1
|
Alarcon HV, Mohl JE, Chong GW, Betancourt A, Wang Y, Leng W, White JC, Xu J. Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source. Appl Environ Microbiol 2024; 90:e0086324. [PMID: 38899885 PMCID: PMC11267869 DOI: 10.1128/aem.00863-24] [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: 05/03/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Purple sulfur bacteria (PSB) are capable of anoxygenic photosynthesis via oxidizing reduced sulfur compounds and are considered key drivers of the sulfur cycle in a range of anoxic environments. In this study, we show that Allochromatium vinosum (a PSB species) is capable of autotrophic growth using pyrite as the electron and sulfur source. Comparative growth profile, substrate characterization, and transcriptomic sequencing data provided valuable insight into the molecular mechanisms underlying the bacterial utilization of pyrite and autotrophic growth. Specifically, the pyrite-supported cell cultures ("py"') demonstrated robust but much slower growth rates and distinct patterns from their sodium sulfide-amended positive controls. Up to ~200-fold upregulation of genes encoding various c- and b-type cytochromes was observed in "py," pointing to the high relevance of these molecules in scavenging and relaying electrons from pyrite to cytoplasmic metabolisms. Conversely, extensive downregulation of genes related to LH and RC complex components indicates that the electron source may have direct control over the bacterial cells' photosynthetic activity. In terms of sulfur metabolism, genes encoding periplasmic or membrane-bound proteins (e.g., FccAB and SoxYZ) were largely upregulated, whereas those encoding cytoplasmic proteins (e.g., Dsr and Apr groups) are extensively suppressed. Other notable differentially expressed genes are related to flagella/fimbriae/pilin(+), metal efflux(+), ferrienterochelin(-), and [NiFe] hydrogenases(+). Characterization of the biologically reacted pyrite indicates the presence of polymeric sulfur. These results have, for the first time, put the interplay of PSB and transition metal sulfide chemistry under the spotlight, with the potential to advance multiple fields, including metal and sulfur biogeochemistry, bacterial extracellular electron transfer, and artificial photosynthesis. IMPORTANCE Microbial utilization of solid-phase substrates constitutes a critical area of focus in environmental microbiology, offering valuable insights into microbial metabolic processes and adaptability. Recent advancements in this field have profoundly deepened our knowledge of microbial physiology pertinent to these scenarios and spurred innovations in biosynthesis and energy production. Furthermore, research into interactions between microbes and solid-phase substrates has directly linked microbial activities to the surrounding mineralogical environments, thereby enhancing our understanding of the relevant biogeochemical cycles. Our study represents a significant step forward in this field by demonstrating, for the first time, the autotrophic growth of purple sulfur bacteria using insoluble pyrite (FeS2) as both the electron and sulfur source. The presented comparative growth profiles, substrate characterizations, and transcriptomic sequencing data shed light on the relationships between electron donor types, photosynthetic reaction center activities, and potential extracellular electron transfer in these organisms capable of anoxygenic photosynthesis. Furthermore, the findings of our study may provide new insights into early-Earth biogeochemical evolutions, offering valuable constraints for understanding the environmental conditions and microbial processes that shaped our planet's history.
Collapse
Affiliation(s)
- Hugo V. Alarcon
- Environmental Science and Engineering Program, the University of Texas at El Paso, El Paso, Texas, USA
| | - Jonathon E. Mohl
- Department of Mathematical Sciences, the University of Texas at El Paso, El Paso, Texas, USA
- Border Biomedical Research Center, the University of Texas at El Paso, El Paso, Texas, USA
| | - Grace W. Chong
- Department of Earth, Environmental and Resource Sciences, the University of Texas at El Paso, El Paso, Texas, USA
| | - Ana Betancourt
- Border Biomedical Research Center, the University of Texas at El Paso, El Paso, Texas, USA
| | - Yi Wang
- The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Weinan Leng
- The National Center for Earth and Environmental Nanotechnology Infrastructure, Blacksburg, Virginia, USA
| | - Jason C. White
- The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Jie Xu
- Environmental Science and Engineering Program, the University of Texas at El Paso, El Paso, Texas, USA
- Department of Earth, Environmental and Resource Sciences, the University of Texas at El Paso, El Paso, Texas, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
2
|
Petushkova E, Khasimov M, Mayorova E, Delegan Y, Frantsuzova E, Bogun A, Galkina E, Tsygankov A. The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways. Microorganisms 2024; 12:391. [PMID: 38399794 PMCID: PMC10892978 DOI: 10.3390/microorganisms12020391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The purple sulfur bacterium Thiocapsa roseopersicina BBS is interesting from both fundamental and practical points of view. It possesses a thermostable HydSL hydrogenase, which is involved in the reaction of reversible hydrogen activation and a unique reaction of sulfur reduction to hydrogen sulfide. It is a very promising enzyme for enzymatic hydrogenase electrodes. There are speculations that HydSL hydrogenase of purple bacteria is closely related to sulfur metabolism, but confirmation is required. For that, the full genome sequence is necessary. Here, we sequenced and assembled the complete genome of this bacterium. The analysis of the obtained whole genome, through an integrative approach that comprised estimating the Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (DDH) parameters, allowed for validation of the systematic position of T. roseopersicina as T. bogorovii BBS. For the first time, we have assembled the whole genome of this typical strain of a new bacterial species and carried out its functional description against another purple sulfur bacterium: Allochromatium vinosum DSM 180T. We refined the automatic annotation of the whole genome of the bacteria T. bogorovii BBS and localized the genomic positions of several studied genes, including those involved in sulfur metabolism and genes encoding the enzymes required for the TCA and glyoxylate cycles and other central metabolic pathways. Eleven additional genes coding proteins involved in pigment biosynthesis was found.
Collapse
Affiliation(s)
- Ekaterina Petushkova
- Institute of Basic Biological Problems, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (M.K.); (E.M.); (A.T.)
| | - Makhmadyusuf Khasimov
- Institute of Basic Biological Problems, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (M.K.); (E.M.); (A.T.)
| | - Ekaterina Mayorova
- Institute of Basic Biological Problems, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (M.K.); (E.M.); (A.T.)
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (Y.D.); (E.F.); (A.B.)
| | - Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (Y.D.); (E.F.); (A.B.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (Y.D.); (E.F.); (A.B.)
| | - Elena Galkina
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia;
| | - Anatoly Tsygankov
- Institute of Basic Biological Problems, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (M.K.); (E.M.); (A.T.)
| |
Collapse
|
3
|
Vargas-Lagunas C, Mora Y, Aguilar A, Reyes-González AR, Arteaga-Ide A, Dunn MF, Encarnación S, Girard L, Peralta H, Mora J. A Tar aspartate receptor and Rubisco-like protein substitute biotin in the growth of rhizobial strains. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35077343 PMCID: PMC8914248 DOI: 10.1099/mic.0.001130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Biotin is a key cofactor of metabolic carboxylases, although many rhizobial strains are biotin auxotrophs. When some of these strains were serially subcultured in minimal medium, they showed diminished growth and increased excretion of metabolites. The addition of biotin, or genetic complementation with biotin synthesis genes resulted in full growth of Rhizobium etli CFN42 and Rhizobium phaseoli CIAT652 strains. Half of rhizobial genomes did not show genes for biotin biosynthesis, but three-quarters had genes for biotin transport. Some strains had genes for an avidin homologue (rhizavidin), a protein with high affinity for biotin but an unknown role in bacteria. A CFN42-derived rhizavidin mutant showed a sharper growth decrease in subcultures, revealing a role in biotin storage. In the search of biotin-independent growth of subcultures, CFN42 and CIAT652 strains with excess aeration showed optimal growth, as they also did, unexpectedly, with the addition of aspartic acid analogues α- and N-methyl aspartate. Aspartate analogues can be sensed by the chemotaxis aspartate receptor Tar. A tar homologue was identified and its mutants showed no growth recovery with aspartate analogues, indicating requirement of the Tar receptor in such a phenotype. Additionally, tar mutants did not recover full growth with excess aeration. A Rubisco-like protein was found to be necessary for growth as the corresponding mutants showed no recovery either with high aeration or aspartate analogues; also, diminished carboxylation was observed. Taken together, our results indicate a route of biotin-independent growth in rhizobial strains that included oxygen, a Tar receptor and a previously uncharacterized Rubisco-like protein.
