In silico transcriptional regulatory networks involved in tomato fruit ripening
ABSTRACTTomato fruit ripening is a complex developmental programme partly mediated by transcriptional regulatory networks. Several transcription factors (TFs) which are members of gene families such as MADS-box and ERF were shown to play a significant role in ripening through interconnections into a...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01234/full |
| _version_ | 1818014772678885376 |
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| author | Stilianos Arhondakis Craita Elena Bita Andreas Perrakis Maria E. Manioudaki Dimitris Kaloudas Panagiotis Kalaitzis |
| author_facet | Stilianos Arhondakis Craita Elena Bita Andreas Perrakis Maria E. Manioudaki Dimitris Kaloudas Panagiotis Kalaitzis |
| author_sort | Stilianos Arhondakis |
| collection | DOAJ |
| description | ABSTRACTTomato fruit ripening is a complex developmental programme partly mediated by transcriptional regulatory networks. Several transcription factors (TFs) which are members of gene families such as MADS-box and ERF were shown to play a significant role in ripening through interconnections into an intricate network. The accumulation of large datasets of expression profiles corresponding to different stages of tomato fruit ripening and the availability of bioinformatics tools for their analysis provide an opportunity to identify TFs which might regulate gene clusters with similar co-expression patterns. We identified two TFs, a SlWRKY22-like and a SlER24 transcriptional activator which were shown to regulate modules by using the LeMoNe algorithm for the analysis of our microarray datasets representing four stages of fruit ripening, breaker, turning, pink and red ripe. The WRKY22-like module comprised a subgroup of six various calcium sensing transcripts with similar to the TF expression patterns according to real time PCR validation. A promoter motif search identified a cis acting element, the W-box, recognized by WRKY TFs that was present in the promoter region of all six calcium sensing genes. Moreover, publicly available microarray datasets of similar ripening stages were also analyzed with LeMoNe resulting in TFs such as SlERF.E1, SlERF.C1, SlERF.B2, SLERF.A2, SlWRKY24, SLWRKY37 and MADS-box/TM29 which might also play an important role in regulation of ripening. These results suggest that the SlWRKY22-like might be involved in the coordinated regulation of expression of the six calcium sensing genes. Conclusively the LeMoNe tool might lead to the identification of putative TF targets for further physiological analysis as regulators of tomato fruit ripening. |
| first_indexed | 2024-04-14T06:48:22Z |
| format | Article |
| id | doaj.art-50c2021256a344bd871a60891b64aced |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-14T06:48:22Z |
| publishDate | 2016-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-50c2021256a344bd871a60891b64aced2022-12-22T02:07:06ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-08-01710.3389/fpls.2016.01234195142In silico transcriptional regulatory networks involved in tomato fruit ripeningStilianos Arhondakis0Craita Elena Bita1Andreas Perrakis2Maria E. Manioudaki3Dimitris Kaloudas4Panagiotis Kalaitzis5Mediterranean Agronomic Institute of Chania (MAICh)Mediterranean Agronomic Institute of Chania (MAICh)Mediterranean Agronomic Institute of Chania (MAICh)Mediterranean Agronomic Institute of Chania (MAICh)Mediterranean Agronomic Institute of Chania (MAICh)Mediterranean Agronomic Institute of Chania (MAICh)ABSTRACTTomato fruit ripening is a complex developmental programme partly mediated by transcriptional regulatory networks. Several transcription factors (TFs) which are members of gene families such as MADS-box and ERF were shown to play a significant role in ripening through interconnections into an intricate network. The accumulation of large datasets of expression profiles corresponding to different stages of tomato fruit ripening and the availability of bioinformatics tools for their analysis provide an opportunity to identify TFs which might regulate gene clusters with similar co-expression patterns. We identified two TFs, a SlWRKY22-like and a SlER24 transcriptional activator which were shown to regulate modules by using the LeMoNe algorithm for the analysis of our microarray datasets representing four stages of fruit ripening, breaker, turning, pink and red ripe. The WRKY22-like module comprised a subgroup of six various calcium sensing transcripts with similar to the TF expression patterns according to real time PCR validation. A promoter motif search identified a cis acting element, the W-box, recognized by WRKY TFs that was present in the promoter region of all six calcium sensing genes. Moreover, publicly available microarray datasets of similar ripening stages were also analyzed with LeMoNe resulting in TFs such as SlERF.E1, SlERF.C1, SlERF.B2, SLERF.A2, SlWRKY24, SLWRKY37 and MADS-box/TM29 which might also play an important role in regulation of ripening. These results suggest that the SlWRKY22-like might be involved in the coordinated regulation of expression of the six calcium sensing genes. Conclusively the LeMoNe tool might lead to the identification of putative TF targets for further physiological analysis as regulators of tomato fruit ripening.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01234/fullMicroarray AnalysisTomatoFruit ripeningregulatory networkWRKYERF |
| spellingShingle | Stilianos Arhondakis Craita Elena Bita Andreas Perrakis Maria E. Manioudaki Dimitris Kaloudas Panagiotis Kalaitzis In silico transcriptional regulatory networks involved in tomato fruit ripening Frontiers in Plant Science Microarray Analysis Tomato Fruit ripening regulatory network WRKY ERF |
| title | In silico transcriptional regulatory networks involved in tomato fruit ripening |
| title_full | In silico transcriptional regulatory networks involved in tomato fruit ripening |
| title_fullStr | In silico transcriptional regulatory networks involved in tomato fruit ripening |
| title_full_unstemmed | In silico transcriptional regulatory networks involved in tomato fruit ripening |
| title_short | In silico transcriptional regulatory networks involved in tomato fruit ripening |
| title_sort | in silico transcriptional regulatory networks involved in tomato fruit ripening |
| topic | Microarray Analysis Tomato Fruit ripening regulatory network WRKY ERF |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01234/full |
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