Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 1999 Oct;153(2):525–538. doi: 10.1093/genetics/153.2.525

Multiple chromosomes in bacteria. The yin and yang of trp gene localization in Rhodobacter sphaeroides 2.4.1.

C Mackenzie 1, A E Simmons 1, S Kaplan 1
PMCID: PMC1460784  PMID: 10511537

Abstract

The existence of multiple chromosomes in bacteria has been known for some time. Yet the extent of functional solidarity between different chromosomes remains unknown. To examine this question, we have surveyed the well-described genes of the tryptophan biosynthetic pathway in the multichromosomal photosynthetic eubacterium Rhodobacter sphaeroides 2.4.1. The genome of this organism was mutagenized using Tn5, and strains that were auxotrophic for tryptophan (Trp(-)) were isolated. Pulsed-field gel mapping indicated that Tn5 insertions in both the large (3 Mb CI) and the small (0.9 Mb CII) chromosomes created a Trp(-) phenotype. Sequencing the DNA flanking the sites of the Tn5 insertions indicated that the genes trpE-yibQ-trpGDC were at a locus on CI, while genes trpF-aroR-trpB were at locus on CII. Unexpectedly, trpA was not found downstream of trpB. Instead, it was placed on the CI physical map at a locus 1.23 Mb away from trpE-yibQ-trpGDC. To relate the context of the R. sphaeroides trp genes to those of other bacteria, the DNA regions surrounding the trp genes on both chromosomes were sequenced. Of particular significance was the finding that rpsA1, which encodes ribosomal protein S1, and cmkA, which encodes cytidylate monophosphate kinase, were on CII. These genes are considered essential for translation and chromosome replication, respectively. Southern blotting suggested that the trp genes and rpsA1 exist in single copy within the genome. To date, this topological organization of the trp "operon" is unique within a bacterial genome. When taken with the finding that CII encodes essential housekeeping functions, the overall impression is one of close regulatory and functional integration between these chromosomes.

