Noronha Fernandes-Brum Christiane, Marinho Rezende Pâmela, Cherubino Ribeiro Thales Henrique, Ricon de Oliveira Raphael, Cunha de Sousa Cardoso Thaís, Rodrigues do Amaral Laurence, de Souza Gomes Matheus, Chalfun-Junior Antonio
Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil.
Departamento de Genética, Universidad de Córdoba (UCO), Córdoba, Spain.
PLoS One. 2017 Apr 27;12(4):e0176333. doi: 10.1371/journal.pone.0176333. eCollection 2017.
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated), and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA) pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.
微小RNA（miRNA）来源于自身互补的发夹结构，而小干扰RNA（siRNA）则来源于双链RNA（dsRNA）或发夹前体。小RNA产生的核心机制涉及类Dicer（DCL）蛋白对小RNA（sRNA）的加工以及AGO蛋白作为沉默效应因子的作用，并且siRNA的生物合成还涉及RNA依赖的RNA聚合酶（RDR）、Pol IV和Pol V在生物合成中的作用。其他几种蛋白质与核心蛋白相互作用，以指导sRNA的生物合成、作用和周转。我们旨在揭示一种具有全球经济意义的非模式植物物种中RNA介导的沉默途径的组成成分和功能。在咖啡（Coffea canephora）基因组中已鉴定出sRNA介导的沉默复合体成员，并通过计算分析在结构、功能和进化水平上对其进行了表征。鉴定出了11种AGO蛋白、9种DCL蛋白（其中包括一种之前未注释的类DCL1蛋白）和8种RDR蛋白。还鉴定出了另外48种与小RNA（sRNA）途径相关的蛋白。此外，我们从113个MIR家族中鉴定出235个miRNA前体和317个成熟miRNA，并对ccp-MIR156、ccp-MIR172和ccp-MIR390进行了表征。对2239个推定靶标的靶标预测和基因本体分析表明，咖啡中的重要途径受到miRNA的靶向作用。我们提供了与sRNA途径相关基因座扩展的证据，通过结构域和催化位点分析对这些蛋白质活性的深入了解，以及基因表达分析。MIR基因座的数量及其靶向途径突出了miRNA在咖啡中的重要性。我们确定了sRNA在咖啡中的几种作用，这为更好地理解这种主要作物的转录和转录后调控提供了大量深入见解。
