vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RASvavilov-117Research ArticleСтатьиArticlesРЕКОНСТРУКЦИЯ МЕХАНИЗМОВ РЕГУЛЯЦИИ ЭКСПРЕССИИ ГЕНА YFIA ESCHERICHIA COLI В УСЛОВИЯХ СТРЕССАRECONSTRUCTION OF MECHANISMS REGULATING THE EXPRESSION OF THE ESCHERICHIA COLI YFIA GENE UNDER STRESS CONDITIONSХлебодароваТ. М.KhlebodarovaT. M.tamara@bionet.nsc.ruОщепковД. Ю.OshchepkovD. Yu.tamara@bionet.nsc.ruТикуноваН. В.TikunovaN. V.БабкинИ. В.BabkinI. V.ГруздевА. Д.GruzdevA. D.tamara@bionet.nsc.ruЛихошвайВ. А.LikhoshvaiV. A.tamara@bionet.nsc.ruФедеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, РоссияРоссияInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaRussian FederationФедеральное государственное бюджетное учреждение науки Институт химической биологии и фундаментальной медицины Сибирского отделения РАН, Новосибирск, РоссияРоссияInstitute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, RussiaRussian FederationФедеральное государственное бюджетное учреждение науки Институт цитологии и генетики Сибирского отделения Российской академии наук, Новосибирск, Россия Новосибирский национальный исследовательский государственный университет, Новосибирск, РоссияРоссияInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaRussian Federation201319122014171104113Copyright © Хлебодарова Т.М., Ощепков Д.Ю., Тикунова Н.В., Бабкин И.В., Груздев А.Д., Лихошвай В.А., 20142014Хлебодарова Т.М., Ощепков Д.Ю., Тикунова Н.В., Бабкин И.В., Груздев А.Д., Лихошвай В.А.Khlebodarova T.M., Oshchepkov D.Y., Tikunova N.V., Babkin I.V., Gruzdev A.D., Likhoshvai V.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/117

С использованием компьютерного ресурса SiteCon и методов математического моделирования проведены реконструкция структуры регуляторной области гена yfiA E. coli и оценка сложности механизмов его экспрессии в условиях окислительного стресса. Моделирование динамики ответа на оксидативный стресс клеток E. coli, трансформированных плазмидой pYfi-gfp, показало, что максимальное совпадение с экспериментальными данными наблюдается в модели, предполагающей комплексное воздействие, которое осуществляется, по-видимому, через ряд транскрипционных факторов (ТФ). Поиск в регуляторной области гена yfiA E. coli потенциальных сайтов связывания ТФ показал высокий уровень достоверности распознавания для ТФ MarA, IscR, MetJ, PurR и SoxS, которые прямо или косвенно могут участвовать в ответе этого гена на окислительный стресс, а также для ТФ CRP, глобального регулятора катаболизма углеводов. Гель-шифт-анализ с очищенными рекомбинантными белками ТФ CRP, MarA и SoxS E. coli подтвердил их присутствие в промоторе гена yfiA E. coli, что позволяет объяснить чувствительность этого гена к митомицину и радикал-образующим агентам.

The regulatory region of the Escherichia coli yfiA gene was reconstructed by using the SiteCon web resource and mathematical modeling, and its expression complexity under oxidative stress was assessed. Simulation of the response of E. coli cells transformed with pYfi-gfp plasmid to oxidative stress indicated that the maximum agreement with experimental data was achieved in a model implying a complex action, apparently mediated by several transcription factors (TFs). The regulatory region of the yfiA gene was searched for potential TF binding sites, and highly reliable recognition was predicted for TFs MarA, IscR, MetJ, PurR, and SoxS, which directly or indirectly participate in the response of the gene to oxidative stress, and for CRP, a global regulator of carbohydrate catabolism. The presence of binding sites for CRP, MarA, and SoxS in the E. coli yfiA promoter was confirmed by electrophoretic mobility shift assay with purified recombinant TFs. This fact explains the sensitivity of yfiA to mitomycin and radical-forming agents.

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The authors declare that there are no conflicts of interest present.