Editing Codon usage bias (section)

== Contributing factors ==

Different factors have been proposed to be related to codon usage bias, including gene expression level (reflecting selection for optimizing the translation process by tRNA abundance), [[guanine-cytosine content]] (GC content, reflecting [[horizontal gene transfer]] or mutational bias), [[guanine-cytosine skew]] (GC skew, reflecting strand-specific mutational bias), [[Conserved sequence|amino acid conservation]], [[Hydrophilicity plot|protein hydropathy]], transcriptional selection, RNA stability, optimal growth temperature, hypersaline adaptation, and dietary nitrogen.<ref name="pmid11719972">{{cite journal | author = Ermolaeva MD | title = Synonymous codon usage in bacteria | journal = Curr Issues Mol Biol | volume = 3 | issue = 4 | pages = 91–7 |date=October 2001 | pmid = 11719972 }}</ref><ref name="pmid12364606">{{cite journal |vauthors=Lynn DJ, Singer GA, Hickey DA | title = Synonymous codon usage is subject to selection in thermophilic bacteria | journal = Nucleic Acids Res. | volume = 30 | issue = 19 | pages = 4272–7 |date=October 2002 | pmid = 12364606 | pmc = 140546 | doi = 10.1093/nar/gkf546 }}</ref><ref name="pmid18397532">{{cite journal |vauthors=Paul S, Bag SK, Das S, Harvill ET, Dutta C | title = Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes | journal = Genome Biol. | volume = 9 | issue = 4 | pages = R70 | year = 2008 | pmid = 18397532 | pmc = 2643941 | doi = 10.1186/gb-2008-9-4-r70 | doi-access = free }}</ref><ref name = "pmid23637123" >{{Cite journal | doi = 10.1534/g3.113.005769| title = Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus| journal = G3| volume = 3| issue = 7| pages = 1069–1083| year = 2013| last1 = Kober | first1 = K. M.| last2 = Pogson | first2 = G. H. | pmid = 23637123 | pmc=3704236}}</ref><ref>{{Cite journal|title = Replicational and transcriptional selection on codon usage in Borrelia burgdorferi|journal = Proceedings of the National Academy of Sciences|date = 1998-09-01|issn = 0027-8424|pmc = 27958|pmid = 9724767|pages = 10698–10703|volume = 95|issue = 18|first = James O.|last = McInerney|doi=10.1073/pnas.95.18.10698|bibcode = 1998PNAS...9510698M|doi-access = free}}</ref><ref name = "pmid27842572" >{{Cite journal | doi = 10.1186/s13059-016-1087-9| title = Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms| journal = Genome Biology| volume = 17| issue = 226| pages = 3–15| year = 2016| last1 = Seward| first1 = Emily| last2 = Kelly | first2 = Steve | pmid = 27842572 | pmc=5109750| doi-access = free}}</ref>