Low-resolution sequencing of 2.A.1: chromosome II is a true chromosome Free

Abstract

The photosynthetic bacterium 2.4.1 has two chromosomes, CI (∼3.0 Mb) and CII (∼0.9 Mb). In this study a low-redundancy sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library. The sum of the lengths of these 23 cosmid inserts was ∼495 kb, which comprised ∼417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each run generating 559±268 bases of sequence to give ∼640 kb of total sequence. After editing, ∼2.8% bases per run were estimated to be ambiguous. After the removal of vector and sequences, the remaining ∼ 565 kb of sequences were assembled, generating ∼291 kb of unique sequences. analysis of these unique sequences suggested that ∼131 kb (45% of the unique sequence) had matches to either known genes, or database ORFs of hypothetical or unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of these matches represented genes encoding a wide variety of functions, e.g. amino acid biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA operons ( and ) and five tRNAs were also identified. The remaining 160 kb of DNA sequence which did not yield database matches was then analysed using from the GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could encode putative ORFs (ports), with the remaining 38 kb (13%) possibly representing non-coding intergenic DNA. From the data so far obtained, CII does not appear to be specialized for encoding any particular metabolic function, physiological state or growth condition. These data suggest that CII contains genes which are functionally as diverse as those found on any other bacterial chromosome and also contains sequences (pORFs) which may prove to be unique to this organism.

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1997-10-01
2024-03-28
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References

  1. Allardet-Servent A., Michaux-Charachon S., Jumas-Bilak E., Karayan L., Ramuz M. 1993; Presence of one linear and one circular chromosome in the agrobacterium tumefaciens c58 genome. J Bacteriol 175:7869–7874
    [Google Scholar]
  2. Ames G.F. 1986; Bacterial periplasmic transport systems: Structure, mechanism and evolution. Annu Rev Biochem 55:397–425
    [Google Scholar]
  3. Bult C.J., White O., Olsen G.J. 37 other authors 1996; Complete genome sequence of the methanogenic archaeon, methanococcus jannaschii . Science 273:1058–1073
    [Google Scholar]
  4. Cheng H., Lessie T.G. 1994; Multiple replicons constituting the genome of pseudomonas cepacia 17616. J Bacteriol 176:4034–4042
    [Google Scholar]
  5. Choudhary M., Mackenzie C., Nereng K.S., Sodergren E.S., Weinstock G.M., Kaplan S. 1994; Multiple chromosomes in bacteria: Structure and function of chromosome ii of rhodobacter sphaeroides 2.4.1t. J Bacteriol 176:7694–7702
    [Google Scholar]
  6. Demolis N., Mallet L., Bussereau F., Jacquet M. 1995; Improved strategy for large-scale dna sequencing using dnase i cleavage for generating random subclones. Biotechniques 18197–201
    [Google Scholar]
  7. Deutch A.H., Rushlow K.E., Smith C.J. 1984; Analysis of the escherichia coli proba locus by dna and protein sequencing. Nucleic Acids Res 126337–6355
    [Google Scholar]
  8. Dryden S.C. 1992 Identification and Characterization of the Ribosomal RNA Operons from Rhodobacter Sphaeroides PhD thesis University of Illinois, Urbana-Champaign;
    [Google Scholar]
  9. Dryden S.C., Kaplan S. 1990; Localization and structural analysis of the ribosomal rna operons of rhodobacter sphaeroides. Nucleic Acids Res 18:7267–7277
    [Google Scholar]
  10. Ehlert K., Holtje J., Templin M.F. 1995; Cloning and expression of a murein hydrolase lipoprotein from escherichia coli. Mol Microbiol 16:761–768
    [Google Scholar]
  11. Ferdows M.S., Barbour G. 1989; Megabase-sized linear dna in the bacterium borrelia burgodorferi, the lyme disease agent. Proc Natl Acad Sci USA 86:5969–5973
    [Google Scholar]
  12. Fichant G.A., Burks C. 1991; Identifying potential trna genes in genomic dna sequence. J Mol Biol 220:659–671
