Synonymous but not the same: the causes and consequences of codon bias

By Joshua B. Plotkin, Grzegorz Kudla. Nature reviews genetics, 2010

1,566 citations recorded by the source corpus.

Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/166fe31c9a7df8f67780a4d06065b9742827eddd

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Citations in the corpus

Toward a Kinetic Understanding of Eukaryotic Translation. (2018, background): “Optimal codons correspond to tRNA species that are abundant and rapidly accommodated into the ribosome during elongation, whereas nonoptimal codons (rare codons) interact with tRNAs that are low in abundance and therefore more slowly accommodated into the A site of the ribosome during elongation (re”
A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape (2014, background): “Codon usage often differs in the beginning of the gene from the rest of the gene, which has been hypothesized to result from a selection against 5 0 mRNA structure and/or a selection for rare codons that provide a slower elongation time at the 5 0 end (Plotkin and Kudla 2011).”
Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage (2011, neutral): “This observation provides support for the functional importance of selective codon usage in mammals 16 .”
A census of human RNA-binding proteins (2014, background): “Furthermore, while tissue-specific variation has been reported for some tRNAs and snoRNAs (Castle et al., 2010; Dittmar et al., 2006; Plotkin and Kudla, 2011), the biogenesis factors of tRNAs and”
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences (2021, background): “Speciﬁcally, it uses synonymous substitutions as a reference baseline (similar to [13]), which, albeit thought to be under weak selection [19–21], has been widely adopted for determining the strength and type of selection operated on coding sequences [22–29].”
Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective (2012, background): “Synonymous mutations are now found to be not so silent and have visible consequences [1801, 1802, 1803], particular on the level of gene expression.”
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition (2016, neutral): “…adaptation index (Sharp & Li, I 987) only explains a small portion of the variance in protein per mRNA in yeast (Ingolia et al, 2009) and bacteria (Plotkin & Kudla, 2011), differences in codon optimality in yeast for individual reporter genes result in different protein output and inferred…”