Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit
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...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2023-12-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/4014 |
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| author | A. R. Volyanskaya E. A. Antropova U. S. Zubairova P. S. Demenkov A. S. Venzel Y. L. Orlov A. A. Makarova T. V. Ivanisenko T. A. Gorshkova A. R. Aglyamova N. A. Kolchanov M. Chen V. A. Ivanisenko |
| author_facet | A. R. Volyanskaya E. A. Antropova U. S. Zubairova P. S. Demenkov A. S. Venzel Y. L. Orlov A. A. Makarova T. V. Ivanisenko T. A. Gorshkova A. R. Aglyamova N. A. Kolchanov M. Chen V. A. Ivanisenko |
| author_sort | A. R. Volyanskaya |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-4ef7e4416da54166b26361c63aa16439 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2023-12-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-4ef7e4416da54166b26361c63aa164392025-02-01T09:58:12ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592023-12-012781031104110.18699/VJGB-23-1181431Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficitA. R. Volyanskaya0E. A. Antropova1U. S. Zubairova2P. S. Demenkov3A. S. Venzel4Y. L. Orlov5A. A. Makarova6T. V. Ivanisenko7T. A. Gorshkova8A. R. Aglyamova9N. A. Kolchanov10M. Chen11V. A. Ivanisenko12Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Novosibirsk State UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of ScienceInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Novosibirsk State UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Kurchatov Genomic Center of ICG SB RASInstitute 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 RussiaInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of ScienceInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Kurchatov Genomic Center of ICG SB RASKazan Institute of Biochemistry and BiophysicsKazan Institute of Biochemistry and BiophysicsInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of ScienceCollege of Life Sciences, Zhejiang UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science; Novosibirsk State University; Kurchatov Genomic Center of ICG SB RASThe 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.https://vavilov.elpub.ru/jour/article/view/4014plant cell walldroughtplantsdifferentially expressed genestext miningmicroarraygene regulatory network |
| spellingShingle | A. R. Volyanskaya E. A. Antropova U. S. Zubairova P. S. Demenkov A. S. Venzel Y. L. Orlov A. A. Makarova T. V. Ivanisenko T. A. Gorshkova A. R. Aglyamova N. A. Kolchanov M. Chen V. A. Ivanisenko Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit Вавиловский журнал генетики и селекции plant cell wall drought plants differentially expressed genes text mining microarray gene regulatory network |
| title | Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit |
| title_full | Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit |
| title_fullStr | Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit |
| title_full_unstemmed | Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit |
| title_short | Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit |
| title_sort | reconstruction and analysis of the gene regulatory network for cell wall function in i arabidopsis thaliana i l leaves in response to water deficit |
| topic | plant cell wall drought plants differentially expressed genes text mining microarray gene regulatory network |
| url | https://vavilov.elpub.ru/jour/article/view/4014 |
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