Sukharicheva N.A., Kiselev S.S., Ozoline O.N., Masulis I.S.
Transcriptional Landscape Variability within the Bacterial oppA-oppB Intergenic Region as Revealed by Computational Search for the Potential Starts of RNA Synthesis
Mathematical Biology & Bioinformatics. 2015;10(2):294-308.
doi: 10.17537/2015.10.294.
References
- Ames G.F.-L., Mimura C., Shyamala V. Bacterial periplasmic permeases belong to a family of transport proteins operating from Escherichia coli to human traffic ATPases. FEMS Microbiol. Rev. 1990;75:429–446. doi: 10.1111/j.1574-6968.1990.tb04110
- Davidson A.L., Dassa E., Orelle C., Chen J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 2008;72:317–364. doi: 10.1128/MMBR.00031-07
- Gilson E., Higgins C.F., Hofnung M., Ames G.F.-L., Nikaido H. Extensive homology between membrane-associated components of histidine and maltose transport systems of Salmonella typhimurium and Escherichia coli. J. Biol. Chem. 1982;257:9915–9918. http://www.jbc.org/content/257/17/9915.full.pdf (accessed 07 June 2015).
- Navarro C., Wu L.F., Mandrand-Berthelot M.A. The nik operon of Escherichia coli encodes a periplasmic binding protein-dependent transport system for nickel. Mol. Microbiol. 1993;9:1181–1191. doi: 10.1111/j.1365-2958.1993.tb01247.x
- Koster W. ABC transporter-mediated uptake of iron, siderophores, heme and vitamin B-12. Res. Microbiol. 2001;152:291–301. doi: 10.1016/S0923-2508(01)01200-1
- Henderson D.P., Payne S.M. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 1994;62:5120–5125. http://iai.asm.org/content/62/11/5120.full.pdf (accessed 07 June 2015).
- Rodriguez G.M., Smith I. Identification of an ABC transporter required for iron acquisition and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2006;188:424–430. doi: 10.1128/JB.188.2.424-430.2006
- Saier M.H., Reddy V.S., Tamang D.G., Vastermark A. The transporter classification database. Nucl. Acids Res. 2014;42:D251–D258. doi: 10.1093/nar/gkt1097
- Transporter Classification Database. http://www.tcdb.org (accessed 07 June 2015).
- Hiles I.D., Gallagher M.P., Jamieson D.J., Higgins C.F. Molecular characterization of the oligopeptide permease of Salmonella typhimurium. J. Mol. Biol. 1987;195:125–142. doi: 10.1016/0022-2836(87)90332-9
- Hogarth B.G., Higgins C.F. Genetic organization of the oligopeptide permease (opp) locus of Salmonella typhimurium and Escherichia coli. J. Bacteriol. 1983;153:1548–1551. http://jb.asm.org/content/153/3/1548.full.pdf (accessed 07 June 2015).
- Lee E.M., Ahn S.H., Park J.H., Lee J.H., Ahn S.C., Kong I.S. Identification of oligopeptide permease (opp) gene cluster in Vibrio fluvialis and characterization of biofilm production by oppA knockout mutation. FEMS Microbiol Lett. 2004;240:21–30. doi: 10.1016/j.femsle.2004.09.007
- Kashiwagi K., Tsuhako M.H., Sakata K., Saisho T., Igarashi A., da Costa S.O., Igarashi K. Relationship between spontaneous aminoglycoside resistance in Escherichia coli and a decrease in oligopeptide binding protein. J. Bacteriol. 1998;180:5484–5488. http://jb.asm.org/content/180/20/5484.full.pdf (accessed 07 June 2015).
