scholarly journals Single-stranded genomic architecture constrains optimal codon usage

Bacteriophage ◽  
2011 ◽  
Vol 1 (4) ◽  
pp. 219-224 ◽  
Author(s):  
Daniel J. Cardinale ◽  
Siobain Duffy
Keyword(s):  
Codon Usage ◽  
Genomic Architecture ◽  
Optimal Codon

scholarly journals Non-optimal codon usage affects expression, structure and function of clock protein FRQ

Nature ◽  
2013 ◽  
Vol 495 (7439) ◽  
pp. 111-115 ◽  
Author(s):  
Mian Zhou ◽  
Jinhu Guo ◽  
Joonseok Cha ◽  
Michael Chae ◽  
She Chen ◽  
...  
Keyword(s):  
Codon Usage ◽  
Structure And Function ◽  
Optimal Codon ◽  
And Function ◽  
Clock Protein

A Synthetic DAF (CD55) Gene Based on Optimal Codon Usage for Transgenic Animals

2001 ◽  
Vol 129 (5) ◽  
pp. 795-801 ◽  
Author(s):  
S. Miyagawa ◽  
M. Yamada ◽  
K. Matsunami ◽  
Y. Koresawa ◽  
M. Ikawa ◽  
...  
Keyword(s):  
Codon Usage ◽  
Transgenic Animals ◽  
Optimal Codon

scholarly journals Experimental determination of codon usage-dependent selective pressure on high copy-number genes in Saccharomyces cerevisiae

2018 ◽  
Author(s):  
Lyne Jossé ◽  
Tarun Singh ◽  
Tobias von der Haar
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Codon Usage ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Selective Pressure ◽  
Recombinant Protein Expression ◽  
High Expression ◽  
Expression Levels ◽  
Optimal Codon

AbstractOne of the central hypotheses in the theory of codon usage evolution is that in highly expressed genes particular codon usage patterns arise because they facilitate efficient gene expression and are thus selected for in evolution. Here we use plasmid copy number assays and growth rate measurements to explore details of the relationship between codon usage, gene expression level, and selective pressure in Saccharomyces cerevisiae. We find that when high expression levels are required optimal codon usage is beneficial and provides a fitness advantage, consistent with evolutionary theory. However, when high expression levels are not required, optimal codon usage is surprisingly and strongly selected against. We show that this selection acts at the level of protein synthesis, and we exclude a number of molecular mechanisms as the source for this negative selective pressure including nutrient and ribosome limitations and proteotoxicity effects. These findings inform our understanding of the evolution of codon usage bias, as well as the design of recombinant protein expression systems.

Whole genome analysis of non-optimal codon usage in secretory signal sequences of Streptomyces coelicolor

Biosystems ◽  
2006 ◽  
Vol 85 (3) ◽  
pp. 225-230 ◽  
Author(s):  
Yu-Dong Li ◽  
Yong-Quan Li ◽  
Jian-shu Chen ◽  
Hui-jun Dong ◽  
Wen-Jun Guan ◽  
...  
Keyword(s):  
Codon Usage ◽  
Genome Analysis ◽  
Streptomyces Coelicolor ◽  
Whole Genome ◽  
Signal Sequences ◽  
Whole Genome Analysis ◽  
Optimal Codon

scholarly journals Genes adopt non‐optimal codon usage to generate cell cycle‐dependent oscillations in protein levels

2012 ◽  
Vol 8 (1) ◽  
pp. 572 ◽  
Author(s):  
Milana Frenkel‐Morgenstern ◽  
Tamar Danon ◽  
Thomas Christian ◽  
Takao Igarashi ◽  
Lydia Cohen ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Codon Usage ◽  
Protein Levels ◽  
Optimal Codon ◽  
Cycle Dependent

Human hemoglobin expression in Escherichia coli: importance of optimal codon usage

Biochemistry ◽  
1992 ◽  
Vol 31 (36) ◽  
pp. 8619-8628 ◽  
Author(s):  
Ronald A. Hernan ◽  
Hilda L. Hui ◽  
Mark E. Andracki ◽  
Robert W. Noble ◽  
Stephen G. Sligar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Codon Usage ◽  
Human Hemoglobin ◽  
Expression In Escherichia Coli ◽  
Optimal Codon
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