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How close can one pack protein and tRNA's genes

| posted 16 Feb, 2017 15:25
Welkin Pope
Nope, the tRNA cassettes are weird, and no you don't have to have a promoter for each of them or for each protein encoding gene interspersed within the cassette. We tend to steer clear of a tRNA and a protein occupying the same space, but there are definitely genomes where they get pretty close (take a look at the Ms). The only promoter rule is still about switching directions– presumably, switching transcriptional directions would still require two promoters even for tRNAs.
Welkin: Based on this statement above ("We tend to steer clear of a tRNA and a protein occupying the same space, but there are definitely genomes where they get pretty close" )

….It seems we should delete the tRNA gene.

Could you take a look at the image linked in my post above and let me know your thoughts on how to deal with this specific situation? Thank you. G
Edited 16 Feb, 2017 15:27
| posted 09 Mar, 2017 15:11
I'm a student in the bioinformatics class and we would really like to finish this genome, as well as my lab partner and I would like to do a presentation concerning what appears to be this anomaly. If anyone does have information, please report this to us!
| posted 13 Mar, 2017 20:32
Yes, Greg, from this picture I think you need to delete the tRNA. I can't tell what cluster this is from the picture, but I am guessing there are many other cluster relatives that likely have the same prediction, and the tRNA was deleted. With no bench evidence one way or the other, I am inclined to go for the protein encoding gene that fits into the operon nicely, and to stay consistent with other cluster relatives.

| posted 15 Mar, 2017 22:36
Thanks Welkin.

We will delete the tRNA. It really seems real.

So is there any empirical evidence that there are not tRNAs overlapping with structural genes? Since these are in the opposite orientation, if seems feasible that both could be real.
| posted 20 Mar, 2017 17:54
Our RNA seq and mass spec data from various clusters supports the guiding principle that the vast majority phage genes and genomes are only transcribed in one direction for any given region. So while I don't have data for this particular instance (and there are always exceptions to every principle), the data that we do have says that you need to choose one or the other when it comes to two genes occupying the same piece of DNA in different frames.
| posted 20 Mar, 2017 17:58
Thanks Welkin! I'll let the students know.

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