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Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses

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Abstract

In tomato, DNA methylation has an inhibitory effect on fruit ripening. The inhibition of DNA methyltransferase by 5-azacytidine results in premature fruit ripening. Methyl CpG binding domain (MBD) proteins are the readers of DNA methylation marks and help in the recruitment of chromatin-modifying enzymes which affect gene expression. Therefore, we investigate their contribution during fruit development. In this study, we identified and analyzed 18 putative genes of Solanum lycopersicum and Solanum pimpinellifolium encoding MBD proteins. We also identified tomato MBD syntelogs in Capsicum annum and Solanum tuberosum. Sixty-three MBD genes identified from four different species of solanaceae were classified into three groups. An analysis of the conserved domains in these proteins identified additional domains along with MBD motif. The transcript profiling of tomato MBDs in wild-type and two non-ripening mutants, rin and Nr, indicated constructive information regarding their involvement during fruit development. When we performed a stage-specific expression analysis during fruit ripening, a gradual decrease in transcript accumulation in the wild-type fruit was detected. However, a very low expression was observed in the ripening mutants. Furthermore, many ethylene-responsive cis-elements were found in SlMBD gene promoters, and some of them were induced in the presence of exogenous ethylene. Further, we detected the possible role of these MBDs in abiotic stresses. We found that few genes were differentially expressed under various abiotic stress conditions. Our results provide an evidence of the involvement of the tomato MBDs in fruit ripening and abiotic stress responses, which would be helpful in further studies on these genes in tomato fruit ripening.

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Acknowledgements

APP acknowledges the Council of Scientific and Industrial Research (CSIR), India for providing research fellowship. AKS acknowledges the Department of Science and Technology, India, for the Purse Grant. The SAP grant of the University Grants Commission to the Department of Plant Molecular Biology for support of infrastructure is also acknowledged.

Funding

This work was supported by a Purse Grant by the Department of Science and Technology, Government of India.

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Authors and Affiliations

  1. Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India

    Adwaita Prasad Parida, Utkarsh Raghuvanshi, Amit Pareek, Vijendra Singh & Arun Kumar Sharma

  2. Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India

    Rahul Kumar

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  1. Adwaita Prasad Parida
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  2. Utkarsh Raghuvanshi
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  3. Amit Pareek
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  4. Vijendra Singh
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  6. Arun Kumar Sharma
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Contributions

AKS: Conceptualized and designed the experiments. APP and RK conducted the data analysis and wrote the manuscript. APP and UR performed gene expression profiling and VS and AP performed the in silico promoter analysis.

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Correspondence to Arun Kumar Sharma.

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Parida, A.P., Raghuvanshi, U., Pareek, A. et al. Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses. Mol Biol Rep 45, 2653–2669 (2018). https://doi.org/10.1007/s11033-018-4435-x

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