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.