Periodic transcriptional organization of the E. coli genome

Journal of Molecular Biology

Volumn 340, Issue 5, 2004, Pages 957-964

  Képès, François ^a,b  

^a University of Paris 5   (France)

^b Parc Scientifique de Luminy   (France)

Author keywords

DNA functional organization; DNA binding proteins; E. coli; replication; transcription

Indexed keywords

BACTERIAL DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CHROMOSOME SIZE; CHROMOSOME STRUCTURE; CISTRON; DNA BINDING; ESCHERICHIA COLI; GENE CLUSTER; GENETIC CODE; GENETIC TRANSCRIPTION; IMMUNOFLUORESCENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION;

ESCHERICHIA COLI; PROKARYOTA;

EID: 3242812952     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.05.039     Document Type: Article

References (36)

1. Müller-Hill B. The function of auxiliary operators. Mol. Microbiol. 29:1998;13-18
2. Dröge P., Müller-Hill B. High local protein concentrations at promoters: strategies in prokaryotic and eukaryotic cells. Bioessays. 23:2001;179-183
3. Miller O.L. Jr, Hamkalo B.A., Thomas C.A. Jr. Visualisation of bacterial genes in action. Science. 169:1970;392-395
4. Thieffry D., Huerta A.M., Pérez-Rueda A., Collado-Vides J. From specific gene regulation to genomic networks: a global analysis to transcriptional regulation in Escherichia coli. Bioessays. 20:1998;433-440
5. Salgado H., Santos-Zavaleta A., Gama-Castro S., Millan-Zarate D., Diaz-Peredo E., Sanchez-Solano F., et al. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucl. Acids Res. 29:2001;72-74
6. Shen-Orr S.S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31:2002;64-68
7. Talukder A.A., Hiraga S., Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells. 5:2000;613-626
8. Lewis P.J., Thaker S.D., Errington J. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J. 19:2000;710-718
9. Pettijohn D.E. Neidhardt F.C. The Nucleoid. 2nd edit. The Nucleoid. vol. 1:1996;158-166 American Society of Microbiology, Washington, DC
10. Woldringh C.L. The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation. Mol. Microbiol. 45:2002;17-29
11. Sinden R.R., Pettijohn D.E. Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling. Proc. Natl Acad. Sci. USA. 78:1981;224-228
12. Staczek P., Higgins N.P. Gyrase and Topo IV modulate chromosome domain size in vivo. Mol. Microbiol. 29:1998;1435-1448
13. Rosenfeld N., Elowitz M.B., Alon U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323:2002;785-793
14. Guelzim N., Bottani S., Bourgine P., Képès F. Topological and causal structure of the yeast transcriptional regulatory network. Nature Genet. 31:2002;60-63
15. Képès F. Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites. J. Mol. Biol. 329:2003;859-865
16. Francois V., Louarn J., Patte J., Rebollo J.E., Louarn J.-M. Constraints in chromosomal inversions in Escherichia coli are not explained by replication pausing at inverted terminator-like sequences. Mol. Microbiol. 4:1990;537-542
17. Niki H., Yamaichi Y., Hiraga S. Dynamic organization of chromosomal DNA in Escherichia coli. Genes Dev. 14:2000;212-223
18. Guijo M.I., Patte J., del Mar Campos M., Louarn J.-M., Rebollo J.E. Localized remodeling of the Escherichia coli chromosome: the patchwork of segments refractory and tolerant to inversion near the replication terminus. Genetics. 157:2001;1413-1423
19. Martin R.G., Rosner J.L. Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data. Mol. Microbiol. 44:2002;1611-1624
20. Worcel A., Burgi E. On the structure of the folded chromosome of Escherichia coli. J. Mol. Biol. 71:1972;127-147
21. Meyer M., De Jong M.A., Woldringh C.L., Nanninga N. Factors affecting the release of folded chromosomes from Escherichia coli. Eur. J. Biochem. 63:1976;469-475
22. Snyder M., Drlica K. DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid. J. Mol. Biol. 131:1979;287-302
23. Sinden R.R., Carlson J.O., Pettijohn D.E. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell. 21:1980;773-783
24. Murphy L.D., Zimmerman S.B. Multiple restraints to the unfolding of spermidine nucleoids from Escherichia coli. J. Struct. Biol. 132:2000;46-62
25. Brunetti R., Prosseda G., Beghetto E., Colonna B., Micheli B. The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains. Biochimie. 83:2001;873-882
26. Audit B., Ouzounis C.A. From genes to genomes: universal scale-invariant properties of microbial chromosome organisation. J. Mol. Biol. 332:2003;617-633
27. Rouvière-Yaniv J., Yaniv M., Germond J.E. E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA. Cell. 17:1979;265-274
28. Murphy L.D., Zimmerman S.B. Stabilization of compact spermidine nucleoids from Escherichia coli under crowded conditions: implications for in vivo nucleoid structure. J. Struct. Biol. 119:1997;336-346
29. Murtin C., Engelhorn M., Geiselmann J., Boccard F. A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell. J. Mol. Biol. 284:1998;949-961
30. Schneider R., Lurz R., Lüder G., Tolksdorf C., Travers A., Muskhelishvili G. An architectural role of the Escherichia coli chromatin protein FIS in organising DNA. Nucl. Acids Res. 29:2001;5107-5114
31. Dame R.T., Goosen N. HU: promoting or counteracting DNA compaction? FEBS Letters. 529:2002;151-156
32. Peterson J.D., Umayam L.A., Dickinson T.M., Hickey E.K., White O. The comprehensive microbial resource. Nucl. Acids Res. 29:2001;123-125
33. Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Burland V., Riley M., et al. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1474
34. Itoh T., Okayama T., Hashimoto H., Takeda J., Davis R.W., Mori H., Gojobori T. A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains. FEBS Letters. 450:1999;72-76
35. Welch R.A., Burland V., Plunkett G., Redford P., Roesch P., Rasko D., et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl Acad. Sci. USA. 99:2002;17020-17024
36. Perna N.T., Plunkett G., Burland V., Mau B., Glasner J.D., Rose D.J., et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 409:2001;529-533