COX assembly and the mitochondrial cycle.

COX (cytochrome c oxidase) assembly is a highly regulated multi-step process involving discrete short-term intermediates, S1, S2, S3 [23]. The table describes the known components involved in COX assembly and the relevant properties of the corresponding mRNAs. MLR (Mitochondria Localization of nuclear-encoded mRNA) characteristics are from [10]; classes indicate whether the mRNAs are translated on Puf3p-dependent (class I), mitochondria-linked (class II) or on free polysomes (class III). Phases A to C correspond to the early time-window of the mitochondrial cycle. The first step of COX assembly is the site-specific translation of the mitochondrially encoded COX subunits. For instance, COX1 mRNA is translated under the control of the translation regulators MSS51 and PET309 (both are class I mRNAs present during phase A, Dataset S3). The second step is the addition of Cox5p and Cox6p; note that Cox5p is the only structural subunit belonging to phase A, consistent with its role in early assembly step [25]. The last step is the addition of the rest of the nuclear-encoded subunits (shield proteins). These two last steps require the presence of the assembly factors. Note that most of the assembly factor transcripts appear during phase A, whereas the shield protein transcripts are present during phase B. In addition, assembly factor transcripts are localized to the vicinity of mitochondria (MLR, class I) and depend on Puf3p for this localization. Shield protein transcripts are translated on free polysomes (MLR class III) and have no Puf3p binding site.细胞色素c氧化酶（cytochrome c oxidase，简称COX）的组装是一个受高度调控的多步骤过程，涉及S1、S2、S3三类离散的短期中间体[23]。本表格详述了COX组装过程中已明确的参与组分，以及对应mRNA的相关属性。核编码mRNA的线粒体定位（Mitochondria Localization of nuclear-encoded mRNA，简称MLR）特征源自文献[10]；分类规则用于标注mRNA的翻译位点：依赖Puf3p的翻译体系（I类）、与线粒体关联的翻译体系（II类），或在游离多聚核糖体上的翻译（III类）。A至C三个时期对应线粒体周期的早期时间窗口。COX组装的第一步为线粒体编码的COX亚基的位点特异性翻译。例如，COX1 mRNA的翻译受翻译调控因子MSS51与PET309的调控（二者均为I类mRNA，且在时期A阶段表达，详见数据集S3）。第二步为添加Cox5p与Cox6p；需注意，Cox5p是唯一归属时期A的结构亚基，这与其在早期组装步骤中的功能高度一致[25]。最后一步则为添加其余核编码亚基（即屏蔽蛋白）。上述后两步均依赖组装因子的参与。值得注意的是，多数组装因子的转录本在时期A阶段出现，而屏蔽蛋白的转录本则于时期B阶段存在。此外，组装因子的转录本定位于线粒体邻近区域（MLR I类），且其定位过程依赖Puf3p；屏蔽蛋白的转录本在游离多聚核糖体上完成翻译（MLR III类），且不携带Puf3p结合位点。