КОМПЬЮТЕРНЫЙ АНАЛИЗ И ФУНКЦИОНАЛЬНАЯ АННОТАЦИЯ САЙТОВ СВЯЗЫВАНИЯ ТРАНСКРИПЦИОННЫХ ФАКТОРОВ AP2/ERF В ГЕНОМЕ ARABIDOPSIS THALIANA L.

У растений этилен участвует как в регуляции процессов развития, так и в ответе на стрессовые воздействия. Сигнал с рецепторов этилена активирует гены одного из самых больших семейств транскрипционных факторов, APETALA2/ETHYLENE RESPONSE FACTORs (ERFs). Сайты связывания ERF транскрипционных факторов содержат специфический GCCGCC-мотив и называются GCC-боксами. В настоящей работе две компьютерные программы для предсказания сайтов связывания транскрипционных факторов (oPWM и SiteGA) применены для анализа последовательностей экспериментально подтвержденных GCC-боксов. Распознаны GCC-боксы и исследовано их распределение в геноме Arabidopsis thaliana L. Проведены функциональная аннотация распознанных GCC-боксов и анализ их роли в ответе на фитогормон этилен.

1. Alonso J.M., Stepanova A., Solano R. et al. Five Components of the Ethylene-Response Pathway Identifi ed in a Screen for Weak Ethylene-Insensitive Mutants in Arabidopsis // Proc. Natl AS USA. 2003. V. 100. No. 5. P. 2992–2997.

2. Bleecker A.B., Kende H. Ethylene: A Gaseous Signal Molecule in Plants // Ann. Rev. Cell Developmental Biology. 2000. V. 16. No. 1. P. 1–18.

3. Cheng M., Liao P., Kuo W., Lin T. The Arabidopsis ETHYLENE RESPONSE FACTOR1 Regulates Abiotic Stress-Responsive Gene Expression by Binding to Different Cis-Acting Elements in Response to Different Stress Signals // Plant Physiology. 2013. V. 162. No. 3. P. 1566–1582.

4. Choudhury S.R., Roy S. et al. Characterization of Differential Ripening Pattern in Association with Ethylene Biosynthesis in the Fruits of Five Naturally Occurring Banana Cultivars and Detection of a GCC-Box-Specific DNA-Binding Protein // Plant Cell Reports. 2008. V. 27. No. 7. P. 1235–1249.

5. Du Z., Zhou X., Ling Y. et al. agriGO: A GO Analysis Toolkit for the Agricultural Community // Nucleic Acids Research. 2010. V. 38. P. 64–70.

6. Fujimoto S., Ohta M. et al. Arabidopsis Ethylene-Responsive Element Binding Factors Act as Transcriptional Activators or Repressors of GCC Box-Mediated Gene Expression // The Plant Cell. 2000. V. 12. No. 3. P. 393–404.

7. Goda H., Sasaki E., Akiyama K. et al. The AtGenExpress Hormone and Chemical Treatment Data Set: Experimental Design, Data Evaluation, Model Data Analysis and Data Access // Plant J.: For Cell Molecular Biology. 2008. V. 55. No. 3. P. 526–542.

8. Grimmig B., Gonzalez-Perez M. et al. Ozone-Induced Gene Expression Occurs via Ethylene-Dependent and Independent Signalling // Plant Molecular Biology. 2003. V. 51. No. 4. P. 599–607.

9. Hess N., Klode M. et al. The Hypoxia Responsive Transcription Factor Genes ERF71/HRE2 and ERF73/HRE1 of Arabidopsis Are Differentially Regulated by Ethylene // Physiologia Plantarum. 2011. V. 143. No. 1. P. 41–49.

10. Ju C., Chang C. Advances in Ethylene Signalling: Protein Complexes at the Endoplasmic Reticulum Membrane // AoB Plants. 2012. No. 1.

11. Kulakovskiy I.V., Boeva V.A., Favorov A.V., Makeev V.J. Deep and Wide Digging for Binding Motifs in ChIP-Seq Data // Bioinformatics. 2010. V. 26. No. 20. P. 2622–2623.

12. Levitsky V.G., Ignatieva E.V., Ananko E.A. et al. Effective Transcription Factor Binding Site Prediction Using a Combination of Optimization, a Genetic Algorithm and Discriminant Analysis to Capture Distant Interactions // BMC Bioinformatics. 2007. V. 8. No. 1. P. 481.

13. Mase K., Ishihama N., Mori H. et al. Ethylene-Responsive AP2/ERF Transcription Factor MACD1 Participates in Phytotoxin-Triggered Programmed Cell Death // Molecular Plant-Microbe Interactions. 2013. V. 26. Nо. 8. P. 868–879.

14. Mironova V., Omelyanchuck N., Levitsky V. Computational analysis of Auxin Responsive Elements in Arabidopsis thaliana Genome // BMC Genomics review. 2014. In print.

15. Nakano T., Suzuki K., Fujimura T., Shinshi H. Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice // Plant Physiology. 2006. V. 140. No. 2. P. 411–432.

