PDF(Pubmed)
Abstract：
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.
摘要：
一些蛋白质家族参与植物中小RNA（sRNA）的生物发生和功能。具有主要角色的包括类似Dicer(DCL)、RNA依赖性RNA聚合酶（RDR），和Argonaute（AGO）蛋白。蛋白质家族，如双链RNA结合（DRB），SERRATE(SE),抑制沉默3（SGS3）作为DCL或RDR蛋白的配偶体。这里,我们提供了对Viridiplantae（又名绿色植物）谱系中196个物种进行的七个sRNA途径蛋白家族的精选注释和系统发育分析。我们的结果表明RDR3蛋白比RDR1/2/6更早出现。RDR6存在于丝状绿藻和所有陆地植物中，表明RDR6蛋白的进化与分阶段小干扰RNA（siRNA）的进化一致。我们将24-nt生殖阶段siRNA相关DCL5蛋白的起源追溯到美国甜旗（Acorusamericanus），最早的分歧，现存的单子叶植物物种。我们对AGO的分析发现了AGO基因丢失的多个重复事件，在分组中保留或进一步重复，表明AGO的进化在单子叶植物中是复杂的。结果还完善了AGO蛋白质的几个进化枝，如AGO4、AGO6、AGO17和AGO18。对AGO蛋白的核定位信号序列和催化三联体的分析揭示了多种AGO的调节作用。总的来说，这项工作为参与植物sRNA生物发生/功能的基因家族提供了一个有组织的和进化上连贯的注释，并提供了对主要sRNA途径进化的见解。