Collapse
Affiliation(s)
- Carmen Vargas-Lagunas
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Yolanda Mora
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alejandro Aguilar
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alma Ruth Reyes-González
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alejandra Arteaga-Ide
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sergio Encarnación
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Humberto Peralta
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jaime Mora
- Programa de Genómica Funcional de Procariotes, Laboratorio de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
4
|
Jakus N, Blackwell N, Straub D, Kappler A, Kleindienst S. Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp. FEMS Microbiol Ecol 2021; 97:6415198. [PMID: 34724047 DOI: 10.1093/femsec/fiab145] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Autotrophic nitrate reduction coupled to Fe(II) oxidation is an important nitrate removal process in anoxic aquifers. However, it remains unknown how changes of O2 and carbon availability influence the community structure of nitrate-reducing Fe(II)-oxidizing (NRFeOx) microbial assemblages and what the genomic traits of these NRFeOx key players are. We compared three metabolically distinct denitrifying assemblages, supplemented with acetate, acetate/Fe(II) or Fe(II), enriched from an organic-poor, pyrite-rich aquifer. The presence of Fe(II) promoted the growth of denitrifying Burkholderiaceae spp. and an unclassified Gallionellaceae sp. This Gallionellaceae sp. was related to microaerophilic Fe(II) oxidizers; however, it did not grow under microoxic conditions. Furthermore, we explored a metagenome and 15 metagenome-assembled genomes from an aquifer-originating, autotrophic NRFeOx culture. The dominant Gallionellaceae sp. revealed the potential to oxidize Fe(II) (e.g. cyc2), fix CO2 (e.g. rbcL) and perform near-complete denitrification leading to N2O formation (e.g. narGHJI,nirK/S and norBC). In addition, Curvibacter spp.,Methyloversatilis sp. and Thermomonas spp. were identified as novel putative NRFeOx taxa. Our findings provide first insights into the genetic traits of the so far only known autotrophic NRFeOx culture originating from an organic-poor aquifer, providing the genomic basis to study mechanisms of nitrate removal in organic-poor subsurface ecosystems.
Collapse
Affiliation(s)
- Natalia Jakus
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, D-72076 Tübingen, Germany.,Microbial Ecology, Center for Applied Geoscience, University of Tübingen, D-72076 Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, D-72076 Tübingen, Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, D-72076 Tübingen, Germany.,Quantitative Biology Center (QBiC), University of Tübingen, D-72076 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, D-72076 Tübingen, Germany.,Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, D-72076 Tübingen, Germany
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, D-72076 Tübingen, Germany
| |
Collapse
|
5
|
Luedin SM, Liechti N, Cox RP, Danza F, Frigaard NU, Posth NR, Pothier JF, Roman S, Storelli N, Wittwer M, Tonolla M. Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno. Sci Rep 2019; 9:1936. [PMID: 30760771 PMCID: PMC6374484 DOI: 10.1038/s41598-018-38202-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/21/2018] [Indexed: 01/07/2023] Open
Abstract
Blooms of purple sulfur bacteria (PSB) are important drivers of the global sulfur cycling oxidizing reduced sulfur in intertidal flats and stagnant water bodies. Since the discovery of PSB Chromatium okenii in 1838, it has been found that this species is characteristic of for stratified, sulfidic environments worldwide and its autotrophic metabolism has been studied in depth since. We describe here the first high-quality draft genome of a large-celled, phototrophic, γ-proteobacteria of the genus Chromatium isolated from the stratified alpine Lake Cadagno, C. okenii strain LaCa. Long read technology was used to assemble the 3.78 Mb genome that encodes 3,016 protein-coding genes and 67 RNA genes. Our findings are discussed from an ecological perspective related to Lake Cadagno. Moreover, findings of previous studies on the phototrophic and the proposed chemoautotrophic metabolism of C. okenii were confirmed on a genomic level. We additionally compared the C. okenii genome with other genomes of sequenced, phototrophic sulfur bacteria from the same environment. We found that biological functions involved in chemotaxis, movement and S-layer-proteins were enriched in strain LaCa. We describe these features as possible adaptions of strain LaCa to rapidly changing environmental conditions within the chemocline and the protection against phage infection during blooms. The high quality draft genome of C. okenii strain LaCa thereby provides a basis for future functional research on bioconvection and phage infection dynamics of blooming PSB.
Collapse
Affiliation(s)
- Samuel M Luedin
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland.
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland.
| | - Nicole Liechti
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Raymond P Cox
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Francesco Danza
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | | | - Nicole R Posth
- Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Copenhagen, Denmark
| | - Joël F Pothier
- Environmental Genomics and System Biology Research Group, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
| | - Nicola Storelli
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Matthias Wittwer
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
| | - Mauro Tonolla
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland.
- Alpine Biology Center Foundation, Bellinzona, Switzerland.
| |
Collapse
|
6
|
Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris. mBio 2018; 9:mBio.00407-18. [PMID: 29636438 PMCID: PMC5893883 DOI: 10.1128/mbio.00407-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5'-Methyl-thioadenosine (MTA) is a dead-end, sulfur-containing metabolite and cellular inhibitor that arises from S-adenosyl-l-methionine-dependent reactions. Recent studies have indicated that there are diverse bacterial methionine salvage pathways (MSPs) for MTA detoxification and sulfur salvage. Here, via a combination of gene deletions and directed metabolite detection studies, we report that under aerobic conditions the facultatively anaerobic bacterium Rhodopseudomonas palustris employs both an MTA-isoprenoid shunt identical to that previously described in Rhodospirillum rubrum and a second novel MSP, both of which generate a methanethiol intermediate. The additional R. palustris aerobic MSP, a dihydroxyacetone phosphate (DHAP)-methanethiol shunt, initially converts MTA to 2-(methylthio)ethanol and DHAP. This is identical to the initial steps of the recently reported anaerobic ethylene-forming MSP, the DHAP-ethylene shunt. The aerobic DHAP-methanethiol shunt then further metabolizes 2-(methylthio)ethanol to methanethiol, which can be directly utilized by O-acetyl-l-homoserine sulfhydrylase to regenerate methionine. This is in contrast to the anaerobic DHAP-ethylene shunt, which metabolizes 2-(methylthio)ethanol to ethylene and an unknown organo-sulfur intermediate, revealing functional diversity in MSPs utilizing a 2-(methylthio)ethanol intermediate. When MTA was fed to aerobically growing cells, the rate of volatile methanethiol release was constant irrespective of the presence of sulfate, suggesting a general housekeeping function for these MSPs up through the methanethiol production step. Methanethiol and dimethyl sulfide (DMS), two of the most important compounds of the global sulfur cycle, appear to arise not only from marine ecosystems but from terrestrial ones as well. These results reveal a possible route by which methanethiol might be biologically produced in soil and freshwater environments.IMPORTANCE Biologically available sulfur is often limiting in the environment. Therefore, many organisms have developed methionine salvage pathways (MSPs) to recycle sulfur-containing by-products back into the amino acid methionine. The metabolically versatile bacterium Rhodopseudomonas palustris is unusual in that it possesses two RuBisCOs and two RuBisCO-like proteins. While RuBisCO primarily serves as the carbon fixation enzyme of the Calvin cycle, RuBisCOs and certain RuBisCO-like proteins have also been shown to function in methionine salvage. This work establishes that only one of the R. palustris RuBisCO-like proteins functions as part of an MSP. Moreover, in the presence of oxygen, to salvage sulfur, R. palustris employs two pathways, both of which result in production of volatile methanethiol, a key compound of the global sulfur cycle. When total available sulfur was plentiful, methanethiol was readily released into the environment. However, when sulfur became limiting, methanethiol release decreased, presumably due to methanethiol utilization to regenerate needed methionine.
