In contrast, a cccA mutant reduced oxygen slightly more rapidly than the parent, suggesting that cccA is expressed but cytochrome c(2) is not involved in electron transfer to cytochrome oxidase. The deletion of cccA increased the sensitivity of the cycB mutant to excess oxygen but decreased the sensitivity of the cycA mutant. Despite many attempts, a double mutant defective in both cytochromes c(4) and c(5) could not be isolated. However, a strain with the ectopically encoded, IPTG-inducible cycB gene with deletions in both cycA and cycB was constructed: the growth and survival of this strain were dependent upon the addition of IPTG, so gonococcal survival is dependent upon the synthesis of either cytochrome c(4) or c(5). These results define the gonococcal electron transfer chain to oxygen in which cytochromes c(4) and c(5), but not cytochrome c(2), provide alternative pathways for electron transfer from the cytochrome bc(1) complex to the terminal oxidase cytochrome cbb(3).
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Affiliation(s)
- Ying Li
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Amanda Hopper
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Tim Overton
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Derrick J. P. Squire
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Jeffrey Cole
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Nicholas Tovell
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
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9
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Sorokin DY, Cherepanov A, Kuenen GJ. Identification of cytochrome c oxidase in the alkaliphilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium 'Thioalcalomicrobium aerophilum' strain AL 3. FEMS Microbiol Lett 1999; 179:91-99. [PMID: 10481092 DOI: 10.1111/j.1574-6968.1999.tb08713.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cytochrome c oxidase from the novel alkaliphilic autotrophic sulfur bacterium 'Thioalcalomicrobium aerophilum' strain AL 3 was isolated and purified 87-fold. Spectroscopic analysis revealed the presence of both c- and b-type hemes as well as copper in a ratio of 3:2:1. The purified enzyme consists of three subunits with apparent molecular masses of 41, 34 and 32 kDa. The two small subunits contain covalently bound heme c. With TMPD as a substrate the pH optimum was determined to be pH 8.0. In the presence of monovalent cations the specific activity of the purified oxidase increased significantly. The enzyme was not able to oxidize external cytochrome c, but accepted electron from its native electron donor. The latter was separated from the other membrane cytochromes during anion-exchange chromatography and was identified as a high potential cytochrome c(551). Overall the data indicate that the cytochrome c oxidase from this alkaliphilic autotrophic bacterium belongs to the heme-copper oxidase superfamily; regarding its subunit composition and content of prosthetic groups, the enzyme is similar in many aspects to the cbb(3)-type cytochrome c oxidases described for several neutrophilic bacteria, including anaerobic phototrophic and aerobic sulfur-oxidizing bacteria.
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Affiliation(s)
- DY Sorokin
- Institute of Microbiology, Russian Academy of Science, Prospect 60-let Octyabrya 7/2, Moscow, Russia
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10
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Toledo-Cuevas M, Barquera B, Gennis RB, Wikström M, García-Horsman JA. The cbb3-type cytochrome c oxidase from Rhodobacter sphaeroides, a proton-pumping heme-copper oxidase. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1365:421-34. [PMID: 9711295 DOI: 10.1016/s0005-2728(98)00095-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rhodobacter sphaeroides expresses a bb3-type quinol oxidase, and two cytochrome c oxidases: cytochrome aa3 and cytochrome cbb3. We report here the characterization of the genes encoding this latter oxidase. The ccoNOQP gene cluster of R. sphaeroides contains four open reading frames with high similarity to all ccoNOQP/fixNOQP gene clusters reported so far. CcoN has the six highly conserved histidines proposed to be involved in binding the low spin heme, and the binuclear center metals. ccoO and ccoP code for membrane bound mono- and diheme cytochromes c. ccoQ codes for a small hydrophobic protein of unknown function. Upstream from the cluster there is a conserved Fnr/FixK-like box which may regulate its expression. Analysis of a R. sphaeroides mutant in which the ccoNOQP gene cluster was inactivated confirms that this cluster encodes the cbb3-type oxidase previously purified. Analysis of proton translocation in several strains shows that cytochrome cbb3 is a proton pump. We also conclude that cytochromes cbb3 and aa3 are the only cytochrome c oxidases in the respiratory chain of R. sphaeroides.
