Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA.
Plant Physiol. 2023 May 31;192(2):1183-1203. doi: 10.1093/plphys/kiad141.
Several protein families participate in the biogenesis and function of small RNAs (sRNAs) in plants. Those with primary roles include Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), and Argonaute (AGO) proteins. Protein families such as double-stranded RNA-binding (DRB), SERRATE (SE), and SUPPRESSION OF SILENCING 3 (SGS3) act as partners of DCL or RDR proteins. Here, we present curated annotations and phylogenetic analyses of seven sRNA pathway protein families performed on 196 species in the Viridiplantae (aka green plants) lineage. Our results suggest that the RDR3 proteins emerged earlier than RDR1/2/6. RDR6 is found in filamentous green algae and all land plants, suggesting that the evolution of RDR6 proteins coincides with the evolution of phased small interfering RNAs (siRNAs). We traced the origin of the 24-nt reproductive phased siRNA-associated DCL5 protein back to the American sweet flag (Acorus americanus), the earliest diverged, extant monocot species. Our analyses of AGOs identified multiple duplication events of AGO genes that were lost, retained, or further duplicated in subgroups, indicating that the evolution of AGOs is complex in monocots. The results also refine the evolution of several clades of AGO proteins, such as AGO4, AGO6, AGO17, and AGO18. Analyses of nuclear localization signal sequences and catalytic triads of AGO proteins shed light on the regulatory roles of diverse AGOs. Collectively, this work generates a curated and evolutionarily coherent annotation for gene families involved in plant sRNA biogenesis/function and provides insights into the evolution of major sRNA pathways.
几个蛋白家族参与了植物中小 RNA（sRNA）的生物发生和功能。其中主要包括 Dicer-like（DCL）、RNA 依赖性 RNA 聚合酶（RDR）和 Argonaute（AGO）蛋白。双链 RNA 结合蛋白（DRB）、SERRATE（SE）和 SUPPRESSION OF SILENCING 3（SGS3）等蛋白家族作为 DCL 或 RDR 蛋白的伴侣发挥作用。在这里，我们对 196 种绿藻门（又名绿色植物）谱系中的七个 sRNA 通路蛋白家族进行了精心注释和系统发育分析。我们的结果表明，RDR3 蛋白比 RDR1/2/6 出现得更早。RDR6 存在于丝状绿藻和所有陆地植物中，这表明 RDR6 蛋白的进化与相分离小干扰 RNA（siRNA）的进化相吻合。我们追溯了 24nt 生殖相分离 siRNA 相关 DCL5 蛋白的起源，可以追溯到最早分化的现存单子叶植物美国菖蒲（Acorus americanus）。我们对 AGOs 的分析确定了 AGO 基因的多个复制事件，这些基因在亚组中丢失、保留或进一步复制，表明 AGOs 在单子叶植物中的进化是复杂的。分析结果还细化了几个 AGO 蛋白支系的进化，如 AGO4、AGO6、AGO17 和 AGO18。对核定位信号序列和 AGO 蛋白催化三联体的分析揭示了不同 AGOs 的调控作用。总的来说，这项工作为参与植物 sRNA 生物发生/功能的基因家族生成了一个精心注释和进化上一致的注释，并为主要 sRNA 途径的进化提供了深入了解。
