Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

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.

• Publication year

  2004

• Venue

  Nature Biotechnology

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/nbt923PMID 14704707
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• The genome encodes 63 signal transduction histidine kinases, 79 response regulator receiver domains, and allocates almost 15% of the genome to transport.

  Confidence 0.95

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• Its genome contains three nitrogenases, five benzene ring cleavage pathways, and four light harvesting 2 systems.

  Confidence 0.97

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• Rhodopseudomonas palustris was reported with a 5,459,213-bp circular chromosome, 4,836 predicted genes, and an 8,427-bp plasmid.

  Confidence 0.98

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review

• benzene ring cleavage pathway

  metabolic pathway

  A biochemical pathway category for breaking down aromatic benzene rings in organic compounds.

  Aliases: ring cleavage pathway

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• circular chromosome

  genome feature

  The main chromosome of the bacterium described here as a closed circular DNA molecule.

  Aliases: chromosome

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• complete genome sequence

  genome resource

  The full DNA sequence resource reported for Rhodopseudomonas palustris in this work.

  Aliases: genome sequence

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• light harvesting 2 system

  protein complex

  A photosynthetic antenna complex category used to capture light energy.

  Aliases: LH2 system, LH2

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• nitrogenase

  enzyme family

  An enzyme complex associated with nitrogen fixation and represented by multiple gene systems in the genome.

  Aliases: nitrogenases

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• plasmid

  genome feature

  A small extrachromosomal DNA molecule present alongside the chromosome in the reported genome.

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• predicted genes

  genomic annotation

  Computationally inferred gene models annotated on the assembled genome.

  Aliases: gene predictions

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• response regulator receiver domain

  protein domain

  A receiver-domain module found in bacterial response regulators that participates in signaling cascades.

  Aliases: receiver domain

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• signal transduction histidine kinase

  protein family

  A sensor kinase protein family involved in bacterial signal transduction.

  Aliases: histidine kinase

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review
• transport genes

  functional category

  Genes annotated as participating in uptake, export, or other membrane transport functions.

  Aliases: transport

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) review

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