Genomic organization of evolutionarily correlated genes in bacteria: Limits and strategies

Journal of Molecular Biology

Volumn 419, Issue 5, 2012, Pages 369-386

  Junier, Ivan ^a,b   Hérisson, Joan ^a   Képès, François ^a  

^a CNRS   (France)

^b Institut des Systèmes Complexes Paris Île de France   (France)

Author keywords

gene expression at the cellular scale; genome functional organization; periodical organization of genes; spatial organization of chromosome; synteny properties

Indexed keywords

ARTICLE; BACTERIAL GENE; CHROMOSOME ANALYSIS; ESCHERICHIA COLI; ESSENTIAL GENE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; HOUSEKEEPING GENE; PERIODICITY; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE; ESCHERICHIA COLI;

EID: 84861527197     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.03.009     Document Type: Article

References (47)

1. Huynen M., and Bork P. Measuring genome evolution Proc. Natl Acad. Sci. USA 95 1998 5849 5856
2. Tamames J. Evolution of gene order conservation in prokaryotes Genome Biol. 2 2001 RESEARCH0020
3. Rocha E.P.C. The organization of the bacterial genome Annu. Rev. Genet. 42 2008 211 233
4. Képès F., and Vaillant C. Transcription-based solenoidal model of chromosomes ComPlexUs 1 2003 171 180
5. Képès F. Periodic transcriptional organization of the E. coli genome J. Mol. Biol. 340 2004 957 964
6. Mercier G., Berthault N., Touleimat N., Képès F., Fourel G., Gilson E., and Dutreix M. A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae Nucleic Acids Res. 33 2005 6635 6643
7. Wright M., Kharchenko P., Church G., and Segrè D. Chromosomal periodicity of evolutionarily conserved gene pairs Proc. Natl Acad. Sci. USA 104 2007 10559
8. Mathelier A., and Carbone A. Chromosomal periodicity and positional networks of genes in Escherichia coli Mol. Syst. Biol. 6 2010 366
9. Junier I., Martin O., and Képès F. Spatial and topological organization of DNA chains induced by gene co-localization PLoS Comput. Biol. 6 2010 e1000678
10. Schoenfelder S., Sexton T., Chakalova L., Cope N.F., Horton A., and Andrews S. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells Nat. Genet. 42 2010 53 61
11. Xu M., and Cook P.R. Similar active genes cluster in specialized transcription factories J. Cell Biol. 181 2008 615 623
12. Cook P. Predicting three-dimensional genome structure from transcriptional activity Nat. Genet. 32 2002 347 352
13. Osborne C.S., Chakalova L., Brown K.E., Carter D., Horton A., and Debrand E. Active genes dynamically colocalize to shared sites of ongoing transcription Nat. Genet. 36 2004 1065 1071
14. Müller J., Oehler S., and Müller-Hill B. Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator J. Mol. Biol. 257 1996 21 29
15. Dröge P., and Müller-Hill B. High local protein concentrations at promoters: strategies in prokaryotic and eukaryotic cells BioEssays 23 2001 179 183
16. Kuhlman T., Zhang Z., Saier M.H., and Hwa T. Combinatorial transcriptional control of the lactose operon of Escherichia coli Proc. Natl Acad. Sci. USA 104 2007 6043 6048
17. Vilar J.M.G., and Leibler S. DNA looping and physical constraints on transcription regulation J. Mol. Biol. 331 2003 981 989
18. Fraser P., and Bickmore W. Nuclear organization of the genome and the potential for gene regulation Nature 447 2007 413 417
19. Kuriyan J., and Eisenberg D. The origin of protein interactions and allostery in colocalization Nature 450 2007 983 990
20. Azam T.A., Hiraga S., and Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid Genes Cells 5 2000 613
21. Lewis P.J., Thaker S.D., and Errington J. Compartmentalization of transcription and translation in Bacillus subtilis EMBO J. 19 2000 710 718
22. Cabrera J., and Jin D. Active transcription of rRNA operons is a driving force for the distribution of RNA polymerase in bacteria: effect of extrachromosomal copies of rrnB on the in vivo localization of RNA polymerase J. Bacteriol. 188 2006 4007 4014
