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Differential transcriptional activation of copia family of different plant retrotransposons

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Abstract

Plant genomes contain a sizeable fraction, ranging from 14 to 75% of retrotransposons (class I elements), predominantly comprising LTR (Long Terminal Repeat) elements. Movement of these elements is mediated via an RNA intermediate by copy-and-paste mechanism. The transposition of the elements is tightly regulated, however, under certain conditions such as stress; they are transcriptionally and possibly transpositionally activated. The 5’-LTRs of retrotransposons contain regulatory sequences required for their transcriptional activation. Each element is usually present in multiple copies and not all copies of an element may be functional possibly due to alterations in its internal sequence domains, without affecting the functionality of their 5’-LTRs. We analyzed the transcriptional activation of six Ty1-copia family of retrotransposons selected from six different plants (two monocots and four dicots) by monitoring pattern of GUS expression directed by 5’-LTRs in transgenic tobacco plants in response to a variety of stress factors (cold, UV, H2O2, HgCl2, CdCl2, CuCl2, 2,4-D, SA, ABA) and tissue-specific (callus, root, leaf, stem and flower) cues. We show that different 5’-LTRs show differential activation under various conditions. Two retroelements which were considered non-functional apparently have functional 5’-LTRs. No apparent correlation between the presence of sequence elements in the 5-LTRs and transcriptional activation of the retroelements in response to stress and tissue-specific signals could be established. The results suggest that the transcriptional activation and possibly silencing of different retrotransposons is a complex process and may be mediated by multiple interconnected pathways.

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Abbreviations

LTR:

Long Terminal Repeat

LINE:

Long Interspersed Nuclear Element

SINE:

Short Interspersed Nuclear Element

ABA:

Absissic acid

SA:

Salicylic acid

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Acknowledgements

Financial assistance of University Grants Commission (UGC) is gratefully acknowledged. SM acknowledges the CSIR for fellowship.

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Authors and Affiliations

  1. School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

    Somnath Mukherjee, Deepak Sharma & Kailash C. Upadhyaya

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  1. Somnath Mukherjee
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  2. Deepak Sharma
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  3. Kailash C. Upadhyaya
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Contributions

SM designed and performed the experiments. KCU conceptualized the study and designed the experiments. DS contributed the lab support and some of the supplies. KCU and SM wrote the manuscript.

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Correspondence to Kailash C. Upadhyaya.

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Mukherjee, S., Sharma, D. & Upadhyaya, K.C. Differential transcriptional activation of copia family of different plant retrotransposons. J. Plant Biochem. Biotechnol. 31, 915–924 (2022). https://doi.org/10.1007/s13562-022-00771-8

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