I was working on the mutations on Rev protein of HIV. We collected variant wise sequence over the year for different variant across the world. While working I noticed that in some variant sequences of some countries encountered with a mutation in stop codon. So now mutations in stop codon means that the length must be extended to the certain stop codon. Interestingly, many of the sequences has mutation in stop codon with no extension. Like it was TAG that mutated to GAG and no extension neither any stop codon is observed. What could be issue behind this? Like isn't it aberrant for a sequence existence without any stop codon? I could exclude that aberrant one and continue my study. But it is observed in more than 60%. It shouldn't be just a error. Should it?
Mutations in stop codons are not uncommon in viral genomes, and they can have various effects on the protein sequence and function. In some cases, the mutation may cause a read-through of the stop codon, resulting in an extended protein sequence. In other cases, the mutation may not result in an extended sequence, but instead may disrupt the normal function of the protein or even lead to its degradation.
The fact that many of the sequences in your dataset have a mutation in the stop codon without an extension or a new stop codon is indeed unusual. However, it is possible that these mutations are not causing a functional change in the protein or that they are compensating for other changes in the genome. It is also possible that some of the sequences are errors or artifacts of the sequencing process, and it would be important to carefully validate the sequences to ensure their accuracy.
In any case, it is important to carefully consider the implications of these mutations for your study. If the mutations are causing a functional change in the protein or are disrupting its normal function, then they may be important to consider in your analysis. However, if the mutations are not causing any functional change or are simply artifacts, then they may not be relevant to your study and could be excluded.
It may also be helpful to compare the sequences with the mutation in the stop codon to other sequences in your dataset and to reference sequences to see if there are any other differences that may be contributing to the observed effects. Additionally, you may want to consider performing further experimental validation to confirm the effects of these mutations on protein function.
Overall, mutations in stop codons can have important implications for protein function and should be carefully considered in any analysis of protein sequences. While the presence of a mutation in the stop codon without an extension or a new stop codon may be unusual, it is not necessarily indicative of an error and should be thoroughly investigated to determine its potential effects on protein function.
Dear Shatila Shahi if you are trying to detect the relevant (mutant) sequences by Western Blot, it is essential to be sure, that mutant sequences are functional in both reporter and replication assays. Otherwise , detections will not be possible. But even if it is the case (that mutant proteins are indeed functional in both reporter and replication assays ), assay may still not detect mutant proteins. I had in the past such observation with truncated Rev-Proteins (but not with extended), although it was clear that all mutant sequences were functional in both reporter and replication assays. To try to exactly answer your questions, i would need more data.
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