Mapping the bacterial cell architecture into the chromosome

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 355, Issue 1394, 2000, Pages 179-190

  Danchin, Antoine ^a   Guerdoux Jamet, Pascale ^b   Moszer, Ivan ^a   Nitschké, Patrick ^c  

^a INSTITUT PASTEUR   (France)

^b PONTCHAILLOU UNIVERSITY HOSPITAL   (France)

^c LABORATOIRE DES SCIENCES DU CLIMAT ET DE L ENVIRONNEMENT   (France)

Author keywords

Codon usage; Genome style; Mesoscopic scale; Neighbourhood; Pathogenicity islands; Translation

Indexed keywords

BACTERIAL GENOME; CELL WALL; CYTOPLASM; GENE LOCATION; GENE STRUCTURE; GENETIC CORRELATION; GENETIC TRANSCRIPTION; MESSENGER RNA; RIBOSOME; SEQUENCE ALIGNMENT; TRANSCRIPTION TERMINATION;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0034728487     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2000.0557     Document Type: Article

References (69)

1. Akiyama, Y. & Ito, K. 1995 A new Escherichia coli gene, fdrA, identified by suppression analysis of dominant negative FtsH mutations. Mol. Gen. Genet. 249, 202-208.
2. Burns, C. M., Richardson, L. V. & Richardson, J. P. 1998 Combinatorial effects of NusA and NusG on transcription elongation and Rho-dependent termination in Escherichia coli. J. Mol. Biol. 278, 307-316.
3. Charlier, D., Hassanzadeh, G., Kholti, A., Gigot, D., Pierard, A. & Glansdorff, N. 1995 carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColEI multimers. J. Mol. Biol. 250, 392-406.
4. Chun, J. T., Gioio, A. E., Crispino, M., Giuditta, A. & Kaplan, B. B. 1996 Differential compartmentalization of mRNAs in squid giant axon. J. Neurochem. 67, 1806-1812.
5. Court, D. L., Patterson, T. A., Baker, T., Costantino, N., Mao, X. & Friedman, D. I. 1995 Structural and functional analyses of the transcription-translation proteins NusB and NusE. J. Bacteriol. 177, 2589-2591.
6. Danchin, A. 1987 Order and necessity. In From enzyme adaptation to natural philosophy: heritage from J. Monod (ed. E. Quagliariello, G. Bernardi & A. Ullmann), pp. 187-196. Amsterdam: Elsevier.
7. Danchin, A. 1997 Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP. DNA Res. 4, 9-18.
8. Danchin, A. 1998 La barque de Delphes. Ce que révéle le texte des génomes. Paris: Odile Jacob.
9. Delrow, J., Gebe, J. & Schurr, J. 1997 Comparison of hard-cylinder and screened Coulomb interactions in the modeling of supercoiled DNAs. Biopolymers 42, 455-470.
10. el-Hajj, H. H., Zhang, H. & Weiss, B. 1988 Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli. J. Bacteriol. 170, 1069-1075.
11. Friedman, D. I., Olson, E. R., Johnson, L. L., Alessi, D. & Craven, M. G. 1990 Transcription-dependent competition for a host factor: the function and optimal sequence of the phage lambda boxA transcription antitermination signal. Genes Dev. 4, 2210-2222.
12. Genty, N., Paly, J., Edery, M., Kelly, P. A., Djiane, J. & Salesse, R. 1994 Endocytosis and degradation of prolactin and its receptor in Chinese hamster ovary cells stably transfected with prolactin receptor cDNA. Mol. Cell. Endocrinol. 99, 221-228.
13. Ginard, M., Lalucat, J., Tummler, B. & Romling, U. 1997 Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations. Int. J. Syst. Bacteriol. 47, 132-143.
14. Glaser, P., Sharpe, M. E., Raether, B., Perego, M., Ohlsen, K. & Errington, J. 1997 Dynamic, mitotic-like behavior of a bacterial protein required for accurate chromosome partitioning. Genes Dev. 11, 1160-1168.
15. Gottesman, S., Roche, E., Zhou, Y. & Sauer, R. T. 1998 The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12, 1338-1347.
16. Guerdoux-Jamet, P. 1997 Mise en oeuvre de logiciels de comparaison de séquences biologiques sur des machines spécialisées symboliques. Applications á l'analyse des génomes. PhD thesis, UFR de Biologie, University of Paris.
17. Hénaut, A., Rouxel, T., Gleizes, A., Moszer, I. & Danchin, A. 1996 Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages. J. Mol. Biol. 257, 574-585.
18. Hénaut, A., Lisacek, F., Nitschké, P., Moszer, I. & Danchin, A. 1998 Global analysis of genomic texts: the distribution of AGCT tetranucleotides in the Escherichia coli and Bacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes. Electrophoresis 19, 515-527.
