Abstract
The genome of Rhodobacter capsulatus has been completely sequenced. It consists of a single chromosome containing 3.5 Mb and a circular plasmid of 134 kb. This effort, started in 1992, began with a fine-structure restriction map of an overlapping set of cosmids that covered the genome. Cosmid sequencing led to a gapped genome that was filled by primer walking on the chromosome and by using lambda clones. Methods had to be developed to handle strong stops in the high GC (68%) inserts. Annotation was done with the ERGO system at Integrated Genomics, as was the reconstruction of the cell's metabolism. It was possible to recognize 3709 orfs of which functional assignments could be made with high confidence to 2392 (65%). Unusual features include the presence of numerous cryptic phage genomes embedded in the chromosome.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bauer CE and Bird TH (1996) Regulatory circuits controlling photosynthesis gene expression. Cell 85: 5–8
Cogdell RJ, Isaacs NW, Howard TD, McLuskey K, Fraser NJ and Prince SM (1999) How photosynthetic bacteria harvest solar energy. J Bacteriol 181: 3869–3879
Cuypers H, Berghofer J and Zumft WG (1995) Multiple nosZ promoters and anaerobic expression of nos genes necessary for Pseudomonas stutzeri nitrous oxide reductase and assembly of its copper centers. Biochim Biophys Acta 1264: 183–190
Fonstein M and Haselkorn R (1993) Chromosomal structure of Rhodobacter capsulatus strain SB 1003: Cosmid encyclopedia and high resolution physical and genetic map. Proc Natl Acad Sci USA 90: 2522–2526
Fonstein M, Zheng S and Haselkorn R (1992) Physical map of the genome of R. capsulatus SB1003. J Bacteriol 174: 4070–4077
Fonstein M, Koshy EG, Nikolskaya T, Mourachov P and Haselkorn R (1995) Refinement of the high resolution physical & genetic map of R. capsulatus and genome surveys using blots of the cosmid encyclopedia. EMBO J 14: 1827–1841
Gurgun V, Kirchner G and Pfennig N (1976) Fermentation of pyruvate by seven species of phototrophic purple bacteria. Z Allg Mikrobiol 16: 573–86
Lang AS and Beatty JT (2001) The gene transfer agent of Rhodobacter capsulatus and ‘constitutive transduction’ in prokaryotes. Arch Microbiol 175: 241–249
Loach PA (2000) Supramolecular complexes in photosynthetic bacteria. Proc Natl Acad Sci USA 97: 5016–5018
Pemberton JM, Horne IM and McEwan AG (1998) Regulation of photosynthetic gene expression in purple bacteria. Microbiol 144: 267–278
Schwintner C, Sabaty M, Berna B, Cahors S and Richaud P (1998) Plasmid content and localization of the genes encoding the denitrification enzymes in two strains of Rhodobacter sphaeroides. FEMS Microbiol Lett 165: 313–321
Schobert M and Gorisch H (1999) Cytochrome c550 is an essential component of the quinoprotein ethanol oxidation system in Pseudomonas aeruginosa: Cloning and sequencing of the genes encoding cytochrome c550 and an adjacent acetaldehyde dehydrogenase. Microbiology 145: 471–481
Vlcek C, Paces V, Maltsev N, Paces J, Haselkorn R and Fonstein M (1997) Sequence of a 189-kb segment of the chromosome of Rhodobacter capsulatus SB1003. Proc Natl Acad Sci USA 94: 9384–9388
Wiebrock A and Zumft WG (1987) Physical mapping of transposon Tn5 insertions defines a gene cluster functional in nitrous oxide respiration by Pseudomonas stutzeri. J Bacteriol 169: 4577–4580
Willis LB and Walker GC (1999) A novel Sinorhizobium meliloti operon encodes an α-glucosidase and a periplasmic-bindingprotein-dependent transport system for α-glucosides.J Bacteriol 181: 4176–4184
Yeliseev A and Kaplan S (2000) TspO of Rhodobacter sphaeroides. J Biol Chem 275: 5657–5667
Youshinari T (1980) N2O reduction by Vibrio succinogenes. Appl Environ Microbiol 39: 81–84
Zeilstra- Ryalls J, Gomelsky M, Eraso JM, Yeliseev A, O'Gara J and Kaplan S (1998) Control of photosystem formation in Rhodobacter sphaeroides. J Bacteriol 180: 2801–2809
Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 533–616
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Haselkorn, R., Lapidus, A., Kogan, Y. et al. The Rhodobacter capsulatus genome. Photosynthesis Research 70, 43–52 (2001). https://doi.org/10.1023/A:1013883807771
Issue Date:
DOI: https://doi.org/10.1023/A:1013883807771