Correction: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

[This corrects the article DOI: 10.1371/journal.pbio.1002015.].

A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

Natural selection favors efficient expression of encoded proteins, but the causes, mechanisms, and fitness consequences of evolved coding changes remain an area of aggressive inquiry. We report a large-scale reversal in the relative translational accuracy of codons across 12 fly species in the Drosophila/Sophophora genus. Because the reversal involves pairs of codons that are read by the same genomically encoded tRNAs, we hypothesize, and show by direct measurement, that a tRNA anticodon modification from guanosine to queuosine has coevolved with these genomic changes. Queuosine modification is present in most organisms but its function remains unclear. Modification levels vary across developmental stages in D. melanogaster, and, consistent with a causal effect, genes maximally expressed at each stage display selection for codons that are most accurate given stage-specific queuosine modification levels. In a kinetic model, the known increased affinity of queuosine-modified tRNA for ribosomes increases the accuracy of cognate codons while reducing the accuracy of near-cognate codons. Levels of queuosine modification in D. melanogaster reflect bioavailability of the precursor queuine, which eukaryotes scavenge from the tRNAs of bacteria and absorb in the gut. These results reveal a strikingly direct mechanism by which recoding of entire genomes results from changes in utilization of a nutrient.

Multiple transcripts from a 3'-UTR reporter vary in sensitivity to nonsense-mediated mRNA decay in Saccharomyces cerevisiae.

Nonsense-mediated mRNA decay (NMD) causes accelerated transcript degradation when a premature translation termination codon disrupts the open reading frame (ORF). Although endogenous transcripts that have uninterrupted ORFs are typically insensitive to NMD, some can nonetheless become prone to NMD when translation terminates at out-of-frame premature stop codons. This occurs when introns containing stop codons fail to be spliced, when translation of an upstream ORF (uORF) terminates in the 5'-untranslated region (5'-UTR) or the coding region, or when the 5'-proximal AUG initiation codon is bypassed and translation initiates at a downstream out-of-frame AUG followed by a stop codon. Some 3'-untranslated regions (3'-UTRs) are also known to trigger NMD, but the mechanism is less well understood. To further study the role of 3'-UTRs in NMD, a reporter system was designed to examine 3'-UTRs from candidate genes known to produce NMD-sensitive transcripts. Out of eight that were tested, the 3'-UTRs from MSH4 and SPO16 caused NMD-dependent mRNA destabilization. Both endogenous genes produce multiple transcripts that differ in length at the 3' end. Detailed studies revealed that the longest of six reporter MSH4-3'-UTR transcripts was NMD-sensitive but five shorter transcripts were insensitive. NMD-dependent degradation of the long transcript required Xrn1, which degrades mRNA from the 5' end. Sensitivity to NMD was not associated with extensive translational read-through past the normal stop codon. To our knowledge, this is the first example where multiple transcripts containing the same ORF are differentially sensitive to NMD in Saccharomyces cerevisiae. The results provide a proof of principle that long 3'-UTRs can trigger NMD, which suggests a potential link between errors in transcription termination or processing and mRNA decay.

Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae.

BACKGROUND: When eukaryotic cells are deprived of amino acids, uncharged tRNAs accumulate and activate the conserved GCN2 protein kinase. Activated Gcn2p up-regulates the general amino acid control pathway through phosphorylation of the translational initiation factor eIF2. In Saccharomyces cerevisiae, Gcn2p is the only kinase that phosphorylates eIF2 to regulate translation through this mechanism. We addressed changes in yeast growth and tRNA aminoacylation, or charging, during amino acid depletion in the presence and absence of GCN2. tRNA charging was measured using a microarray technique which simultaneously measures all cytosolic tRNAs. A fully prototrophic strain, and its isogenic gcn2 Delta counterpart, were used to study depletion for each of the 20 amino acids, with a focus on Trp, Arg, His and Leu, which are metabolically distinct and together provide a good overview on amino acid metabolism. RESULTS: While the wild-type strain had no observable phenotype upon depletion for any amino acid, the gcn2 Delta strain showed slow growth in media devoid of only Trp or Arg. Consistent with the growth phenotypes, profiles of genome-wide tRNA charging revealed significant decrease in cognate tRNA charging only in the gcn2 Delta strain upon depletion for Trp or Arg. In contrast, there was no change in tRNA charging during His and Leu depletion in either the wild-type or gcn2 Delta strains, consistent with the null effect on growth during loss of these amino acids. We determined that the growth phenotype of Trp depletion is derived from feedback inhibition of aromatic amino acid biosynthesis. By removing Phe and Tyr from the media in addition to Trp, regular growth was restored and tRNATrp charging no longer decreased. The growth phenotype of Arg depletion is derived from unbalanced nitrogen metabolism. By supplementing ornithine upon Arg depletion, both growth and tRNAArg charging were partially restored. CONCLUSION: Under mild stress conditions the basal activity of Gcn2p is sufficient to allow for proper adaptation to amino acid depletion. This study highlights the importance of the GCN2 eIF2 kinase pathway for maintaining metabolic homeostasis, contributing to appropriate tRNA charging and growth adaptation in response to culture conditions deficient for the central amino acids, tryptophan and arginine.

Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast.

Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as gamma-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.

Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p.

When cells are subjected to nutritional stress, uncharged tRNAs accumulate and activate Gcn2p phosphorylation of eukaryotic initiation factor-2 (eIF2) and the general amino acid control pathway. The Gcn2p regulatory domain homologous to histidyl-tRNA synthetases is proposed to bind to uncharged tRNA, directly contributing to activation of Gcn2p. Here we apply a microarray technology to analyze genome-wide changes in tRNA charging in yeast upon activation of Gcn2p in response to amino acid starvation and high salinity, a stress not directly linked to nutritional deficiency. This microarray technology is applicable for all eukaryotic cells. Strains were starved for histidine, leucine, or tryptophan and shown to rapidly induce Gcn2p phosphorylation of eIF2. The relative charging level of all tRNAs was measured before and after starvation, and Gcn2p activation and the intracellular levels of the starved amino acid correlate with the observed decrease in tRNA charging. Interestingly, in some cases, tRNAs not charged with the starved amino acid became deacylated more rapidly than tRNAs charged with the starved amino acid. This increase in uncharged tRNA levels occurred although the intracellular levels for these non-starved amino acids remained unchanged. Additionally, treatment of a wild-type strain with high salinity stress showed transient changes in the charging of several different tRNAs. These results suggest that Gcn2p can be activated by many different tRNA species in the cell. These results also depict a complex cellular relationship between tRNA charging, amino acid availability, and non-nutrient stress. These relationships are best revealed by simultaneous monitoring of the charging level of all tRNAs.

Nickel2+-mediated assembly of an RNA-amino acid complex.

The RNA species SHR1 reacts with biocytin (epsilon-biotinoyl-L-lysine) in the presence of Ni(2+) or Pt(2+) to produce a metal-bridged complex that migrates more slowly than unreacted RNA in the presence of streptavidin (StrAv) on denaturing polyacrylamide gels. Mapping of reverse transcription pause sites identified G79 as a reactive nucleotide. G79 is near the 3' end of a 37 nucleotide core motif that is nearly as reactive as SHR1. SHR1 reacts with biocytin in the presence of Pt(2+) to yield a product that comigrates with the Ni(2+) product but that is much more stable, suggesting that the metal ion used in the reaction is present in the product, possibly linking the RNA to the amino acid. In support of this model, SHR1 shows a strong affinity for Ni(2+) in immobilized metal ion chromatography.