16. Ohme-Takagi M., Shinshi H. Ethylene-Inducible DNA Binding Proteins That Interact with an Ethylene-Responsive Element // Plant Cell. 1995. V. 7. No. 2. P. 173–182.

17. Olmedo G., Guo H., Gregory B. et al. ETHYLENE-INSENSITIVE5 Encodes a 5´→3´ Exoribonuclease Required for Regulation of the EIN3-Targeting F-Box Proteins EBF1/2 // Proc. Natl AS USA. 2006. V. 103. No. 36. P. 13286–13293.

18. Osnato M., Stile M.R., Wang Y. et al. Cross Talk between the KNOX and Ethylene Pathways Is Mediated by Intron-Binding Transcription Factors in Barley // Plant Physiology. 2010. V. 154. No. 4. P. 1616–1632.

19. Qiao H., Shen Z., Huang S. et al. Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas // Science. 2012. V. 338. No. 6105. P. 390–393.

20. Samac D. A., Hironaka C.M., Yallaly P.E., Shah D.M. Isolation and Characterization of the Genes Encoding Basic and Acidic Chitinase in Arabidopsis Thaliana // Plant Physiology. 1990. V. 93. No. 3. P. 907–914.

21. Sato F., Kitajima S. et al. Ethylene-Induced Gene Expression of Osmotin-like Protein, a Neutral Isoform of Tobacco PR-5, Is Mediated by the AGCCGCC Cis-Sequence // Plant Cell Physiology. 1996. V. 37. No. 3. P. 249–255.

22. Sears M., Zhang H., Rushton P. et al. NtERF32: A Non-NIC2 Locus AP2/ERF Transcription Factor Required in Jasmonate-Inducible Nicotine Biosynthesis in Tobacco // Plant Molecular Biology. 2014. V. 84. No. 1-2. P. 49–66.

23. Sessa G., Meller Y., Fluhr R. A GCC Element and a G-Box Motif Participate in Ethylene-Induced Expression of the PRB-1b Gene // Plant Molecular Biology. 1995. V. 28. No. 1. P. 145–153.

24. Shakeel S.N., Wang X., Binder B.M., Schaller G.E. Mechanisms of Signal Transduction by Ethylene: Overlapping and Non-Overlapping Signalling Roles in a Receptor Family // AoB Plants. 2013. V. 5. No. 1.

25. Shinshi H., Usami S., Ohme-Takagi M. Identification of an Ethylene-Responsive Region in the Promoter of a Tobacco Class I Chitinase Gene // Plant Molecular Biology. 1995. V. 27. No. 5. P. 923–932.

26. Solano R., Stepanova A., Chao Q., Ecker J.R. Nuclear Events in Ethylene Signaling: A Transcriptional Cascade Mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1 // Genes Development. 1998. V. 12. No. 23. P. 3703–3714.

27. Son G.H., Wan J., Kim H. et al. Ethylene-Responsive Element-Binding Factor 5, ERF5, Is Involved in Chitin-Induced Innate Immunity Response // Molecular Plant-Microbe Interactions. 2012. V. 25. No. 1. P. 48–60.

28. Stepanova A.N., Ecker J.R. Ethylene Signaling: From Mutants to Molecules // Current Opinion Plant Biology. 2000. V. 3. No. 5. P. 353–360.

29. Stepanova A.N., Yun J., Likhacheva A.V., Alonso J.M. Multilevel Interactions between Ethylene and Auxin in Arabidopsis Roots // Plant Cell. 2007. V. 19. No. 7. P. 2169–2185.

30. Stergachis A., Haugen E. et al. Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution // Science. 2013. V. 342. No. 6164. P. 1367–1372.

31. Tournier B., Sanchez-Ballesta M. et al. New Members of the Tomato ERF Family Show Specifi c Expression Pattern and Diverse DNA-Binding Capacity to the GCC Box Element // FEBS Letters. 2003. V. 550. No. 1-3. P. 149–154.

32. Wang P., Du Y., Zhao X. et al. The MPK6-ERF6-ROSResponsive Cis-Acting Element7/GCC Box Complex

33. Modulates Oxidative Gene Transcription and the Oxidative Response in Arabidopsis // Plant Physiology. 2013. V. 161. No. 3. P. 1392–1408.

34. Zarei A., Körbes A.P., Younessi P. et al. Two GCC Boxes and AP2/ERF-Domain Transcription Factor ORA59 in Jasmonate/ethylene-Mediated Activation of the PDF1.2 Promoter in Arabidopsis // Plant Molecular Biology. 2011. V. 75. No. 4-5. P. 321–231.

35. Zhang Z., Zhang H., Quan R., Wang X.C., Huang R. Transcriptional Regulation of the Ethylene Response Factor LeERF2 in the Expression of Ethylene Biosynthesis Genes Controls Ethylene Production in Tomato and Tobacco // Plant Physiology. 2009. V. 150. No. 1. P. 365–377.