Full Text

The Full Text of this article is available as a PDF (329.9 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Allardet-Servent A., Michaux-Charachon S., Jumas-Bilak E., Karayan L., Ramuz M. Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome. J Bacteriol. 1993 Dec;175(24):7869–7874. doi: 10.1128/jb.175.24.7869-7874.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Allen L. N., Hanson R. S. Construction of broad-host-range cosmid cloning vectors: identification of genes necessary for growth of Methylobacterium organophilum on methanol. J Bacteriol. 1985 Mar;161(3):955–962. doi: 10.1128/jb.161.3.955-962.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baril C., Herrmann J. L., Richaud C., Margarita D., Girons I. S. Scattering of the rRNA genes on the physical map of the circular chromosome of Leptospira interrogans serovar icterohaemorrhagiae. J Bacteriol. 1992 Dec;174(23):7566–7571. doi: 10.1128/jb.174.23.7566-7571.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Calero S., Fernandez de Henestrosa A. R., Barbé J. Molecular cloning, sequence and regulation of expression of the recA gene of the phototrophic bacterium Rhodobacter sphaeroides. Mol Gen Genet. 1994 Jan;242(1):116–120. doi: 10.1007/BF00277356. [DOI] [PubMed] [Google Scholar]
  5. Choudhary M., Mackenzie C., Mouncey N. J., Kaplan S. RsGDB, the Rhodobacter sphaeroides Genome Database. Nucleic Acids Res. 1999 Jan 1;27(1):61–62. doi: 10.1093/nar/27.1.61. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Choudhary M., Mackenzie C., Nereng K. S., Sodergren E., Weinstock G. M., Kaplan S. Multiple chromosomes in bacteria: structure and function of chromosome II of Rhodobacter sphaeroides 2.4.1T. J Bacteriol. 1994 Dec;176(24):7694–7702. doi: 10.1128/jb.176.24.7694-7702.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Choudhary M., Mackenzie C., Nereng K., Sodergren E., Weinstock G. M., Kaplan S. Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome. Microbiology. 1997 Oct;143(Pt 10):3085–3099. doi: 10.1099/00221287-143-10-3085. [DOI] [PubMed] [Google Scholar]
  8. Crawford I. P. Evolution of a biosynthetic pathway: the tryptophan paradigm. Annu Rev Microbiol. 1989;43:567–600. doi: 10.1146/annurev.mi.43.100189.003031. [DOI] [PubMed] [Google Scholar]
  9. Deckert G., Warren P. V., Gaasterland T., Young W. G., Lenox A. L., Graham D. E., Overbeek R., Snead M. A., Keller M., Aujay M. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 1998 Mar 26;392(6674):353–358. doi: 10.1038/32831. [DOI] [PubMed] [Google Scholar]
  10. Dryden S. C., Kaplan S. Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides. Nucleic Acids Res. 1990 Dec 25;18(24):7267–7277. doi: 10.1093/nar/18.24.7267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fricke J., Neuhard J., Kelln R. A., Pedersen S. The cmk gene encoding cytidine monophosphate kinase is located in the rpsA operon and is required for normal replication rate in Escherichia coli. J Bacteriol. 1995 Feb;177(3):517–523. doi: 10.1128/jb.177.3.517-523.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gray M. W. Origin and evolution of organelle genomes. Curr Opin Genet Dev. 1993 Dec;3(6):884–890. doi: 10.1016/0959-437x(93)90009-e. [DOI] [PubMed] [Google Scholar]
  13. Hallenbeck P. L., Lerchen R., Hessler P., Kaplan S. Phosphoribulokinase activity and regulation of CO2 fixation critical for photosynthetic growth of Rhodobacter sphaeroides. J Bacteriol. 1990 Apr;172(4):1749–1761. doi: 10.1128/jb.172.4.1749-1761.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hallenbeck P. L., Lerchen R., Hessler P., Kaplan S. Roles of CfxA, CfxB, and external electron acceptors in regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase expression in Rhodobacter sphaeroides. J Bacteriol. 1990 Apr;172(4):1736–1748. doi: 10.1128/jb.172.4.1736-1748.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hasona A., Ray R. M., Shanmugam K. T. Physiological and genetic analyses leading to identification of a biochemical role for the moeA (molybdate metabolism) gene product in Escherichia coli. J Bacteriol. 1998 Mar;180(6):1466–1472. doi: 10.1128/jb.180.6.1466-1472.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Heath J. D., Perkins J. D., Sharma B., Weinstock G. M. NotI genomic cleavage map of Escherichia coli K-12 strain MG1655. J Bacteriol. 1992 Jan;174(2):558–567. doi: 10.1128/jb.174.2.558-567.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kishan V., Hillen W. Molecular cloning, nucleotide sequence, and promoter structure of the Acinetobacter calcoaceticus trpFB operon. J Bacteriol. 1990 Oct;172(10):6151–6155. doi: 10.1128/jb.172.10.6151-6155.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kitakawa M., Isono K. An amber mutation in the gene rpsA for ribosomal protein S1 in Escherichia coli. Mol Gen Genet. 1982;185(3):445–447. doi: 10.1007/BF00334137. [DOI] [PubMed] [Google Scholar]
  19. Kuykendall L. D., Hunter W. J. The sequence of a symbiotically essential Bradyrhizobium japonicum operon consisting of trpD, trpC and a moaC-like gene. Biochim Biophys Acta. 1997 Feb 28;1350(3):277–281. doi: 10.1016/s0167-4781(96)00237-0. [DOI] [PubMed] [Google Scholar]
  20. Mackenzie C., Chidambaram M., Sodergren E. J., Kaplan S., Weinstock G. M. DNA repair mutants of Rhodobacter sphaeroides. J Bacteriol. 1995 Jun;177(11):3027–3035. doi: 10.1128/jb.177.11.3027-3035.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Michaux S., Paillisson J., Carles-Nurit M. J., Bourg G., Allardet-Servent A., Ramuz M. Presence of two independent chromosomes in the Brucella melitensis 16M genome. J Bacteriol. 1993 Feb;175(3):701–705. doi: 10.1128/jb.175.3.701-705.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Neidle E. L., Kaplan S. Expression of the Rhodobacter sphaeroides hemA and hemT genes, encoding two 5-aminolevulinic acid synthase isozymes. J Bacteriol. 1993 Apr;175(8):2292–2303. doi: 10.1128/jb.175.8.2292-2303.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Neidle E. L., Kaplan S. Rhodobacter sphaeroides rdxA, a homolog of Rhizobium meliloti fixG, encodes a membrane protein which may bind cytoplasmic [4Fe-4S] clusters. J Bacteriol. 1992 Oct;174(20):6444–6454. doi: 10.1128/jb.174.20.6444-6454.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ohta N., Sato N., Kawano S., Kuroiwa T. The trpA gene on the plastid genome of Cyanidium caldarium strain RK-1. Curr Genet. 1994 Apr;25(4):357–361. doi: 10.1007/BF00351490. [DOI] [PubMed] [Google Scholar]
  25. Rice P. A., Yang S., Mizuuchi K., Nash H. A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 1996 Dec 27;87(7):1295–1306. doi: 10.1016/s0092-8674(00)81824-3. [DOI] [PubMed] [Google Scholar]
  26. Rodley P. D., Römling U., Tümmler B. A physical genome map of the Burkholderia cepacia type strain. Mol Microbiol. 1995 Jul;17(1):57–67. doi: 10.1111/j.1365-2958.1995.mmi_17010057.x. [DOI] [PubMed] [Google Scholar]
  27. Suwanto A., Kaplan S. Chromosome transfer in Rhodobacter sphaeroides: Hfr formation and genetic evidence for two unique circular chromosomes. J Bacteriol. 1992 Feb;174(4):1135–1145. doi: 10.1128/jb.174.4.1135-1145.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Suwanto A., Kaplan S. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: genome size, fragment identification, and gene localization. J Bacteriol. 1989 Nov;171(11):5840–5849. doi: 10.1128/jb.171.11.5840-5849.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Suwanto A., Kaplan S. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. J Bacteriol. 1989 Nov;171(11):5850–5859. doi: 10.1128/jb.171.11.5850-5859.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Tabita F. R., Gibson J. L., Bowien B., Dijkhuizen L., Meijer W. G. Uniform designation for genes of the Calvin-Benson-Bassham reductive pentose phosphate pathway of bacteria. FEMS Microbiol Lett. 1992 Dec 1;78(2-3):107–110. doi: 10.1111/j.1574-6968.1992.tb05551.x. [DOI] [PubMed] [Google Scholar]
  31. Trucksis M., Michalski J., Deng Y. K., Kaper J. B. The Vibrio cholerae genome contains two unique circular chromosomes. Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14464–14469. doi: 10.1073/pnas.95.24.14464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Winterstein C., Ludwig B. Genes coding for respiratory complexes map on all three chromosomes of the Paracoccus denitrificans genome. Arch Microbiol. 1998 Apr;169(4):275–281. doi: 10.1007/s002030050572. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES