Russian version English version
Volume 9   Issue 2   Year 2014
Glazunova O.A., Kiselev S.S., Shavkunov K.S., Bykov A.A., Panyukov V.V., Ozoline O.N.

Promoter Islands in the Genome of E. coli: Comparative Analysis against AT-Rich Sequences

Mathematical Biology & Bioinformatics. 2014;9(2):563-574.

doi: 10.17537/2014.9.563.

References

  1. Shavkunov KS, Masulis IS, Tutukina MN, Deev AA, Ozoline ON. Gains and unexpected lessons from genome-scale promoter mapping. Nucl. Acids Res. 2009;37:4919-4931. doi: 10.1093/nar/gkp490
  2. Panyukov VV, Ozoline ON. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS ONE. 2013;8:e62601. doi: 10.1371/journal.pone.0062601
  3. Panyukov VV, Kiselev SS, Shavkunov KS, Masulis IS, Ozoline ON. Mixed promoter islands as genomic regions with specific structural and functional properties. Mathematical Biology and Bioinformatics. 2013;8:t12-t26. doi:  10.17537/2013.8.t12
  4. Shavkunov KS, Tutukina MN, Masulis IS, Ozoline ON. Promoter islands: the novel elements in bacterial genomes. J. Biomol. Struct. Dyn. 2011;28:1128-1129.
  5. Syvanen M. Evolutionary implications of horizontal gene transfer. Annu. Rev. Genet. 2012;46:341-358. doi: 10.1146/annurev-genet-110711-155529
  6. Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, Hinton JC. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog. 2006;2:e81. doi: 10.1371/journal.ppat.0020081
  7. Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, Libby SJ, Fang FC. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science. 2006;313:236-238. doi: 10.1126/science.1128794
  8. Dorman CJ. Horizontally acquired homologues of the nucleoid-associated protein H-NS: implications for gene regulation. Mol. Microbiol. 2010;75:264-267. doi: 10.1111/j.1365-2958.2009.06996.x
  9. Dorman CJ. Genome architecture and global gene regulation in bacteria: making progress towards a unified model? Nat. Rev. Microbiol. 2013;11:349-355. doi: 10.1038/nrmicro3007
  10. Dorman CJ. H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria. Plasmid. 2014;75:1-11. doi: 10.1016/j.plasmid.2014.06.004
  11. Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucl. Acids Res. 2013;41:D203-D213. doi: 10.1093/nar/gks1201
  12. Panyukov VV, Nazipova NN, Ozoline ON. Software Package aSHAPE as a Tool to Study the Spatial Conformation of the Bacterial Genome Sites. Mathematical Biology and Bioinformatics. 2011;6(2):t36-t52. doi: 10.17537/2011.6.t36
  13. Okonechnikov K, Golosova O, Fursov M., the UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28:1166-1167. doi: 10.1093/bioinformatics/bts091
  14. Reppas NB, Wade JT, Church GM, Struhl K. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol. Cell. 2006;24:747-757. doi: 10.1016/j.molcel.2006.10.030
  15. Kahramanoglou C, Seshasayee ASN, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, Luscombe NM. Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucl. Acids Res. 2011;39:2073-2091. doi: 10.1093/nar/gkq934
  16. Dornenburg JE, DeVita AM, Palumbo MJ, Wade JT. Widespread antisense transcription in Escherichia coli. mBio. 2010;1:e00024-10.
  17. Lawrence JG, Ochman H. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA. 1998;95:9413-9417. doi: 10.1073/pnas.95.16.9413
  18. Nakamura Y, Itoh T, Matsuda H, Gojobori T. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 2004;36:760-766. doi: 10.1038/ng1381
  19. Price MN, Dehal PS, Arkin AP. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 2008;9:R4. doi: 10.1186/gb-2008-9-1-r4
  20. Huang Q, Cheng X, Cheung MK, Kiselev SS, Ozoline ON, Kwan HS. High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS ONE. 2012;7:e33759. doi: 10.1371/journal.pone.0033759
  21. Langille MG, Brinkman FS. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics. 2009;25:664-665. doi: 10.1093/bioinformatics/btp030
  22. Ozoline ON, Deev AA. Predicting antisense RNAs in the genomes of Escherichia coli and Salmonella typhimurium using promoter-search algorithm PlatProm. J. Bioinf. Comput. Biol. 2006;4:443-454. doi: 10.1142/S0219720006001916
  23. Kiselev SS, Ozoline ON. Structure-specific modules as indicators of promoter DNA in bacterial genomes. Mathematical Biology and Bioinformatics. 2011;6:t1-t13. doi: 10.17537/2011.6.t1
  24. Oshima T, Ishikawa S, Kurokawa K, Aiba H, Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res. 2006;13:141-153. doi: 10.1093/dnares/dsl009
  25. Dorman CJ. H-NS, the genome sentinel. Nat. Rev. Microbiol. 2007;5:157-161. doi: 10.1038/nrmicro1598
Table of Contents Original Article
Math. Biol. Bioinf.
2014;9(2):563-574
doi: 10.17537/2014.9.563
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References Translation into English
Math. Biol. Bioinf.
2015;10(Suppl.):t29-t38
doi: 10.17537/2015.10.t29

Full text (eng., pdf)

 

  Copyright IMPB RAS © 2005-2022