- Yu D., Pi B., Yu M., Wang Y., Ruan Z., Feng Y., Yu Y. Diversity and evolution of oligopeptide permease systems in staphylococcal species. Genomics. 2014;104:8–13. doi: 10.1016/j.ygeno.2014.04.003
- Berntsson R.P., Smits S.H., Schmitt L., Slotboom D.J., Poolman B. A structural classification of substrate-binding proteins. FEBS Lett. 2010;584:2606–2617. doi: 10.1016/j.febslet.2010.04.043
- Medrano M.S., Ding Y., Wang X.G., Lu P., Coburn J., Hu L.T. Regulators of expression of the oligopeptide permease A proteins of Borrelia burgdorferi. J. Bacteriol. 2007;189:2653–2659. doi: 10.1128/JB.01760-06
- Pletzer D., Lafon C., Braun Y., Kohler T., Page M.G., Mourez M., Weingart H. High-throughput screening of dipeptide utilization mediated by the ABC transporter DppBCDF and its substrate-binding proteins DppA1-A5 in Pseudomonas aeruginosa. PLoS ONE. 2014;9:e111311. doi: 10.1371/journal.pone.0111311
- RegulonDB. http://regulondb.ccg.unam.mx (accessed 07 June 2015).
- Salgado H., Peralta-Gil M., Gama-Castro S., Santos-Zavaleta A., Muniz-Rascado L., Garcia-Sotelo J.S., Weiss V., Solano-Lira H., Martinez-Flores I., Medina-Rivera A., Salgado-Osorio G., Alquicira-Hernandez S., Alquicira-Hernandez K., Lopez-Fuentes A., Porron-Sotelo L., Huerta A.M., Bonavides-Martinez C., Balderas-Martinez Y.I., Pannier L., Olvera M., Labastida A., Jimenez-Jacinto V., Vega-Alvarado L., Del Moral-Chavez V., Hernandez-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
- Shavkunov K.S., Masulis I.S., Tutukina M.N., Deev A.A., Ozoline O.N. Gains and unexpected lessons from genome-scale promoter mapping. Nucl. Acids Res. 2009;37:4919–4931. doi: 10.1093/nar/gkp490
- Panyukov V.V., Kiselev S.S., Shavkunov K.S., Masulis I.S., Ozoline O.N. Mixed promoter islands as genomic regions with specific structural and functional properties. Mathematical Biology and Bioinformatics. 2013;8(2):t12-t26. doi: 10.17537/2013.8.432.
- GenBank Catalog of Bacterial Genomes. ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ (accessed 07 June 2015).
- Kiselev S.S., Ozoline O.N. Structure-specific modules as indicators of promoter DNA in bacterial genomes. Mathematical Biology and Bioinformatics. 2011;6(1):t1-t13. doi: 10.17537/2011.6.39.
- Woese C.R., Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA. 1977;74:5088–5090. doi: 10.1073/pnas.74.11.5088
- Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 2013;30:2725–2729. doi: 10.1093/molbev/mst197
- Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993;10:512–526. http://mbe.oxfordjournals.org/content/10/3/512.full.pdf (accessed 07 June 2015).
- Ozoline O.N., Tsyganov M.A. Structure of open promoter complexes with Escherichia coli RNA polymerase as revealed by the DNaseI footprinting technique: compilation analysis. Nucl. Acids Res. 1995;23:4533–4541. doi: 10.1093/nar/23.22.4533
- Panyukov V.V., Ozoline O.N. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS ONE. 2013;8:e62601. doi: 10.1371/journal.pone.0062601
- Wang L., Wang F.F., Qian W. Evolutionary rewiring and reprogramming of bacterial transcription regulation. J. Genet. Genomics. 2011;38:279–288. doi: 10.1016/j.jgg.2011.06.001
- Porcelli I., Reuter M., Pearson B.M., Wilhelm T., van Vliet A.H. Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria. BMC Genomics. 2013;14:616. doi: 10.1186/1471-2164-14-616
- EMBOSS Needle. http://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html (accessed 07 June 2015).
- Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970;48:443–453. doi: 10.1016/0022-2836(70)90057-4
- EMBOSS Water. http://www.ebi.ac.uk/Tools/psa/emboss_water/nucleotide.html (accessed 07 June 2015).
- Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981;147:195–197. doi: 10.1016/0022-2836(81)90087-5
- Microbial Nucleotide BLAST. http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes (accessed 07 June 2015).
- EMBOSS Matcher. http://www.ebi.ac.uk/Tools/psa/emboss_matcher/nucleotide.html (accessed 07 June 2015).
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