1887

Abstract

The standard strategies of genome sequencing based on -vector or cosmid libraries are only partially applicable to AT-rich Gram-positive bacteria because of the problem of instability of their chromosomal DNA in heterologous hosts like . One complete collection of ordered clones known for such bacteria is that of , established by using yeast artificial chromosomes (YACs). This paper reports the results of the direct use of one of the YAC clones from the above collection for the sequencing of the region cloned in it. The strategy applied consisted of the following: (i) construction of M13 banks of the partially purified YAC DNA and sequencing of 800 M13 clones chosen at random; (ii) directed selection of M13 clones to sequence by using marginal contig fragments as hybridization probes; (iii) direct sequencing of joining PCR fragments obtained by combinations of primers corresponding to the ends of representative contigs. The complete 104 109 bp insert sequence of this YAC clone was thus established. The strategy used allowed us to avoid resequencing the two largest, previously sequenced, contigs (13695 and 20303 bp) of the YAC insert. We propose that the strategy used can be applied to the sequencing of the whole bacterial genome without intermediate cloning, as well as for larger inserts of eukaryotic origin cloned ir YACs. Sequencing of the insert of the YAC clone 15-6B allowed us to establish the contiguous sequence of 127 kb from to The organization of the newly determined region is presented. Of the 138 ORFs identified in the region, 57 have no clear putative function from their homology to proteins in the databases.

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1996-08-01
2021-08-05
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References

  1. Ahnn J., March P.E., Takiff H.E., Inouye M. 1986; A GTP- binding protein of Escherichia coli has homology to yeast RAS proteins. Proc Natl Acad Sci USA 838849–8853
    [Google Scholar]
  2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410
    [Google Scholar]
  3. Anand R., Villasante A., Tyler-Smith C. 1989; Construction of yeast artificial chromosome libraries with large inserts using fractionation by pulsed-field electrophoresis. Nucleic Acids Res 17:3425–3433
    [Google Scholar]
  4. Azevedo V., Alvarez E., Zumstein E., Damiani G., Sgaramella V., Ehrlich S.D., Serror P. 1993a; An ordered collection of Bacillus suhtilis DNA segments cloned in yeast artificial chromosomes. Proc Natl Acad Sci USA 906047–6051
    [Google Scholar]
  5. Azevedo V., Sorokin A.V., Ehrlich S.D., Serror P. 1993b; The transcriptional organisation of the Bacillus subtilis 168 chromosome region between the spoVAF and serA genetic loci. Mol Microbiol 10:397–405
    [Google Scholar]
  6. Baigori M., Grau R., Morbidoni H.R., Mendoza D. 1991; Isolation and characterisation of Bacillus subtilis mutants blocked in the synthesis of pantothenic acid. J Bacteriol 173:4240–4242
    [Google Scholar]
  7. Barnes W.M. 1994; PCR amplification of up to 35-kb DNA with high fidelity and high yield from λ bacteriophage templates. Proc Natl Acad Sci USA 912216–2220
    [Google Scholar]
  8. Bower S., Perkins J., Yocum R.R., Serror P., Sorokin A., Rahaim P., Howitt C.L., Prasad N., Ehrlich S.D., Pero J. 1995; Cloning and characterization of the Bacillus subtilis birA gene encoding a repressor of the biotin operon. J Bacteriol 177:2572–2575
    [Google Scholar]
  9. Bruand C., Sorokin A., Serror P., Ehrlich S.D. 1995; Nucleotide sequence of the Bacillus subtilis dnaD gene. Microbiology 141:321–322
    [Google Scholar]
  10. Burke D.T., Carle G.F., Olson M.V. 1987; Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236:806–812
    [Google Scholar]
  11. Condemine G., Robert-Baudouy J. 1991; Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation. Mol Microbiol 5:2191–2202
    [Google Scholar]
  12. Cheng S., Fockler C., Barnes W.M., Higuchi R. 1994; Effective amplification of long targets from cloned inserts and human genomic DNA. Proc Natl Acad Sci USA 915695–5699
    [Google Scholar]