23. Berger M., Farcas A., Geertz M., Zhelyazkova P., Brix K., Travers A., and Muskhelishvili G. Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU EMBO Rep. 11 2009 59 64
24. Montero Llopis P., Jackson A.F., Sliusarenko O., Surovtsev I., Heinritz J., Emonet T., and Jacobs-Wagner C. Spatial organization of the flow of genetic information in bacteria Nature 466 2010 77 81
25. Taniguchi Y., Choi P.J., Li G.W., Chen H., Babu M., and Hearn J. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 329 2010 533 538
26. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., and Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles Proc. Natl Acad. Sci. USA 96 1999 4285 4288
27. Junier I., Hérisson J., and Képès F. Periodic pattern detection in sparse boolean sequences Algorithms Mol. Biol. 5 2010 31
28. Koonin E.V. Orthologs, paralogs, and evolutionary genomics Annu. Rev. Genet. 39 2005 309 338
29. Espeli O., and Boccard F. Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications J. Struct. Biol. 156 2006 304 310
30. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., and Cherry J.M. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 25 2000 25 29
31. Boyle E.I., Weng S., Gollub J., Jin H., Botstein D., Cherry J.M., and Sherlock G. GO:TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Bioinformatics 20 2004 3710 3715
32. Gil R., Silva F.J., Peretó J., and Moya A. Determination of the core of a minimal bacterial gene set Microbiol. Mol. Biol. Rev. 68 2004 518 537
33. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., and Baba M. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 2 2006 2006.0008
34. Fang G., Rocha E.P.C., and Danchin A. Persistence drives gene clustering in bacterial genomes BMC Genomics 9 2008 4
35. Allen T.E., Herrgard M.J., Liu M., Qiu Y., Glasner J.D., Blattner F.R., and Palsson B.∅. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets J. Bacteriol. 185 2003 6392 6399
36. Glasner J.D., Liss P., Plunkett G., Darling A., Prasad T., and Rusch M. ASAP, a systematic annotation package for community analysis of genomes Nucleic Acids Res. 31 2003 147 151
37. Alm E.J., Huang K.H., Price M.N., Koche R.P., Keller K., Dubchak I.L., and Arkin A.P. The MicrobesOnline web site for comparative genomics Genome Res. 15 2005 1015 1022
38. Jeong K.S., Ahn J., and Khodursky A.B. Spatial patterns of transcriptional activity in the chromosome of Escherichia coli Genome Biol. 5 2004 R86
39. Postow L., Hardy C.D., Arsuaga J., and Cozzarelli N.R. Topological domain structure of the Escherichia coli chromosome Genes Dev. 18 2004 1766 1779
40. Deng S., Stein R.A., and Higgins N.P. Organization of supercoil domains and their reorganization by transcription Mol. Microbiol. 57 2005 1511 1521
41. Kolesov G., Wunderlich Z., Laikova O.N., Gelfand M.S., and Mirny L.A. How gene order is influenced by the biophysics of transcription regulation Proc. Natl Acad. Sci. USA 104 2007 13948
42. Wang X., Liu X., Possoz C., and Sherratt D.J. The two Escherichia coli chromosome arms locate to separate cell halves Genes Dev. 20 2006 1727 1731
43. Wiggins P.A., Cheveralls K.C., Martin J.S., Lintner R., and Kondev J. Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament Proc. Natl Acad. Sci. USA 107 2010 4991 4995
44. Cabrera J.E., and Jin D.J. The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues Mol. Microbiol. 50 2003 1493 1505
45. Saberi S., and Emberly E. Chromosome driven spatial patterning of proteins in bacteria PLoS Comput. Biol. 6 2010 e1000986
46. Shaffer J. Multiple hypothesis testing Annu. Rev. Psychol. 46 1995 561 584
47. Tatusov R., Natale D., Garkavtsev I., Tatusova T., Shankavaram U., and Rao B.S. The COG database: new developments in phylogenetic classification of proteins from complete genomes Nucleic Acids Res. 29 2001 22