We are analyzing https://link.springer.com/article/10.1007/s00239-004-0277-3.

Title:
Relationships Among Stop Codon Usage Bias, Its Context, Isochores, and Gene Expression Level in Various Eukaryotes | Journal of Molecular Evolution
Description:
It is well known that stop codons play a critical role in the process of protein synthesis. However, little effort has been made to investigate whether stop codon usage exhibits biases, such as widely seen for synonymous codon usage. Here we systematically investigate stop codon usage bias in various eukaryotes as well as its relationships with its context, GC3 content, gene expression level, and secondary structure. The results show that there is a strong bias for stop codon usage in different eukaryotes, i.e., UAA is overrepresented in the lower eukaryotes, UGA is overrepresented in the higher eukaryotes, and UAG is least used in all eukaryotes. Different conserved patterns for each stop codon in different eukaryotic classes are found based on information content and logo analysis. GC3 contents increase with increasing complexity of organisms. Secondary structure prediction revealed that UAA is generally associated with loop structures, whereas UGA is more uniformly present in loop and stem structures, i.e., UGA is less biased toward having a particular structure. The stop codon usage bias, however, shows no significant relationship with GC3 content and gene expression level in individual eukaryotes. The results indicate that genomic complexity and GC3 content might contribute to stop codon usage bias in different eukaryotes. Our results indicate that stop codons, like synonymous codons, exhibit biases in usage. Additional work will be needed to understand the causes of these biases and their relationship to the mechanism of protein termination.
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Keywords {🔍}

article, google, scholar, codon, pubmed, usage, stop, gene, content, eukaryotes, expression, termination, bias, mol, acids, res, level, translation, genes, nucleic, information, molecular, synonymous, access, privacy, cookies, analysis, journal, research, context, biases, structure, selection, biol, publish, search, evolution, isochores, september, codons, protein, secondary, open, human, genome, genetics, cerevisiae, drosophila, mrna, evol,

Topics {✒️}

mottagui-tabar la isaksson month download article/chapter jinlin xu & jianhua luo pubmed google scholar molecular evolution aims saccharomyces cerevisiae eur highly expressed genes simple model based amino-acid usage codon usage trends stop codon usage european economic area full article pdf translational stop signal privacy choices/manage cookies gene expression level codon usage biases synonymous codon usage amino acids stop codons play state key program selection explains trends secondary structure codon adaptation index sequence analysis suggests translational termination efficiency genomically recoded organism moon dm bedwell coghlan kh wolfe chandonia se brenner duan ma antezana fast-growing bacteria maside aw lee broek van den stoehr ma tuli hakak jr walker synonymous codon choice conditions privacy policy jianhua luo tetra-nucleotides signal mrna expression levels large-scale analysis article sun author information authors accepting optional cookies translation termination efficiency cassan jp rousset stop codon journal finder publish gc3 contents increase

Questions {❓}

L Kisselev M Ehrenberg L Frolova (2003) New EMBO member’s review: Termination of translation: Interplay of mRNA, rRNAs and release factors?
WP Tate ES Poole ME Dalphin LL Major DJG Crawford SA Mannering (1996) The translational stop signal: Codon with a context, or extended factor recognition element?

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         CAI value
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         Animal Genetics and Genomics
         Cell Biology
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