Dataset Information

Complete Genome Sequence of Rhodopseudomonas palustris RCB100, an Anoxygenic Phototroph That Degrades 3-Chlorobenzoate.

ABSTRACT: The purple nonsulfur bacterium Rhodopseudomonas palustris RCB100 anaerobically degrades 3-chlorobenzoate (3-CBA), a halogenated pollutant. R. palustris RCB100 uses 3-CBA as a carbon source, while most R. palustris strains cannot. We report the complete genome sequence of strain RCB100 to help gain insight into how this bacterium degrades 3-CBA.

SUBMITTER: Haq IU

PROVIDER: S-EPMC8050959 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Complete Genome Sequence of Rhodopseudomonas palustris RCB100, an Anoxygenic Phototroph That Degrades 3-Chlorobenzoate.

Haq Irshad Ui IU Fixen Kathryn R KR

Microbiology resource announcements 20210415 15

The purple nonsulfur bacterium Rhodopseudomonas palustris RCB100 anaerobically degrades 3-chlorobenzoate (3-CBA), a halogenated pollutant. R. palustris RCB100 uses 3-CBA as a carbon source, while most R. palustris strains cannot. We report the complete genome sequence of strain RCB100 to help gain insight into how this bacterium degrades 3-CBA. ...[more]

PMID: 33858917

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Project description:UnlabelledRhodopseudomonas palustris is an alphaproteobacterium that has served as a model organism for studies of photophosphorylation, regulation of nitrogen fixation, production of hydrogen as a biofuel, and anaerobic degradation of aromatic compounds. This bacterium is able to transition between anaerobic photoautotrophic growth, anaerobic photoheterotrophic growth, and aerobic heterotrophic growth. As a starting point to explore the genetic basis for the metabolic versatility of R. palustris, we used transposon mutagenesis and Tn-seq to identify 552 genes as essential for viability in cells growing aerobically on semirich medium. Of these, 323 have essential gene homologs in the alphaproteobacterium Caulobacter crescentus, and 187 have essential gene homologs in Escherichia coli. There were 24 R. palustris genes that were essential for viability under aerobic growth conditions that have low sequence identity but are likely to be functionally homologous to essential E. coli genes. As expected, certain functional categories of essential genes were highly conserved among the three organisms, including translation, ribosome structure and biogenesis, secretion, and lipid metabolism. R. palustris cells divide by budding in which a sessile cell gives rise to a motile swarmer cell. Conserved cell cycle genes required for this developmental process were essential in both C. crescentus and R. palustris. Our results suggest that despite vast differences in lifestyles, members of the alphaproteobacteria have a common set of essential genes that is specific to this group and distinct from that of gammaproteobacteria like E. coli.ImportanceEssential genes in bacteria and other organisms are those absolutely required for viability. Rhodopseudomonas palustris has served as a model organism for studies of anaerobic aromatic compound degradation, hydrogen gas production, nitrogen fixation, and photosynthesis. We used the technique of Tn-seq to determine the essential genes of R. palustris grown under heterotrophic aerobic conditions. The transposon library generated in this study will be useful for future studies to identify R. palustris genes essential for viability under specialized growth conditions and also for survival under conditions of stress.

Project description:BACKGROUND: Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria. METHODS: The complete genomic sequence of Cfl. aurantiacus has been determined, analyzed and compared to the genomes of other photosynthetic bacteria. RESULTS: Abundant genomic evidence suggests that there have been numerous gene adaptations/replacements in Cfl. aurantiacus to facilitate life under both anaerobic and aerobic conditions, including duplicate genes and gene clusters for the alternative complex III (ACIII), auracyanin and NADH:quinone oxidoreductase; and several aerobic/anaerobic enzyme pairs in central carbon metabolism and tetrapyrroles and nucleic acids biosynthesis. Overall, genomic information is consistent with a high tolerance for oxygen that has been reported in the growth of Cfl. aurantiacus. Genes for the chimeric photosystem, photosynthetic electron transport chain, the 3-hydroxypropionate autotrophic carbon fixation cycle, CO2-anaplerotic pathways, glyoxylate cycle, and sulfur reduction pathway are present. The central carbon metabolism and sulfur assimilation pathways in Cfl. aurantiacus are discussed. Some features of the Cfl. aurantiacus genome are compared with those of the Roseiflexus castenholzii genome. Roseiflexus castenholzii is a recently characterized FAP bacterium and phylogenetically closely related to Cfl. aurantiacus. According to previous reports and the genomic information, perspectives of Cfl. aurantiacus in the evolution of photosynthesis are also discussed. CONCLUSIONS: The genomic analyses presented in this report, along with previous physiological, ecological and biochemical studies, indicate that the anoxygenic phototroph Cfl. aurantiacus has many interesting and certain unique features in its metabolic pathways. The complete genome may also shed light on possible evolutionary connections of photosynthesis.

Dataset Information

Complete Genome Sequence of Rhodopseudomonas palustris RCB100, an Anoxygenic Phototroph That Degrades 3-Chlorobenzoate.

Publications

Complete Genome Sequence of Rhodopseudomonas palustris RCB100, an Anoxygenic Phototroph That Degrades 3-Chlorobenzoate.

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