Comprehensive phylogenetic analysis of evolutionarily conserved rRNA adenine dimethyltransferase suggests diverse bacterial contributions to the nucleus-encoded plastid proteome

Phylogenetic Reconstruction Shows Independent Evolutionary Origins of Mitochondrial Transcription Factors from an Ancient Family of RNA Methyltransferase Proteins

“…Therefore, Lineages 1 and 2 were probably both present in the ancestral Proteobacterium that was the progenitor of the mitochondrial endosymbiont (Kurland and Andersson 2000) were laterally transferred into the eukaryotic domain via the mitochondrial endosymbiosis event. Additionally, our phylogeny is consistent with a prior study (Park et al 2009) showing a complex relationship among RAMTases originating from plastids in Virdiplanteae and other photosynthetic eukaryotes, here represented by photosynthetic Chromerida and vestigial-plastid-bearing Apicomplexa (Sato 2011) of the Alveolata. The plastid RAMTases of both Virdiplanteae and other photosynthetic eukaryotes evolved within Lineage 2 but are only distantly related to one another (Fig.…”

“…The mtTFB1 clade includes the duo-functional amoebozoan mtTFB (hereafter, mtTFB1) based on phylogeny and common domain architecture (Manna et al 2013; Shutt and Gray 2006). Additionally, previous phylogenetic analyses found that the RAMTases that localize to plastids entered the eukaryotic lineage at least twice: once within Viridiplantae and once within all other sampled plastid-bearing lineages, such as Rhodophyta, some “Excavata,” and Alveolata (Park et al 2009). Thus, the origins of the RAMTases that localize to plastids appear inconsistent with both eukaryotic and plastid evolution, in which Viridiplantae and Rhodophyta are sister phyla that obtained their plastids through a single endosymbiosis event involving a bacterium, while the other lineages trace their plastids to secondary or tertiary endosymbiosis events involving a photosynthetic eukaryote (McFadden and van Dooren 2004).…”

“…In addition to the presence of RAMTases within the three domains of life, proteins of this family were likely also encoded in the genomes of the endosymbiotic progenitors of plastids and mitochondria (Lisowsky and Michaelis 1988; Patron et al 2005; Rife 2009; Shutt and Gray 2006). In extant eukaryotes, plastid and mitochondrial RAMTase genes have been transferred to the nucleus, but their protein products localize to the respective organelles where they retain their function of methylating organellar rSSUs (Lisowsky and Michaelis 1988; Park et al 2009; Patron et al 2005). …”

“…Prior phylogenetic analyses of the RAMTase family depict several complex evolutionary events, especially related to the presence of the family in eukaryotic lineages (Cotney and Shadel 2006; Park et al 2009; Shutt and Gray 2006). Notably, all mtTFBs with neofunctionalized roles solely or primarily in transcription comprise a clade in which the mtTFB2s of Metazoa and the mtTFBs of other lineages (hereafter mtTFB2s) are mutually monophyletic (Cotney and Shadel 2006; Park et al 2009; Shadel and Clayton 1995; Shutt and Gray 2006).…”

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

“…It stimulates, but is not necessary for transcription initiation (Diffley and Stillman, 1991;Fisher et al, 1992;Xu and Clayton, 1992;Parisi et al, 1993). Mitochondrial mtTFBs are related to a family of rRNA methyltransferases which dimethylate two adenosines near the 3 end of the rRNA in the small ribosomal subunit (Schubot et al, 2001;Park et al, 2009;Richter et al, 2010). Two yeast mtTFB homologs, mtTFB1 and mtTFB2 were identified in humans as well as in mice.…”