Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2

Molecular Microbiology

Volumn 22, Issue 1, 1996, Pages 175-191

  Sensen, C W ^a,b   Klenk, H P ^c,g   Singh, R K ^b   Allard, G ^d   Chan, C C Y ^d   Liu, Q Y ^d   Penny, S L ^b   Young, F ^d   Schenk, M E ^c   Gaasterland, T ^a,e,f   Doolittle, W F ^a,c   Ragan, M A ^a,b   Charlebois, R L ^a,d  

^a CANADIAN INSTITUTE FOR ADVANCED RESEARCH   (Canada)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^c DALHOUSIE UNIVERSITY   (Canada)

^d UNIVERSITY OF OTTAWA   (Canada)

^e ARGONNE NATIONAL LABORATORY   (United States)

^f THE UNIVERSITY OF CHICAGO   (United States)

^g J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENETIC ANALYSIS; GRAM NEGATIVE CHEMOLITHOTROPHIC AND METHANE PRODUCING BACTERIA; MOLECULAR CLONING; NONHUMAN; OPEN READING FRAME; OPERON; PRIORITY JOURNAL;

CHROMOSOMES, BACTERIAL; CLONING, MOLECULAR; COSMIDS; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; REGULATORY SEQUENCES, NUCLEIC ACID; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, BACTERIAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; SULFOLOBUS; TRANSCRIPTION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; SULFOLOBUS SOLFATARICUS;

EID: 10144228402     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.1996.tb02666.x     Document Type: Article

References (90)

