A single sequence context cannot satisfy all non-AUG initiator codons in yeast†

Chang, Chia Pei; Chen, Shun Jia; Lin, Chen; Wang, Tzu Ling; Wang, Chien Chia

doi:10.1186/1471-2180-10-188

Cited by 21 publications

(25 citation statements)

References 29 publications

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“…It is also unclear why other near-cognate triplets in an optimal context in the leader of GCN4 mRNA, and presumably many other genes, were not detectably translated in vivo (88). Results from a separate study suggested that nucleotides besides the critical Ϫ3 position significantly affect initiation from certain nearcognate triplets (30).…”

Section: Metmentioning

confidence: 97%

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes

Hinnebusch

2011

Microbiol Mol Biol Rev

362

415

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SUMMARY The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5′ end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNA i Met ) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an “open” conformation of the 40S subunit with Met-tRNA i Met bound in a low-affinity state conducive to scanning and in triggering rearrangement into a “closed” conformation incompatible with scanning, which features Met-tRNA i Met more tightly bound to the “P” site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded “landing pad” for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.

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Section: Metmentioning

confidence: 97%

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes

Hinnebusch

2011

Microbiol Mol Biol Rev

362

415

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“…It has been observed through several studies has proved for example in yeast in 2010, that thought investigating different genes like ALA1 encodes alanyl-tRNA synthase and GRS1 encodes glycyltRNA synthase use ACG and TTG as their alternative translation start codon. It has been proved by [5] that except for AAG and AGG, all triplets that differ from ATG by a single nucleotide were able to serve as initiator codons in ALA1. It has been concluded that from these initiator codons, TTG, CTG, ACG, and ATT that had *50 % initiating activities compared to that of ATG, they indicated that the GTG, ATA, and ATC had *20 % initiating activities compared to that of ATG.…”

Section: Sequence Analysis and Phylogenetic Comparisons Within Mastermentioning

confidence: 99%

“…Unexpectedly, these non-AUG initiator codons showed different favoring actions toward different sequence backgrounds. Specifically, GTG was one of the most efficient non-ATG initiator codons [5,7].…”

Section: Sequence Analysis and Phylogenetic Comparisons Within Mastermentioning

confidence: 99%

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

2015

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This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.

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“…Non-AUG initiator codons refer to triplets that differ from AUG by 1 nucleotide, such as GUG, UUG, AUU, and ACG (23). However, relatively few examples of non-AUG initiation have been found in lower eukaryotes.…”

mentioning

confidence: 99%

“…Although translation initiation from an AUG codon is not affected by its surrounding sequence in yeast (24)(25)(26), translation initiation from a non-AUG codon is greatly affected by its surrounding sequence. The best sequence context for a non-AUG initiator codon is AAA at its relative Ϫ3 to Ϫ1 positions (23,27), and a non-AUG initiator codon requires at least an A at its relative Ϫ3 position to be properly functional. A peculiar feature of ALA1 is that the gene uses AUG1 as the translation initiation codon of its cytoplasmic form while using two upstream consecutive ACG codons (ACG/ACG) as the translation initiation codons of its mitochondrial isoform (12).…”

mentioning

confidence: 99%

Divergent Alanyl-tRNA Synthetase Genes of Vanderwaltozyma polyspora Descended from a Common Ancestor through Whole-Genome Duplication Followed by Asymmetric Evolution

Chang

Lee

Lin

et al. 2015

Molecular and Cellular Biology

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bCytoplasmic and mitochondrial forms of a eukaryotic aminoacyl-tRNA synthetase (aaRS) are generally encoded by two distinct nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. However, in most known yeasts, only the mitochondrial-origin alanyl-tRNA synthetase (AlaRS) gene is retained and plays a dual-functional role. Here, we present a novel scenario of AlaRS evolution in the yeast Vanderwaltozyma polyspora. V. polyspora possesses two significantly diverged AlaRS gene homologues, one encoding the cytoplasmic form and the other its mitochondrial counterpart. Clever selection of transcription and translation initiation sites enables the two isoforms to be localized and thus functional in their respective cellular compartments. However, the two isoforms can also be stably expressed and function in the reciprocal compartments by insertion or removal of a mitochondrial targeting signal. Synteny and phylogeny analyses revealed that the AlaRS homologues of V. polyspora arose from a dual-functional common ancestor through whole-genome duplication (WGD). Moreover, the mitochondrial form had higher synonymous (1.6-fold) and nonsynonymous (2.8-fold) substitution rates than did its cytoplasmic counterpart, presumably due to a lesser constraint imposed on components of the mitochondrial translational apparatus. Our study suggests that asymmetric evolution confers the divergence between the AlaRS paralogues of V. polyspora.

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A single sequence context cannot satisfy all non-AUG initiator codons in yeast†

Cited by 21 publications

References 29 publications

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

Divergent Alanyl-tRNA Synthetase Genes of Vanderwaltozyma polyspora Descended from a Common Ancestor through Whole-Genome Duplication Followed by Asymmetric Evolution

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