19. Henkin, T. M. 1994 tRNA-directed transcription antitermination. Mol. Microbiol. 13, 381-387.
20. Henkin, T. M. 1996 Control of transcription termination in prokaryotes. A. Rev. Genet. 30, 35-57.
21. Herman, C., Thevenet, D., Bouloc, P., Walker, G. C. & D'Ari, R. 1998 Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HAB (FtsH). Genes Dev. 12, 1348-1355.
22. Himeno, H., Nameki, N., Tadaki, T., Sato, M., Hanawa, K., Fukushima, M., Ishii, M., Ushida, C. & Muto, A. 1997a Escherichia coli tmRNA (10Sa RNA) in trans-translation. Nucl. Acids Symp. Ser. 37, 185-186.
23. Himeno, H., Sato, M., Tadaki, T., Fukushima, M., Ushida, C. & Muto, A. 1997b In vitro trans translation mediated by alanine-charged 10Sa RNA. J. Mol. Biol. 268, 803-808.
24. Huenges, M., Rolz, C., Gschwind, R., Peteranderl, R., Berglechner, F., Richter, G., Bacher, A., Kessler, H. & Gemmecker, G. 1998 Solution structure of the antitermination protein NusB of Escherichia coli: a novel all-helical fold for an RNA-binding protein. EMBO J. 17, 4092-4100.
25. Kaberdin, V. R., Miczak, A., Jakobsen, J. S., Lin-Chao, S., McDowall, K. J. & Von Gabain, A. 1998 The endoribonucleolytic N-terminal half of Escherichia coli RNasc E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Proc. Natl Acad. Sci. USA 95, 11 637-11 642.
26. Karlin, S., Mrazek, J. & Campbell, A. M. 1997 Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179, 3899-3913.
27. Kebbekus, P., Draper, D. & Hagerman, P. 1995 Persistence length of RNA. Biochemistry 34, 4354-4357.
28. Keiler, K. C., Waller, P. R. & Sauer, R. T. 1996 Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990-993.
29. Komissarova, N. & Kashlev, M. 1997 Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl Acad. Sci. USA 94, 1755-1760.
30. Krohn, M. & Wagner, R. 1996 Transcriptional pausing of RNA polymerase in the presence of guanosine tetraphosphate depends on the promoter and gene sequence. J. Biol. Chem. 271, 23 884-23 894.
31. Kryzek, R. A. & Rogers, P. 1976 Dual regulation by arginine of the expression of the Escherichia coli argECBH operon. J. Bacteriol. 126, 348-364.
32. Kunst, F. (and 150 others) 1997 The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390, 249-256.
33. Landais, S., Gounon, P., Laurent-Winter, C., Mazić, J. C., Danchin, A., Barzu, O. & Sakamoto, H. 1999 Immunochemical analysis of UMP kinase from Escherichia coli. J. Bacteriol. 181, 833-840.
34. Lazdins, I. B., Delannoy, M. & Sollner-Webb, B. 1997 Analysis of nucleolar transcription and processing domains and pre-rRNA movements by in situ hybridization. Chromosoma 105, 481-495.
35. Lebart, L., Morineau, A. & Warwick, K. A. 1984 Multivariate descriptive statistical analysis. New York: Wiley.
36. Lemon, K. & Grossman, A. 1998 Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science 282, 1516-1519.
37. Lewis, P. J. & Errington, J. 1996 Use of green fluorescent protein for detection of cell-specific gene expression and subcellular protein localization during sporulation in Bacillus subtilis. Microbiology 142, 733-740.
38. Mackie, G. A. 1998 Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395, 720-722.
39. Médigue, C., Rouxel, T., Vigier, P., Hénaut, A. & Danchin, A. 1991 Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222, 851-856.
40. Moszer, I. 1996 Représentation et analyse des génomes: application au projet de séquençage du génome de Bacillus subtilis. PhD thesis, UFR de Biologie, University of Paris.
41. Moszer, I., Glaser, P. & Danchin, A. 1996 SubtiList: a relational database for the Bacillus subtilis genome. Microbiology 141, 261-268.
42. Muto, A., Sato, M., Tadaki, T., Fukushima, M., Ushida, C. & Himeno, H. 1996 Structure and function of 10Sa RNA: trans-translation system. Biochimie 78, 985-991.
43. Muto, A., Ushida, C. & Himeno, H. 1998 A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem. Sci. 23, 25-29.
44. Myhill, J. 1952 Some philosophical implications of mathematical logic. I. Three classes of ideas. Rev. Metaphys. 6, 165-198.
45. Nilsen, H., Yazdankhah, S. P., Eftedal, I. & Krokan, H. E. 1995 Sequence specificity for removal of uracil from U.A pairs and U.G mismatches by uracil-DNA glycosylase from Escherichia coli, and correlation with mutational hotspots. FEBS Lett. 362, 205-209.