1. Asahara, H., Wistort, P.M., Bank, J.F., Bakerian, R.H., and Cunningham, R.P. (1989) Purification and characterization of Escherichia coli endonuclease III from the cloned nth gene. Biochemistry 28: 4444-4449.
2. Blattner, F.R. (1994) A contiguous 1.6 megabases of the Escherichia coli K-12 genome (minutes 67.4-4.1). Third International E. coli Genome Meeting, University of Wisconsin-Madison.
3. Bork, P., Ouzounis, C., Casari, G., Schneider, R., Sander, C., Dolan, M., Gilbert, W., and Gillevet, P.M. (1995) Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol Microbiol 16: 955-967.
4. Brown, J.R., and Doolittle, W.F. (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92: 2441-2445.
5. Burland, V., Plunkett, III, G., Daniels, D.L., and Blattner, F.R. (1993) DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16: 551-561.
6. Burland, V., Plunkett, III, G., Sofia, H.J., Daniels, D.L., and Blattner, F.R. (1995) Analysis of the Escherichia coli genome Vl: DNA sequence of the region from 92.8 through 100 minutes. Nucl Acids Res 23: 2105-2119.
7. Bussey, H., Kaback, D.B., Zhong, W., Vo, D.T., Clark, M.W., Fortin, N., Hall, J., Ouellette, B.F.F., Keng, T., Barton, A.B., Su, Y., Davies, C.J., and Storms, R.K. (1995) The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. Proc Natl Acad Sci USA 92: 3809-3813.
8. Charlebois, R.L., Schalkwyk, L.C., Hofman, J.D., and Doolittle, W.F. (1991) Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2. J Mol Biol 222: 509-524.
9. Christie, P.J., Ward, Jr., J.E., Gordon, M.P., and Nester, E.W. (1989) A gene required for transfer of T-DNA to plants encodes an ATPase with autophosphorylating activity. Proc Natl Acad Sci USA 86: 9677-9681.
10. Cohen, A., Lam, W.L., Charlebois, R.L., Doolittle, W.F., and Schalkwyk, L.C. (1992) Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea. Proc Natl Acad Sci USA 89: 1602-1606.
11. Colombo, S., Toietta, G., Zecca, L., Vanoni, M., and Tortora, P. (1995) Molecular cloning, nucleotide sequence, and expression of a carboxypeptidase-encoding gene from the archaebacterium Sulfolobus solfataricus. J Bacteriol 177: 5561-5566.
12. Cowan, D.A. (1992) Enzymes from thermophilic archaebacteria: current and future applications in biotechnology. Biochem Soc Symp 58: 149-169.
13. Cubellis, M.V., Rozzo, C., Nitti, G., Arnone, M.I., Marino, G., and Sannia, G. (1989) Cloning and sequencing of the gene coding for aspartate aminotransferase from the thermoacidophilic archaebacterium Sulfolobus solfataricus. Eur J Biochem 186: 375-381.
14. Dams, E., Londei, P., Cammarano, P., Vandenberghe, A., and De Wachter, R. (1983) Sequences of the 5S RNAs of the thermo-acidophilic archaebacterium Sulfolobus solfataricus (Caldariella acidophila) and the thermophilic eubacteria Bacillus acidocaldarius and Thermus aquations. Nucl Acids Res 11: 4667-4676.
15. Trp gene of an archaebacterium, Halobacterium volcanii. J Biol Chem 260: 3132-3134.
16. Daniels, D.L., Plunkett, III, G., Burland, V., and Blattner, F. (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5-86.5 minutes. Science 257: 771-778.
17. Daube, G., Simon, P., and Kaeckenbeeck, A. (1993) IS1151, an IS-like element of Clostridium perfingens. Nucl Acids Res 21: 352.
18. De Smet, K.A.L., Jamil, S., and Stoker, N.G. (1993) TropistS: a cosmid vector for simplified mapping of both G+C-rich and A+T-rich genomic DNA. Gene 136: 215-219.
19. Donadio, S., and Staver, M.J. (1993) IS1136, an insertion element in the erythromycin gene cluster of Saccharopolyspora erythraea. Gene 126: 147-151.
20. Doolittle, W.F., and Brown, J.R. (1994) Tempo, mode, the progenote, and the universal root. Proc Natl Acad Sci USA 91: 6721-6728.
21. van der Drift, A.C.M., Sluiter, W., and Berends, F. (1987) Hydrodynamic characterization of the size and shape of atropinesterase from Pseudomonas putida. Biochim Biophys Acta 912: 167-177.
