The result of my bacterial genome annotation showed that there is a gene that has lost its stop codon, resulting the gene to be joined in one big ORF together with an adjacent gene. Is it biologically plausible to have this? (I know that the reverse, i.e. having stop codons interrupting a gene's CDS, exists and is known as gene split.) If it is, are there known effects to the coded protein? I'm imagining one big protein with two different domains that have really different functions... (if the protein managed to fold correctly, anyway). Or is it because there must have been something wrong in the annotation and/or genome sequencing/assembly? Thank you for your input.
What I would first do is check for two things:
- will your combined protein contain the second one in the correct reading frame?
- does the sequence for you interstitial protein (the one between the two known ones) show any similarity to any other known protein (blast nr)
if the answer is no to both questions then I would doubt that your resulting protein is functional - although crazier things could happen in bacteria
Whenever something like that happens to me, I automatically think the assembly and/or annotation is to blame. However,...
It is definitely possible that a fusion protein was made, and that could be really neat.
It is almost impossible to predict the effects of fusion proteins like that. It really depends on whether two domains were fused, what the functions of the individual domains are/were. E.g. imagine a DNA binding protein fusing to a transcription factor, this could have some funky consequences...
But as I mentioned, rule out errors/bugs in the annotation first!