PPR proteins are a diverse family of RNA binding factors found in all Eukaryotic lineages. They perform multiple functions in the expression of organellar genes, mostly on the post-transcriptional level. PPR proteins are also significant determinants of evolutionary nucleo-organellar compatibility. Plant PPR proteins recognize their RNA substrates using a simple modular code. No target sequences recognized by animal or yeast PPR proteins were identified prior to the present study, making it impossible to assess whether this plant PPR code is conserved in other organisms. Dmr1p (Ccm1p, Ygr150cp) is a S. cerevisiae PPR protein essential for mitochondrial gene expression and involved in the stability of 15S ribosomal RNA. We demonstrate that in vitro Dmr1p specifically binds a motif composed of multiple AUA repeats occurring twice in the 15S rRNA sequence as the minimal 14 nucleotide (AUA)4AU or longer (AUA)7 variant. Short RNA fragments containing this motif are protected by Dmr1p from exoribonucleolytic activity in vitro. Presence of the identified motif in mtDNA of different yeast species correlates with the compatibility between their Dmr1p orthologues and S. cerevisiae mtDNA. RNA recognition by Dmr1p is likely based on a rudimentary form of a PPR code specifying U at every third position, and depends on other factors, like RNA structure.

中文翻译：

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酵母五肽蛋白 Dmr1（Ccm1）结合小亚基线粒体核糖体 RNA 中富含 AU 的重复基序

PPR 蛋白是在所有真核细胞谱系中发现的多种 RNA 结合因子家族。它们在细胞器基因的表达中发挥多种功能，主要是在转录后水平上。PPR 蛋白也是进化核细胞器兼容性的重要决定因素。植物 PPR 蛋白使用简单的模块化代码识别其 RNA 底物。在本研究之前，没有鉴定出动物或酵母 PPR 蛋白识别的靶序列，因此无法评估该植物 PPR 代码在其他生物体中是否保守。Dmr1p (Ccm1p, Ygr150cp) 是一种酿酒酵母 PPR 蛋白，对线粒体基因表达至关重要，并参与 15S 核糖体 RNA 的稳定性。我们证明体外 Dmr1p 特异性结合由在 15S rRNA 序列中作为最小 14 个核苷酸 (AUA)4AU 或更长 (AUA)7 变体出现两次的多个 AUA 重复组成的基序。含有该基序的短 RNA 片段受到 Dmr1p 的保护，使其免受体外核糖核酸外切活动的影响。不同酵母物种的 mtDNA 中已识别基序的存在与其 Dmr1p 直向同源物和酿酒酵母 mtDNA 之间的兼容性相关。Dmr1p 的 RNA 识别可能基于 PPR 代码的基本形式，在每三个位置指定 U，并取决于其他因素，如 RNA 结构。不同酵母物种的 mtDNA 中已识别基序的存在与其 Dmr1p 直向同源物和酿酒酵母 mtDNA 之间的兼容性相关。Dmr1p 对 RNA 的识别可能基于 PPR 代码的基本形式，在每三个位置指定 U，并取决于其他因素，如 RNA 结构。不同酵母物种的 mtDNA 中已识别基序的存在与其 Dmr1p 直向同源物和酿酒酵母 mtDNA 之间的兼容性相关。Dmr1p 对 RNA 的识别可能基于 PPR 代码的基本形式，在每三个位置指定 U，并取决于其他因素，如 RNA 结构。