22. Dujon, B. et al. (1994) Complete DNA sequence of yeast chromosome Xl. Nature 369: 371-378.
23. Dums, F., Dow, J.M., and Daniels, M.J. (1991) Structural characterization of protein secretion genes of the bacterial phytopathogen Xanthomonas campestris pathovar campestris: relatedness to secretion systems of other Gram-negative bacteria. Mol Gen Genet 229: 357-364.
24. Durovic, P., Kutay, U., Schleper, C., and Dennis, P.P. (1994) Strain identification and 5S RNA gene characterization of the hyperthermophilic archaebacterium Sulfolobus acidocaldarius. J Bacteriol 176: 514-517.
25. Fath, M.J., and Kolter, R. (1993) ABC transporters: bacterial exporters. Microbiol Revs. 57: 995-1017.
26. Feldmann, H. et al. (1994) Complete DNA sequence of yeast chromosome II. EMBO J 13: 5795-5809.
27. Fichant, G.A., and Burks, C. (1991) Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol220: 659-671.
28. Fleischmann, R.D. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
29. Fraser, C.M et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
30. Gaasterland, T., and Sensen, C.W. (1996a) MAGPIE: automated genome interpretation. Trends Genet 12: 76-78.
31. Gaasterland, T., and Sensen, C.W. (1996b) MAGPIE: a multipurpose automated genome project investigation environment for ongoing sequencing projects. In Bacterial Genomes: Physical Structure and Analysis. De Bruijn, F.J., Lupski, J.R., and Weinstock, G. (eds). New York: Chapman and Hall, in press.
32. Glaser, P. et al. (1993) Bacillus subtilis genome project: cloning and sequencing of the 97kb region from 325° to 333°. Mol Microbiol 10: 371-384.
33. +-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 86: 6661-6665.
34. Grogan, D.W. (1989) Phenotypic characterization of the archaebacterial genus Sulfolobus: comparison of five wildtype strains. J Bacteriol 171: 6710-6719.
35. Guilfoile, P.G., and Hutchinson, C.R. (1991) A bacterial analog of the mcfrgene of mammalian tumor cells is present in Streptomyces peucetius, the producer of daunorubicin and doxorubicin. Proc Natl Acad Sci USA 88: 8553-8557.
36. Gutiérrez, M.C., Ventosa, A., and Ruiz-Berraquero, F. (1989) DNA-DNA homology studies among strains of Haloferax and other halobacteria. Curr Microbiol 18: 253-256.
37. Hain, J., Reiter, W.D., Hüdepohl, U., and Zillig, W. (1992) Elements of an archaeal promoter defined by mutational analysis. Nucl Acids Res 20: 5423-5428.
38. Hawkins, C.F., Borges, A., and Perham, R.N. (1989) A common structural motif in thiamin pyrophosphate-binding enzymes. FEBS Lett 255: 77-82.
39. von Heijne, G. (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225: 487-494.
40. Higgins, C.F. (1992) ABC transporters: from microorganisms to man. Annu Rev Cell Biol 8: 67-113.
41. Hrdy, I., and Müller, M. (1995) Primary structure and eubacterial relationships of the pyruvate: ferredoxin oxidoreductase of the amitochondriate eukaryote Trichomonas vaginalis. J Mol Evol 41: 388-396.
42. Huang, S., and Deutscher, M.P. (1992) Sequence and transcriptional analysis of the Escherichia coli rnt gene encoding RNase T. J Biol Chem 267: 25609-25613.
43. Hundle, B., Alberti, M., Nievelstein, V., Beyer, P., Kleinig, H., Armstrong, G.A., Burke, D.H., and Hearst, J.E. (1994) Functional assignment of Erwinia herbicola Eho10 carotenoid genes expressed in Escherichia coli. Mol Gen Genet 245: 406-416.
44. Iwabe, N., Kuma, K., Hasegawa, M., Osaw, S., and Miyata, T. (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86: 9355-9359.
45. Johnston, M. et al. (1994) Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII. Science 265: 2077-2082.
46. Kaine, B.P. (1987) Intron-containing tRNA genes of Sulfolobus solfataricus. J Mol Evol 25: 248-254.
47. Kaine, B.P. (1990) Structure of the archaebacterial 7S RNA molecule. Mol Gen Genet 221: 315-321.
48. Kaine, B.P., Gupta, R., and Woese, C.R. (1983) Putative introns in tRNA genes of prokaryotes. Proc Natl Acad Sci USA 80: 3309-3312.
