Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.
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TLDR
This analysis suggests an evolved function for codon optimality in regulating the rhythm of elongation to facilitate cotranslational polypeptide folding, beyond its previously proposed role of adapting to the cost of expression.Citations
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In vivo aspects of protein folding and quality control
TL;DR: A new view of protein folding is emerging, whereby the energy landscapes that proteins navigate during folding in vivo may differ substantially from those observed during refolding in vitro.
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Codon Optimality Is a Major Determinant of mRNA Stability
Vladimir Presnyak,Najwa Alhusaini,Ying Hsin Chen,Sophie G. Martin,Nathan Morris,Nicholas Kline,Sara Olson,David E. Weinberg,Kristian E. Baker,Brenton R. Graveley,Jeff Coller +10 more
TL;DR: It is shown that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function, demonstrating that codon optimization exists as a mechanism to finely tune levels of m RNAs and, ultimately, proteins.
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Codon Bias as a Means to Fine-Tune Gene Expression
TL;DR: How understanding the principles of codon bias and translation can contribute to improved protein production and developments in synthetic biology is discussed.
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Causes and effects of N-terminal codon bias in bacterial genes.
Daniel B. Goodman,Daniel B. Goodman,Daniel B. Goodman,George M. Church,George M. Church,Sriram Kosuri +5 more
TL;DR: It is demonstrated that reduced RNA structure and not codon rarity itself is responsible for expression increases, which resolve controversies over the roles of N-terminal codon bias and suggest a straightforward method for optimizing heterologous gene expression in bacteria.
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Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers
Fran Supek,Fran Supek,Belén Miñana,Juan Valcárcel,Juan Valcárcel,Toni Gabaldón,Toni Gabaldón,Ben Lehner,Ben Lehner,Ben Lehner +9 more
TL;DR: It is estimated that between one in two and one in five silent mutations in oncogenes have been selected, equating to ~6%- 8% of all selected single-nucleotide changes in these genes.
References
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Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
Journal ArticleDOI
Protein secondary structure prediction based on position-specific scoring matrices
TL;DR: A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST and achieved an average Q3 score of between 76.5% to 78.3% depending on the precise definition of observed secondary structure used, which is the highest published score for any method to date.
Journal ArticleDOI
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
TL;DR: A ribosomesome-profiling strategy based on the deep sequencing of ribosome-protected mRNA fragments is presented and enables genome-wide investigation of translation with subcodon resolution and is used to monitor translation in budding yeast under both rich and starvation conditions.
Journal ArticleDOI
A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity
Chava Kimchi-Sarfaty,Jung Mi Oh,In-Wha Kim,Zuben E. Sauna,Anna Maria Calcagno,Suresh V. Ambudkar,Michael M. Gottesman +6 more
TL;DR: It is hypothesized that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.
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