SEA-PHAGES | Is there any recent evidence of a tRNA overlapping a protein gene, even by a few bp?

Link to this post \| posted 14 Apr, 2022 21:52
fbaliraine	I am asking this question to have this issue settled and possibly suggest that a note be included in the Resource Guide regarding tRNA annotation. Phage IkeLoa reverse draft gene 134 at 92938-9390 bp overlaps a tRNA by 27 bp; even if we change the start, it still overlaps by a few bp. Its sequence is: MLYQLSYDGGAAGETSQPSRLRVMSPVCLPSTTIPARVTDEDLTFVKPLSZ According to the forum post, “How close can one pack protein and tRNA's genes” of Feb 24, 2016, Dr Pope stated that, “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.” We have been following this rule and I am inclined to delete this protein gene, but I want to be sure in case something has changed recently, because it is matching q1:s1, 100% with recently annotated genes in phagesDB and phamerator (years 2017-2020; see attached). Thanks! Fred 267Kb

Link to this post | posted 14 Apr, 2022 21:52

I am asking this question to have this issue settled and possibly suggest that a note be included in the Resource Guide regarding tRNA annotation.

Phage IkeLoa reverse draft gene 134 at 92938-9390 bp overlaps a tRNA by 27 bp; even if we change the start, it still overlaps by a few bp. Its sequence is: MLYQLSYDGGAAGETSQPSRLRVMSPVCLPSTTIPARVTDEDLTFVKPLSZ

According to the forum post, “How close can one pack protein and tRNA's genes” of Feb 24, 2016, Dr Pope stated that, “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.”
We have been following this rule and I am inclined to delete this protein gene, but I want to be sure in case something has changed recently, because it is matching q1:s1, 100% with recently annotated genes in phagesDB and phamerator (years 2017-2020; see attached).
Thanks!
Fred

Link to this post \| posted 15 Apr, 2022 02:31
debbie	Hi Fred, I have to look into this. What Welkin wrote was our best prediction at the time. However, we can show examples of exceptions of every 'rule' we make. We have found an example of a tRNA in the same region as a protein coding gene. BOTH are expressed. However, the tRNA is in the opposite direction. More to come. debbie

Link to this post \| posted 18 Apr, 2022 19:26
debbie	Fred, The tRNAs that I would like to be sure I keep are the ones that are called in Spud and ScottMcG. Would you provide the DNA Master file so i can take a closer look? Thanks, debbie Edited 18 Apr, 2022 19:26

Link to this post \| posted 19 Apr, 2022 02:30
fbaliraine	Hi Debbie, Please find the DNA Master file attached. The tRNAs look legit, but the question is whether to delete the reverse gene at 92938-93090 bp, given that it is currently in pham 14023 with 31 members and hits various phage genes (including very recently annotated phages such as Ronan gp 160, GenBank submission 01-JUN-2020, and Mangeria GenBank Accn # YP_010057792.1) in phagesDb with q1:s1, 100% identity and e-values such as 6e-22. Thanks, Fred 811Kb

Link to this post | posted 19 Apr, 2022 02:30

fbaliraine

Hi Debbie,
Please find the DNA Master file attached. The tRNAs look legit, but the question is whether to delete the reverse gene at 92938-93090 bp, given that it is currently in pham 14023 with 31 members and hits various phage genes (including very recently annotated phages such as Ronan gp 160, GenBank submission 01-JUN-2020, and Mangeria GenBank Accn # YP_010057792.1) in phagesDb with q1:s1, 100% identity and e-values such as 6e-22.
Thanks,
Fred

Link to this post \| posted 21 Apr, 2022 17:55
debbie	Fred, I would delete this gene. The coding potential is "greatest" in the open reading frame in question, is closer to 93100 - so there really is no coding potential in the space between where the tRNAs reside. If you BlastN the sequence in question, it is VERY well conserved across the C1s, but my money is on some kind of RNA thing and not a protein coding gene. This area was well reviewed by an RNA guy back in the day, and for now, without additional data, I think I would like to refrain from calling this a gene. And yes, others called it, but I would disagree. What do you think? debbie

Link to this post | posted 21 Apr, 2022 17:55

debbie

Fred,
I would delete this gene. The coding potential is "greatest" in the open reading frame in question, is closer to 93100 - so there really is no coding potential in the space between where the tRNAs reside. If you BlastN the sequence in question, it is VERY well conserved across the C1s, but my money is on some kind of RNA thing and not a protein coding gene. This area was well reviewed by an RNA guy back in the day, and for now, without additional data, I think I would like to refrain from calling this a gene.
And yes, others called it, but I would disagree.
What do you think?
debbie

Link to this post \| posted 21 Apr, 2022 23:19
fbaliraine	Hi Debbie, I concur. Case closed! Thank you for critically looking at this and clearing the air about calling genes that overlap with tRNAs. Perhaps a note in the resource guide can help eliminate future possibilities of someone calling such protein genes simply based on previous calls or significant BLASTp matches. Fred

Link to this post \| posted 22 Apr, 2022 11:22
debbie	Fred, Terrific. I think the note is there. https://seaphagesbioinformatics.helpdocsonline.com/article-40 The 're-look' was a good thing. I am glad we took the time and weighed the evidence. debbie

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Is there any recent evidence of a tRNA overlapping a protein gene, even by a few bp?