How would we identify a specific gene responsible for a novel peptide produced by a bacteria?
The first step is to identify the protein sequence. This can be done by some sort of stepwise reaction using gas chromatography or HPLC, but it’s probably best using Mass Spectrometry. However, once you get that – and assuming this peptide is not known (thus ‘novel’) you would need to do your best at trying to lock down the mRNA sequence. Because of the degeneracy of the codons, however, you might not be able to get a perfect match. If you can find a region of moderate homology, you might be able to perform a Northern Blot – creating a anti-sense DNA probe and probing through an RNA library. However, this would depend on how accurate your mRNA sequence is due to the degeneracy. In theory, one of the given variations of the DNA sequence should give you a match when searching the genome of the animal (by nucleotide BLAST), but this (again) would depend on the accuracy of the reverse translation. Bottom line – if you know very little about it, finding the gene can be really hard.