Collapse
|
7
|
North JA, Miller AR, Wildenthal JA, Young SJ, Tabita FR. Microbial pathway for anaerobic 5'-methylthioadenosine metabolism coupled to ethylene formation. Proc Natl Acad Sci U S A 2017; 114:E10455-E10464. [PMID: 29133429 PMCID: PMC5715764 DOI: 10.1073/pnas.1711625114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Numerous cellular processes involving S-adenosyl-l-methionine result in the formation of the toxic by-product, 5'-methylthioadenosine (MTA). To prevent inhibitory MTA accumulation and retain biologically available sulfur, most organisms possess the "universal" methionine salvage pathway (MSP). However, the universal MSP is inherently aerobic due to a requirement of molecular oxygen for one of the key enzymes. Here, we report the presence of an exclusively anaerobic MSP that couples MTA metabolism to ethylene formation in the phototrophic bacteria Rhodospirillum rubrum and Rhodopseudomonas palustris In vivo metabolite analysis of gene deletion strains demonstrated that this anaerobic MSP functions via sequential action of MTA phosphorylase (MtnP), 5-(methylthio)ribose-1-phosphate isomerase (MtnA), and an annotated class II aldolase-like protein (Ald2) to form 2-(methylthio)acetaldehyde as an intermediate. 2-(Methylthio)acetaldehyde is reduced to 2-(methylthio)ethanol, which is further metabolized as a usable organic sulfur source, generating stoichiometric amounts of ethylene in the process. Ethylene induction experiments using 2-(methylthio)ethanol versus sulfate as sulfur sources further indicate anaerobic ethylene production from 2-(methylthio)ethanol requires protein synthesis and that this process is regulated. Finally, phylogenetic analysis reveals that the genes corresponding to these enzymes, and presumably the pathway, are widespread among anaerobic and facultatively anaerobic bacteria from soil and freshwater environments. These results not only establish the existence of a functional, exclusively anaerobic MSP, but they also suggest a possible route by which ethylene is produced by microbes in anoxic environments.
Collapse
Affiliation(s)
- Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - Anthony R Miller
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - John A Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - Sarah J Young
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
| |
Collapse
|
8
|
Buchanan BB, Sirevåg R, Fuchs G, Ivanovsky RN, Igarashi Y, Ishii M, Tabita FR, Berg IA. The Arnon-Buchanan cycle: a retrospective, 1966-2016. PHOTOSYNTHESIS RESEARCH 2017; 134:117-131. [PMID: 29019085 DOI: 10.1007/s11120-017-0429-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
For the first decade following its description in 1954, the Calvin-Benson cycle was considered the sole pathway of autotrophic CO2 assimilation. In the early 1960s, experiments with fermentative bacteria uncovered reactions that challenged this concept. Ferredoxin was found to donate electrons directly for the reductive fixation of CO2 into alpha-keto acids via reactions considered irreversible. Thus, pyruvate and alpha-ketoglutarate could be synthesized from CO2, reduced ferredoxin and acetyl-CoA or succinyl-CoA, respectively. This work opened the door to the discovery that reduced ferredoxin could drive the Krebs citric acid cycle in reverse, converting the pathway from its historical role in carbohydrate breakdown to one fixing CO2. Originally uncovered in photosynthetic green sulfur bacteria, the Arnon-Buchanan cycle has since been divorced from light and shown to function in a variety of anaerobic chemoautotrophs. In this retrospective, colleagues who worked on the cycle at its inception in 1966 and those presently working in the field trace its development from a controversial reception to its present-day inclusion in textbooks. This pathway is now well established in major groups of chemoautotrophic bacteria, instead of the Calvin-Benson cycle, and is increasingly referred to as the Arnon-Buchanan cycle. In this retrospective, separate sections have been written by the authors indicated. Bob Buchanan wrote the abstract and the concluding comments.
Collapse
Affiliation(s)
- Bob B Buchanan
- Department of Plant & Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA.
| | - Reidun Sirevåg
- Department of Biosciences, University of Oslo, Blindern, Box 1066, 0316, Oslo, Norway
| | - Georg Fuchs
- Mikrobiologie, Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Ruslan N Ivanovsky
- Department of Microbiology, M.V. Lomonosov Moscow State University, 1/12 Lenin's Hills, Moscow, Russia, 119991
| | - Yasuo Igarashi
- Southwest University, Chongqing, 2 Tiansheng Rd, Beibei Qu, Chongqing Shi, 400700, China
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - Ivan A Berg
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149, Münster, Germany
| |
Collapse
|
9
|
Orlova MV, Tarlachkov SV, Dubinina GA, Belousova EV, Tutukina MN, Grabovich MY. Genomic insights into metabolic versatility of a lithotrophic sulfur-oxidizing diazotrophic AlphaproteobacteriumAzospirillum thiophilum. FEMS Microbiol Ecol 2016; 92:fiw199. [DOI: 10.1093/femsec/fiw199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/14/2022] Open
|
10
|
Metabolic Regulation as a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum rubrum. mBio 2016; 7:mBio.00855-16. [PMID: 27406564 PMCID: PMC4958253 DOI: 10.1128/mbio.00855-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Rhodospirillum rubrum possesses a novel oxygen-independent, aerobic methionine salvage pathway (MSP) for recycling methionine from 5-methylthioadenosine (MTA), the MTA-isoprenoid shunt. This organism can also metabolize MTA as a sulfur source under anaerobic conditions, suggesting that the MTA-isoprenoid shunt may also function anaerobically as well. In this study, deep proteomics profiling, directed metabolite analysis, and reverse transcriptase quantitative PCR (RT-qPCR) revealed metabolic changes in response to anaerobic growth on MTA versus sulfate as sole sulfur source. The abundance of protein levels associated with methionine transport, cell motility, and chemotaxis increased in the presence of MTA over that in the presence of sulfate. Purine salvage from MTA resulted primarily in hypoxanthine accumulation and a decrease in protein levels involved in GMP-to-AMP conversion to balance purine pools. Acyl coenzyme A (acyl-CoA) metabolic protein levels for lipid metabolism were lower in abundance, whereas poly-β-hydroxybutyrate synthesis and storage were increased nearly 10-fold. The known R. rubrum aerobic MSP was also shown to be upregulated, to function anaerobically, and to recycle MTA. This suggested that other organisms with gene homologues for the MTA-isoprenoid shunt may also possess a functioning anaerobic MSP. In support of our previous findings that ribulose-1,5-carboxylase/oxygenase (RubisCO) is required for an apparently purely anaerobic MSP, RubisCO transcript and protein levels both increased in abundance by over 10-fold in cells grown anaerobically on MTA over those in cells grown on sulfate, resulting in increased intracellular RubisCO activity. These results reveal for the first time global metabolic responses as a consequence of anaerobic MTA metabolism compared to using sulfate as the sulfur source. In nearly all organisms, sulfur-containing byproducts result from many metabolic reactions. Unless these compounds are further metabolized, valuable organic sulfur is lost and can become limiting. To regenerate the sulfur-containing amino acid methionine, organisms typically employ one of several variations of a “universal” methionine salvage pathway (MSP). A common aspect of the universal MSP is a final oxygenation step. This work establishes that the metabolically versatile bacterium Rhodospirillum rubrum employs a novel MSP that does not require oxygen under either aerobic or anaerobic conditions. There is also a separate, dedicated anaerobic MTA metabolic route in R. rubrum. This work reveals global changes in cellular metabolism in response to anaerobic MTA metabolism compared to using sulfate as a sulfur source. We found that cell mobility and transport were enhanced, along with lipid, nucleotide, and carbohydrate metabolism, when cells were grown in the presence of MTA.
