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Literature DB >> 22249164

Strong association between mRNA folding strength and protein abundance in S. cerevisiae.

Abstract

One of the open questions in regulatory genomics is how the efficiency of gene translation is encoded in the coding sequence. Here we analyse recently generated measurements of folding energy in Saccharomyces cerevisiae, showing that genes with high protein abundance tend to have strong mRNA folding (mF; R=0.68). mF strength also strongly correlates with ribosomal density and mRNA levels, suggesting that this relation at least partially pertains to the efficiency of translation elongation, presumably by preventing aggregation of mRNA molecules.

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Year: 2012 PMID： 22249164 PMCID： PMC3323128 DOI： 10.1038/embor.2011.262

Source DB: PubMed Journal: EMBO Rep ISSN： 1469-221X Impact factor: 8.807

36 in total

1. Precision and functional specificity in mRNA decay.

Authors: Yulei Wang; Chih Long Liu; John D Storey; Robert J Tibshirani; Daniel Herschlag; Patrick O Brown
Journal: Proc Natl Acad Sci U S A Date: 2002-04-23 Impact factor: 11.205

2. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae.

Authors: A Coghlan; K H Wolfe
Journal: Yeast Date: 2000-09-15 Impact factor: 3.239

3. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.

Authors: Yoav Arava; Yulei Wang; John D Storey; Chih Long Liu; Patrick O Brown; Daniel Herschlag
Journal: Proc Natl Acad Sci U S A Date: 2003-03-26 Impact factor: 11.205

4. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.

Authors: Dmitri M Krylov; Yuri I Wolf; Igor B Rogozin; Eugene V Koonin
Journal: Genome Res Date: 2003-10 Impact factor: 9.043

5. A unification of mosaic structures in the human genome.

Authors: Martin J Lercher; Araxi O Urrutia; Adam Pavlícek; Laurence D Hurst
Journal: Hum Mol Genet Date: 2003-07-29 Impact factor: 6.150

6. Solving the riddle of codon usage preferences: a test for translational selection.

Authors: Mario dos Reis; Renos Savva; Lorenz Wernisch
Journal: Nucleic Acids Res Date: 2004-09-24 Impact factor: 16.971

Review 7. Controlling messenger RNA stability in bacteria: strategies for engineering gene expression.

Authors: T A Carrier; J D Keasling
Journal: Biotechnol Prog Date: 1997 Nov-Dec

8. Widespread selection for local RNA secondary structure in coding regions of bacterial genes.

Authors: Luba Katz; Christopher B Burge
Journal: Genome Res Date: 2003-09 Impact factor: 9.043

9. Composite effects of gene determinants on the translation speed and density of ribosomes.

Authors: Tamir Tuller; Isana Veksler-Lublinsky; Nir Gazit; Martin Kupiec; Eytan Ruppin; Michal Ziv-Ukelson
Journal: Genome Biol Date: 2011-11-03 Impact factor: 13.583

10. The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation.

Authors: I Iost; M Dreyfus
Journal: EMBO J Date: 1995-07-03 Impact factor: 11.598

54 in total

1. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants.

Authors: Tuval Ben-Yehezkel; Shimshi Atar; Hadas Zur; Alon Diament; Eli Goz; Tzipy Marx; Rafael Cohen; Alexandra Dana; Anna Feldman; Ehud Shapiro; Tamir Tuller
Journal: RNA Biol Date: 2015 Impact factor: 4.652

2. Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins.

Authors: Rostam M Razban
Journal: Mol Biol Evol Date: 2019-09-01 Impact factor: 16.240

Strong association between mRNA folding strength and protein abundance in S. cerevisiae.

1. Precision and functional specificity in mRNA decay.

2. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae.

3. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.

4. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.

5. A unification of mosaic structures in the human genome.

6. Solving the riddle of codon usage preferences: a test for translational selection.

Review 7. Controlling messenger RNA stability in bacteria: strategies for engineering gene expression.

8. Widespread selection for local RNA secondary structure in coding regions of bacterial genes.

9. Composite effects of gene determinants on the translation speed and density of ribosomes.

10. The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation.

1. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants.

2. Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins.

3. Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly.

Review 4. Synonymous codons, ribosome speed, and eukaryotic gene expression regulation.

Review 5. Insights into RNA structure and function from genome-wide studies.

6. Leveraging the complementary nature of RNA-Seq and shotgun proteomics data.

7. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.

8. Changing the Codon Usage of hfq Gene has Profound Effect on Phenotype and Pathogenicity of Salmonella Typhimurium.

9. Plasmodium falciparum translational machinery condones polyadenosine repeats.

10. The effect of tRNA levels on decoding times of mRNA codons.