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

Aj Harris Aj Harris,Aaron David Goldman

doi:10.1007/s00239-018-9842-z

Abstract

Here, we generate a robust phylogenetic framework for the rRNA adenine N(6)-methyltransferase (RAMTase) protein family that shows a more ancient and complex evolutionary history within the family than previously reported. RAMTases occur universally by descent across the three domains of life, and typical orthologs within the family perform methylation of the small subunits of ribosomal RNA (rRNA). However, within the RAMTase family, two different groups of mitochondrial transcription factors, mtTFB1 and mtTFB2, have evolved in eukaryotes through neofunctionalization. Previous phylogenetic analyses have suggested that mtTFB1 and mtTFB2 comprise sister clades that arose via gene duplication, which occurred sometime following the endosymbiosis event that produced the mitochondrion. Through dense and taxonomically broad sampling of RAMTase family members especially within bacteria, we found that these eukaryotic mitochondrial transcription factors, mtTFB1 and mtTFB2, have independent origins in phylogenetically distant clades such that their divergence most likely predates the last universal common ancestor of life. The clade of mtTFB2s comprises orthologs in Opisthokonts and the clade of mtTFB1s includes orthologs in Amoebozoa and Metazoa. Thus, we clearly demonstrate that the neofunctionalization producing the transcription factor function evolved twice independently within the RAMTase family. These results are consistent with and help to elucidate outcomes from prior experimental studies, which found that some members of mtTFB1 still perform the ancestral rRNA methylation function, and the results have broader implications for understanding the evolution of new protein functions. Our phylogenetic reconstruction is also in agreement with prior studies showing two independent origins of plastid RAMTases in Viridiplantae and other photosynthetic autotrophs. We believe that this updated phylogeny of RAMTases should provide a robust evolutionary framework for ongoing studies to identify and characterize the functions of these proteins within diverse organisms.

Highlights

The enzymatic ribosomal RNA (rRNA) adenine N(6)-methyltransferase protein (RAMTase) family occurs in all three domains of life and is responsible for the methylation of two adjacent adenosine molecules in the highly conserved 3′ terminal hairpin loop of ribosomal small subunits
RAMTase is dependent on S-adenosylmethionine, or SAM, from which it obtains four methyl groups to split between its two adenosine targets (McCulloch et al 2002)
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 ribosomal small subunits (rSSU) (Lisowsky and Michaelis 1988; Park et al 2009; Patron et al 2005)

Summary

Introduction

The enzymatic rRNA adenine N(6)-methyltransferase protein (RAMTase) family occurs in all three domains of life and is responsible for the methylation of two adjacent adenosine molecules in the highly conserved 3′ terminal hairpin loop of ribosomal small subunits (rSSU; O’Farrell et al 2006, 2008). Unknowns are presented by question marks; especially parts of the plastid history and events prior to the duplication of Lineages 1 and 2 can deliver methyl groups to proteins with conserved SAM domains (Cheng and Roberts 2001; Lu 2000).

Results

Conclusion