A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase

Abstract

The modified nucleoside 1-methyladenosine (m(1)A) is found in the T-loop of many tRNAs from organisms belonging to the three domains of life (Eukaryota, Bacteria, Archaea). In the T-loop of eukaryotic and bacterial tRNAs, m(1)A is present at position 58, whereas in archaeal tRNAs it is present at position(s) 58 and/or 57, m(1)A57 being the obligatory intermediate in the biosynthesis of 1-methylinosine (m(1)I57). In yeast, the formation of m(1)A58 is catalysed by the essential tRNA (m(1)A58) methyltransferase (MTase), a tetrameric enzyme that is composed of two types of subunits (Gcd14p and Gcd10p), whereas in the bacterium Thermus thermophilus the enzyme is a homotetramer of the TrmI polypeptide. Here, we report that the TrmI enzyme from the archaeon Pyrococcus abyssi is also a homotetramer. However, unlike the bacterial site-specific TrmI MTase, the P.abyssi enzyme is region-specific and catalyses the formation of m(1)A at two adjacent positions (57 and 58) in the T-loop of certain tRNAs. The stabilisation of P.abyssi TrmI at extreme temperatures involves intersubunit disulphide bridges that reinforce the tetrameric oligomerisation, as revealed by biochemical and crystallographic evidences. The origin and evolution of m(1)A MTases is discussed in the context of different hypotheses of the tree of life.

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor

“…Although m 1 A58 in the T loop of tRNA has also been shown to be essential for the viability of yeast (Anderson et al 2000), due to its role in maintaining steady-state levels of eukaryotic initiator tRNA (Anderson et al 1998), it is not uniformly present in human cells (Saikia et al 2010) and is rare in bacteria, indicating that it is not a broad-based antimicrobial target. Also, while m 1 A58 is synthesized by the TrmI enzyme in bacteria (Roovers et al 2004;Varshney et al 2004) but by a Trm6-Trm61 complex in eukaryotes (Anderson et al 1998), the bacterial TrmI shares homology with the eukaryotic Trm61, indicating an orthologous relationship between the two enzymes.…”

Crystal Structure of Thermus thermophilus tRNA m1A58 Methyltransferase and Biophysical Characterization of Its Interaction with tRNA

“…6 This hypothesis was demonstrated experimentally for the bacterial orthologs in Thermus thermophilus and Mycobacterium tuberculosis and for the archaeal ortholog in Pyrococcus abyssi. 3,[7][8][9] These proteins are α 4 homotetramers of Trm61p-like proteins, hereafter called TrmI. Interestingly, orthologs of the Trm6p protein could only be found in eukaryotes.…”

The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans

“…In keeping with the conventional nomenclature of tRNA modification enzymes from yeast, GCD10 and GCD14 are now referred to as TRM6 and TRM61, respectively (Kadaba et al 2004). While structural and functional homologs of Trm61p have been identified in Archaea and Eubacteria (Bujnicki 2001;Gupta et al 2001;Droogmans et al 2003;Roovers et al 2004;Varshney et al 2004), homologs of Trm6p have not been found in the sequenced genomes of organisms 1 Present address: The College of St. Scholastica, Duluth, MN 55811, USA.…”