Collapse
|
11
|
Dey S, North JA, Sriram J, Evans BS, Tabita FR. In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways. J Biol Chem 2015; 290:30658-68. [PMID: 26511314 DOI: 10.1074/jbc.m115.691295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/19/2022] Open
Abstract
All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO2 as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilation. In addition, sulfur salvage pathways are necessary to ensure that key sulfur-containing compounds are both available and, where necessary, detoxified in the cell. Using knock-out mutations and metabolomics in the bacterium Rhodospirillum rubrum, we show here that Rubisco concurrently catalyzes key and essential reactions for seemingly unrelated but physiologically essential central carbon and sulfur salvage metabolic pathways of the cell. In this study, complementation and mutagenesis studies indicated that representatives of all known extant functional Rubisco forms found in nature are capable of simultaneously catalyzing reactions required for both CO2-dependent growth as well as growth using 5-methylthioadenosine as sole sulfur source under anaerobic photosynthetic conditions. Moreover, specific inactivation of the CO2 fixation reaction did not affect the ability of Rubisco to support anaerobic 5-methylthioadenosine metabolism, suggesting that the active site of Rubisco has evolved to ensure that this enzyme maintains both key functions. Thus, despite the coevolution of both functions, the active site of this protein may be differentially modified to affect only one of its key functions.
Collapse
Affiliation(s)
- Swati Dey
- From the Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| | - Justin A North
- From the Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| | - Jaya Sriram
- From the Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| | - Bradley S Evans
- the Donald Danforth Plant Science Center, St. Louis, Missouri, 63132
| | - F Robert Tabita
- From the Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| |
Collapse
|
12
|
Hamilton TL, Bovee RJ, Thiel V, Sattin SR, Mohr W, Schaperdoth I, Vogl K, Gilhooly WP, Lyons TW, Tomsho LP, Schuster SC, Overmann J, Bryant DA, Pearson A, Macalady JL. Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake. GEOBIOLOGY 2014; 12:451-68. [PMID: 24976102 DOI: 10.1111/gbi.12092] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/30/2014] [Indexed: 05/10/2023]
Abstract
Mahoney Lake represents an extreme meromictic model system and is a valuable site for examining the organisms and processes that sustain photic zone euxinia (PZE). A single population of purple sulfur bacteria (PSB) living in a dense phototrophic plate in the chemocline is responsible for most of the primary production in Mahoney Lake. Here, we present metagenomic data from this phototrophic plate--including the genome of the major PSB, as obtained from both a highly enriched culture and from the metagenomic data--as well as evidence for multiple other taxa that contribute to the oxidative sulfur cycle and to sulfate reduction. The planktonic PSB is a member of the Chromatiaceae, here renamed Thiohalocapsa sp. strain ML1. It produces the carotenoid okenone, yet its closest relatives are benthic PSB isolates, a finding that may complicate the use of okenone (okenane) as a biomarker for ancient PZE. Favorable thermodynamics for non-phototrophic sulfide oxidation and sulfate reduction reactions also occur in the plate, and a suite of organisms capable of oxidizing and reducing sulfur is apparent in the metagenome. Fluctuating supplies of both reduced carbon and reduced sulfur to the chemocline may partly account for the diversity of both autotrophic and heterotrophic species. Collectively, the data demonstrate the physiological potential for maintaining complex sulfur and carbon cycles in an anoxic water column, driven by the input of exogenous organic matter. This is consistent with suggestions that high levels of oxygenic primary production maintain episodes of PZE in Earth's history and that such communities should support a diversity of sulfur cycle reactions.
Collapse
Affiliation(s)
- T L Hamilton
- Department of Geosciences, Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Schada von Borzyskowski L, Rosenthal RG, Erb TJ. Evolutionary history and biotechnological future of carboxylases. J Biotechnol 2013; 168:243-51. [PMID: 23702164 DOI: 10.1016/j.jbiotec.2013.05.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/08/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
Carbon dioxide (CO2) is a potent greenhouse gas whose presence in the atmosphere is a critical factor for global warming. At the same time atmospheric CO2 is also a cheap and readily available carbon source that can in principle be used to synthesize value-added products. However, as uncatalyzed chemical CO2-fixation reactions usually require quite harsh conditions to functionalize the CO2 molecule, not many processes have been developed that make use of CO2. In contrast to synthetical chemistry, Nature provides a multitude of different carboxylating enzymes whose carboxylating principle(s) might be exploited in biotechnology. This review focuses on the biochemical features of carboxylases, highlights possible evolutionary scenarios for the emergence of their reactivity, and discusses current, as well as potential future applications of carboxylases in organic synthesis, biotechnology and synthetic biology.
Collapse
|
14
|
Eddie BJ, Hanson TE. Chlorobaculum tepidum TLS displays a complex transcriptional response to sulfide addition. J Bacteriol 2013; 195:399-408. [PMID: 23161024 PMCID: PMC3553837 DOI: 10.1128/jb.01342-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/08/2012] [Indexed: 11/20/2022] Open
Abstract
Chlorobaculum tepidum is a green sulfur bacterium (GSB) that is a model system for phototrophic sulfur oxidation. Despite over 2 decades of research, conspicuous gaps exist in our understanding of its electron donor metabolism and regulation. RNA sequencing (RNA-seq) was used to provide a global picture of the C. tepidum transcriptome during growth on thiosulfate as the sole electron donor and at time points following the addition of sulfide to such a culture. Following sulfide addition, 121 to 150 protein-coding genes displayed significant changes in expression depending upon the time point. These changes included a rapid decrease in expression of thiosulfate and elemental sulfur oxidation genes. Genes and gene loci with increased expression included CT1087, encoding a sulfide:quinone oxidoreductase required for growth in high sulfide concentrations; a polysulfide reductase-like complex operon, psrABC (CT0496 to CT0494); and, surprisingly, a large cluster of genes involved in iron acquisition. Finally, two genes that are conserved as a cassette in anaerobic bacteria and archaea, CT1276 and CT1277, displayed a strong increase in expression. The CT1277 gene product contains a DNA-binding domain, suggesting a role for it in sulfide-dependent gene expression changes.
Collapse
Affiliation(s)
- Brian J Eddie
- College of Earth, Ocean, and Environment and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | | |
Collapse
|
15
|
Weissgerber T, Zigann R, Bruce D, Chang YJ, Detter JC, Han C, Hauser L, Jeffries CD, Land M, Munk AC, Tapia R, Dahl C. Complete genome sequence of Allochromatium vinosum DSM 180(T). Stand Genomic Sci 2011; 5:311-30. [PMID: 22675582 PMCID: PMC3368242 DOI: 10.4056/sigs.2335270] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacterium belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus Allochromatium contains currently five species. All members were isolated from freshwater, brackish water or marine habitats and are predominately obligate phototrophs. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the Chromatiaceae within the purple sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp genome with its 3,302 protein-coding and 64 RNA genes was sequenced within the Joint Genome Institute Community Sequencing Program.
