In general there is a perception that if we over-express a eukaryotic gene into a plant (say Arabidopsis), it will have better expression compared to a prokaryotic gene, due to closer/similar codon uses. I know there could be many more factors to control expression, but has anyone come across (or have literature) the opposite ie. a similar gene from prokaryotic origins performs much better than that of eukaryotic origin? The phenomenon could be specific to a certain class of gene, but I am not sure. Kindly share your experience and references.
This assumption is general and superficial very much at the same time. Most likely it is true in most cases, but overlooks the really important points.
- First of all, the comparison must be restricted to ORFs for which codon usage is an issue at all.
- Effects of introns are also completely ignored. Therefore it is also very important whether we are speaking about genomic DNA fragments or cDNS (mRNA derived copies) of eukaryotes?
- About promoters and other regulatory elements one can not state such “thumb rule” despite they are crucial elements of gene expression.
- You will also find incredible differences whether you try to express another dicot plant gene, a monocot gene (can be as problematic as a mammalian one) or a gene form a fungus, like yeast. And all these are eukaryots…
The most experience on this field emerged form the commercial use of GMO plants. Companies, developers worked a lot on increasing the expression of a given gene by optimizing codon usage according to the host plant.
In your question, probably you did not count on chloroplast transformation, which works, but it is tricky and far less common than nuclear gene transfer. However, in chloroplast, only prokaryotic type genes are working properly, since chloroplast is organellum derived from ancient cyanobacteria (blue-green algae).
Taken together, except for the expression in chloroplast where prokaryotic codon usage is preferred, I do not know any cases, where bacterial genes would work better than their eukaryotic orthologues.
Thanks alot Dr. Györgyey,
I do agree what you pointed but as I observed this, I thought to have opinions of other.
Moreover, I mean was in terms of cDNA/ORF only and not whole gene with regulatory elements.
Thanks once again.
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