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Identification, cloning and characterization of AcMSH1 from Onion (Allium cepa L.)

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Abstract

Background

MSH1 (MutS homolog1) is a nuclear-encoded protein that plays a crucial role in maintaining low mutation rates and stability of the organellar genome. While plastid MSH1 maintains nuclear epigenome plasticity and affects plant development patterns, mitochondrial MSH1 suppresses illegitimate recombination within the mitochondrial genome, affects mitochondrial genome substoichiometric shifting activity and induces cytoplasmic male sterility (CMS) in crops. However, a detailed functional investigation of onion MSH1 has yet to be achieved.

Materials and results

The homology analysis of onion genome database identified a single copy of the AcMSH1 gene in the onion cv. Bhima Super. In silico analysis of AcMSH1 protein sequence revealed the presence of 6 conserved functional domains including a unique MSH1-specific GIY-YIG endonuclease domain at the C-terminal end. At N-terminal end, it has signal peptide sequences targeting chloroplast and mitochondria. The concentration of AcMSH1 was found to be highest in isolated mitochondria, followed by chloroplasts, and negligible in the cytoplasmic fraction; which proved its localization to the mitochondria and chloroplasts. Quantitative expression analysis revealed that AcMSH1 protein levels were highest in leaves, followed by flower buds, root tips, flowers, and umbels, with the lowest amount found in callus tissue.

Conclusion

Onion genome has single copy of MSH1, with characteristic GIY-YIG endonuclease domain. AcMSH1 targeted towards both chloroplasts and mitochondria. The identification and characterisation of AcMSH1 may provide valuable insights into the development of CMS lines in onion.

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Data Availability

All data are included in the manuscript.

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Acknowledgements

Authors are thankful to Department of Science and Technology - Science and Engineering Research Board for financial support and fellowship provided to author SKK is gratefully acknowledged. Authors are highly thankful to Dr. Major Singh, ICAR-DOGR, Rajgurunagar for his suggestions during the entire work.

Funding

This research work was supported by a grant from the Department of Science and Technology - Science and Engineering Research Board (DST-SERB) (Grant No. CRG/2019/000830).

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    Authors and Affiliations

    1. ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, 410 505, Maharashtra, India

      Pawan Mainkar, Tushar Kashinath Manape, Snehal Krishna Kad & Sivalingam Anandhan

    2. Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa, 50010, USA

      Viswanathan Satheesh

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    1. Pawan Mainkar
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    Contributions

    PM and SA conceived and designed the experiments. PM, TKM and SKK conducted all the experiments. PM, TKM and SKK drafted the manuscript. SA and VS carried out the data analysis and manuscript editing. SA supervised the entire work.

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    Correspondence to Sivalingam Anandhan.

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    Mainkar, P., Manape, T.K., Kad, S.K. et al. Identification, cloning and characterization of AcMSH1 from Onion (Allium cepa L.). Mol Biol Rep 50, 5147–5155 (2023). https://doi.org/10.1007/s11033-023-08414-4

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