Вопросы вирусологии. 2015; 60: 32-37
Стратегия использования синонимичных кодонов в кодирующих последовательностях вируса клещевого энцефалита
Аннотация
Список литературы
1. Вотяков В.И., Злобин В.И., Мишаева Н.П. Клещевые энцефалиты Евразии. Новосибирск: Наука; 2002.
2. Козлова И.В., Верхозина М.М., Демина Т.В., Джиоев Ю.П., Ткачев С.Е., Карань Л.С. и др. Комплексная характеристика оригинальной группы штаммов вируса клещевого энцефалита, изолированных с территории Восточной Сибири. Сибирский медицинский журнал (Иркутск). 2012; 111 (4): 80–5.
3. Карганова Г.Г. Хозяин-специфические детерминанты в геноме вируса клещевого энцефалита. В кн.: Фундаментальные и прикладные аспекты изучения паразитических членистоногих в XXI в: материалы международной конференции. СПб.; 2013: 71–3.
4. Леонова Г.Н. Клещевой энцефалит в Приморском крае. Владивосток: Дальнаука; 1997.
5. Погодина В.В., Карань Л.С., Колясникова Н.М., Левина Л.С., Герасимов С.Г., Маленко Г.В. и др. Сибирский подтип вируса клещевого энцефалита, доминирующий на территории России. Распространение и патогенность. Медицинская вирусология. 2013; 27 (1): 36.
6. Лукашев В.В. Молекулярная эволюция и филогенетический анализ. М.: БИНОМ; 2009.
7. Wong E.Н.М., Smith D.K., Rabadan R., Peiris M., Poon L.L.M. Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evol. Biol. 2010; 10: 253. Available at: http://www.biomedcentral.com/1471-2148/10/253.
8. Belalov I.S., Lukashev A.N. Causes and Implications of Codon Usage Bias in RNA Viruses. PLoS One. 2013; 8 (2). Available at: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056642.
9. Qian W., Yang J.R., Pearson N.M., Maclean C., Zhang J. Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency. PLoS Genet. 2012; 8 (3). Available at: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002603.
10. Schubert A.M., Putonti C. Evolution of the sequence composition of Flaviviruses. Infect. Genet. Evol. 2010; 10 (1): 129–36.
11. Perriere G., Thioulouse J. Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Research. 2002; 30 (20): 4548–55.
12. Shah P., Gilchrist M.A. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc. Natl. Acad. Sci. U S A. 2011; 108 (25): 10 231–6.
13. Su M.W., Lin H.M., Yuan H.S., Chu W.C. Categorizing host-dependent RNA viruses by principal component analysis of their codon usage preferences. J. Comput. Biol. 2009; 16 (11): 1539–47.
14. Plotkin J.B., Robins H., Levine A.J. Tissue-specific codon usage and the expression of human genes. Proc. Natl. Acad. Sci. USA. 2004; 101: 12 588–91.
15. Tello M., Saavedra J.M., Spencer E. Analysis of the use of codon pairs in the HE gene of the ISA virus shows a correlation between bias in HPR codon-pair use and mortality rates caused by the virus. Virol. J. 2013; 10. Available at: http://www.virologyj.com/content/10/1/180.
16. Frias D., Monteiro-Cunha J.P., Mota-Miranda A.C., Fonseca V.S., Oliveira T., Galvao-Castro B. et al. Human Retrovirus codon Usage from tRnA point of View: Therapeutic Insights. Bioinform. Biol. Insights. 2013; 7: 335–45.
17. Grantham R., Gautier C., Gouy M., Mercier R., Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980; 8 (1): 49–62.
18. Cardinale D.J., DeRosa K., Duffy S. Base composition and translational selection are insufficient to explain codon usage bias in plant viruses. Viruses. 2013; 5 (1): 162–81.
19. Sharp P.M., Tuohy T.M., Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986; 14 (13): 5125–43.
20. Бутвиловский А.В., Бутвиловский В.Э., Черноус Е.А. Изучение стратегии кодирования белков. Медицинский журнал. 2009; 2 (28): 29–33.
21. Халафян А.А. Учебник STATISTIСA 6. Статистический анализ данных. М.: Бином; 2007.
22. Орлов А.И. Прикладная статистика: учебник. М.: Экзамен; 2006.
23. Демина Т.В. Вопросы генотипирования и анализ генетической вариабельности вируса клещевого энцефалита: Дисс. … д-ра биол. наук. Иркутск; 2012.
24. Стародуб З.Ф., Рачков А.Э. Избирательность трансляции матричных рнк эукариот. Биополимеры и клетка. 1986; 2 (4): 167–78.
25. Dittmar K.A., Goodenbour J.M., Pan T. Tissue-Specific Differences in Human Transfer RNA Expression. PLoS Genetics. 2006; 2 (12). Available at: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0020221.
26. Nougairede A., Fabritus L., Aubry F., Gould E.A., Holmes E.C., Lamballerie X. Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells. PLOS Pathog. 2013; 9 (2). Available at: http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003172
27. Тюлько Ж.С., Якименко В.В. Вариабельность нуклеотидных последовательностей геномов вируса клещевого энцефалита, связанная с их структурой. Сибирский медицинский журнал (Иркутск). 2012; 111 (4): 27–30.
