Link to this post | posted 02 Mar, 2017 19:15

vbrownk

Question! (Also posted this on the external questions because I forgot my login). In viral genes, when there is start configuration like this: ATGATG … Is there some rule in bacteria/viruses that the second ATG is correct? We have several ORFs where the annotated START in other genomes (thus in STARTerator) choose ATG #2; however, ATG #1 would allow for a 4bp overlap with the upstream ORF, and if the subject in question already has its STOP overlapped 4bp with the downstream ORF - this would be a beautiful operon, but in direct conflict with STARTerator. -Victoria Kalah2_draft start@ 51741 vs. 51738 (REV). Pham 8105

Link to this post | posted 03 Mar, 2017 16:54

debbie

Victoria, Mass spec data of a few of these instances shows the protein starting at the amino acid next to the second start. Since it is common that the first methionine gets chopped of in post-translation processing, that NO methionine is present in the mass spec reads, it is likely that the second methionine initiated translation. So in this example, the 4 bp overlap gets 'trumped'. This decision is based on the simplest possible answer. and never forget, things do not have to be simple!

Link to this post | posted 26 Feb, 2023 19:09
jawsWPI	The Guiding Principles point 12 has been updated to choose the second of any two tandem (i.e. back-to-back) start sites based on the mass spec data and consideration of basic biology principles. guiding principles, point 12 subpoint f. Edited 26 Feb, 2023 19:10

Link to this post | posted 15 Feb, 2024 17:50

EWisner

Hello! I have a follow up question realted to this. One of my students is evaluating two tandem starts in AWGoat Gene stop 8723 (Potential starts: 8409 and 8412). Unlike in the example above, these are not both ATG starts. Instead, the 8409 start is an ATG and the 8412 is a GTG. We are wondering if the rule of calling the second start only applies to two methionines in a row. We have included a screenshot of the 6-frame translation. 22Kb

Link to this post | posted 15 Feb, 2024 20:12
debbie	I don't think that it matters if they are ATG, GTG, or TTG. Starts are starts and the amino acids chain start with an fMet. debbie

Link to this post | posted 20 Feb, 2024 19:53

EWisner

Thanks Debbie! I have a quick follow up. Because the second possible start is a GTG, couldn't it actually be coding for the amino acid valine? The DNA looks like this: ATGGTG 1) If we called start 8409 It would be: f-Met - Val 2) If we called start 8412 It would be: Met (not included) - f-Met That is why we weren't sure here if it still followed the two-starts in a row rule, since in 1) above it isn't actually two Mets in a row.

Link to this post | posted 20 Feb, 2024 22:45

balish

My two cents here. Yes, if you started at 8409, then translation would begin with fMet-Val-Glu. If you started at 8412, it would begin with fMet-Glu. Although the only way to know for sure is to analyze the protein in an infected bacterial cell itself, the rule of thumb is always to use the last among consecutive start codons. In this particular situation there are arguments that could be made for either case being correct, but by applying this rule, at least everyone is consistent. -Mitch

Link to this post | posted 21 Feb, 2024 12:44
EWisner	Thanks Mitch and Debbie. This sounds good, I appreciate it.