  13. Cheo D.L., Bayles K.W., Yasbin R.E. 1991; Cloning and characterization of DNA damage-inducible promoter regions from Bacillus subtilis. . J Bacteriol 173:1696–1703
    [Google Scholar]
  14. Daniels D.L., Plunkett G. III Burland V., Blattner F.R. 1992; Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257:771–778
    [Google Scholar]
  15. Dear S., Staden R. 1991; A sequence assembly and editing program for efficient management of large projects. Nucleic Acids Res 19:3907–3911
    [Google Scholar]
  16. Diêp Lê K.H., Lederer F. 1991; Amino acid sequence of long chain ɑ-hydroxy acid oxidase from rat kidney, a member of the family of FMN-dependent ɑ-hydroxy acid oxidizing enzymes. J Biol Chem 266:20877–20881
    [Google Scholar]
  17. Donovan W., Zheng L, Sandman K., Losick R. 1987; Genes encoding spore coat polypeptides from Bacillus subtilis. . J Mol Biol 196:1–10
    [Google Scholar]
  18. Dower W.J., Miller J.F., Ragsdale C.W. 1988; High-efficiency transformation of E. coli by high-voltage electroporation. Nucleic Acids Res 16:6127–6145
    [Google Scholar]
  19. Dujon B., Alexandraki D., André B., Ansorge W., Baladron V., Ballesta J.P., Banrevi A., Bolle P.A., Bolotin-Fukuhara M., Bossier P.et al. 1994; Complete DNA sequence of yeast chromosome XI. Nature 369:371–378
    [Google Scholar]
  20. Fleishmann R.D., Adams M.D., White O. and 37 other authors 1995; Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512
    [Google Scholar]
  21. Fraser C.M., Gocayne J.D., White O. and 26 other authors 1995; The minimal gene complement of Mycoplasma genitalium. . Science 270:397–403
    [Google Scholar]
  22. Freese E.B., Oh Y.K. 1974; Adenosine 5ʹ-triphosphate release and membrane collapse in glycerol-requiring mutants of Bacillus subtilis. . J Bacteriol 120:507–515
    [Google Scholar]
  23. Fricke J., Neuhard J., Kellin R.A., Pedersen S. 1995; 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 177:517–523
    [Google Scholar]
  24. Glaser P., Danchin A., Kunst F, Debarbouille M., Vertes A., Dedonder R. 1990; A gene encoding a tyrosine-tRNA synthetase is located near sacS in Bacillus subtilis. . DNA Seq 1:251–261
    [Google Scholar]
  25. Glaser P., Kunst F., Arnaud M. and 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]
  26. Goldman M., Blumenthal H.J. 1963; Pathways of glucose in Bacillus subtilis. . J Bacteriol 86:303–311
    [Google Scholar]
  27. Gollop N., March P.E. 1991; A GTP-binding protein (Era) has an essential role in growth rate and cell cycle control in Escherichia coli. . J Bacteriol 173:2265–2270
    [Google Scholar]
  28. Grundy F.J., Henkin T.M. 1993; tRNA as a positive regulator of transcription antitermination in Bacillus subtilis. . Cell 74:475–482
    [Google Scholar]
  29. Henner D., Gollnick P., Moir A. 1990; Analysis of an 18 kilobasepair region of the Bacillus subtilis chromosome containing the mtr and gerC operons and the aro-trp-aro supraoperon. In Proceedings of the 6th International Symposium on Genetics of Industrial Microorganisms 2: pp. 675–665
    [Google Scholar]
  30. Henner D., Yanofski Ch. 1993; Biosynthesis of aromatic amino acids. In Bacillus subtilis and Other Gram-positive Bacteria pp. 269–280 Sonenshein A.L., Hoch J.A., Losick R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  31. Hoch J., Mathews J. 1972; Genetic studies in Bacillus subtilis. . In Spores V pp. 113–116 Halvorson H.O., Hanson R., Campbell L.L. Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  32. Honoré N., Bergh S., Chonteau S. and 15 other authors 1993; Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the rif-str regions. Mol Microbiol 7:207–214
    [Google Scholar]
  33. Hugouvieux-Cotte-Pattat N., Robert-Baudouy J. 1994; Molecular analysis of the Erwinia chrysanthemi region containing the kdgA and zwf genes. Mol Microbiol 11:67–75
    [Google Scholar]
  34. Irino N., Nakayama K., Nakayama H. 1986; The recQ gene of Escherichia coli K12: primary structure and evidence for SOS regulation. Mol Gen Genet 205:298–304
    [Google Scholar]
  35. Jacob F., Monod J. 1961; Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356