    [Google Scholar]
  13. Finan T.M., Kunkel B., Vos G.F.W., Signer E.R. 1986; Second symbiotic megaplasmid in rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes. J Bacteriol 167:66–72
    [Google Scholar]
  14. Fleischmann Adams R.D.M.D., White O. 37 other authors 1995; Whole-genome random sequencing and assembly of haemophilus influenzae rd. Science 269:496–512
    [Google Scholar]
  15. Fonstein M., Haselkorn R. 1995; Physical mapping of bacterial genomes. J Bacteriol 177:3361–3369
    [Google Scholar]
  16. Frantz B., Chakrabarty A.M. 1986; Degradative plasmids in pseudomonas. In The Bacteria, Vol. X, the Biology of the Pseudomonads pp. 295–323 Edited by Sokatch J. R. New York: Academic Press;
    [Google Scholar]
  17. Fraser C.M., Jeannine D.G., White O. 26 other authors 1995; The minimal gene complement of mycoplasma genitalium. Science 270:397–403
    [Google Scholar]
  18. Freiberg G., Ferret X., Broughton W.J., Rosenthal A. 1996; Sequencing the 500-kb gc-rich symbiotic replicon of rhizobium sp. Ngr234 using dye terminators and a thermostable ‘sequenase’: A beginning. Genome Res 6:590–600
    [Google Scholar]
  19. Freiberg G., Fellay R., Balroch A., Broughton W.J., Rosenthal A., Perret X. 1997; Molecular basis of symbiosis between rhizobium and legumes. Nature 387:394–401
    [Google Scholar]
  20. Gest H. 1972; Energy conservation and generation of reducing power in bacterial photosynthesis. Adv Microb Physiol 7:243–282
    [Google Scholar]
  21. Glaser P., Kunst F., Amaud M. 14 other authors 1993; Bacillus subtilis genome project: Cloning and sequencing of the 97 kb region from 325° to 333°. Mol Microbiol 10:371–384
    [Google Scholar]
  22. Hallenbeck P.L., Lerchen R., Hessler P., Kaplan S. 1990; Roles of cfxa, cfxb, and external electron acceptors in regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase expression in rhodobacter sphaeroides. J Bacteriol 172:1736–1748
    [Google Scholar]
  23. Hallenbeck P.L., Lerchen R., Hessler P., Kaplan S. 1990; Phosphoribulokinase activity and regulation of co2 fixation critical for photosynthetic growth of rhodobacter sphaeroides. J Bacteriol 172:1749–1761
    [Google Scholar]
  24. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li Bi-Chen, Herrmann R. 1996; Complete sequence analysis of the genome of the bacterium mycoplasma pneumoniae. Nucleic Acids Res 24:4420–4449
    [Google Scholar]
  25. Kiley P.J., Kaplan S. 1988; Molecular genetics of photosynthetic membrane biosynthesis in rhodobacter sphaeroides. Microbiol Rev 52:50–69
    [Google Scholar]
  26. Kosuge T., Tabata K., Hoshino T. 1994; Molecular cloning and sequence analysis of the proba operon from an extremely therophilic eubacterium thermus thermophilus. FEMS Micrio- Biol Lett 5562:123
    [Google Scholar]
  27. Krawiec S., Riley M. 1990; Organization of the bacterial chromosome. Microbiol Rev 54:502–539
    [Google Scholar]
  28. Labedan B., Riley M. 1995; Gene products of escherichia coli: Sequence comparison and common ancestries. Mol Biol Evol 12:980–987
    [Google Scholar]
  29. Lee W.T., Terleshy K.C., Tabita F.R. 1997; Cloning and characterization of two groesl operons of rhodobacter sphaeroides: Transcriptional regulation of the heat-induced groesl operon. J Bacteriol 179:487–495
    [Google Scholar]
  30. Lin Y., Kieser H.M., Hopwood D.A., Chen C.W. 1993; The chromosomal dna of streptomyces lividans 66 is linear. Mol Microbiol 10:923–933
    [Google Scholar]
  31. Mackenzie C., Chidambaram M., Sodergren E., Kaplan S., Weinstock G.M. 1995; Repair mutants of rhodobacter sphaeroides. J Bacteriol 177:3027–3035
    [Google Scholar]
  32. Mackenzie C., Chidambaram M., Choudhary M., Nereng , Kaplan, Weinstock K.S.S.G.M. 1997; Sequence skimming of chromosome ii of rhodobacter sphaeroides 2.4.1T . In Bacterial Genomes: Physical Structure and Analysis Edited by de Bruijn F. J., Lupski F. R., Weinstock G. M. New York: Chapman & Hall; (in press)
    [Google Scholar]
