Эволюция участков связывания бактериальных факторов транскрипции в последовательностях ДНК
Диссертация
Произведен обзор механизмов выработки антибактериальных пептидовбактериоцинов грамположительными бактериями. Систематически описано устройство всех локусов, содержащих гены регуляторных систем, транспорта, иммунитета, процессинга и посттрансляционной модификации антибактериальных пептидов. Показано, что эволюционное дерево транскрипционных регуляторов ответа соответствует дереву узнаваемых ими… Читать ещё >
Список литературы
- Allison G.E., Worobo R.W., Stiles М.Е., Klaenhammer T.R. Heterologous expression of the lactacin F peptides by Carnobacterium piscicola LV17. Appl Environ Microbiol. 1995. V. 61. N. 4. P.1371−1377
- Altena K., Guder A., Cramer C., Bierbaum G. Biosynthesis of the lantibiotic mersacidin: organization of a type В lantibiotic gene cluster. Appl.Envirom.Microbiol. 2000. V. 66. N. 6. P. 2565−2571.
- Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment tool. J. Mol. Biol. 1990- V. 215. N. 3. P. 403−410.
- Axelsson L. and Hoick A. The genes involved in production of and immunity to sakacin A, a bacteriocin from Lactobacillus sake Lb706. J. Bacterid. 1995. V. 177. N. 8. P. 21 252 137.
- Benos P. V., Bulyk M.L. and Stormo G. D. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Research. 2002. V. 30 N. 20
- Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Res. 2003.31:23−7.
- BergJ., Willmann S., LassigM. Adaptive evolution of transcription factor binding sites. BMC Evol Biol. 2004. 4(1):42.
- Berg O.G., von HippelP.H. Selection of DNA binding sites by regulatory proteins. J. Mol. Biol. 1987. 193,723−750.
- Berg O.G. The evolutionary selection of DNA base pairs in gene-regulatory binding sites. Proc.Natl. Acad. Sci. USA. 1992. V.89. P. 7501−7505.
- Bierbaum G., Brotz H., Koller K.P. and Sahl E.G. Cloning, sequencing and production of the lantibiotic mersacidin. FEMS Microbiol. Lett. 1995. V. 127. P. 121−126.
- Bromham L., and Penny D. The modern molecular clock. Nat Rev Genet 2003.4:216−24.
- Brurberg M.B., Nes I.F. and Eijsink V.G. Pheromone-induced production of antimicrobial peptides in Lactobacillus. Mol. Microbiol. 1997. V. 26 N. 2. P. 347−360.
- Buckler N.E., Gerland U., Hwa T. On schemes of combinatorial transcription logic. Proc. Natl. Acad. Sci. USA. 2003. 100: 5136−5141.
- Bulyk M.L., Johnson P.L., and Church G.M. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 2002. 30: 1255−1261.
- Bussemaker H.J., Li H., and Siggia E.D. Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis. Proc.Natl. Acad. Sci. USA. 2000. V. 97. P. 10 096−10 100
- Casaus P., Nilsen Т., Cintas L.M., Nes I.F., Hernandez P.E., Holo H. Enterocin B, a new bacteriocin from Enterococcus faecium T136 which can act synergistically with enterocin A. Microbiology. 1997. V. 143. N. 7. P.2287−2294
- Cintas L.M., Casaus P., Holo H., Hernandez P.E., Nes I.F., Havarstein L.S. Enterocins L50A and L50B, two novel bacteriocins from Enterococcus faecium L50, are related to staphylococcal hemolysins. J Bacteriol. 1998. V. 180. N. 8. P. 1988−1994.
- Claverie J. M, Audic S. The statistical significance of nucleotide position-weight matrix matches. Comput Appl Biosci. 1996. N 12. P 431−9.
- Day W.H., McMorris F.R. A consensus program for molecular sequences. Comput Appl Biosci. 1993. 9(6):653−6.
- Diep D.B., Havarstein L.S., and Nes I.F. Characterization of the locus responsible for bacteriocin production in Lactobacillus plantarum CI 1. J. Bacteriol. 1996. V. 178. p. 44 724 483.
- Djordjevic M., Sengupta A. M., Shraiman B.I. A biophysical approach to transcription factor binding site discovery. Genome Res. 2003.13(11):2381−90.
- Donvito В., Etienne J., Denoroy L., Greenland Т., Benito Y., Vandenesch F. Synergistic hemolytic activity of Staphylococcus lugdunensis is mediated by three peptides encoded by a non-agr genetic locus. Infect Immun. 1997. V. 65. N. 1. P. 95−100.
- Dufour A., Rince A., Uguen P. and Le Pennec J.P. IS 1675, a Novel Lactococcal Insertion Element, Forms a Transposon-Like Structure Including the Lacticin 481 Lantibiotic Operon. J. Bacteriol. 2000. V. 182. N. 19. P. 5600−5605.
- Durbin R., Eddy S., KroghA., Mitchison G. Biological sequence analysis. Probabilistic models of proteins and nucleic acids. Cambridge University Press. 1998.
- Ehrmann M.A., Remiger A., Eijsink KG. and Vogel R.F. A gene cluster encoding plantaricin 1.25beta and other bacteriocin-like peptides in Lactobacillus plantarum TMW1.25. Biochim. Biophys. Acta. 2000. V. 1490. N. 3. P. 355−361.
- Eijsink F.G.H., Brurberg M.B., Middelhoven P.H., and Nes I.F. Induction of bacteriocin production in Lactobacillus sake by secreted peptide. J. Bacteriol. 1996. V. 178. N. 8. P. 2232−2237.