    [Google Scholar]
  36. Kane J.F., Wakim J., Fisher R.S. 1981; Regulation of glutamate dehydrogenase in Bacillus subtilis. . J Bacteriol 148:1002–1005
    [Google Scholar]
  37. Kimura K. 1975; A new flavin enzyme catalysing the reduction of dihydropicolinate in sporulating Bacillus subtilis. I. Purification and properties. J Biochem 77:405–413
    [Google Scholar]
  38. Kimura K., Goto T. 1977; Dihydrodipicolinate reductases from Bacillus cereus and Bacillus megaterium. I. Purification and properties. J Biochem 81:1367–1373
    [Google Scholar]
  39. Kimura K., Goto T., Ujita S. 1978; Two differentiatable types of dihydropicolinate reductases from sporulating bacilli. In Spores VII pp. 308–311 Chambliss G., Vary J.C. Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  40. Kunst F., Devine K. 1991; The project of sequencing the entire Bacillus subtilis genome. Res Microbiol 142:905–912
    [Google Scholar]
  41. Kunst F., Vassarotti A., Danchin A. 1995; Organization of the European Bacillus subtilis genome sequencing project. Microbiology 141:249–255
    [Google Scholar]
  42. Lerner C.G., Inoye M. 1991; Pleiotropic changes resulting from depletion of Era, an essential GTP-binding protein in Escherichia coli. . Mol Microbiol 5:951–957
    [Google Scholar]
  43. Lindgren V., Rutberg L. 1974; Glycerol metabolism in Bacillus subtilis-. gene-enzyme relationships. J Bacterial 119:431–442
    [Google Scholar]
  44. Lonetto M.A., Brown K.L., Rudd K.E., Buttner M.J. 1994; Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase σ factors involved in the regulation of extracytoplasmic functions. Proc Natl Acad Sci USA 917573–7577
    [Google Scholar]
  45. McLaughlin J.R., Murray C.L., Rabinowitz J.C. 1981; Unique features in the ribosome-binding site sequence of the Grampositive Staphylococcus aureus β-lactamase gene. J Biol Chern 256:11283–11291
    [Google Scholar]
  46. Ogasawara N., Nakai S., Yoshikawa Y. 1994; Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin. DNA Res 1:1–6
    [Google Scholar]
  47. Ogasawara N., Fujita Y., Kobayashi Y., Sadaie Y., Tanaka T., Takahashi H., Yamane K., Yoshikawa H. 1995; Systematic sequencing of the Bacillus subtilis genome: progress report of the Japanese group. Microbiology 141:257–259
    [Google Scholar]
  48. Oh Y.K., Freese E.B., Freese E. 1973; Abnormal septation and inhibition of sporulation by accumulation of L-ɑ-glycerophosphate in Bacillus subtilis mutants. J Bacteriol 113:1034–1045
    [Google Scholar]
  49. Oliver S.G., van der Aart Q.J., Agostoni-Carbone M.L. and 144 other authors 1992; The complete DNA sequence of yeast chromosome III. Nature 357:38–46
    [Google Scholar]
  50. Pearson W.R., Lipman D.J. 1988; Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 852444–2448
    [Google Scholar]
  51. Popham D.L., Setlow P. 1995; Cloning, nucleotide sequence and mutagenesis of the Bacillus subtilis ponA operon, which codes for penicillin-binding protein (PBP) 1 and a PBP-related factor. J Bacteriol 177:326–335
    [Google Scholar]
  52. Popham D.L., Illades-Aniar B., Setlow P. 1995; The Bacillus subtilis dacB gene, encoding penicillin-binding protein 5, is part of a three-gene operon required for proper spore cortex synthesis and spore core dehydration. J Bacteriol 177:4721–4729
    [Google Scholar]
  53. Putzer H., Gendron N., Grunberg-Manago M. 1992; Coordinate expression of the two threonyl-tRNA synthetase genes in Bacillus subtilis-. control by transcriptional antitermination involving a conserved regulatory sequence. EAIBO J 11:3117–3127
    [Google Scholar]
  54. Reich C., Gardiner K.J., Olsen G.J., Pace B., Marsh T.L., Pace N.R. 1986; The RNA component of the Bacillus subtilis RNase P. Sequence, activity and partial secondary structure. J Biol Chem 261:7888–7893
    [Google Scholar]
  55. Reverchon S., Nasser W., Robert-Baudouy J. 1991; Characterisation of kdgR, a gene of Erwinia chrysanthemi that regulates pectin degradation. Mol Microbiol 5:2203–2216
    [Google Scholar]
