GC-content of tRNA genes classifies archaea into two groups

Kawai, Yoshio; Maeda, Yoshimi

doi:10.2323/jgam.55.403

Cited by 2 publications

(2 citation statements)

References 19 publications

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“…P. novymonadis genome with the GC content higher than 56% and all these genes encode tRNAs. This is in agreement with an earlier observation that in prokaryotes the GC content of such genes does not correlate with that of the whole genome ( Kawai and Maeda, 2009 ).…”

Section: Resultssupporting

confidence: 93%

Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas

et al. 2017

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We have sequenced, annotated, and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it has all the hallmarks of the endosymbionts’ genomes, such as significantly reduced size, extensive gene loss, low GC content, numerous gene rearrangements, and low codon usage bias. In addition, Ca. P. novymonadis lacks mobile elements, has a strikingly low number of pseudogenes, and almost all genes are single copied. This suggests that it already passed the intensive period of host adaptation, which still can be observed in the genome of Polynucleobacter necessarius, a certainly recent endosymbiont. Phylogenetically, Ca. P. novymonadis is more related to P. necessarius, an intracytoplasmic bacterium of free-living ciliates, than to Ca. Kinetoplastibacterium spp., the only other known endosymbionts of trypanosomatid flagellates. As judged by the extent of the overall genome reduction and the loss of particular metabolic abilities correlating with the increasing dependence of the symbiont on its host, Ca. P. novymonadis occupies an intermediate position P. necessarius and Ca. Kinetoplastibacterium spp. We conclude that the relationships between Ca. P. novymonadis and N. esmeraldas are well-established, although not as fine-tuned as in the case of Strigomonadinae and their endosymbionts.

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Section: Resultssupporting

confidence: 93%

Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas

et al. 2017

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“…While several studies in both archaea (58) and bacteria (59,60) have shown that the nucleotide content of tRNA genes does not comply with the genomic GC content but is rather restricted by habitat temperature through constraints on folding stability, the wobble position, which does not contribute to structure stability, might be free from these constraints and conform to nucleotide content bias.…”

Section: Discussionmentioning

confidence: 99%

Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics

Wald

Margalit

2014

Nucleic Acids Research

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Decoding of all codons can be achieved by a subset of tRNAs. In bacteria, certain tRNA species are mandatory, while others are auxiliary and are variably used. It is currently unknown how this variability has evolved and whether it provides an adaptive advantage. Here we shed light on the subset of auxiliary tRNAs, using genomic data from 319 bacteria. By reconstructing the evolution of tRNAs we show that the auxiliary tRNAs are highly dynamic, being frequently gained and lost along the phylogenetic tree, with a clear dominance of loss events for most auxiliary tRNA species. We reveal distinct co-gain and co-loss patterns for subsets of the auxiliary tRNAs, suggesting that they are subjected to the same selection forces. Controlling for phylogenetic dependencies, we find that the usage of these tRNA species is positively correlated with GC content and may derive directly from nucleotide bias or from preference of Watson–Crick codon–anticodon interactions. Our results highlight the highly dynamic nature of these tRNAs and their complicated balance with codon usage.

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GC-content of tRNA genes classifies archaea into two groups

Abstract: 404Vol. 55 KAWAI and MAEDA

Cited by 2 publications

References 19 publications

Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas

Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas

Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics

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