Journal of Environment and Sociobiology

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Repetitive Sequences in Monocot MICRORNAs – Targets for Future Bioengineering Strategies for Climate Resilient Crops


Affiliations
1 Post Graduate Department of Botany, Barasat Government College, Barasat., India
2 Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata., India
3 Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata., India
     

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miRNAs are a de novo class of endogenous, small, non-coding RNAs (19–21 nucleotides long) that are evolutionarily conserved and have a direct impact on the processes of development, differentiation, growth, metabolism, and disease resistance. Micro (mi)RNAs having high base- pair complementarity exert their effect by post-transcriptional silencing of targets. miRNAs functions by acting upon target mRNA induce cleavage and subsequent degradation of it. Further more, they can also repress the translational targets. mRNA deadenylation and their subsequent degradation is caused by the induction of translational repression of miRNAs in animals. Plant miRNA not only differ in their mechanism of gene regulation but they also differ from biogenesis point of view. Majority of the miRNAs function as negative switches to control the expression of important genes, like transcription factors, which affects how the body reacts to stress and during development. With the impact of climate change the mean average temperatures are on the rise. Thus, the need of the hour is to identify or develop crops that can be grown in areas even under above normal temperatures. For this the microRNA regulatory pathways offers us with the necessary tweaking cascade that can be explored further. This work focuses on the identification of internal repeats in microRNA sequences which not only enables us to identify and map the occurrence of the specific molecules but also enables us to formulate methods for their regulation. Results indicate that there is a strong correlation between the occurrence of internal repeats and miRNA stability.

Keywords

Climate Change, MicroRNAs, Internal Repeats.
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  • Bonnet, E., Wuyts, J., Rouzé, P. and Van de Peer, Y. 2004. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 20(17): 2911-2917.

  • Devi, K. J., Chakraborty, S., Deb, B. and Rajwanshi, R. 2016. Computational identification and functional annotation of microRNAs and their targets from expressed sequence tags (ESTs) and genome survey sequences (GSSs) of coffee (Coffea arabicaL.). Plant Gene, 6: 30-42.

  • Dexheimer, P. J. and Cochella, L. 2020. MicroRNAs: from mechanism to organism. Front. Cell Dev. Biol., 8: 409. DOI: 10.3389/fcell.2020.00409

  • Djami-Tchatchou, A. T., Sanan-Mishra, N., Ntushelo, K. and Dubery, I. A. 2017. Functional roles of microRNAs in agronomically important plants-potential as targets for crop improvement and protection. Front. Plant Sci., 8: 378. https:// doi.org/10.3389/fpls.2017.00378.

  • Dong, Q. H., Han, J., Yu, H-P., Wang, C., Zhao, M-Z., Liu, H., Ge, A-J. and Fang, J-G. 2012. Computational identification of microRNAs in strawberry expressed sequence tags and validation of their precise sequences by miR-RACE. J. Hered, 103(2): 268-277. DOI: 10.1093/jhered/esr127

  • Griffiths-Jones, S., Saini, H. K., Van Dongen, S. and Enright, A. J. 2008. miRBase: tools for microRNA genomics. Nucleic Acids Res., 36 (Issue Suppl. 1): D154– D158. https://doi.org/10.1093/nar/gkm952.

  • http://bioserver1.physics.iisc.ernet.in/cgi-bin/fair4/fair/indx.pl http://www.unafold. org/mfold/applications/rna-folding-form.php http://www.mirbase.org/cgi-bin/ browse.pl

  • Lindow, M. and Krogh, A. 2005. Computational evidence for hundreds of non- conserved plant microRNAs. BMC Genomics, 6(1): 119. DOI: 10.1186/1471-2164-6-119

  • Magner, D., Nowak, R., Onyekaa, E. L., Pasternak, A. and Kierzek, R. 2022. A structural potential of rare trinucleotide repeat tracts in RNA. Int. J. Mol. Sci., 23(10): 5850. https://doi.org/10.3390/ijms23105850

  • Mak, C. H. and Phan, E. N. H. 2021. Diagrammatic approaches to RNA structures with trinucleotide repeats. Biophys. J., 120(11): 2343-2354. https://doi. org/10.1016/j.bpj.2021.04.010

  • Millar A. A. 2020. The function of miRNAs in plants. Plants (Basel), 9(2): 198. https:// doi.org/10.3390/plants9020198

  • Patanun, O., Lertpanyasampatha, M., Sojikul, P., Viboonjun, U. and Narangajavana, J. 2013. Computational identification of microRNAs and their targets in Cassava (Manihot esculentaCrantz.). Mol. Biotechnol., 53(3): 257-269. DOI: 10.1007/ s12033-012-9521-z

  • Rhoades, M. W., Reinhart, B. J., Lim, L. P., Burge, C. B., Bartel, B. and Bartel, D. P. 2002. Prediction of plant microRNA targets. Cell, 110(4): 513-520. https:// doi.org/10.1016/s0092-8674(02)00863-2

  • Richard, G-F., Kerrest, A. and Dujon, B. 2008. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol. Mol. Biol. Rev., 72(4): 686-727. https://doi.org/10.1128/MMBR.00011-08.

  • Schwab, R., Palatnik, J. F., Riester, M., Schommer, C., Schmid, M. and Weigel, D. 2005. Specific effects of microRNAs on the plant transcriptome. Dev Cell., 8(4): 517-527. DOI: 10.1016/j.devcel.2005.01.018

  • Sobczak, K., Michlewski, G., De Mezer, M., Kierzek, E., Krol, J., Olejniczak, M., Kierzek, R. and Krzyzosiak, W. J. 2010. Structural diversity of triplet repeat RNAs. J. Biol. Chem., 285(17): 12755-12764. DOI: 10.1074/jbc.M109.078790

  • Yin, Z., Li, C., Han, X. and Shen, F. 2008. Identification of conserved micro RNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 414(1-2): 60-66. DOI: 10.1016/j.gene.2008.02.007


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  • Repetitive Sequences in Monocot MICRORNAs – Targets for Future Bioengineering Strategies for Climate Resilient Crops

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Authors

Sohini Ganguli Gupta
Post Graduate Department of Botany, Barasat Government College, Barasat., India
Souradip Basu
Post Graduate Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata., India
Sayak Ganguli
Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata., India

Abstract


miRNAs are a de novo class of endogenous, small, non-coding RNAs (19–21 nucleotides long) that are evolutionarily conserved and have a direct impact on the processes of development, differentiation, growth, metabolism, and disease resistance. Micro (mi)RNAs having high base- pair complementarity exert their effect by post-transcriptional silencing of targets. miRNAs functions by acting upon target mRNA induce cleavage and subsequent degradation of it. Further more, they can also repress the translational targets. mRNA deadenylation and their subsequent degradation is caused by the induction of translational repression of miRNAs in animals. Plant miRNA not only differ in their mechanism of gene regulation but they also differ from biogenesis point of view. Majority of the miRNAs function as negative switches to control the expression of important genes, like transcription factors, which affects how the body reacts to stress and during development. With the impact of climate change the mean average temperatures are on the rise. Thus, the need of the hour is to identify or develop crops that can be grown in areas even under above normal temperatures. For this the microRNA regulatory pathways offers us with the necessary tweaking cascade that can be explored further. This work focuses on the identification of internal repeats in microRNA sequences which not only enables us to identify and map the occurrence of the specific molecules but also enables us to formulate methods for their regulation. Results indicate that there is a strong correlation between the occurrence of internal repeats and miRNA stability.

Keywords


Climate Change, MicroRNAs, Internal Repeats.

References