Nature Biotechnology
22, 55 - 61 (2003)
Published online: 14 December 2003; | doi:10.1038/nbt923
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustrisFrank W Larimer1, 2, Patrick Chain2, 3, Loren Hauser1, 2, Jane Lamerdin2, 3, 7, Stephanie Malfatti2, 3, Long Do2, 3, 7, Miriam L Land1, 2, Dale A Pelletier1, 2, J Thomas Beatty4, Andrew S Lang4, F Robert Tabita5, Janet L Gibson5, Thomas E Hanson5, 7, Cedric Bobst5, Janelle L Torres y Torres6, Caroline Peres6, 7, Faith H Harrison6, Jane Gibson6
& Caroline S Harwood61
Genome Analysis and Systems Modeling, Oak Ridge National Laboratory, One Bethel Valley Rd., Oak Ridge, Tennessee 37831, USA. 2
Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California 94598, USA. 3
Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, California 94550, USA. 4
Department of Microbiology and Immunology, The University of British Columbia, 6174 University Blvd., Vancouver, British Columbia, Canada V6T 1Z3. 5
Department of Microbiology, The Ohio State University, 484 West 12th Ave., Columbus, Ohio 43210, USA. 6
Department of Microbiology, 3-432 Bowen Science Bldg., The University of Iowa, Iowa City, Iowa 52242, USA. 7
Present addresses: Odyssey Thera, 4550 Norris Canyon Rd., San Ramon, California 94583, USA (J.L.), Department of Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, California 92093, USA (L.D.), Delaware Biotechnology Institute, The University of Delaware, 15 Innovation Way, Newark, Delaware 19711, USA (T.E.H.), Genencor International, 925 Page Mill Rd., Palo Alto, California 94304, USA (C.P.).
Correspondence should be addressed to Caroline S Harwood caroline-harwood@uiowa.edu
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.
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