Once a phage is isolated and characterized, a FASTA file is created which is the genome sequence. We upload this file into a program called DNA master where we can see each gene in the sequence and the amino acid sequence for each of the genes.
Due to the importance of stomatin protein in regulation of ion channels and membrane trafficking, can it be realistically hypothesized that most bacteriophage, or at least most siphoviridae bacteriophage, will have gene 48 present in the genome? Are there other proteins that can substitute for stomatin?
Yes, similar genes that encode for stomatin were found in other L subclusters as well as the O cluster. There could be other genes that encode for a stomatin protein in other phage outside if these clusters, but these are the ones with a stomatin similar to the one found in Enceladus. As far as substitution, it is hard to say. Since the exact function of stomatin in bacteriophage is still not 100% clear, it is hard to say if there is something that could substitute it. However, stomatin does belong to a subfamily of proteins that have similar functions that could possibly take the place of this stomatin.
When looking at the genes my partner and I annotated, this one sparked interest because of the lack of research regarding stomatin in bacteriophage. I thought it would be interesting to really research it thoroughly to find the function it most likely plays in phage. Yes, there were many phage that had unknown functions and so they were hypothetical proteins because they didn’t match with any proteins already existing with a known function.
There were a lot of genes that didn’t have a function or highly match with anything. I would like to look into these more to see if I can determine a function.
Yes of course. So we were given the sequence of the genome and then we used a variety of programs such as DNA master, HHPred, phamerator, starterator, and NCBI BLAST to find the functions of each gene as well as find some key characteristics of each gene. From this information, I found gene product 48 which encoded for the stomatin and researched that further. Hope that makes more sense.
Thank you! I think bacteriophage are very interesting in general and the diversity between all of them is really cool. I think it is also great that these phage have the potential to be used in phage therapy to treat disease. I would like to continue with this research because of those reasons and because I have already research phage for the past two semesters.
I would like to find a definitive function of the stomatin protein. I think it would be really cool to be the one to discover the function. As stated in the presentation, I would create a variety of mutation to the stomatin protein or remove it completely and see how that affects the phage.
Stomatin is located in the intracellular space so it wouldn’t be able to act as a pore since in is not integrated within the membrane. It does interact with some of those integral membrane proteins though.
Is there other comparable genes that can take over/fulfill Stomatin’s function? Were there other similar genes from different phages that could suggest another function of this gene?
Yes, stomatin is a part of a superfamily of proteins that all share similar functions which could probably fulfill the stomatin function. All of the top hits on HHPred pointed to the stomatin protein so the likelihood of this gene having a different function is very low.
How did you find or isolate the amino acid sequence of gene 48?
Once a phage is isolated and characterized, a FASTA file is created which is the genome sequence. We upload this file into a program called DNA master where we can see each gene in the sequence and the amino acid sequence for each of the genes.
Due to the importance of stomatin protein in regulation of ion channels and membrane trafficking, can it be realistically hypothesized that most bacteriophage, or at least most siphoviridae bacteriophage, will have gene 48 present in the genome? Are there other proteins that can substitute for stomatin?
Yes, similar genes that encode for stomatin were found in other L subclusters as well as the O cluster. There could be other genes that encode for a stomatin protein in other phage outside if these clusters, but these are the ones with a stomatin similar to the one found in Enceladus. As far as substitution, it is hard to say. Since the exact function of stomatin in bacteriophage is still not 100% clear, it is hard to say if there is something that could substitute it. However, stomatin does belong to a subfamily of proteins that have similar functions that could possibly take the place of this stomatin.
How does the alpha helix structure relate to the function of the protein?
That is a really good question that I would have to look more into to answer!
Why did you chose to investigate gene 48 specifically? Are there any other genes with a poorly understood function in your phage?
When looking at the genes my partner and I annotated, this one sparked interest because of the lack of research regarding stomatin in bacteriophage. I thought it would be interesting to really research it thoroughly to find the function it most likely plays in phage. Yes, there were many phage that had unknown functions and so they were hypothetical proteins because they didn’t match with any proteins already existing with a known function.
What other gene products would you like to understand further? apart from gene 48
There were a lot of genes that didn’t have a function or highly match with anything. I would like to look into these more to see if I can determine a function.
Could you discuss your methods one more time and make them more clear?
Yes of course. So we were given the sequence of the genome and then we used a variety of programs such as DNA master, HHPred, phamerator, starterator, and NCBI BLAST to find the functions of each gene as well as find some key characteristics of each gene. From this information, I found gene product 48 which encoded for the stomatin and researched that further. Hope that makes more sense.
Hi Zoe, really good presentation! What specifically about bacteriophages and proteins interests you to do all this further research on them? Thanks!
Thank you! I think bacteriophage are very interesting in general and the diversity between all of them is really cool. I think it is also great that these phage have the potential to be used in phage therapy to treat disease. I would like to continue with this research because of those reasons and because I have already research phage for the past two semesters.
You listed a lot of potential future directions, which one would you do if you could continue this research?
I would like to find a definitive function of the stomatin protein. I think it would be really cool to be the one to discover the function. As stated in the presentation, I would create a variety of mutation to the stomatin protein or remove it completely and see how that affects the phage.
Is the circular structure of stomatin like a pore for a membrane?
Stomatin is located in the intracellular space so it wouldn’t be able to act as a pore since in is not integrated within the membrane. It does interact with some of those integral membrane proteins though.
Is there other comparable genes that can take over/fulfill Stomatin’s function? Were there other similar genes from different phages that could suggest another function of this gene?
Yes, stomatin is a part of a superfamily of proteins that all share similar functions which could probably fulfill the stomatin function. All of the top hits on HHPred pointed to the stomatin protein so the likelihood of this gene having a different function is very low.