46. Nitschké, P., Guerdoux-Jamet, P., Chiapello, H., Faroux, G., Hénaut, C., Hénaut, A. & Danchin, A. 1998 Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol. Rev. 22, 207-227.
47. Nudler, E., Mustaev, A., Lukhtanov, E. & Goldfarb, A. 1997 The RNA DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89, 33-41.
48. Nudler, E., Gusarov, I., Avetissova, E., Kozlov, M. & Goldfarb, A. 1998 Spatial organization of transcription elongation complex in Escherichia coli. Science 281, 424-428.
49. Ollivier, E., Delorme, M. O. & Hénaut, A. 1995 DosDNA occurs along yeast chromosomes, regardless of functional significance of the sequence. C. R. Acad. Sci. III 318, 599-608.
50. Rivals, E., Delgrange, O., Delahaye, J. P., Dauchet, M., Delorme, M. O., Hénaut, A. & Ollivier, E. 1997 Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences. Comput. Appl. Biosci. 13, 131-136.
51. Rivetti, C., Walker, C. & Bustamante, C. 1998 Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J. Mol. Biol. 280, 41-59.
52. Rocha, E. P. C., Danchin, A. & Viari, A. 1999a Universal replication biases in bacteria. Mol. Microbiol. 32, 11-16.
53. Rocha, E. P. C., Viari, A. & Danchin, A. 1999b Long repeats reveal alternative evolutionary mechanisms in competent prokaryotes. J. Mol. Evol. (In the press.)
54. Sagot, M.-F. 1994 Formalisation et approches combinatoires du problème de ressemblance lexicale et structurale entre macromolécules biologiques. Marne-la Vallée, France: Université Gaspar Monge.
55. Sagot, M. F. & Myers, E. W. 1998 Identifying satellites and periodic repetitions in biological sequences. J. Comput. Biol. 5, 539-553.
56. Schlick, T., Li, B. & Olson, W. 1994 The influence of salt on the structure and energetics of supercoiled DNA. Biophys. J. 67, 2146-2166.
57. Turner, L. R., Olson, J. W. & Lory, S. 1997 The XcpR protein of Pseudomonas aeruginosa dimerizes via its N-terminus. Mol. Microbiol. 26, 877-887.
58. Ueguchi, C., Seto, C., Suzuki, T. & Mizuno, T. 1997 Clarification of the dimerization domain and its functional significance for the Escherichia coli nucleoid protein H-NS. J. Mol. Biol. 274, 145-151.
59. Uptain, S. M. & Chamberlin, M. J. 1997 Escherichia coli RNA polymerase terminates transcription efficiently at rho-independent terminators on single-stranded DNA templates. Proc. Natl Acad. Sci. USA 94, 13 548-13 553.
60. Uptain, S. M., Kane, C. M. & Chamberlin, M. J. 1997 Basic mechanisms of transcript elongation and its regulation. A. Rev. Biochem. 66, 117-172.
61. Van Gilst, M. R. & Von Hippel, P. H. 1997 Assembly of the N-dependent antitermination complex of phage lambda: NusA and RNA bind independently to different unfolded domains of the N protein. J. Mol. Biol. 274, 160-173.
62. Vogel, U. & Jensen, K. F. 1994 Effects of guanosine 3′,5′-bisdiphosphate (ppGpp) on rate of transcription elongation in isoleucine-starved Escherichia coli. J. Biol. Chem. 269, 16 236-16 241.
63. Vogel, U. & Jensen, K. F. 1997 NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA. J. Biol. Chem. 272, 12 265-12 271.
64. Watanabe, T., Sugita, M. & Sugiura, M. 1998 Identification of 10Sa RNA (tmRNA) homologues from the cyanobacterium Synechococcus sp. strain PCC6301 and related organisms. Biochim. Biophys. Acta 1396, 97-104.
65. Weiss, B. & el-Hajj, H. H. 1986 The repair of uracil-containing DNA. Basic Life Sci. 38, 349-356.
66. Whalen, W. A. & Das, A. 1990 Action of an RNA site at a distance: role of the nut genetic signal in transcription antitermination by phage-lambda N gene product. New Biol. 2, 975-991.
67. Williams, R. M., Rimsky, S. & Buc, H. 1996 Probing the structure, function, and interactions of the Escherichia coli H-NS and StpA proteins by using dominant negative derivatives. J. Bacteriol. 178, 4335-4343.
68. Wu, L. J., Feucht, A. & Errington, J. 1998 Prespore-specific gene expression in Bacillus subtilis is driven by sequestration of SpoIIE phosphatase to the prespore side of the asymmetric septum. Genes Dev. 12, 1371-1380.
69. Zacharias, M. & Hagerman, P. 1996 The influence of symmetric internal loops on the flexibility of RNA. J. Mol. Biol. 257, 276-289.