Collapse
Affiliation(s)
- Thomas Weissgerber
- Institute for Microbiology & Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Renate Zigann
- Institute for Microbiology & Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Yun-juan Chang
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Christiane Dahl
- Institute for Microbiology & Biotechnology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| |
Collapse
|
16
|
Roles of RubisCO and the RubisCO-like protein in 5-methylthioadenosine metabolism in the Nonsulfur purple bacterium Rhodospirillum rubrum. J Bacteriol 2009; 192:1324-31. [PMID: 20038587 DOI: 10.1128/jb.01442-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the assimilation of atmospheric CO(2) into organic matter and is thus central to the existence of life on earth. The beginning of the 2000s was marked by the discovery of a new family of proteins, the RubisCO-like proteins (RLPs), which are structural homologs of RubisCO. RLPs are unable to catalyze CO(2) fixation. The RLPs from Chlorobaculum tepidum, Bacillus subtilis, Geobacillus kaustophilus, and Microcystis aeruginosa have been shown to participate in sulfur metabolism. Whereas the precise function of C. tepidum RLP is unknown, the B. subtilis, G. kaustophilus, and M. aeruginosa RLPs function as tautomerases/enolases in a methionine salvage pathway (MSP). Here, we show that the form II RubisCO enzyme from the nonsulfur purple bacterium Rhodospirillum rubrum is also able to function as an enolase in vivo as part of an MSP, but only under anaerobic conditions. However, unlike B. subtilis RLP, R. rubrum RLP does not catalyze the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate. Instead, under aerobic growth conditions, R. rubrum RLP employs another intermediate of the MSP, 5-methylthioribulose-1-phosphate, as a substrate, resulting in the formation of different products. To further determine the interrelationship between RubisCOs and RLPs (and the potential integration of cellular carbon and sulfur metabolism), the functional roles of both RubisCO and RLP have been examined in vivo via the use of specific knockout strains and complementation studies of R. rubrum. The presence of functional, yet separate, MSPs in R. rubrum under both aerobic (chemoheterotrophic) and anaerobic (photoheterotrophic) growth conditions has not been observed previously in any organism. Moreover, the aerobic and anaerobic sulfur salvage pathways appear to be differentially controlled, with novel and previously undescribed steps apparent for sulfur salvage in this organism.
Collapse
|
17
|
Tourova TP, Spiridonova EM. Phylogeny and evolution of the ribulose 1,5-bisphosphate carboxylase/oxygenase genes in prokaryotes. Mol Biol 2009. [DOI: 10.1134/s0026893309050033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev 2009; 33:999-1043. [PMID: 19645821 DOI: 10.1111/j.1574-6976.2009.00187.x] [Citation(s) in RCA: 289] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.
Collapse
Affiliation(s)
- Wriddhiman Ghosh
- Department of Microbiology, University of Burdwan, West Bengal, India.
| | | |
Collapse
|
19
|
Abstract
Phototrophic sulfur bacteria are characterized by oxidizing various inorganic sulfur compounds for use as electron donors in carbon dioxide fixation during anoxygenic photosynthetic growth. These bacteria are divided into the purple sulfur bacteria (PSB) and the green sulfur bacteria (GSB). They utilize various combinations of sulfide, elemental sulfur, and thiosulfate and sometimes also ferrous iron and hydrogen as electron donors. This review focuses on the dissimilatory and assimilatory metabolism of inorganic sulfur compounds in these bacteria and also briefly discusses these metabolisms in other types of anoxygenic phototrophic bacteria. The biochemistry and genetics of sulfur compound oxidation in PSB and GSB are described in detail. A variety of enzymes catalyzing sulfur oxidation reactions have been isolated from GSB and PSB (especially Allochromatium vinosum, a representative of the Chromatiaceae), and many are well characterized also on a molecular genetic level. Complete genome sequence data are currently available for 10 strains of GSB and for one strain of PSB. We present here a genome-based survey of the distribution and phylogenies of genes involved in oxidation of sulfur compounds in these strains. It is evident from biochemical and genetic analyses that the dissimilatory sulfur metabolism of these organisms is very complex and incompletely understood. This metabolism is modular in the sense that individual steps in the metabolism may be performed by different enzymes in different organisms. Despite the distant evolutionary relationship between GSB and PSB, their photosynthetic nature and their dependency on oxidation of sulfur compounds resulted in similar ecological roles in the sulfur cycle as important anaerobic oxidizers of sulfur compounds.
Collapse
|
20
|
Functional analysis of three sulfide:quinone oxidoreductase homologs in Chlorobaculum tepidum. J Bacteriol 2008; 191:1026-34. [PMID: 19028893 DOI: 10.1128/jb.01154-08] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sulfide:quinone oxidoreductase (SQR) catalyzes sulfide oxidation during sulfide-dependent chemo- and phototrophic growth in bacteria. The green sulfur bacterium Chlorobaculum tepidum (formerly Chlorobium tepidum) can grow on sulfide as the sole electron donor and sulfur source. C. tepidum contains genes encoding three SQR homologs: CT0117, CT0876, and CT1087. This study examined which, if any, of the SQR homologs possess sulfide-dependent ubiquinone reduction activity and are required for growth on sulfide. In contrast to CT0117 and CT0876, transcripts of CT1087 were detected only when cells actively oxidized sulfide. Mutation of CT0117 or CT1087 in C. tepidum decreased SQR activity in membrane fractions, and the CT1087 mutant could not grow with >or=6 mM sulfide. Mutation of both CT0117 and CT1087 in C. tepidum completely abolished SQR activity, and the double mutant failed to grow with >or=4 mM sulfide. A C-terminal His(6)-tagged CT1087 protein was membrane localized, as was SQR activity. Epitope-tagged CT1087 was detected only when sulfide was actively consumed by cells. Recombinantly produced CT1087 and CT0117 proteins had SQR activity, while CT0876 did not. In summary, we conclude that, under the conditions tested, both CT0117 and CT1087 function as SQR proteins in C. tepidum. CT0876 may support the growth of C. tepidum at low sulfide concentrations, but no evidence was found for SQR activity associated with this protein.
Collapse
|
21
|
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms. Philos Trans R Soc Lond B Biol Sci 2008; 363:2629-40. [PMID: 18487131 PMCID: PMC2606765 DOI: 10.1098/rstb.2008.0023] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) catalyses the key reaction by which inorganic carbon may be assimilated into organic carbon. Phylogenetic analyses indicate that there are three classes of bona fide RubisCO proteins, forms I, II and III, which all catalyse the same reactions. In addition, there exists another form of RubisCO, form IV, which does not catalyse RuBP carboxylation or oxygenation. Form IV is actually a homologue of RubisCO and is called the RubisCO-like protein (RLP). Both RubisCO and RLP appear to have evolved from an ancestor protein in a methanogenic archaeon, and comprehensive analyses indicate that the different forms (I, II, III and IV) contain various subgroups, with individual sequences derived from representatives of all three kingdoms of life. The diversity of RubisCO molecules, many of which function in distinct milieus, has provided convenient model systems to study the ways in which the active site of this protein has evolved to accommodate necessary molecular adaptations. Such studies have proven useful to help provide a framework for understanding the molecular basis for many important aspects of RubisCO catalysis, including the elucidation of factors or functional groups that impinge on RubisCO carbon dioxide/oxygen substrate discrimination.
Collapse
|
22
|
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol Mol Biol Rev 2008; 71:576-99. [PMID: 18063718 DOI: 10.1128/mmbr.00015-07] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
About 30 years have now passed since it was discovered that microbes synthesize RubisCO molecules that differ from the typical plant paradigm. RubisCOs of forms I, II, and III catalyze CO(2) fixation reactions, albeit for potentially different physiological purposes, while the RubisCO-like protein (RLP) (form IV RubisCO) has evolved, thus far at least, to catalyze reactions that are important for sulfur metabolism. RubisCO is the major global CO(2) fixation catalyst, and RLP is a somewhat related protein, exemplified by the fact that some of the latter proteins, along with RubisCO, catalyze similar enolization reactions as a part of their respective catalytic mechanisms. RLP in some organisms catalyzes a key reaction of a methionine salvage pathway, while in green sulfur bacteria, RLP plays a role in oxidative thiosulfate metabolism. In many organisms, the function of RLP is unknown. Indeed, there now appear to be at least six different clades of RLP molecules found in nature. Consideration of the many RubisCO (forms I, II, and III) and RLP (form IV) sequences in the database has subsequently led to a coherent picture of how these proteins may have evolved, with a form III RubisCO arising from the Methanomicrobia as the most likely ultimate source of all RubisCO and RLP lineages. In addition, structure-function analyses of RLP and RubisCO have provided information as to how the active sites of these proteins have evolved for their specific functions.
