Figure 3. α-proteobacteria have different types of COX operons and catalytic subunits of aa₃ oxidase.

A – Graphical representation of aa₃ oxidase gene clusters.

The different COX clusters of α-proteobacteria are classified by considering gene sequence variations and the features of flanking genes (see also “Classification of bacterial COX operons” in File S1). Specific graphical symbols identify COX subunits as indicated; other types of proteins are labelled as follows: white hexagon, enzyme working with RNA or DNA; red diamond with enclosed c, cytochrome c type protein; truncated triangle pointing left, ABC transporter/permease; grey sharp triangle, transcription regulator; PQQ, PQQ-dependent dehydrogenase; white diamond, protein belonging to a DUF family [41], e.g. DUF983; question mark within hexagon, completely unknown protein. Note that SURF1 (Surfeit locus protein 1) and SCO (Synthesis of cytochrome c oxidase) are also involved in the biogenesis of oxidases. Distance between genes is arbitrary. COX operon type a-I is attached to a Nrf-like gene cluster, also called Alternative Complex III or Act [50], containing two homologues of the membrane subunit NrfD (called NrfD2 and NrfD-like here, as shown at the side of the figure). The synthenic diads of protist mitochondria [48] are shown below the blue line. Each of the recognised subfamilies of COX3 [41] is represented by a different colour, as indicated in the middle of the illustration. B - Representative distance tree of COX 1 proteins. The tree was obtained with Neighbour Joining (maximal distance 0.9) using the DELTABLAST program [80] with the COX1 protein of Methylobacterium extorquens PA1 (Accession: YP_001637594) as query. The group containing bacterial and mitochondrial proteins (mito.) is enclosed in the blue square. Protein length and type of COX operon are annotated on the right of the tree. C – Simplified pattern of typical phylogenetic trees of COX 1 proteins.The tree is modelled to match distance trees of nitrate reductase (Fig. 2C) and COX1 (part B). Branch length is arbitrary.