Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

Frank W. Larimer; Patrick Chain; Loren Hauser; Jane Lamerdin; Stephanie Malfatti; Long Do; Miriam L. Land; Dale A. Pelletier; J. Thomas Beatty; Andrew S. Lang; F. Robert Tabita; Janet L. Gibson; Thomas E. Hanson; Cedric Bobst; Janelle L. Torres Y Torres; Caroline Peres; Faith H. Harrison; Jane Gibson; Caroline S. Harwood

doi:10.1038/nbt923

Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

Frank W. Larimer, Patrick Chain, Loren Hauser, Jane Lamerdin, Stephanie Malfatti, Long Do, Miriam L. Land, Dale A. Pelletier, J. Thomas Beatty, Andrew S. Lang, F. Robert Tabita, Janet L. Gibson, Thomas E. Hanson, Cedric Bobst, Janelle L. Torres Y Torres, Caroline Peres, Faith H. Harrison, Jane Gibson, Caroline S. Harwood

Integrative Microbiomics

Research output: Contribution to journal › Article › peer-review

623 Scopus citations

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.

Original language	English
Pages (from-to)	55-61
Number of pages	7
Journal	Nature Biotechnology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1038/nbt923
State	Published - Jan 2004

Funding

The Biological and Environmental Research program of the US Department of Energy’s Office of Science funded this research. The Joint Genome Institute managed the overall sequencing effort. The University of California, Lawrence Livermore National Laboratory, carried out genome finishing under the auspices of the US Department of Energy (DOE). Computational annotation was carried out at the Oak Ridge National Laboratory, managed by UT-BATTELLE for the DOE. The DOE provided additional support to J.T.B., F.R.T. and C.S.H. The US Army Research Office provided support to C.S.H.

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Larimer, F. W., Chain, P., Hauser, L., Lamerdin, J., Malfatti, S., Do, L., Land, M. L., Pelletier, D. A., Beatty, J. T., Lang, A. S., Tabita, F. R., Gibson, J. L., Hanson, T. E., Bobst, C., Torres Y Torres, J. L., Peres, C., Harrison, F. H., Gibson, J., & Harwood, C. S. (2004). Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nature Biotechnology, 22(1), 55-61. https://doi.org/10.1038/nbt923

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title = "Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris",

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.",

author = "Larimer, {Frank W.} and Patrick Chain and Loren Hauser and Jane Lamerdin and Stephanie Malfatti and Long Do and Land, {Miriam L.} and Pelletier, {Dale A.} and Beatty, {J. Thomas} and Lang, {Andrew S.} and Tabita, {F. Robert} and Gibson, {Janet L.} and Hanson, {Thomas E.} and Cedric Bobst and {Torres Y Torres}, {Janelle L.} and Caroline Peres and Harrison, {Faith H.} and Jane Gibson and Harwood, {Caroline S.}",

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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 Y Torres, JL, Peres, C, Harrison, FH, Gibson, J & Harwood, CS 2004, 'Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris', Nature Biotechnology, vol. 22, no. 1, pp. 55-61. https://doi.org/10.1038/nbt923

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Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

Abstract

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