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Affiliation(s)
- M Toledo-Cuevas
- Depàrtamento de Bioquímica, UNAM, Ciudad Universitaria, Mexico D.F., Mexico
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Cheesman MR, Zumft WG, Thomson AJ. The MCD and EPR of the heme centers of nitric oxide reductase from Pseudomonas stutzeri: evidence that the enzyme is structurally related to the heme-copper oxidases. Biochemistry 1998; 37:3994-4000. [PMID: 9521721 DOI: 10.1021/bi972437y] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
EPR spectra at liquid helium temperatures and MCD spectra at room temperature and 4.2 K are presented for fully oxidized nitric oxide reductase (NOR) from Pseudomonas stutzeri. The MCD spectra show that the enzyme contains three heme groups at equivalent concentrations but distinctive in their axial coordination. Two, in the low-spin ferric state at all temperatures, give rise to infrared charge-transfer transitions which show the hemes to have bis-histidine and histidine-methionine ligation, respectively. The EPR spectra show them to be magnetically isolated. The third heme has an unusual temperature-dependent spin state and spectroscopic features which are consistent with histidine-hydroxide coordination. No EPR signals have been detected from this heme. Together with its unusual near-infrared MCD, this suggests a spin-spin interaction between this heme and another paramagnet. The three hemes account for only 75% of the iron content, and it is concluded that the additional paramagnet is a mononuclear ferric ion. These results provide further evidence that NOR is indeed structurally related to heme-copper oxidases and that it contains a heme/non-heme iron spin-coupled pair at the active site.
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Affiliation(s)
- M R Cheesman
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences, University of East Anglia, Norwich, U.K.
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Visser JM, Robertson LA, Van Verseveld HW, Kuenen JG. Sulfur production by obligately chemolithoautotrophic thiobacillus species. Appl Environ Microbiol 1997; 63:2300-5. [PMID: 16535627 PMCID: PMC1389182 DOI: 10.1128/aem.63.6.2300-2305.1997] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transient-state experiments with the obligately autotrophic Thiobacillus sp. strain W5 revealed that sulfide oxidation proceeds in two physiological phases, (i) the sulfate-producing phase and (ii) the sulfur- and sulfate-producing phase, after which sulfide toxicity occurs. Specific sulfur-producing characteristics were independent of the growth rate. Sulfur formation was shown to occur when the maximum oxidative capacity of the culture was approached. In order to be able to oxidize increasing amounts of sulfide, the organism has to convert part of the sulfide to sulfur (HS(sup-)(symbl)S(sup0) + H(sup+) + 2e(sup-)) instead of sulfate (HS(sup-) + 4H(inf2)O(symbl)SO(inf4)(sup2-) + 9 H(sup+) + 8e(sup-)), thereby keeping the electron flux constant. Measurements of the in vivo degree of reduction of the cytochrome pool as a function of increasing sulfide supply suggested a redox-related down-regulation of the sulfur oxidation rate. Comparison of the sulfur-producing properties of Thiobacillus sp. strain W5 and Thiobacillus neapolitanus showed that the former has twice the maximum specific sulfide-oxidizing capacity of the latter (3.6 versus 1.9 (mu)mol/mg of protein/min). Their maximum specific oxygen uptake rates were very similar. Significant mechanistic differences in sulfur production between the high-sulfur-producing Thiobacillus sp. strain W5 and the moderate-sulfur-producing species T. neapolitanus were not observed. The limited sulfide-oxidizing capacity of T. neapolitanus appears to be the reason that it can convert only 50% of the incoming sulfide to elemental sulfur.
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