Collapse
|
23
|
Chan LK, Weber TS, Morgan-Kiss RM, Hanson TE. A genomic region required for phototrophic thiosulfate oxidation in the green sulfur bacterium Chlorobium tepidum (syn. Chlorobaculum tepidum). Microbiology (Reading) 2008; 154:818-829. [DOI: 10.1099/mic.0.2007/012583-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Leong-Keat Chan
- College of Marine and Earth Studies and Delaware Biotechnology Institute, University of Delaware, Rm 127 DBI, 15 Innovation Way, Newark, DE 19711, USA
| | - Timothy S. Weber
- College of Marine and Earth Studies and Delaware Biotechnology Institute, University of Delaware, Rm 127 DBI, 15 Innovation Way, Newark, DE 19711, USA
| | - Rachael M. Morgan-Kiss
- College of Marine and Earth Studies and Delaware Biotechnology Institute, University of Delaware, Rm 127 DBI, 15 Innovation Way, Newark, DE 19711, USA
| | - Thomas E. Hanson
- College of Marine and Earth Studies and Delaware Biotechnology Institute, University of Delaware, Rm 127 DBI, 15 Innovation Way, Newark, DE 19711, USA
| |
Collapse
|
24
|
Genomic Insights into the Sulfur Metabolism of Phototrophic Green Sulfur Bacteria. SULFUR METABOLISM IN PHOTOTROPHIC ORGANISMS 2008. [DOI: 10.1007/978-1-4020-6863-8_17] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
25
|
|
26
|
Meyer B, Imhoff JF, Kuever J. Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria – evolution of the Sox sulfur oxidation enzyme system. Environ Microbiol 2007; 9:2957-77. [PMID: 17991026 DOI: 10.1111/j.1462-2920.2007.01407.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Birte Meyer
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | | | | |
Collapse
|
27
|
Zhou F, Hanson TE, Johnston MV. Intact Protein Profiling of Chlorobium tepidum by Capillary Isoelectric Focusing, Reversed-Phase Liquid Chromatography, and Mass Spectrometry. Anal Chem 2007; 79:7145-53. [PMID: 17711353 DOI: 10.1021/ac071147c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Capillary isoelectric focusing (CIEF) coupled with reversed-phase liquid chromatography (RPLC) and electrospray ionization (ESI) mass spectrometry (MS) is shown to provide a liquid-based alternative to 2D-PAGE for intact protein profiling. This combination exhibits high resolution, sensitivity and throughput for protein profiling based on pI vs MW. The CIEF-RPLC-MS system described here facilitates the use of IEF markers for internal calibration of pI. It also provides a high dynamic range as evidenced by the detection of 100 pg (3 fmol) of a test protein spiked into 1 microg of a complex protein mixture. About 1200 individual proteins/polypeptides were detected from lysates of the green sulfur bacterium Chlorobium tepidum in a single <8 h run. The pI vs MW profile obtained from CIEF-RPLC-MS compares favorably with theoretical data derived from the C. tepidum genome and experimental data obtained from 2D-PAGE.
Collapse
Affiliation(s)
- Feng Zhou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, 19716, USA
| | | | | |
Collapse
|
28
|
Chen ZW, Liu YY, Wu JF, She Q, Jiang CY, Liu SJ. Novel bacterial sulfur oxygenase reductases from bioreactors treating gold-bearing concentrates. Appl Microbiol Biotechnol 2007; 74:688-98. [PMID: 17111141 DOI: 10.1007/s00253-006-0691-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 09/12/2006] [Accepted: 09/15/2006] [Indexed: 11/30/2022]
Abstract
The microbial community and sulfur oxygenase reductases of metagenomic DNA from bioreactors treating gold-bearing concentrates were studied by 16S rRNA library, real-time polymerase chain reaction (RT-PCR), conventional cultivation, and molecular cloning. Results indicated that major bacterial species were belonging to the genera Acidithiobacillus, Leptospirillum, Sulfobacillus, and Sphingomonas, accounting for 6.3, 66.7, 18.8, and 8.3%, respectively; the sole archaeal species was Ferroplasma sp. (100%). Quantitative RT-PCR revealed that the 16S rRNA gene copy numbers (per gram of concentrates) of bacteria and archaea were 4.59 x 10(9) and 6.68 x 10(5), respectively. Bacterial strains representing Acidithiobacillus, Leptospirillum, and Sulfobacillus were isolated from the bioreactors. To study sulfur oxidation in the reactors, pairs of new PCR primers were designed for the detection of sulfur oxygenase reductase (SOR) genes. Three sor-like genes, namely, sor (Fx), sor (SA), and sor (SB) were identified from metagenomic DNAs of the bioreactors. The sor (Fx) is an inactivated SOR gene and is identical to the pseudo-SOR gene of Ferroplasma acidarmanus. The sor (SA) and sor (SB) showed no significant identity to any genes in GenBank databases. The sor (SB) was cloned and expressed in Escherichia coli, and SOR activity was determined. Quantitative RT-PCR determination of the gene densities of sor (SA) and sor (SB) were 1,000 times higher than archaeal 16S rRNA gene copy numbers, indicating that these genes were mostly impossible from archaea. Furthermore, with primers specific to the sor (SB) gene, this gene was PCR-amplified from the newly isolated Acidithiobacillus sp. strain SM-1. So far as we know, this is the first time to determine SOR activity originating from bacteria and to document SOR gene in bioleaching reactors and Acidithiobacillus species.
Collapse
MESH Headings
- Acidithiobacillus
- Archaea/classification
- Archaea/enzymology
- Archaea/isolation & purification
- Bacteria/classification
- Bacteria/enzymology
- Bacteria/isolation & purification
- Bacterial Proteins/genetics
- Base Sequence
- Bioreactors
- Cloning, Molecular
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Dosage
- Gene Expression
- Gold/metabolism
- Molecular Sequence Data
- Oxidoreductases Acting on Sulfur Group Donors/genetics
- Oxidoreductases Acting on Sulfur Group Donors/metabolism
- Polymerase Chain Reaction/methods
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Z-W Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100080, People's Republic of China
| | | | | | | | | | | |
Collapse
|
29
|
Hensen D, Sperling D, Trüper HG, Brune DC, Dahl C. Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Mol Microbiol 2006; 62:794-810. [PMID: 16995898 DOI: 10.1111/j.1365-2958.2006.05408.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two different pathways for thiosulphate oxidation are present in the purple sulphur bacterium Allochromatium vinosum: oxidation to tetrathionate and complete oxidation to sulphate with obligatory formation of sulphur globules as intermediates. The tetrathionate:sulphate ratio is strongly pH-dependent with tetrathionate formation being preferred under acidic conditions. Thiosulphate dehydrogenase, a constitutively expressed monomeric 30 kDa c-type cytochrome with a pH optimum at pH 4.2 catalyses tetrathionate formation. A periplasmic thiosulphate-oxidizing multienzyme complex (Sox) has been described to be responsible for formation of sulphate from thiosulphate in chemotrophic and phototrophic sulphur oxidizers that do not form sulphur deposits. In the sulphur-storing A. vinosum we identified five sox genes in two independent loci (soxBXA and soxYZ). For SoxA a thiosulphate-dependent induction of expression, above a low constitutive level, was observed. Three sox-encoded proteins were purified: the heterodimeric c-type cytochrome SoxXA, the monomeric SoxB and the heterodimeric SoxYZ. Gene inactivation and complementation experiments proved these proteins to be indispensable for thiosulphate oxidation to sulphate. The intermediary formation of sulphur globules in A. vinosum appears to be related to the lack of soxCD genes, the products of which are proposed to oxidize SoxY-bound sulphane sulphur. In their absence the latter is instead transferred to growing sulphur globules.