- Felix, J.V., Papathanasopoulos.M.A., Smith, A.A., von Holy, A. and Hastings, J.W. Characterization of leucocin B-Talla: a bacteriocin from Leuconostoc carnosum Talla isolated from meat. Curr. Microbiol. 1994. V. 29. N. 4. P. 207−212.
- Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981- 17(6):368−76.
- Fields D.S., He Y" Al-Uzri A.Y., Stormo G.D. Quantitative specificity of the Mnt repressor. J Mol Biol. 1997. V. 271. N. 2. P. 178−94.
- Fremaux C., Hechard Y. and Cenatiempo Y. Mesentericin Y105 gene clusters in Leuconostoc mesenteroides Y105. Microbiology 1995. V. 141. N. 7. P. 1637−1645.
- Garver K.I., Muriana P.M. Purification and partial amino acid sequence of curvaticin FS47, a heat-stable bacteriocin produced by Lactobacillus curvatus FS47. Appl Environ Microbiol. 1994. V. 60. N. 6. P. 2191−2195.
- Gelfand M.S. Recognition of regulatory sites by genomic comparsion. Res. Microbiol. 1999. V. 150. P. 755−771.
- Gelfand M.S., Koonin E.V., Mironov A.A. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res. 2000. V. 28. P. 695 705.
- Gerasimova A.V., Rodionov D.A., Mironov A.A., Gel’fand M.S. Computer analysis of regulatory signals in bacterial genomes. Fnr binding segments. Mol Biol (Mosk). 2001. 35. 1001−1009.
- Gerland U., Hwa T. On the selection and evolution of regulatory DNA motifs. J.Mol. Evol. 2002. V. 55. P.386−400.
- Giacomini A., Squartini A. and Nuti M.P. Nucleotide sequence and analysis of plasmid pMD136 from Pediococcus pentosaceus FBB61 (ATCC43200) involved in pediocin A production. Plasmid. 2000. V. 43. N. 2. P. 111−122
- Guder A., Wiedemann I., Sahl H.-G. Posttranslationally Modified Bacteriocins The Lantibiotics. Biopolymers (Peptide Science). 2000. V. 55. P. 62−73.
- Jack R.W., TaggJ.R., and Ray B. Bacteriocins of Gram-Positive Bacteria. Microbiological Reviews. 1995. V. 59. N. 2. P. 171−200.
- Hastings J.W., Sailer M., Johnson K, Roy K.L., Vederas J.C. and Stiles M.E. Characterization of leucocin A-UAL 187 and cloning of the bacteriocin gene from Leuconostoc gelidum. J. Bacteriol. 1991. V. 173. N. 23. P. 7491−7500.
- Hechard Y., Berjeaud J.M. and Cenatiempo Y. Characterization of the mesB gene and expression of bacteriocins by leuconostoc mesenteroides YI05. Curr. Microbiol. 1999. V. 39. N. 5. P. 265−269.
- Hertz G.Z., Hartzell G.W. 3rd, Stormo G.D. Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci. 1990. V. 6. N. 2. P. 81−92.
- Hertz G.Z., Stormo G.D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 1999. V. 15. N. 7−8. P. 563−77.
- Holo H., Jeknic Z., Daeschel M" Stevanovic S., Nes I.F. Plantaricin W from Lactobacillus plantarum belongs to a new family of two-peptide lantibiotics. Microbiology. 2001. V. 147. N. 3. P. 643−51.
- Holo H., Nilssen O., and Nes I. F. Lactococcin A, a new bacteriocin from Lactococcus lactis subsp. cremoris: isolation and characterization of the protein and its gene. J. Bacteriol. 1991. V. 173. P. 3879−3887.
- Hynes W.L., Ferretti J.J. and Tagg J.R. Cloning of the gene encoding Streptococcin A-FF22, a novel lantibiotic produced by Streptococcus pyogenes, and determination of its nucleotide sequence. Appl. Environ. Microbiol. 1993. V. 59. N. 6. P. 1969−1971.
- Jukes Т.Н. and Cantor C. Evolution of protein molecules. Mammalian Protein Metabolism. 1969. Acadenuc Press. P. 21−132.
- Kaiser A.L., Montville T.J. Purification of the bacteriocin bavaricin MN and characterization of its mode of action against Listeria monocytogenes Scott A cells and lipid vesicles. // Appl Environ Microbiol. 1996. V. 62. N. 12. P. 4529−35
- Kaletta C., Entian K.D. and Jung G. Prepeptide sequence of cinnamycin (Ro 09−0198): the first structural gene of a duramycin-type lantibiotic. Eur. J. Biochem. 1991. V. 199. N. 2. P. 411−415.
- Kalmokoff M.L., Banerjee S.K., Cyr Т., Hefford MA, Gleeson T. Identification of a New Plasmid-Encoded sec-Dependent Bacteriocin Produced by Listeria innocua 743. Appl Environ Microbiol. 2001. V. 67. N. 9. P. 4041−4047
- Kanatani K, Oshimura M" and SanoK. Isolation and characterization of acidocin A and cloning of the bacteriocin gene from Lactobacillus acidophilus. Appl. Environ. Microbiol. 1995. V. 61. N. 3.P. 1061−1067.
- Kanatani K., Tahara Т., Oshimura M., Sano K. and Umezawa C. Cloning and nucleotide sequence of the gene for acidocin 8912, a bacteriocin from Lactobacillus acidophilus TK8912. Lett. Appl. Microbiol. 1995. V. 21. N. 6. P. 384−386.63