  56. Roels S., Driks A., Losick R. 1992; Characterisation of spoiIVA, a sporulation gene involved in coat morphogenesis in Bacillus subtilis. . J Bacteriol 174:575–585
    [Google Scholar]
  57. Saier M.H. JR Reizer J. 1992; Proposed uniform nomenclature for the proteins and protein domains of the bacterial phospho-enolpyruvate: sugar phosphotransferase system. J Bacteriol 174:1433–1438
    [Google Scholar]
  58. Schreier H.J. 1993; Biosynthesis of glutamine and the assimilation of ammonia. In Bacillus subtilis and Other Gram-positive Bacteria pp. 281–298 Sonnenshein A.L., Hoch J.A., Losick R. Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  59. Schönbächler M., Horvath A., Fassler J., Riezman H. 1995; he yeast SPT14 gene is homologous to the human PIG-A gene and is required for GPI anchor synthesis. EMBO J 14:1637–1645
    [Google Scholar]
  60. Smith D.R., Smyth A.P., Moir D.T. 1990; Amplification of large artificial chromosomes. Proc Natl Acad Sci USA 878242–8246
    [Google Scholar]
  61. Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P. 1993; The organisation of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci. Mol Microbiol 10:385–395
    [Google Scholar]
  62. Sorokin A., Serror P., Pujic P., Azevedo V., Ehrlich S.D. 1995; The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mss A and rpsA gene products. Microbiology 141:311–319
    [Google Scholar]
  63. Stallings R.L., Doggott N.A., Ford A., Langmire J., Hildebrand C.E., Deaven L.L., Deaven L.L., Moyzis R.K. 1994; Application of cosmid libraries in genome mapping and sequencing efforts. In Automated DNA Sequencing and Analysis pp. 80–88 Adams M.D., Fields Ch., Venter J.C. Edited by New York: Academic Press;
    [Google Scholar]
  64. Stevens C.M., Daniel R., Illing N., Errington J. 1992; Characterisation of a sporulation gene, spoIVA, involved in spore coat morphogenesis in Bacillus subtilis. . J Bacteriol 174:586–594
    [Google Scholar]
  65. Sun G., Sharkova E., Chesnut R., Birkey S., Duggan M.F., Sorokin A., Pujic P., Ehrlich S.D., Hulett F.M. 1996; Regulators of aerobic and anaerobic respiration in Bacillus subtilis. . J Bacteriol 178:1374–1385
    [Google Scholar]
  66. Trach K., Hoch J. 1989; The Bacillus subtilis spoOB stage 0 sporulation operon encodes an esential GTP-binding protein. J Bacteriol 171:1362–1371
    [Google Scholar]
  67. Trumpower B.L. 1990; Cytochrome bc 1 complexes of microorganisms. Microbiol Rev 54:101–129
    [Google Scholar]
  68. Vaudin M., Roopra A., Hillier L., Brinkman R., Sulston J., Wilson R.K., Waterston R.H. 1995; The construction and analysis of M13 libraries prepared from YAC DNA. Nucleic Acids Res 23:670–674
    [Google Scholar]
  69. Völker U., Engelmann S., Maul B., Riethdorf S., Völker A., Schmid R., Mach H., Hecker M. 1994; Analysis of the induction of general stress proteins of Bacillus subtilis. . Microbiology 140:741–752
    [Google Scholar]
  70. Walch N.S., Ingraham J.L. 1976; Pyrimidine mono- phosphokinase and the mode of RNA turnover in Bacillus subtilis. . Arch Microbiol 110:49–54
    [Google Scholar]
  71. Weijland A., Parmeggiani A. 1993; Toward a model for the interaction between elongation factor Tu and the ribosome. Science 259:1311–1314
    [Google Scholar]
  72. Williams N. 1995; Closing in on the complete yeast genome sequence. Science 268:1560–1561
    [Google Scholar]
  73. Wilson R., Ainscough R., Anderson K. and 52 other authors 1994; 2·2 Mb of contiguous nucleotide sequence from chrom-osome III of C. elegans. . Nature 368:32–38
    [Google Scholar]
  74. Yamashita Y., Takehara T., Kuramotsu H.K. 1993; Molecular characterization of a Streptococcus mutants mutant altered in en-vironmental stress responses. J Bacterial 175:6220–6228
    [Google Scholar]
  75. Yu J., Hederstedt L., Piggot P. 1995; The cytochrome be complex (menaquinone: cytochrome c reductase) in Bacillus subtilis has a non-traditional subunit organisation. J Bacteriol 77:6751–6760
    [Google Scholar]
  76. Zheng L., Losick R. 1990; Cascade regulation of spore coat gene expression in Bacillus subtilis. . J Mol Biol 212:645–660
    [Google Scholar]
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