tRNAs as a Driving Force of Genome Evolution in Yeast

Guimarães, Ana Rita; Correia, Inês; Sousa, Inês; Oliveira, Carla Roma; Moura, Gabriela; Bezerra, Ana R.; Santos, Manuel A. S.

doi:10.3389/fmicb.2021.634004

Cited by 10 publications

(5 citation statements)

References 68 publications

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“…The RNAi-independent function of Dcr1 mediates the removal of RPII from genomic regions, including tDNAs [ 38 ]; the functional role of RPII at tDNAs is unknown, but R-loops, which could be generated by RPIII at tDNAs, serve as intrinsic RPII promoters [ 63 ]. tDNAs can slow replicative progression and tDNA rich sites are overrepresented at sites of genomic rearrangements, including translocations [ 64 , 65 ]. These factors led us to hypothesize that in the absence of Dcr1, Tsn1 is required to suppress inter-molecular recombination at loci which required Dcr1 to eject RPII, such as tDNAs.…”

Section: Resultsmentioning

confidence: 99%

Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency

et al. 2022

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The conserved nucleic acid binding protein Translin contributes to numerous facets of mammalian biology and genetic diseases. It was first identified as a binder of cancer-associated chromosomal translocation breakpoint junctions leading to the suggestion that it was involved in genetic recombination. With a paralogous partner protein, Trax, Translin has subsequently been found to form a hetero-octomeric RNase complex that drives some of its functions, including passenger strand removal in RNA interference (RNAi). The Translin-Trax complex also degrades the precursors to tumour suppressing microRNAs in cancers deficient for the RNase III Dicer. This oncogenic activity has resulted in the Translin-Trax complex being explored as a therapeutic target. Additionally, Translin and Trax have been implicated a wider range of biological functions ranging from sleep regulation to telomere transcript control. Here we reveal a Trax- and RNAi-independent function for Translin in dissociating RNA polymerase II from its genomic template, with loss of Translin function resulting in increased transcription-associated recombination and elevated genome instability. This provides genetic insight into the longstanding question of how Translin might influence chromosomal rearrangements in human genetic diseases and provides important functional understanding of an oncological therapeutic target.

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Section: Resultsmentioning

confidence: 99%

Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency

et al. 2022

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“…Discordant tRNA expression may also raise the prospect of adaptive translation, which exploits translation infidelity to diversify the proteome [53][54][55] . Notably, experimentally manipulated tRNA mis-expression is associated with adaptive genome instabilities in yeast [56][57][58] , emphasizing the prominent influence of tRNAs during the evolution of genome.…”

Section: Discussionmentioning

confidence: 99%

Amino acid usage and tRNA expression underlies proteome adaptation inPlasmodium falciparum

Vetter

Sahin

et al. 2023

Preprint

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Plasmodium falciparum has an AT-rich genome with highly biased codon and amino acid usage that is not balanced by the tRNA genes repertoire. To determine whether individual tRNA genes can be differentially expressed to compensate for the tRNA-codon imbalance, we characterized the tRNA profiles of the parasite. While we found that the parasite stably maintained a biased expression of different tRNAs throughout the intraerythrocytic cycle (IDC), the tRNA-codon imbalance remains. Specifically, the requirements for a limited tRNA subset in the codons of a gene negatively correlated with its mRNA level. A detailed analysis revealed that these observations implicate host adaptation during P. falciparum genome evolution, whereby housekeeping genes evolved to minimize dependence on exogenous amino acids, allowing these genes to mitigate the negative effects during acute nutrient deprivation. We found that these host-adapted features can derive a decentralized nutrient-dependent regulatory programme via sensing isoleucine as a proxy for nutrient stress, which causes a reduction in aminoacylated Ile-tRNA level. This, in turn, rapidly reprogrammes the global protein output and transcriptome in a targeted fashion. Our findings provide strong evidence showing that the primary sequences of proteins underlie gene expression programmes, suggesting new perspectives on protein evolution.

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“…It was also noticed that the correlations in tRNA and 5S rRNA genes were stronger than those in 16S rRNA and 23S rRNA genes. The tRNA genes are known for their evolutionary flexibility, as they mutate quickly and are sites of genomic instability (49)(50)(51). On the other hand, the ribosomal RNA genes are known for their conservation in evolution.…”

Section: Discussionmentioning

confidence: 99%

Relationship between prokaryotic GC content and environmental salinity

Sun

Niu

2023

Preprint

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BackgroundMany environmental factors are associated with GC content evolution. However, the relationship between GC content and halophilicity has been poorly explored. Higher GC contents have been linked to halophiles because of a few solitary archaeal cases. The only previous statistical study on the relationship ignored the phylogenetic non-independence of species. The habitats of halophilic archaea typically have high-intensity ultraviolet radiation. Avoiding the DNA photoproduct is widely believed as a selective force to increase GC content in archaea living in high saline/ultraviolet-radiation environments.ResultsUsing phylogenetic generalized least squares (PGLS), we examined the relationship between GC content and halophilicity in 1226 bacteria and 181 archaea. Significant positive correlations have been found in bacteria but not in archaea. We suspect that the crowding of most archaeal halophiles in a few phylogenetic lineages dramatically reduces the effective sample size and probably makes the PGLS method less efficient in detecting correlations. The GC contents of different genomic components were explored separately. Bacterial intergenic sequences have GC contents more strongly correlated with halophilicity than protein-coding genes, and 5S rRNA and tRNA genes have GC contents more strongly correlated with halophilicity than 16S and 23S rRNA genes. Using PGLS, we measured the relationship between GC content and photoreactivity, a measure of the vulnerability of DNA sequences under ultraviolet radiation. No significant correlation was observed in the 1226 bacteria or the 181 archaea.ConclusionsWe proposed that the correlation between bacterial GC content and environmental salinity should be attributed to the GC-biased DNA repairing process and the insertion of GC-rich sequences.

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tRNAs as a Driving Force of Genome Evolution in Yeast

Cited by 10 publications

References 68 publications

Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency

Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency

Amino acid usage and tRNA expression underlies proteome adaptation inPlasmodium falciparum

Relationship between prokaryotic GC content and environmental salinity

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