tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote

Abstract

ABSTRACTtRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of wholegenome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced relative to the other yeasts, while genes for synonymous wobble iso-acceptors are amplified, indicating wobble use not apparent in any other eukaryote. We identified a subset of japonicus-specific wobbles that improves correlation of codon use and tRNA gene content in japonicus. We conclude that tgCNV is high among Schizo species and occurs in related laboratory strains of S. pombe (and expectedly other species), and tRNAome-codon analyses can provide insight into species-specific wobble decoding.

Lack of tRNA Modification Isopentenyl-A37 Alters mRNA Decoding and Causes Metabolic Deficiencies in Fission Yeast

“…Misreading is largely affected by competition among tRNAs for ribosome fit and codon match, and depending on the system at hand, rates can vary from 10 Ϫ3 to 10 Ϫ5 (13)(14)(15). A potential source of differing rates might be the species-specific composition of the tRNA gene complement (tRNAome) (16). Consistent with this possibility are mutants in Maf1, a repressor of tRNA synthesis, that exhibit asymmetric increases in the levels of different tRNAs and increased translational fidelity at UAA and UAG codons (17).…”

Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA

“…It is important to note here that S. cerevisiae, S. pombe and humans modify different subsets of tRNAs with i6A37, both the cy-and mt-tRNAs (Lamichhane et al 2011(Lamichhane et al , 2013bHorvath and Chinnery 2015;Wei et al 2015). Differences in tRNA-i6A37 subsets is part of a wider variability in the overall tRNA gene content of different eukaryotic genomes and in the tRNA anticodon modification systems, which together with corresponding codon-content may contribute to plasticity of genetic information (Iben and Maraia 2012;Maraia and Iben 2014). That tRNA Tyr is most limiting in S. pombe should not necessarily be expected to be extrapolable to other species.…”

Different types of secondary information in the genetic code

“…Relative numbers of tRNA isoacceptor genes is markedly different in related Schizosaccharomyces species, and among individual persons, particularly relevant to wobble decoding Maraia 2012, 2013). A wide variability in Schizosaccharomyces tRNAomes exists despite similar genome size and remarkable conservation of other features of the genomes (Iben and Maraia 2012). In addition to variance in tRNA gene number, there was a striking reorganization of the fractional content of isoacceptor tRNA genes in these species: Lack of any genes for tRNA Ala AGC is specific to Schizosaccharomyces japonicas, and this was accompanied by amplification of the tRNA Ala UGC gene necessitating wobble decoding of GCU codons not required in the other species (Iben and Maraia 2012).…”

“…In addition to variance in tRNA gene number, there was a striking reorganization of the fractional content of isoacceptor tRNA genes in these species: Lack of any genes for tRNA Ala AGC is specific to Schizosaccharomyces japonicas, and this was accompanied by amplification of the tRNA Ala UGC gene necessitating wobble decoding of GCU codons not required in the other species (Iben and Maraia 2012). Gene numbers for tRNA Ser UGA, tRNA Gly UCC, and tRNA Val UAC have similarly diverged among Schizosaccharomyces, all encoding U34, the most versatile of the wobble bases and most deterministic of synonymous decoding (Iben and Maraia 2012). Variability of these highly related tRNAomes presumably reflects their readiness to evolve (Yona et al 2013;Bloom-Ackermann et al 2014).…”

“…An independent variable is the tRNA complement, which can differ significantly in gene copy number not only among related species (Chan and Lowe 2009;Iben and Maraia 2012) but also in different strains of a single yeast species (Iben et al 2011;Iben and Maraia 2012) and among different humans (Iben and Maraia 2013;Parisien et al 2013). tRNAome variability can be a determinant of expression of specific mRNAs, at least in some microorganisms (Bulmer 1987).…”