vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-23-118vavilov-4014Research ArticleСИСТЕМНАЯ И КОМПЬЮТЕРНАЯ БИОЛОГИЯSYSTEMS AND COMPUTATIONAL BIOLOGYРеконструкция и анализ регуляторной генной сети функционирования клеточной стенки листьев Arabidopsis thaliana L. при ответе на водный дефицитReconstruction and analysis of the gene regulatory network for cell wall function in Arabidopsis thaliana L. leaves in response to water deficithttps://orcid.org/0009-0003-8472-4945ВолянскаяА. Р.VolyanskayaA. R.

Новосибирск

Novosibirsk

https://orcid.org/0000-0003-2158-3252АнтроповаЕ. А.AntropovaE. A.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-0730-9145ЗубаироваУ. С.ZubairovaU. S.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-9433-8341ДеменковП. С.DemenkovP. S.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-7419-5168ВензельА. С.VenzelA. S.

Новосибирск

Novosibirsk

ОрловЮ. Л.OrlovY. L.

Новосибирск

Москва

Novosibirsk

Moscow

https://orcid.org/0009-0005-1844-7921МакароваА. А.MakarovaA. A.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-0005-9155ИванисенкоТ. В.IvanisenkoT. V.

Новосибирск

Novosibirsk

ГоршковаТ. А.GorshkovaT. A.

Казань

Kazan

АгълямоваА. Р.AglyamovaA. R.

Казань

Kazan

https://orcid.org/0000-0001-6800-8787КолчановН. А.KolchanovN. A.

Новосибирск

Novosibirsk

ЧенМ.ChenM.

Ханчжоу

Hangzhou

https://orcid.org/0000-0002-1859-4631ИванисенкоВ. А.IvanisenkoV. A. 

Новосибирск

Novosibirsk

salix@bionet.nsc.ruФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Novosibirsk State UniversityRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of ScienceRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Курчатовский геномный центр ИЦиГ СО РАНРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Kurchatov Genomic Center of ICG SB RASRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Первый Московский государственный медицинский университет им. И.М. Сеченова Министерства здравоохранения Российской Федерации (Сеченовский Университет); Российский университет дружбы народов имени Патриса ЛумумбыРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University); Peoples’ Friendship University of RussiaRussian FederationКазанский институт биохимии и биофизики – обособленное структурное подразделение Федерального исследовательского центра «Казанский научный центр Российской академии наук»РоссияKazan Institute of Biochemistry and BiophysicsRussian FederationКолледж наук о жизни, Чжэцзянский университет науки и техникиКитайCollege of Life Sciences, Zhejiang UniversityChinaФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университет; Курчатовский геномный центр ИЦиГ СО РАНРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Novosibirsk State University; Kurchatov Genomic Center of ICG SB RASRussian Federation20232912202327810311041Copyright © Волянская А.Р., Антропова Е.А., Зубаирова У.С., Деменков П.С., Вензель А.С., Орлов Ю.Л., Макарова А.А., Иванисенко Т.В., Горшкова Т.А., Агълямова А.Р., Колчанов Н.А., Чен М., Иванисенко В.А., 20232023Волянская А.Р., Антропова Е.А., Зубаирова У.С., Деменков П.С., Вензель А.С., Орлов Ю.Л., Макарова А.А., Иванисенко Т.В., Горшкова Т.А., Агълямова А.Р., Колчанов Н.А., Чен М., Иванисенко В.А.Volyanskaya A.R., Antropova E.A., Zubairova U.S., Demenkov P.S., Venzel A.S., Orlov Y.L., Makarova A.A., Ivanisenko T.V., Gorshkova T.A., Aglyamova A.R., Kolchanov N.A., Chen M., Ivanisenko V.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4014

Растительная клеточная стенка представляет собой внешний компартмент растительной клетки, который во многом обеспечивает физический барьер и запуск сигнальных каскадов при действии био- и абиотических стрессоров. Засуха негативно влияет как на рост, так и развитие растений. Белки клеточной стенки (БКС) играют существенную роль в ответе растений на водный дефицит. Механизмы адаптации клеточной стенки к потере воды могут быть использованы для выявления важных генетических факторов, определяющих устойчивость растений к засухе, и предоставляют ценные данные о биомаркерах для дальнейшей селекции, направленной на повышение урожайности культурных растений. С помощью ANDSystem реконструирована генная сеть, позволяющая описывать регуляцию БКС в условиях ограничения полива. Анализ генной сети совместно с анализом транскриптомных данных позволил провести приоритизацию транскрипционных факторов (ТФ) по их обогащенности регулируемыми дифференциально экспрессирующимися генами. В результате были рассчитаны веса, являющиеся индикаторами ассоциации ТФ с водным дефицитом. По значениям весов отобраны восемь наиболее значимых ТФ. Наибольшим приоритетом обладал ТФ GBF3. Приоритизация БКС проведена по критерию суммирования весов транскрипционных факторов, регулирующих эти гены. К наиболее приоритетным БКС отнесены ген AT5G03350, кодирующий лектин-подобный белок; AT4G20860, кодирующий фермент берберинового моста BBE-like 22 (berberine bridge enzyme-like 22), необходимый для окисления продуктов распада целлюлозы, и AT4G37800, кодирующий ксилоглюкан эндотрансгликозилазу/гидролазу 7.

The plant cell wall represents the outer compartment of the plant cell, which provides a physical barrier and triggers signaling cascades under the influence of biotic and abiotic stressors. Drought is a factor that negatively affects both plant growth and development. Cell wall proteins (CWP) play an important role in the plant response to water deficit. The adaptation mechanisms of the cell wall to water loss are of interest for identifying important genetic factors determining plant drought resistance and provide valuable information on biomarkers for further selection aimed at increasing the yield of crop plants. Using ANDSystem, a gene network describing the regulation of CWPs under water restriction conditions was reconstructed. The analysis of the gene network and the transcriptome data analysis allowed prioritizing transcription factors (TF) based on their enrichment of differentially expressed genes regulated by them. As a result, scores were calculated, acting as indicators of the association of TFs with water deficit. On the basis of the score values, eight most significant TFs were selected. The highest priority was given to the TF GBF3. CWPs were prioritized according to the criterion of summing up the scores of transcription factors regulating these genes. Among the most prioritized CWPs were the AT5G03350 gene encoding a lectin-like protein, AT4G20860 encoding BBE-like 22 required for the oxidation of cellulose degradation products, and AT4G37800 encoding xyloglucan endotransglucosy lase/hydrolase 7. Overall, the implemented algorithm could be used for prediction of regulatory interactions between transcription factors and target genes encoding cell wall proteins in plants.

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