Codon preference refers to the tendency of an organism to use certain codons to encode for specific amino acids during protein expression. While all organisms use the same genetic code, the preferred codons can vary between taxa. In E. coli and Salmonella, codon preference is very similar. In higher organisms, GC content influences codon choice for a given gene. Several hypotheses attempt to explain biased codon usage, such as selection for more efficient translation by using abundant tRNAs or codons that bind tRNAs more strongly. While high codon bias is often associated with highly expressed genes, some research finds it also in lowly and broadly expressed genes. Engineering additional tRNA genes can help express foreign genes by increasing the tRNA pool for preferred cod

1. CODON PREFERENCE IN
DIFFERENT ORGANISMS
Subject: Trends in Biotechnology
Assignment # 01
Submitted by: Ahmed Madni
Registration # SP18-R02-002
Submitted to: Dr. Raza Ahmad
Submission Date: 02-April-2018

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Codon Preference
A codon is a sequence of three nucleotides that encodes a specific amino acid of a polypeptide
chain. Codon preference is the codon (three nucleotides) used by particular organism expression
system to form particular polypeptide chain. This thing has created challenges for scientist to
express foreign gene in other organisms because that sequence of triplet codon might encodes for
different amino acid in that system which is not of interest.
There are 64 codons in which only 20 translated into amino acids include one start codon and three
stop codons. The overabundance of codon numbers allow the many amino acids to be encoded by
more than one codon this leads to term known as degenerative codon (one amino acid encoded by
more than one codon). In organism system, for expression of gene those genetic code is preferred
which encodes the similar amino acid in formation of particular polypeptide chain. Almost all
organisms show same codon assignment for each amino acid. For example Escherichia coli and
Salmonella typhimurium have very similar codon preference. The preferred of individual codons
vary greatly among taxonomic groups. In higher organisms, codon choice depends upon GC bias
of the specific DNA sequence presenting the gene.
The process of biased use of codon is often explained by selection to improve translation of gene.
Several hypothesis confirms that the use of optimal codons can increase translation efficiency and
accuracy. The use of Codon is biased towards the use of some of the most abundant tRNAs in the
tRNA pool or towards the codons that bind to their own related tRNA stronger than other synonym
codons. Codon's bias avoids slowly translated codes, which are more likely to combine with the
wrong amino acid. Although the bias of the use of codon in the highly expressed genes appears to
be due to the choice of optimal codes associated with the most common DNA genes, the increase
in the frequency of these tRNA genes also results from the bias of the use of codon. This leads to

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the concept of co-evolution that left the expression of highly expressive genes a more efficient or
the idea that different developments of mobile DNA evolved directly from existing codon biases.
Secondly, key codes are always used preferentially by very expressive genes, regardless of the
secondary structure of the protein. This suggests that the abundance of tRNA is the result of codon
bias.
Another one is the expression, in recent research, suggests that high codon bias is not necessarily
indicative of highly expressed genes. For example, a study of the human genome has found that
some lowly expressed genes, as well as highly expressed genes, are characterized by high codon
bias. In other research in humans which studied the relationship between gene expression level
and gene expression breadth and codon bias and showed that codon usage is more strongly related
to breadth of expression than to maximum expression level.
Conclusion
For amplification of foreign gene which does not require any sort of modification or codon
preference because in that case the gene number is increased but when to come to expression of
gene, codon preference is ought. Firstly, abundance of tRNA is checked in target organisms and
secondly the expression level of gene in that organism. Genetic engineering is one of strategy that
is employed to increase the tRNA pool (gene encodes the tRNA sequence) by transferring it and
thus help in expression of foreign gene.
References
Andersson, S. G., & Kurland, C. G. (1990). Codon preferences in free-living
microorganisms. Microbiological Reviews, 54(2), 198-210.
Kotlar, D., & Lavner, Y. (2006). The action of selection on codon bias in the human genome is
related to frequency, complexity, and chronology of amino acids. BMC Genomics, 7(1), 67.

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Lavner, Y., & Kotlar, D. (2005). Codon bias as a factor in regulating expression via translation
rate in the human genome. Gene, 345(1), 127-138.
Salim, H. M., & Cavalcanti, A. R. (2008). Factors influencing codon usage bias in
genomes. Journal of the Brazilian Chemical Society, 19(2), 257-262.