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The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome

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Abstract

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We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement.

Abstract

Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed.

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Acknowledgements

The authors wish to thank the University of Helsinki Language Centre, Finland for outstanding editing and proofreading of the manuscript. We sincerely thank the anonymous reviewers for their valuable time and insightful comments, which greatly improved the quality of the manuscript. We apologize to those whose original work(s) could not be included in this review owing to space limitations.

Funding

Preparation of this review was supported by a grant from the Jiangxi “Shuangqian” Programme (S2019DQKJ2030), the Qing Lan Project of Jiangsu Higher Education Institutions, the Natural Science Foundation for Distinguished Young Scholars of Nanjing Forestry University (JC2019004), the Project for Groundbreaking Achievements of Nanjing Forestry University (202211), a project funded by the Priority Academic Programme Development of Jiangsu Higher Education Institutions, and also the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (OR11465424). The authors are also grateful for the support of Metasequoia Faculty Research Start-up Funding (grant number 163100028) at the Bamboo Research Institute, Nanjing Forestry University for the first author MR.

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Authors and Affiliations

  1. Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China

    Muthusamy Ramakrishnan, Zishan Ahmad & Qiang Wei

  2. State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin’an, Hangzhou, 311300, Zhejiang, China

    Pradeep K. Papolu, Mingbing Zhou & Anket Sharma

  3. Department of Zoology, St. Albert’s College (Autonomous), Kochi, 682018, Kerala, India

    Sileesh Mullasseri

  4. Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin’an, Hangzhou, 311300, Zhejiang, China

    Mingbing Zhou

  5. Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA

    Anket Sharma

  6. Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China

    Viswanathan Satheesh

  7. Helsinki Institute of Life Science HiLIFE, University of Helsinki, Biocenter 3, Viikinkaari 1, F1-00014, Helsinki, Finland

    Ruslan Kalendar

  8. Institute of Plant Biology and Biotechnology (IPBB), Timiryazev Street 45, 050040, Almaty, Kazakhstan

    Ruslan Kalendar

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  1. Muthusamy Ramakrishnan
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  2. Pradeep K. Papolu
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  3. Sileesh Mullasseri
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  4. Mingbing Zhou
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  5. Anket Sharma
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  7. Viswanathan Satheesh
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  8. Ruslan Kalendar
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  9. Qiang Wei
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Contributions

MR, PKP and SM planned, designed and wrote the review. MR, SM, QW, RK and MZ outlined and edited the review. MR, PKP, RK and QW made the table and the images. MR, RK, QW, SM, AS, ZA, VS, and MZ edited and revised the review.

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Correspondence to Ruslan Kalendar or Qiang Wei.

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Communicated by Wusheng Liu.

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Ramakrishnan, M., Papolu, P.K., Mullasseri, S. et al. The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome. Plant Cell Rep 42, 3–15 (2023). https://doi.org/10.1007/s00299-022-02945-z

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