Problems of Virology. 2015; 60: 32-37
Strategy of synonymous codon usage in encoding sequences of the tick-borne encephalitis virus
Abstract
References
1. Votyakov V.I., Zlobin V.I., Mishaeva N.P. Kleshchevye entsefality Evrazii. Novosibirsk: Nauka; 2002.
2. Kozlova I.V., Verkhozina M.M., Demina T.V., Dzhioev Yu.P., Tkachev S.E., Karan' L.S. i dr. Kompleksnaya kharakteristika original'noi gruppy shtammov virusa kleshchevogo entsefalita, izolirovannykh s territorii Vostochnoi Sibiri. Sibirskii meditsinskii zhurnal (Irkutsk). 2012; 111 (4): 80–5.
3. Karganova G.G. Khozyain-spetsificheskie determinanty v genome virusa kleshchevogo entsefalita. V kn.: Fundamental'nye i prikladnye aspekty izucheniya paraziticheskikh chlenistonogikh v XXI v: materialy mezhdunarodnoi konferentsii. SPb.; 2013: 71–3.
4. Leonova G.N. Kleshchevoi entsefalit v Primorskom krae. Vladivostok: Dal'nauka; 1997.
5. Pogodina V.V., Karan' L.S., Kolyasnikova N.M., Levina L.S., Gerasimov S.G., Malenko G.V. i dr. Sibirskii podtip virusa kleshchevogo entsefalita, dominiruyushchii na territorii Rossii. Rasprostranenie i patogennost'. Meditsinskaya virusologiya. 2013; 27 (1): 36.
6. Lukashev V.V. Molekulyarnaya evolyutsiya i filogeneticheskii analiz. M.: BINOM; 2009.
7. Wong E.N.M., Smith D.K., Rabadan R., Peiris M., Poon L.L.M. Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evol. Biol. 2010; 10: 253. Available at: http://www.biomedcentral.com/1471-2148/10/253.
8. Belalov I.S., Lukashev A.N. Causes and Implications of Codon Usage Bias in RNA Viruses. PLoS One. 2013; 8 (2). Available at: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056642.
9. Qian W., Yang J.R., Pearson N.M., Maclean C., Zhang J. Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency. PLoS Genet. 2012; 8 (3). Available at: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002603.
10. Schubert A.M., Putonti C. Evolution of the sequence composition of Flaviviruses. Infect. Genet. Evol. 2010; 10 (1): 129–36.
11. Perriere G., Thioulouse J. Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Research. 2002; 30 (20): 4548–55.
12. Shah P., Gilchrist M.A. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc. Natl. Acad. Sci. U S A. 2011; 108 (25): 10 231–6.
13. Su M.W., Lin H.M., Yuan H.S., Chu W.C. Categorizing host-dependent RNA viruses by principal component analysis of their codon usage preferences. J. Comput. Biol. 2009; 16 (11): 1539–47.
14. Plotkin J.B., Robins H., Levine A.J. Tissue-specific codon usage and the expression of human genes. Proc. Natl. Acad. Sci. USA. 2004; 101: 12 588–91.
15. Tello M., Saavedra J.M., Spencer E. Analysis of the use of codon pairs in the HE gene of the ISA virus shows a correlation between bias in HPR codon-pair use and mortality rates caused by the virus. Virol. J. 2013; 10. Available at: http://www.virologyj.com/content/10/1/180.
16. Frias D., Monteiro-Cunha J.P., Mota-Miranda A.C., Fonseca V.S., Oliveira T., Galvao-Castro B. et al. Human Retrovirus codon Usage from tRnA point of View: Therapeutic Insights. Bioinform. Biol. Insights. 2013; 7: 335–45.
17. Grantham R., Gautier C., Gouy M., Mercier R., Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980; 8 (1): 49–62.
18. Cardinale D.J., DeRosa K., Duffy S. Base composition and translational selection are insufficient to explain codon usage bias in plant viruses. Viruses. 2013; 5 (1): 162–81.
19. Sharp P.M., Tuohy T.M., Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986; 14 (13): 5125–43.
20. Butvilovskii A.V., Butvilovskii V.E., Chernous E.A. Izuchenie strategii kodirovaniya belkov. Meditsinskii zhurnal. 2009; 2 (28): 29–33.
21. Khalafyan A.A. Uchebnik STATISTISA 6. Statisticheskii analiz dannykh. M.: Binom; 2007.
22. Orlov A.I. Prikladnaya statistika: uchebnik. M.: Ekzamen; 2006.
23. Demina T.V. Voprosy genotipirovaniya i analiz geneticheskoi variabel'nosti virusa kleshchevogo entsefalita: Diss. … d-ra biol. nauk. Irkutsk; 2012.
24. Starodub Z.F., Rachkov A.E. Izbiratel'nost' translyatsii matrichnykh rnk eukariot. Biopolimery i kletka. 1986; 2 (4): 167–78.
25. Dittmar K.A., Goodenbour J.M., Pan T. Tissue-Specific Differences in Human Transfer RNA Expression. PLoS Genetics. 2006; 2 (12). Available at: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0020221.
26. Nougairede A., Fabritus L., Aubry F., Gould E.A., Holmes E.C., Lamballerie X. Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells. PLOS Pathog. 2013; 9 (2). Available at: http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003172
27. Tyul'ko Zh.S., Yakimenko V.V. Variabel'nost' nukleotidnykh posledovatel'nostei genomov virusa kleshchevogo entsefalita, svyazannaya s ikh strukturoi. Sibirskii meditsinskii zhurnal (Irkutsk). 2012; 111 (4): 27–30.