Collapse
Affiliation(s)
- Daniela Hensen
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
| | | | | | | | | |
Collapse
|
30
|
Carré-Mlouka A, Méjean A, Quillardet P, Ashida H, Saito Y, Yokota A, Callebaut I, Sekowska A, Dittmann E, Bouchier C, de Marsac NT. A New Rubisco-like Protein Coexists with a Photosynthetic Rubisco in the Planktonic Cyanobacteria Microcystis. J Biol Chem 2006; 281:24462-71. [PMID: 16737967 DOI: 10.1074/jbc.m602973200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two genes encoding proteins related to large subunits of Rubisco were identified in the genome of the planktonic cyanobacterium Microcystis aeruginosa PCC 7806 that forms water blooms worldwide. The rbcL(I) gene belongs to the form I subfamily typically encountered in cyanobacteria, green algae, and land plants. The second and newly discovered gene is of the form IV subfamily and widespread in the Microcystis genus. In M. aeruginosa PCC 7806 cells, the expression of both rbcL(I) and rbcL(IV) is sulfur-dependent. The purified recombinant RbcL(IV) overexpressed in Escherichia coli cells did not display CO(2) fixation activity but catalyzed enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate, and the rbcL(IV) gene rescued a Bacillus subtilis MtnW-deficient mutant. Therefore, the Microcystis RbcL(IV) protein functions both in vitro and in vivo and might be involved in a methionine salvage pathway. Despite variations in the amino acid sequences, RbcL(IV) shares structural similarities with all members of the Rubisco superfamily. Invariant amino acids within the catalytic site may thus represent the minimal set for enolization, whereas variations, especially located in loop 6, may account for the limitation of the catalytic reaction to enolization. Even at low protein concentrations in vitro, the recombinant RbcL(IV) assembles spontaneously into dimers, the minimal unit required for Rubisco forms I-III activity. The discovery of the coexistence of RbcL(I) and RbcL(IV) in cyanobacteria, the ancestors of chloroplasts, enlightens episodes of the chaotic evolutionary history of the Rubiscos, a protein family of major importance for life on Earth.
Collapse
Affiliation(s)
- Alyssa Carré-Mlouka
- Département de Microbiologie, Unité des Cyanobactéries (CNRS-URA 2172) and Plate-forme Génomique-Pasteur Génopole Ile de France, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Ferreira S, Hjernø K, Larsen M, Wingsle G, Larsen P, Fey S, Roepstorff P, Salomé Pais M. Proteome profiling of Populus euphratica Oliv. upon heat stress. ANNALS OF BOTANY 2006; 98:361-77. [PMID: 16740589 PMCID: PMC2803470 DOI: 10.1093/aob/mcl106] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress. METHODS Heat effects were evaluated through electrolyte leakage on leaf discs, and LT(50) was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45 % of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82 % of the selected spots. KEY RESULTS Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism. CONCLUSIONS Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.
Collapse
Affiliation(s)
- Sílvia Ferreira
- Unit of Molecular Biology and Plant Biotechnology, Institute of Applied Science and Technology, Science Faculty of Lisbon University, Campo Grande, 1749-016 Lisbon, Portugal.
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Cottrell MT, Yu L, Kirchman DL. Sequence and expression analyses of Cytophaga-like hydrolases in a Western arctic metagenomic library and the Sargasso Sea. Appl Environ Microbiol 2006; 71:8506-13. [PMID: 16332841 PMCID: PMC1317373 DOI: 10.1128/aem.71.12.8506-8513.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of environmental DNA promises to provide new insights into the ecology and biogeochemistry of uncultured marine microbes. In this study we used the Sargasso Sea Whole Genome Sequence (WGS) data set to search for hydrolases used by Cytophaga-like bacteria to degrade biopolymers such as polysaccharides and proteins. Analysis of the Sargasso WGS data for contigs bearing both the 16S rRNA genes of Cytophaga-like bacteria and hydrolase genes revealed a cellulase gene (celM) most similar to the gene found in Cytophaga hutchinsonii. A BLAST search of the entire Sargasso Sea WGS data set indicated that celM was the most abundant cellulase-like gene in the Sargasso Sea. However, the similarity between CelM-like cellulases and peptidases belonging to metalloprotease family M42 led us to question whether CelM is involved in the degradation of polysaccharides or proteins. PCR primers were designed for the celM genes in the Sargasso Sea WGS data set and used to identify celM in a fosmid library constructed with prokaryotic DNA from the western Arctic Ocean. Expression analysis of the Cytophaga-like Arctic CelM, which is 63% identical and 77% similar to CelM in C. hutchinsonii, indicated that there was peptidase activity, whereas cellulase activity was not detected. Our analysis suggests that the celM gene plays a role in the degradation of protein by Cytophaga-like bacteria. The abundance of peptidase genes in the Cytophaga-like fosmid clone provides further evidence for the importance of Cytophaga-like bacteria in the degradation of protein in high-molecular-weight dissolved organic matter.
Collapse
|
33
|
Saga Y, Osumi S, Higuchi H, Tamiaki H. Bacteriochlorophyll-c homolog composition in green sulfur photosynthetic bacterium Chlorobium vibrioforme dependent on the concentration of sodium sulfide in liquid cultures. PHOTOSYNTHESIS RESEARCH 2005; 86:123-30. [PMID: 16172931 DOI: 10.1007/s11120-005-5301-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 04/11/2005] [Indexed: 05/04/2023]
Abstract
Green sulfur photosynthetic bacteria Chlorobium (Chl.) vibrioforme (DSM 263 strain and NCIB 8327 substrain possessing BChl-c) and Chl. tepidum (ATCC 49652) were photoautotrophically grown in liquid cultures containing different concentrations of sodium sulfide (Na2S). BChl-c homologs possessing a methyl group at the 12-position tended to increase in cells of the two strains of Chl. vibrioforme cultured under high Na2S concentrations. In contrast, the Na2S concentration in liquid cultures did not affect the relative composition of BChl-c homologs in Chl. tepidum. 8-Propyl-12-methyl([P,M])-BChl-c homolog, which has been little observed in usual cultivations, could be isolated by reverse-phase high-performance liquid chromatography from the cells of Chl. vibrioforme grown under high Na2S contents. The [P,M]-BChl-c homolog has the R-configuration at the 3(1)-position, which was determined by 1H-NMR analyses.
Collapse
Affiliation(s)
- Yoshitaka Saga
- Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, 525-8577, Kusatsu, Shiga, Japan
| | | | | | | |
Collapse
|
34
|
Li H, Sawaya MR, Tabita FR, Eisenberg D. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure 2005; 13:779-89. [PMID: 15893668 DOI: 10.1016/j.str.2005.02.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 02/17/2005] [Accepted: 02/19/2005] [Indexed: 11/24/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the incorporation of atmospheric CO(2) into ribulose 1,5-bisphosphate (RuBP). RuBisCOs are classified into four forms based on sequence similarity: forms I, II and III are bona fide RuBisCOs; form IV, also called the RuBisCO-like protein (RLP), lacks several of the substrate binding and catalytic residues and does not catalyze RuBP-dependent CO(2) fixation in vitro. To contribute to understanding the function of RLPs, we determined the crystal structure of the RLP from Chlorobium tepidum. The overall structure of the RLP is similar to the structures of the three other forms of RuBisCO; however, the active site is distinct from those of bona fide RuBisCOs and suggests that the RLP is possibly capable of catalyzing enolization but not carboxylation. Bioinformatic analysis of the protein functional linkages suggests that this RLP coevolved with enzymes of the bacteriochlorophyll biosynthesis pathway and may be involved in processes related to photosynthesis.
