Short tRNA anticodon stem and mutant eRF1 allow stop codon reassignment

Kachale, Ambar; Pavlíková, Zuzana; Nenarokova, Anna; Roithová, Adriana; Durante, Ignacio Miguel; Miletínová, Petra; Záhonová, Kristína; Nenarokov, Serafim; Votýpka, Jan; Horáková, Eva; Ross, Robert L; Yurchenko, Vyacheslav; Beznosková, Petra; Paris, Zdeněk; Valášek, Leoš Shivaya; Lukeš, Julius

doi:10.1038/s41586-022-05584-2

Cited by 34 publications

(71 citation statements)

References 57 publications

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“…AF288091.2 ) evolved and, in some species, both TAA and TAG were recoded to tyrosine (normally encoded by TAT and TAC) ( 10 ). All three stop codons have been recoded in the nuclear genomes of the ciliate Condylostoma magnum ( 92 ) and the kinetoplastid genus Blastocrithidia ( 93 , 94 ). In both cases, TGA encodes tryptophan, and TAA and TAG encode glutamine (normally encoded only by CAA and CAG).…”

Section: Resultsmentioning

confidence: 99%

Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

Macher

Coots

Poh

et al. 2023

mBio

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Section: Resultsmentioning

confidence: 99%

Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

Macher

Coots

Poh

et al. 2023

mBio

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“…Overall, most of the detected amino acid misincorporations can be explained by the single nucleotide mismatch between the tRNA anticodon and the stop codon. Similarly, organisms that exhibit stop-to-sense reassignment of stop codons include TAG and TAA reassignment to Glutamine 38 and TGA reassignment to Tryptophan 39 . Further, our results corroborate previous observations reported for S. cerevisiae where TAG and TAA were found to be replaced by glutamine, lysine, and tyrosine, and TGA - by tryptophan, cysteine, and arginine 40 .…”

Section: Resultsmentioning

confidence: 99%

Environment Modulates Protein Heterogeneity Through Transcriptional and Translational Stop Codon Miscoding

Romero-Romero

Kirilenko

Poehls

et al. 2023

Preprint

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Stop codon miscoding events give rise to longer proteins, which may alter the protein's function and thereby generate short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon miscoding events, we designed a library of reporters. We introduced premature stop codons into mScarlet that enabled high-throughput quantification of protein synthesis termination errors in E.coli using fluorescent microscopy. We found that under stress conditions, stop codon miscoding may occur with a rate as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon miscoding events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon miscoding. The RNA polymerase is more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon miscoding by mass spectrometry revealed that temperature regulates the expression of cryptic sequences generated by stop codon miscoding in E.coli. Overall, our findings suggest that the environment influences the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.

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“…For example, in the mitochondrial genome of certain thraustochytrid stramenopiles, a new stop codon (TTA) (GenBank: AF288091.2) evolved and, in some species, both TAA and TAG were recoded to Tyrosine (normally encoded by TAT and TAC) (10). All three stop codons have been recoded in the nuclear genomes of the ciliate Condylostoma magnum (92) and the kinetoplastid genus Blastocrithidia (93, 94). In both cases, TGA = Tryptophan, and TAA and TAG = Glutamine (normally encoded only by CAA and CAG).…”

Section: Resultsmentioning

confidence: 99%

“…In both cases, TGA = Tryptophan, and TAA and TAG = Glutamine (normally encoded only by CAA and CAG). For Blastocrithidia , authors showed that highly expressed genes have fewer TAA and TAG codons and speculate that changes in tRNA usage enable ribosomes to read through TAA and TAG sense codons in the middle of moderate and lowly expressed genes while TAA is still used as a termination codon at the end of transcripts (93, 94). Here, we identify a similar example in radiolarian mitochondria where all three stop codons are likely recoded to sense codons.…”

Section: Resultsmentioning

confidence: 99%

Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria)

Macher

Coots

Poh

et al. 2023

Preprint

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Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria- the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we present two complete mitochondrial genomes of Foraminifera and two near-complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes encode a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and encode only 14-15 protein-coding genes, including nad1, 3, 4, 4L, 5, 7, cob, cox1, 2, 3, atp1, 6, and 9, with forams and radiolarians additionally encoding nad2 and nad6, respectively. In radiolarian mitogenomes, a non-canonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases.

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Short tRNA anticodon stem and mutant eRF1 allow stop codon reassignment

Cited by 34 publications

References 57 publications

Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

Environment Modulates Protein Heterogeneity Through Transcriptional and Translational Stop Codon Miscoding

Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria)

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