49. Kaine, B.P., Schurke, C.M., and Stetter, K.O. (1989) Genes for the 16S and 5S ribosomal RNAs and the 7S RNA of Pyrodictium occultum. Syst Appl Microbiol 12: 8-14.
50. Kaneko, T., Tanaka, A., Sato, S., Kotani, H., Sazuka, T., Miyajima, N., Sugiura, M., and Tabata, S. (1995) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC680. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome. DNA Res 2: 153-166, 191-198.
51. Kates, M., Kushner, D.J., and Matheson, A.T. (eds). (1993) The Biochemistry of the Archaea (Archaebacteria). Amsterdam: Elsevier.
52. Kato, M., Kettoku, M., Miura, Y., Komeda, T., Konishi, Y., Shindo, K., Kobayashi, K., and Iwamatsu, A. (1995a) Sulfolobus solfataricus gene for alpha-amylase. DDBJ Accession Number D64130.
53. Kato, M., Kettoku, M., Miura, Y., Komeda, T., Konishi, Y., Shindo, K., Kobayashi, K., and Iwamatsu, A. (1995b) Sulfolobus acidocaldarius gene for alpha-amylase. DDBJ Accession Number D64131.
54. Keeling, P.J., and Doolittle, W.F. (1995) Archaea: narrowing the gap between prokaryotes and eukaryotes. Proc Natl Acad Sci USA 92: 5761-5764.
55. Kletzin, A. (1992) Molecular characterization of a DNA ligase gene of the extremely thermophilic archaeon Desulphurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucl Acids Res 20: 5389-5396.
56. Kletzin, A., and Adams, M.W.W. (1996) Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Tnermofoga maritima, J Bacteriol 178: 248-257.
57. Kuo, C.-F., McRee, D.E., Fisher, C.L., O'Handley, S.F., Cunningham, R.P., and Tainer, J.A. (1992) Atomic structure of the DNA repair [4Fe-4S]enzyme endonuclease III. Science 258: 434-440.
58. Kyte, J., and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
59. Lam, W.L., Cohen, A., Tsouluhas, D., and Doolittle, W.F. (1990) Genes for tryptophan biosynthesis in the archaebacterium Hatoferax volcanii. Proc Natl Acad Sci USA 87: 6614-6618.
60. Langer, D., Hain, J., Thuriaux, P., and Zillig, W. (1995) Transcription in Archaea: similarity to that in Eucarya. Proc Natl Acad Sci USA 92: 5768-5772.
61. Marino, G., Nitti, G., Arnone, M.I., Sannia, G., Gambacorta, A., and De Rosa, M. (1988) Purification and characterization of aspartate aminotransferase from the thermoacidophilic archaebacterium Sulfolobus solfataricus. J Biol Chem 263: 12305-12309.
62. Mazel, D., Bernard, C., Schwarz, R., Castets, A.M., Houmard, J., and de Marsac, T. (1991) Characterization of two insertion sequences, IS707 and IS702, from the cyanobacterium Calothrix species PCC 7601. Mol Microbiol 5: 2165-2170.
63. Mehta, P.K., Hale, T.I., and Christen, P. (1989) Evolutionary relationships among aminotransferases. Tyrosine aminotransferase, histidinol-phosphate aminotransferase, and aspartate aminotransferase and homologous proteins. Eur J Biochem 186: 249-253.
64. Menn, F.-M., Zylstra, G.J., and Gibson, D.T. (1991) Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2, 4-dienoate hydrolase in Pseudomonas putida F1. Gene 104: 91-94.
65. Misawa, N., Nakagawa, M., Kobayashi, K., Yamano, S., Izawa, Y., Nakamura, K., and Harashima, K. (1990) Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli. J Bacteriol 172: 6704-6712.
66. Nordlund, I., and Shingler, V. (1990) Nucleotide sequences of the mete-cleavage pathway enzymes 2-hydroxymuconic semialdehyde dehydrogenase and 2-hydroxymuconic semialdehyde hydrolase from Pseudomonas CF600. Biochim Biophys Acta 1049: 227-230.
67. Ohnuma, S.-i., Suzuki, M., and Nishino, T. (1994) Archaebacterial ether-linked lipid biosynthetic gene. Expression cloning, sequencing, and characterization of geranylgeranyldiphosphate synthase. J Biol Chem 269: 14792-14797.
68. Oliver, S.G. et al. (1992) Th∈ complete DNA sequence of yeast chromosome III. Nature 357: 38-46.
69. Pfeifer, F. (1988) Genetics of Halobacteria. In Halophilic Bacteria. Vol. 2. Rodriguez-Valera, F. (ed.). Boca Raton: CRC Press, pp. 105-133.
