SEA-PHAGES | Frame-shift mutation splitting Tape Measure

Link to this post \| posted 04 Mar, 2020 17:07
BobHarms	Annotating phage Magel and there appears to be a 92-base deletion causing a frame-shift in the middle of Tape Measure. Aligns 100% with relatives Kerry, Tanis, Odesza except for this deletion. Both 'halves' of the gene have nearly 100% identity with Tape Measure. Has anyone seen this before? Any ideas on which ORF would be the functioning Tape Measure? (I was going to post the phamerator screenshot, but for the life of me, can't get it copied into the post). If you pull up Magel in phamerator with the above phages, ORFs 30 & 31 are the ones in question.

Link to this post | posted 04 Mar, 2020 17:07

Annotating phage Magel and there appears to be a 92-base deletion causing a frame-shift in the middle of Tape Measure. Aligns 100% with relatives Kerry, Tanis, Odesza except for this deletion. Both 'halves' of the gene have nearly 100% identity with Tape Measure.

Has anyone seen this before?
Any ideas on which ORF would be the functioning Tape Measure?

(I was going to post the phamerator screenshot, but for the life of me, can't get it copied into the post). If you pull up Magel in phamerator with the above phages, ORFs 30 & 31 are the ones in question.

Link to this post \| posted 04 Mar, 2020 18:16
debbie	Bob, The simple answer is that yes, the tape measure in Magel is in two pieces. However, that does not imply a programmed frameshift as we see in the tail assembly chaperone genes. Much bench work would be needed to confirm that there is a ribosomal slippage. It would be great to say that the upstream gene is a particular domain of the tape measure gene, but I don't think that is obvious. However more investigation could help to elucidate if the upstream gene has a particular function that we could identify. debbie

Link to this post | posted 04 Mar, 2020 18:16

debbie

Bob,
The simple answer is that yes, the tape measure in Magel is in two pieces. However, that does not imply a programmed frameshift as we see in the tail assembly chaperone genes. Much bench work would be needed to confirm that there is a ribosomal slippage. It would be great to say that the upstream gene is a particular domain of the tape measure gene, but I don't think that is obvious. However more investigation could help to elucidate if the upstream gene has a particular function that we could identify.
debbie

Link to this post \| posted 05 Mar, 2020 16:37
BobHarms	Thanks Debbie,it certainly is interesting. The highly conserved nature of both pieces would indicate that the mutation happened very recently in this lineage or perhaps each piece does represent a functional domain of the protein. Would the tail length provide a clue? Magel has a tail length very similar to it's relatives with a single, large tape measure gene.

Link to this post \| posted 05 Mar, 2020 16:42
debbie	Yes, the tail length might reflect the differences. However, if the two genes are stitched back together, the tail would be the same length. It would be a great exercise to ask students to provide an explanation for how that could happen, by checking out the literature. Fin, right? debbie

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Frame-shift mutation splitting Tape Measure