vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-23-33vavilov-3738Research ArticleГЕНЕТИКА МИКРООРГАНИЗМОВMICROBIAL GENETICSОбнаружение генных кластеров биодеструкции алканов и ароматических соединений в геноме Rhodococcus qingshengii VKM Ac-2784DDetection of gene clusters for biodegradation of alkanes and aromatic compounds in the Rhodococcus qingshengii VKM Ac-2784D genomehttps://orcid.org/0000-0001-7767-4204МарковаЮ. А.MarkovaYu. A.

Иркутск

Irkutsk

https://orcid.org/0000-0002-8788-5352ПетрушинИ. С.PetrushinI. S.

Иркутск

Irkutsk

ivan.kiel@gmail.comhttps://orcid.org/0000-0001-5922-3397БеловежецЛ. А.BelovezhetsL. A.

Иркутск

Irkutsk

Сибирский институт физиологии и биохимии растений Сибирского отделения Российской академии наукРоссияSiberian Institute of Plant Physiology and Biochemistry of the Siberian Branch of the Russian Academy of SciencesRussian FederationСибирский институт физиологии и биохимии растений Сибирского отделения Российской академии наук; Иркутский государственный университетРоссияSiberian Institute of Plant Physiology and Biochemistry of the Siberian Branch of the Russian Academy of Sciences; Irkutsk State UniversityRussian FederationИркутский институт химии им. А.Е. Фаворского Сибирского отделения Российской академии наукРоссияA.E. Favorsky Irkutsk Institute of Chemistry of the Siberian Branch of the Russian Academy of SciencesRussian Federation202302062023273276282Copyright © Маркова Ю.А., Петрушин И.С., Беловежец Л.А., 20232023Маркова Ю.А., Петрушин И.С., Беловежец Л.А.Markova Y.A., Petrushin I.S., Belovezhets L.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3738

Многие представители рода Rhodococcus известны как активные биодеструкторы компонентов нефти (в том числе алканов) и ароматических соединений. Пристальное внимание, которое стали уделять родококкам в последнее время, является следствием их высокого катаболического потенциала. Ранее нами выделен штамм Rhodococcus qingshengii VKM Ac-2784D из ризосферы пырея, произраставшего на нефтезагрязненной почве. По результатам филогенетического анализа этот штамм может быть отнесен к виду Rhodococcus qingshengii. На сегодняшний день расшифрованы пути и идентифицированы гены деструкции многих загрязнителей. Для оценки способности рассматриваемого штамма к деградации нефти и нефтепродуктов мы исследовали генные кластеры, ассоциированные с такой способностью. Ферменты деструкции алканов представлены двумя кластерами и пятью отдельно расположенными генами alkB. Деструкция ароматических соединений состоит из двух этапов: периферического и центрального. Геном R. qingshengii VKM Ac-2784D содержит четыре из восьми известных центральных путей деструкции ароматических соединений. Структура генных кластеров сходна с описанными в литературе штаммами R. jostii RHA1 и R. ruber Chol-4. Периферические пути представлены кластерами генов, кодирующих белки деструкции бензойной кислоты, ген бифенил 2,3-диоксигеназы и два гена бифенил-2,3-диол 1,2-диоксигеназы, участвующих в катаболизме бифенила. Присутствие генов бифенил 2,3-диоксигеназы, кластера генов бензоатного и 2-гидроксипентадиеноатного путей указывает на способность исследуемого штамма деструктировать полихлорированные бифенилы. Усилить активность биодеструкции загрязнителей помогают сурфактанты, улучшающие доступность разлагаемых веществ. Для некоторых видов Rhodococcus описаны биосурфактанты на основе трегалозы. В геноме R. qingshengii VKM Ac-2784D присутствуют гены, кодирующие белки биосинтеза сурфактантов – otsA, otsB, treY, treZ. Данные биоинформационного анализа согласуются с результатами ранее проведенных биохимических исследований. Знание метаболического потенциала отдельного организма, полученное в результате анализа генома, позволит создавать адаптированные к заданным условиям смеси бактериальных штаммов, объединяющие микроорганизмы с разным спектром метаболических путей деструкции.

Bacterial species of the genus Rhodococcus are known to be efficient degraders of hydrocarbons in contaminated soil. They are also employed for bioremediation of polluted environments. These bacteria are widely met in soil, water and living organisms. Previously, we have isolated the Rhodococcus qingshengii strain VKM Ac-2784D from the rhizosphere of couch grass growing on oil-contaminated soil. This strain can effectively degrade oil and some model compounds (naphthalene, anthracene and phenanthrene). The results of phylogenetic analysis show that this strain belongs to the species R. qingshengii. To understand the catabolic properties of this strain, we have studied its gene clusters possessing such properties. The alkane destruction genes are represented by two clusters and five separate alkB genes. The destruction of aromatic compounds involves two stages, namely central and peripheral. The R. qing­ shengii VKM Ac-2784D genome contains four out of eight known central metabolic pathways for the destruction of aromatic compounds. The structure of the gene clusters is similar to that of the known strains R. jostii RHA1 and R. ru­ ber Chol-4. The peripheral pathways include the genes encoding proteins for benzoic acid destruction. The presence of biphenyl 2,3-dioxygeneses as well as gene clusters of benzoate and 2-hydroxypentandienoate pathways suggests that R. qingshengii VKM Ac-2784D could degrade polychlorinated biphenyls. The biodegradation ability can be enhanced by biosurfactants, which are known to be synthesized by Rhodococcus. The R. qingshengii VKM Ac-2784D genome contains the otsA, otsB, treY, treZ genes. The bioinformatics data are supported by the previous biochemical experiments that allow a mixture of species with a wide variation of metabolic pathways to be obtained.

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