Data from: Evolution and diversification of the organellar release factor family

Translation termination is accomplished by proteins of the Class I release factor family (RF) that recognize stop codons and catalyze the ribosomal release of the newly synthesized peptide. Bacteria have two canonical RFs: RF1 recognizes UAA and UAG, RF2 recognizes UAA and UGA. Despite that these 2 release factor proteins are sufficient for de facto translation termination, the eukaryotic organellar RF protein family, which has evolved from bacterial release factors, has expanded considerably, comprising multiple subfamilies, most of which have not been functionally characterized or formally classified. Here we integrate multiple sources of information to analyze the remarkable differentiation of the RF family among organelles. We document the origin, phylogenetic distribution and sequence structure features of the mitochondrial and plastidial release factors: mtRF1a, mtRF1, mtRF2a, mtRF2b, mtRF2c, ICT1, C12orf65, pRF1 and pRF2, and review published relevant experimental data. The canonical release factors (mtRF1a, mtRF2a, pRF1 and pRF2) and ICT1 are derived from bacterial ancestors, while the others have resulted from gene duplications of another release factor. These new RF family members have all lost one or more specific motifs relevant for bona fide release factor function but are mostly targeted to the same organelle as their ancestor. We also characterize the subset of canonical release factor proteins that bear non-classical PxT/SPF tripeptide motifs, and provide a molecular-model-based rationale for their retained ability to recognize stop codons. Finally we analyze the co-evolution of canonical RFs with the organellar genetic code. Although the RF presence in an organelle and its stop codon usage tend to co-evolve, we find three taxa that encode an RF2 without using UGA stop codons, and one reverse scenario, where mamiellales green algae use UGA stop codons in their mitochondria without having a mitochondrial type RF2. For the latter we put forward a “stop-codon re-invention” hypothesis that involves the retargeting of the plastid release factor to the mitochondrion.翻译终止过程由I类释放因子家族（Class I release factor family，RF）的蛋白质完成，这类因子可识别终止密码子并催化核糖体释放新合成的肽链。细菌拥有两种经典释放因子：RF1识别UAA与UAG，RF2识别UAA与UGA。尽管这两种释放因子蛋白已足以实现实际的翻译终止，但从细菌释放因子演化而来的真核生物细胞器释放因子蛋白家族已发生显著扩增，包含多个亚家族，其中绝大多数尚未得到功能表征或正式分类。本研究整合多源信息，分析细胞器中释放因子家族的显著分化情况。我们对线粒体与质体释放因子（包括mtRF1a、mtRF1、mtRF2a、mtRF2b、mtRF2c、ICT1、C12orf65、pRF1及pRF2）的起源、系统发育分布及序列结构特征进行了梳理，并综述了已发表的相关实验数据。经典释放因子（mtRF1a、mtRF2a、pRF1与pRF2）及ICT1均起源于细菌祖先，而其余家族成员则源自另一释放因子的基因重复事件。这些新出现的释放因子家族成员均丢失了一个或多个与真正释放因子功能相关的特异性结构基序，但大多仍与祖先蛋白一样靶向至同一细胞器。我们还对携带非经典PxT/SPF三肽基序的经典释放因子蛋白亚群进行了表征，并基于分子模型为其仍保留识别终止密码子的能力提供了理论依据。最后我们分析了经典释放因子与细胞器遗传密码的共进化关系。尽管细胞器中释放因子的存在与其终止密码子使用偏好性往往存在共进化现象，但我们发现三个类群编码RF2却不使用UGA终止密码子，以及一种反向情况：微胞藻目（mamiellales）绿藻的线粒体基因组中使用UGA作为终止密码子，却未编码线粒体型RF2。针对后者，我们提出了“终止密码子重塑”假说，该假说涉及将质体释放因子重靶向至线粒体中。