I want to optimize codon usage of a human gene for expression in a plant (Nicotiana tabacum). How can to do it? Is codon harmonization necessary or not?
It would be necessary if there are important differences in codon usage bias between humans and tobacco (I would expect so). With this optimization you would ensure (in theory) efficient translation of the protein encoded by the transgene.
To have an idea on how efficient would be the translation of the original sequence, you can calculate the CAI (Codon Adaptation Index) for the gene of interest according to the codon usage of tabacco.
For CAI calculation: http://genomes.urv.es/CAIcal/
The codon usage table for Nicotiana tabacum: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4097
Now, for codon optimization you can try these online tools:
https://www.idtdna.com/CodonOpt (includes tobacco as target organism).
http://genomes.urv.es/OPTIMIZER/ (you need to include the codon usage table mentioned above).
Good luck!
It would be necessary if there are important differences in codon usage bias between humans and tobacco (I would expect so). With this optimization you would ensure (in theory) efficient translation of the protein encoded by the transgene.
To have an idea on how efficient would be the translation of the original sequence, you can calculate the CAI (Codon Adaptation Index) for the gene of interest according to the codon usage of tabacco.
For CAI calculation: http://genomes.urv.es/CAIcal/
The codon usage table for Nicotiana tabacum: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4097
Now, for codon optimization you can try these online tools:
https://www.idtdna.com/CodonOpt (includes tobacco as target organism).
http://genomes.urv.es/OPTIMIZER/ (you need to include the codon usage table mentioned above).
Good luck!
Tnx Gustavo
What is your idea about codon harmonization?
http://www.ncbi.nlm.nih.gov/pubmed/21125377
It looks interesting, since for codon adjustment it takes into account not only the most frequent codons in the host species, but also the relative frequence of each codon to make it comparable between the original species and the new one. The rationale behind this is that some pauses during translation might be necessary for proper folding of the nascent protein.
I've only heard of examples regarding codon optimization from people I know, and it seems to improve significantly protein expression in plants. I don't know if codon harmonization works that well in organisms other than bacteria. Sorry I can't help :(
It was kind of protein depends! Sometimes,codon optimization is very efficient,sometimes not,
Most gene synthesis companies will do this for you free of charge. Sometimes it makes a big difference, sometimes not.
Well certainly it is not necessary, situation dependent and may not improve upon the expression levels compared to unoptimized codons. but here you will be expressing human gene in a plant and i would strongly recommend codon optimization, as Gustavo has already explained the reason.
There's a very easy-to-use software application that performs codon optimization, and has options for codon usage harmonization.
It's called eugene: http://bioinformatics.ua.pt/eugene
To get good expression codon optimization is necessary. Considering codon biasness optimization of a particular organism should done.
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