  33. Meijer W.G., Tabita R. 1992; Isolation and characterization of the nifusvw-rpon gene cluster from rhodobacter sphaeroides. J Bacteriol 174:3855–3866
    [Google Scholar]
  34. Michaux S., Paillisson J., Carles-Nurit M.-J., Bourg G., Allardet- Servent A., Ramuz M. 1993; Presence of two independent chromosomes in the brucella melitensis 16m genome. J Bacteriol 175:701–705
    [Google Scholar]
  35. Moore M.D., Kaplan S. 1992; Identification of intrinsic high- level resistance to rare-earth oxides and oxyanions in members of the class proteobacteria: Characterization of tellurite, selenite, and rhodium sesquioxide reduction in rhodobacter sphaeroides. J Bacteriol 174:1505–1514
    [Google Scholar]
  36. Neidle E.L., Kaplan S. 1992; Rhodobacter sphaeroides rdxa, a homolog of rhizobium meliloti fixg, encodes a membrane protein which may bind cytoplasmic [4fe-4s] clusters. J Bacteriol 174:6444–6454
    [Google Scholar]
  37. Neidle E.L., Kaplan S. 1993; Expression of the rhodobacter sphaeroides hem a and hemt genes encoding two 5-aminolevulinic acid synthase isozymes. J Bacteriol 175:2292–2303
    [Google Scholar]
  38. Ogawa J., Long S.R. 1995; The rhizobium meliloti groelc locus is required for regulation of early nod genes by the transcription activator. Nodd. Genes Dev 9:714–729
    [Google Scholar]
  39. Omori K., Suzuku S., Imai Y., Komatsubara S. 1991; Analysis of the serratia marcescens proba operon and feedback control of proline biosynthesis. J Gen Microbiol 137:509–517
    [Google Scholar]
  40. Pardo M.A., Lagunez J., Miranda J., Martinez E. 1994; Nodulating ability of rhizobium tropici is conditioned by a plasmid-encoded citrate synthase. Mol Microbiol 11:315–321
    [Google Scholar]
  41. Riley M. 1993; Functions of the gene products of escherichia coli. Microbiol Rev 57:862–952
    [Google Scholar]
  42. Rodley P.D., Romling U., Burkhard T. 1995; A physical genome map of the burkholderia cepacia type strain. Mol Micriobiol 17:57–67
    [Google Scholar]
  43. Sambrook J., Fritsch E.F., Maniatis T. 1989 Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  44. Schnler J., Thamm S., Lurz R., Hussain A., Faist G., Dobrinski B. 1988; Cloning and characterization of a gene from rhizobium meliloti 2011 coding for ribosomal protein si. Nucleic Acids Res 16:3075–3089
    [Google Scholar]
  45. Sensen G.W., Klenk H., Singh R.K. 10 other authors 1996; Organizational characteristics and information content of an archael genome: 156 kb of sequence from sulfolobus solfataricus p2. Mol Microbiol 22:175–191
    [Google Scholar]
  46. Sobral B.W.S., Honeycutt R.J., Atherly A.G., McClelland M. 1991; Electrophoretic separation of the three rhizobium meliloti replicons. J Bacteriol 173:5173–5180
    [Google Scholar]
  47. Suwanto A., Kaplan S. 1989; Physical and genetic mapping of the rhodobacter sphaeroides 2.4.1 genome: Presence of two unique circular chromosomes. J Bacteriol 171:5850–5859
    [Google Scholar]
  48. Suwanto A., Kaplan S. 1992; Chromosome transfer in rhodobacter sphaeroides: Hfr formation and genetic evidence for two unique circular chromosomes. J Bacteriol 174:1135–1145
    [Google Scholar]
  49. Tabita F.R., Gibson J.L., Bowien B., Dijkhuizen L., Meijer W.G. 1992; Uniform designation for genes of the calvin- benson-bassham reductive pentose phosphate pathway of bacteria. FEMS Microbiol Lett 99:107–110
    [Google Scholar]
  50. Woese C.R., Stackebrandt E., Weisburg W.G. 8 other authors 1984; The phylogeny of the purple bacteria: The alpha subdivision. Syst Appl Microbiol 5:315–326
    [Google Scholar]
  51. Yang O., Oyaizu Y., Oyaizu H., Olsen G.J., Woese C.R. 1985; Mitochondrial origins. Proc Natl Acad Sci USA 82:4443–4447
    [Google Scholar]
  52. Zuerner R.L., Herrmann J.L., Saint Girons I. 1993; Comparison of genetic maps for two leptospira interrogans serovars provides evidence for two chromosomes and intraspecies heterogeneity. J Bacteriol 175:5445–5451
    [Google Scholar]
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