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Open AccessArticle

Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway

1
Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice, 62500 Brno, Czech Republic
2
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice, 62500 Brno, Czech Republic
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Department of Biomolecular Sciences, Weizmann Institute of Sciences, Rehovot 7610001, Israel
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Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
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Centre for Structural Biology, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice, 62500 Brno, Czech Republic
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Institute of Science and Technology (IST Austria), 3400 Klosterneuburg, Austria
*
Author to whom correspondence should be addressed.
Equal contribution.
Plants 2020, 9(3), 299; https://doi.org/10.3390/plants9030299
Received: 31 December 2019 / Revised: 21 February 2020 / Accepted: 24 February 2020 / Published: 1 March 2020
(This article belongs to the Special Issue The Evolution of Protein Structure and Function in Plants)
Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes. View Full-Text
Keywords: small RNA (smRNAs); Dawdle (DDL); Tough (TGH); Serrate (SE/ARS2); Argonaute (AGO); Dicer-Like (DCR/DCL); evolution; phylogeny small RNA (smRNAs); Dawdle (DDL); Tough (TGH); Serrate (SE/ARS2); Argonaute (AGO); Dicer-Like (DCR/DCL); evolution; phylogeny
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Moturu, T.R.; Sinha, S.; Salava, H.; Thula, S.; Nodzyński, T.; Vařeková, R.S.; Friml, J.; Simon, S. Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway. Plants 2020, 9, 299.

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