Editing Codon usage bias (section)

== Consequences of codon composition ==

=== Effect on RNA secondary structure ===
Because [[nucleic acid secondary structure|secondary structure]] of the [[5' end|5’ end]] of mRNA influences translational efficiency, synonymous changes at this region on the mRNA can result in profound effects on gene expression. Codon usage in [[noncoding DNA]] regions can therefore play a major role in RNA secondary structure and downstream protein expression, which can undergo further selective pressures. In particular, strong secondary structure at the [[ribosomal binding site|ribosome-binding site]] or [[start codon|initiation codon]] can inhibit translation, and mRNA folding at the 5’ end generates a large amount of variation in protein levels.<ref name = "pmid22921354">{{Cite journal
 | pmid = 22921354
| year = 2012
| last1 = Novoa
| first1 = E. M.
| title = Speeding with control: Codon usage, tRNAs, and ribosomes
| journal = Trends in Genetics
| volume = 28
| issue = 11
| pages = 574–81
| last2 = Ribas De Pouplana
| first2 = L
| doi = 10.1016/j.tig.2012.07.006
}}</ref>

=== Effect on transcription or gene expression ===
[[Heterologous expression|Heterologous gene expression]] is used in many biotechnological applications, including protein production and [[metabolic engineering]]. Because tRNA pools vary between different organisms, the rate of [[transcription (genetics)|transcription]] and translation of a particular coding sequence can be less efficient when placed in a non-native context. For an overexpressed [[transgene]], the corresponding mRNA makes a large percent of total cellular RNA, and the presence of rare codons along the [[primary transcript|transcript]] can lead to inefficient use and depletion of ribosomes and ultimately reduce levels of heterologous protein production. In addition, the composition of the gene (e.g. the total number of rare codons and the presence of consecutive rare codons) may also affect translation accuracy.<ref name = "pmid17017124">{{Cite journal | pmid = 17017124| pmc = 6032470| year = 2006|author1=Shu, P. |author2=Dai, H. |author3=Gao, W. |author4=Goldman, E. | title = Inhibition of translation by consecutive rare leucine codons in E. coli: absence of effect of varying mRNA stability. | journal = Gene Expr. | volume = 13| issue = 2| pages = 97–106| doi = 10.3727/000000006783991881}}</ref><ref name = "pmid31509345">{{Cite journal | pmid = 31509345 | year = 2019|author1=Correddu, D. |author2=Montaño López, J. d. J. |author3=Angermayr, S. A. |author4=Middleditch, M. J. |author5=Payne, L. S. |author6=Leung, I. K. H. | title = Effect of Consecutive Rare Codons on the Recombinant Production of Human Proteins in Escherichia coli. | journal = [[IUBMB Life]] | volume = 72| issue = 2| pages = 266–274| doi =10.1002/iub.2162 | hdl = 11343/286411| s2cid = 202555575| hdl-access = free}}</ref> However, using codons that are optimized for tRNA pools in a particular host to overexpress a heterologous gene may also cause amino acid starvation and alter the equilibrium of tRNA pools. This method of adjusting codons to match host tRNA abundances, called [[codon optimization]], has traditionally been used for expression of a heterologous gene. However, new strategies for optimization of heterologous expression consider global nucleotide content such as local mRNA folding, codon pair bias, a codon ramp, [[codon harmonization]] or codon correlations.<ref name = "pmid29624661">{{Cite journal | pmid = 29624661| year = 2018|author1=Mignon, C. |author2=Mariano, N. |author3=Stadthagen, G. |author4=Lugari, A. |author5=Lagoutte, P. |author6=Donnat, S. |author7=Chenavas, S. |author8=Perot, C. |author9=Sodoyer, R. |author10=Werle, B. | title = Codon harmonization - going beyond the speed limit for protein expression. | journal = [[FEBS Letters]] | volume = 592| issue = 9| pages = 1554–1564| doi = 10.1002/1873-3468.13046| doi-access = free}}</ref><ref name = "pmid21102527">{{Cite journal | pmid = 21102527| pmc = 3074964| year = 2011| last1 = Plotkin| first1 = J. B.| title = Synonymous but not the same: The causes and consequences of codon bias| journal = Nature Reviews Genetics| volume = 12| issue = 1| pages = 32–42| last2 = Kudla| first2 = G| doi = 10.1038/nrg2899}}</ref> With the number of nucleotide changes introduced, [[artificial gene synthesis]] is often necessary for the creation of such an optimized gene.

Specialized codon bias is further seen in some [[endogenous]] genes such as those involved in amino acid starvation. For example, [[amino acid synthesis|amino acid biosynthetic]] enzymes preferentially use codons that are poorly adapted to normal tRNA abundances, but have codons that are adapted to tRNA pools under starvation conditions. Thus, codon usage can introduce an additional level of transcriptional regulation for appropriate gene expression under specific cellular conditions.<ref name = "pmid21102527" />

=== Effect on speed of translation elongation ===
Generally speaking for highly expressed genes, translation elongation rates are faster along transcripts with higher codon adaptation to tRNA pools, and slower along transcripts with rare codons. This correlation between codon translation rates and cognate tRNA concentrations provides additional modulation of translation elongation rates, which can provide several advantages to the organism. Specifically, codon usage can allow for global regulation of these rates, and rare codons may contribute to the accuracy of translation at the expense of speed.<ref name = "doi1">{{Cite journal | doi = 10.5936/csbj.201204006| pmid = 24688635| pmc = 3962081| title = Genetic Code Redundancy and Its Influence on the Encoded Polypeptides| journal = Computational and Structural Biotechnology Journal| volume = 1| pages = 1–8| year = 2012| last1 = Spencer | first1 = P. S. | last2 = Barral | first2 = J. M. }}</ref>

=== Effect on protein folding ===
[[Protein folding]] ''in vivo'' is [[Vectorial space|vectorial]], such that the [[N-terminus]] of a protein exits the translating ribosome and becomes solvent-exposed before its more [[C-terminal]] regions. As a result, co-translational protein folding introduces several spatial and temporal constraints on the nascent polypeptide chain in its folding trajectory. Because mRNA translation rates are coupled to protein folding, and codon adaptation is linked to translation elongation, it has been hypothesized that manipulation at the sequence level may be an effective strategy to regulate or improve protein folding. Several studies have shown that pausing of translation as a result of local mRNA structure occurs for certain proteins, which may be necessary for proper folding. Furthermore, [[synonymous mutations]] have been shown to have significant consequences in the folding process of the nascent protein and can even change substrate specificity of enzymes. These studies suggest that codon usage influences the speed at which [[peptide|polypeptides]] emerge vectorially from the ribosome, which may further impact protein folding pathways throughout the available structural space.<ref name = "doi1" />