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Question

It is well established that Paramecium translate UAG and UAA mRNA codons to amino acid, although they are STOP codons in most other eukaryotes. (https://www.nature.com/articles/314188a0)

Suppose I wish to express a particular bacterial gene in Paramecium by translation of its mRNA in a similar fashion to the SARS-CoV-2 (COVID-19) vaccines. The gene is AlkB from Alcanivorax borkumensis, which encodes foralkane hydroxylase (https://www.ncbi.nlm.nih.gov/nuccore/AB110225).

The coding DNA sequence of this gene ends with TAA (UAA in mRNA). As explained above, this won't be translated correctly by Paramecium. Could I simply replace the DNA TAA/mRNA UAA with DNA TGA / RNA UGA in order to get it translated to the same protein in Paramecium?

Evidence of Research

This is only some of the research I have done for this question. More can be provided, if required.

Search on this site for previous similar questions
https://biology.stackexchange.com/search?*q=can+i+switch+codons+with+their+equivalents yielded nothing

Paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409834/
Not useful because it only states that switching mRNAs that mean the same thing may make translation take longer due to rare tRNAs. The only STOP tRNA in Paramecium has the anti codon ACU, as proved above.

Paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549826/
Not useful because it's about bacteria.

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  • $\begingroup$ Welcome to SE Biology. I have edited your question to improve the likelihood of its receiving attention and a positive response. This consisted of removing much inessential and repetitive material, and the over "loud" appearance through abnormally large text in headings. I also replaced the opening statement that "It is commonly known". Your view of what biological facts are known to this audience is irrelevant to the question, and off by a mile, in a way that antagonizes people who do not know. Likewise, we don't need to be told to click on links to find something out. But I'll answer it. $\endgroup$
    – David
    Feb 15, 2023 at 13:53
  • $\begingroup$ Hi @David! Thank you so much for your lovely edits & answer, it made the question a lot better! I didn't mean to really offend anyone, thank you for correcting the language used. :) $\endgroup$ Feb 15, 2023 at 23:44

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Preamble

The choice of the organism and gene for expression is not explained, although I gather the bacterium is able to degrade oil components using this enzyme. However one wonders why anyone should wish to express the enzyme in Paramecium, which to my knowledge has not been used to express foreign nucleic acid sequences. The mode of delivery of foreign genes or mRNAs is an important consideration in their expression, but I shall ignore this in my answer. However as Covid vaccines are invoked in the question, a study of papers reviewing the structural features of mRNAs that facilitated their expression (e.g. this one) is advised.

Answer

  1. In principle, replacing a UAA stop codon by a UGA stop codon should still allow termination of translation, especially in an environment in which UAA is the only stop codon. The only possible problem I can see is that of possible readthough, which can occur in certain sequence environments. However if the protein is terminated properly in the bacterium, there seems no reason to expect a disfavoured environment in Paramecium.

  2. As we are considering the expression of a bacterial mRNA in a eukaryotic environment, the differences in bacterial and eukaryotic translational initiation (see any decent biochemistry text or search this site) need to be considered as well as termination. In brief, eukaryotic initiation occurs at a capped 5′-end, with the ribosomes then progressing to what is generally (but not always) the first AUG. An mRNA containing the bacterial coding sequence would have to be synthesized that facilitates this. In addition, polyadenylation of the 3′-end is required to ensure a stable mRNA. A close examination of the features of Paramecium mRNA sequences would be prudent before undertaking such a project.

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    $\begingroup$ Thank you - that answer is so great and I understand now 🎉 Unfortunately I cannot up-vote yet, but it is a great answer well-written well answer well worthy of one. $\endgroup$ Feb 15, 2023 at 23:46
  • $\begingroup$ I'll definitely do the research you suggested, looks like a great rabbit hole to go down... $\endgroup$ Feb 15, 2023 at 23:49

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