Collapse
Affiliation(s)
- Huiying Li
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Box 951570, Los Angeles, California 90095, USA
| | | | | | | |
Collapse
|
35
|
Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J. Prokaryotic sulfur oxidation. Curr Opin Microbiol 2005; 8:253-9. [PMID: 15939347 DOI: 10.1016/j.mib.2005.04.005] [Citation(s) in RCA: 315] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 04/20/2005] [Indexed: 11/28/2022]
Abstract
Recent biochemical and genomic data differentiate the sulfur oxidation pathway of Archaea from those of Bacteria. From these data it is evident that members of the Alphaproteobacteria harbor the complete sulfur-oxidizing Sox enzyme system, whereas members of the beta and gamma subclass and the Chlorobiaceae contain sox gene clusters that lack the genes encoding sulfur dehydrogenase. This indicates a different pathway for oxidation of sulfur to sulfate. Acidophilic bacteria oxidize sulfur by a system different from the Sox enzyme system, as do chemotrophic endosymbiotic bacteria.
Collapse
Affiliation(s)
- Cornelius G Friedrich
- Department of Biochemical and Chemical Engineering, University of Dortmund, D-44221 Dortmund, Germany.
| | | | | | | | | |
Collapse
|
36
|
Dahl C, Engels S, Pott-Sperling AS, Schulte A, Sander J, Lübbe Y, Deuster O, Brune DC. Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum. J Bacteriol 2005; 187:1392-404. [PMID: 15687204 PMCID: PMC545617 DOI: 10.1128/jb.187.4.1392-1404.2005] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seven new genes designated dsrLJOPNSR were identified immediately downstream of dsrABEFHCMK, completing the dsr gene cluster of the phototrophic sulfur bacterium Allochromatium vinosum D (DSM 180(T)). Interposon mutagenesis proved an essential role of the encoded proteins for the oxidation of intracellular sulfur, an obligate intermediate during the oxidation of sulfide and thiosulfate. While dsrR and dsrS encode cytoplasmic proteins of unknown function, the other genes encode a predicted NADPH:acceptor oxidoreductase (DsrL), a triheme c-type cytochrome (DsrJ), a periplasmic iron-sulfur protein (DsrO), and an integral membrane protein (DsrP). DsrN resembles cobyrinic acid a,c-diamide synthases and is probably involved in the biosynthesis of siro(heme)amide, the prosthetic group of the dsrAB-encoded sulfite reductase. The presence of most predicted Dsr proteins in A. vinosum was verified by Western blot analysis. With the exception of the constitutively present DsrC, the formation of Dsr gene products was greatly enhanced by sulfide. DsrEFH were purified from the soluble fraction and constitute a soluble alpha(2)beta(2)gamma(2)-structured 75-kDa holoprotein. DsrKJO were purified from membranes pointing at the presence of a transmembrane electron-transporting complex consisting of DsrKMJOP. In accordance with the suggestion that related complexes from dissimilatory sulfate reducers transfer electrons to sulfite reductase, the A. vinosum Dsr complex is copurified with sulfite reductase, DsrEFH, and DsrC. We therefore now have an ideal and unique possibility to study the interaction of sulfite reductase with other proteins and to clarify the long-standing problem of electron transport from and to sulfite reductase, not only in phototrophic bacteria but also in sulfate-reducing prokaryotes.
Collapse
Affiliation(s)
- Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Abstract
Several sequencing projects unexpectedly uncovered the presence of genes that encode ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) in anaerobic archaea. RubisCO is the key enzyme of the Calvin-Benson-Bassham (CBB) reductive pentose phosphate pathway, a scheme that does not appear to contribute greatly, if at all, to net CO2 assimilation in these organisms. Recombinant forms of the archaeal enzymes do, however, catalyze a bona fide RuBP-dependent CO2 fixation reaction, and it was recently shown that Methanocaldococcus (Methanococcus) jannaschii and other anaerobic archaea synthesize catalytically active RubisCO in vivo. To complete the CBB pathway, there is a need for an enzyme, i.e., phosphoribulokinase (PRK), to catalyze the formation of RuBP, the substrate for the RubisCO reaction. Homology searches, as well as direct enzymatic assays with M. jannaschii, failed to reveal the presence of PRK. The apparent lack of PRK raised the possibility that either there is an alternative pathway to generate RuBP or RubisCO might use an alternative substrate in vivo. In the present study, direct enzymatic assays performed with alternative substrates and extracts of M. jannsachii provided evidence for a previously uncharacterized pathway for RuBP synthesis from 5-phospho-D-ribose-1-pyrophosphate (PRPP) in M. jannaschii and other methanogenic archaea. Proteins and genes involved in the catalytic conversion of PRPP to RuBP were identified in M. jannaschii (Mj0601) and Methanosarcina acetivorans (Ma2851), and recombinant Ma2851 was active in extracts of Escherichia coli. Thus, in this work we identified a novel means to synthesize the CO2 acceptor and substrate for RubisCO in the absence of a detectable kinase, such as PRK. We suggest that the conversion of PRPP to RuBP might be an evolutional link between purine recycling pathways and the CBB scheme.
Collapse
Affiliation(s)
- Michael W Finn
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210-1292, USA
| | | |
Collapse
|
38
|
Frigaard NU, Bryant DA. Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch Microbiol 2004; 182:265-76. [PMID: 15340781 DOI: 10.1007/s00203-004-0718-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2004] [Revised: 07/21/2004] [Accepted: 07/22/2004] [Indexed: 10/26/2022]
Abstract
Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria. However, members of the two taxa that comprise this group, the green sulfur bacteria (Chlorobi) and the filamentous anoxygenic phototrophic bacteria ("Chloroflexales"), are otherwise quite different, both physiologically and phylogenetically. This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus and the oxidation of inorganic sulfur compounds in two model organisms that represent these taxa, Chlorobium tepidum and Chloroflexus aurantiacus. The genes involved in bacteriochlorophyll (BChl) c and carotenoid biosynthesis in these two organisms were identified by sequence homology with known BChl a and carotenoid biosynthesis enzymes, gene cluster analysis in Cfx. aurantiacus, and gene inactivation studies in Chl. tepidum. Based on these results, BChl a and BChl c biosynthesis is similar in the two organisms, whereas carotenoid biosynthesis differs significantly. In agreement with its facultative anaerobic nature, Cfx. aurantiacus in some cases apparently produces structurally different enzymes for heme and BChl biosynthesis, in which one enzyme functions under anoxic conditions and the other performs the same reaction under oxic conditions. The Chl. tepidum mutants produced with modified BChl c and carotenoid species also allow the functions of these pigments to be studied in vivo.
Collapse
Affiliation(s)
- Niels-Ulrik Frigaard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA.
| | | |
Collapse
|
39
|
Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres JLTY, Peres C, Harrison FH, Gibson J, Harwood CS. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 2003; 22:55-61. [PMID: 14704707 DOI: 10.1038/nbt923] [Citation(s) in RCA: 482] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2003] [Accepted: 11/03/2003] [Indexed: 01/26/2023]
Abstract
Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic compounds, for energy. It acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. Here we describe the genome sequence of R. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways and four light harvesting 2 systems. R. palustris encodes 63 signal transduction histidine kinases and 79 response regulator receiver domains. Almost 15% of the genome is devoted to transport. This genome sequence is a starting point to use R. palustris as a model to explore how organisms integrate metabolic modules in response to environmental perturbations.
Collapse
Affiliation(s)
- Frank W Larimer
- Genome Analysis and Systems Modeling, Oak Ridge National Laboratory, One Bethel Valley Rd., Oak Ridge, Tennessee 37831, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|