Hello!
I need any explanation. I have to express plant protein in Pichia pastoris, but the codon usage of hosts plant is unknown yet ( i searched for it on kazusa). I found several articles on this topic. Authors optimized codons of gene of this protein according to Pichia pastoris codon usage. I think, it was doing by use online resources. I checked several of them, and got different results, different expression profiles. I understand that optimizing codons we want to achieve the translation rate by ribosome and correct folding. But does it make sense to optimize codons, if the hosts codon usage is unknown? In any case, any optimization does not lead to the correct nucleotide sequence.
Hello
We usually optimize codons based on the expression host, in your case Pichia. You are right about getting different results of optimization from different web-tools! I recommend to use the optimization service from where you order your gene synthesis.
Hello Ruslan, not all the tRNA there are exactly equal-represented in all organisms, for instance, for the amino acid A your vegetal will use one triplet, and maybe this tRNA doesn't exist in Pichia, so you will going to have a stop or delay in the translation process. In general, more evolutive distance increase the possibility to have codon-bias. In your situation this is the case, I recommend you a codon optimization to express in Pichia. There are many tools online, with the aa-sequence run an optimization for pichia, and that's it.
You didn't answer my question. If we don't know codon usage of host organism how do we know the optimization for recipient organism is correct? What if some rare codons coincide in these organisms, and the program substitutes it a widespread?
Yes I did. Again, to express in pichia a tyrannosaurus-protein you need the pichia codon-usage. Tyrannosaurus usage and/or rare codons... guess what: does not matter.
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