Codon Usage Bias in Phylogenetic Systematics: A review
Authors
Justin Miller
Michael Whiting
Perry Ridge
Novelty of Approach
-Describes phylogenetic approaches using codon usage
-Proposes future avenues of research
Causes of Codon Usage Bias
-The ramp sequence consists of rare, slowly translated codons that increase ribosomal spacing, reduce mRNA secondary structure, and slow initial translation.
-tRNA are recharged with amino acids for synonymous codon translation when synonymous codons are in close proximity to each other. Recharging allows the tRNA to stay attached to the ribosome and significantly increases translation efficiency.
-tRNA are recharged with amino acids for identical codon translation when identical codons are in close proximity to each other. Recharging allows the tRNA to stay attached to the ribosome and significantly increases translation efficiency.
-Cognate, near-cognate, and non-cognate tRNA may attempt to bind to an mRNA codon. If relatively few cognate tRNA are available, translation will slow because other tRNA attempt to bind to the same codon. This process is essential for translation elongation, efficiency, and accuracy.
-Overall GC content in a gene is highly correlated with GC content at the third codon position. GC content influences over two-thirds of codon variation.