Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway

Abstract

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.

MicroRNA miR-146a-5p inhibits the inflammatory response and injury of airway epithelial cells via targeting TNF receptor-associated factor 6

“…MicroRNA (miRNA), known as non-coding small RNA with about 19 ~ 25nt in length, plays a regulatory role in various biological activities at the posttranscriptional level [7][8][9]. MiRNA, as reported, is vital in modulating airway inflammation in asthma [10,11].…”

Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation

“…Phylogenetic analyses on the miRNA biogenesis machinery confirmed the presence of the majority of microprocessor proteins in representatives of all major green plant lineages, including green algae, bryophytes, ferns, and seed plants [ 41 , 161 , 162 , 163 , 164 , 165 ]. Currently living green plants ( Viridiplantae ) can be subdivided into two lineages: Chlorophyta (majority of the green algae), and Streptophyta (embryophytes and their closest algal relatives, a grade collectively known as streptophyte algae).…”

“…Similarly to HYL1 evolutionary conservation, we found that homologs of the SE protein contain conserved SERRATE_Ars2_N—ARS2 domain architecture, regardless of the taxonomic position of the plant studied. Phylogenetic studies published in recent years have shown that single copies of SE orthologs are present in all lineages of the plant and animal kingdoms but were not identified in prokaryotes, suggesting that the SE protein encoding gene emerged as a single copy in the last eucaryotic common ancestor (LECA) [ 161 , 163 , 164 ]. Interestingly, in representatives of some embryophytes, such as moss Physcomitrium patens, water lily Nymphaea colorata or parasitic dicot Striga asiatica, the SE gene underwent a duplication event.…”

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

“…Furthermore, JsCBF5 and JsICE1b had more protein interaction relationships compared to other CBF and ICE proteins. In plants, miRNAs play many biological functions by regulating the expression of target genes, such as in clod tolerance [44][45][46]. There is no published miRNA database in psRNATarget for walnut species, so we predicted the interaction network between the CBF and ICE proteins in walnuts and the putative miRNA in Arabidopsis for target prediction.…”