70. Pfeifer, O., Pelletier, I., Altenbucher, J., and van Pée, K.-H. (1992) Molecular cloning and sequencing of a non-haem bromoperoxidase gene from Streptomyces aureofaciens ATCC 10762. J Gen Microbiol 138: 1123-1131.
71. Pühler, G., Lottspeich, G., and Zillig, W. (1989) Organization and nucleotide sequence of the genes encoding the large subunits A, B and C of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus solfataricus. Nucl Acids Res 17: 4517-4534.
72. Reiter, W.-D., Palm, P., Voos, W., Kaniecki, J., Grampp, B., Schulz, W., and Zillig, W. (1987) Putative promoter elements for the ribosomal RNA genes of the thermoacidophilic archaebacterium Sulfolobus sp. strain B12. Nucl Acids Res 15: 5581-5595.
73. Reiter, W.-D., Palm, P., and Zillig, W. (1988) Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. Nucl Acids Res 16: 2445-2459.
74. Rezsöhazy, R., Hallet, B., and Delcour, J. (1992) IS231D, E and F, three new insertion sequences in Bacillus thuringiensis: extension of the IS231 family. Mol Microbiol 6: 1959-1967.
75. Riley, M. (1993) Functions of the gene products of Escherichia coli. Microbiol Rev 57: 862-952.
76. Salmond, G.P.C., and Reeves, P.J. (1993) Membrane traffic wardens and protein secretion in Gram-negative bacteria. Trends Biochem Sci 18: 7-12.
77. Schleper, C., Kubo, K., and Zillig, W. (1992) The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. Proc Natl Acad Sci USA 89: 7645-7649.
78. Schleper, C., Roder, R., Singer, T., and Zillig, W. (1994) An insertion element of the extremely thermophilic archaeon Sulfolobus solfataricus transposes into the endogenous beta-galactosidase gene. Mol Gen Genet 243: 91-96.
79. Schleper, C., Holz, I., Janekovic, D., Murphy, J., and Zillig, W. (1995) A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating. J Bacteriol 117: 4417-4426.
80. Selkov, E., Basmanova, S., Gaasterland, T., Goryanin, I., Gretchkin, Yu., Maltsev, N., Nenashev, V., Overbeek, R., Panyushkina, E., Pronevitch, L., Selkov, Jr, E., and Yunus, I. (1996) The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucl Acids Res 24: 26-28.
81. Sensen, C.W., Charlebois, R.L., Singh, R.K., Klenk, H.-P., Ragan, M.A., and Doolittle, W.F. (1996) Sequencing the genome of Sutfolobus solfatericus P2. In Bacterial Genomes: Physical Structure and Analysis. De Bruijn, F.J., Lupski, J.R., and Weinstock, G. (eds). New York: Chapman and Hall, in press.
82. Singh, R.K., Penny, S.L., Sensen, C.W., and Ragan, M.A. (1995) Direct cosmid sequencing (40-kB inserts) for ABI automated sequencers. NRC-IMB Int Rep 75: 1-5.
83. Sobek, H., and Görisch, H. (1989) Further kinetic and molecular characterization of an extremely heat-stable carboxylesterase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. Biochem J 261: 993-998.
84. Stahl, D., Luehrsen, K., Woese, C., and Pace, N. (1981) An unusual 5S RNA from Sulfolobus acidocaldarius and its implications for a general 5S RNA structure. Nucl Acids Res 9: 6129-6137.
85. Thompson, D.V., Melchers, L.S., Idler, K.B., Schilperoort, R.A., and Hooykaas, P.J.J. (1988) Analysis of the complete nucleotide sequence of the Agrobacterium tumefaciens virB operon. Nucl Acids Res 16: 4621-4636.
86. Vashakidze, R.P., and Prangishvili, D.A. (1987) Simple repetitive sequences in the genomes of archaebacteria. FEBS Lett 216: 217-220.
87. Whiteway, M., and Szostak, J.W. (1985) The ARD1 gene of yeast functions in the switch between the mitotic cell cycle and alternative developmental pathways. Cell 43: 483-492.
88. Wich, G., Leinfelder, W., and Bock, A. (1987) Genes for stable RNA in the extremely thermophilic Thermoproteus tenax: introns and transcription signals. EMBO J 6: 523-528.
89. Winefield, C.S., Farnden, K.J.F., Reynolds, P.H.S., and Marshall, C.J. (1995) Evolutionary analysis of aspartate aminotransferases. J Mol Evol 40: 455-463.
90. Yoshikawa, A., Isono, S., Sheback, A., and Isono, K. (1987) Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12. Mol Gen Genet 209: 481-488.