What are the implications of these two genes being linked?
If they are separate genes, do you think they have different functions as glycosyltransferases?
I can only assume based on the BLASTp that if the genes were to be linked they would make an illegitimate gene, given one half of the gene is meant to perform as a GT-2 (glycosyltransferase) and the other is meant to perform as a GT-25.
Great job! You mentioned in your future directions that you want to investigate the commonality between the genes in the F1 cluster, what methods would you use to investigate those similarities?
I would primarily use Phamerator and BLAST. I’ve been having a lot of issues with Tootsieroll’s genome map on Phamerator but once all the annotations are done (our class is finishing them now) it will be easier to compare and contrast other F1 cluster phages that also have glycosyltranferases. Phamerator can also tell me which phage in other clusters share this gene and BLAST can tell me other organisms that share the gene.
I know there’s a program that helps you build phylogenetic relationships. I’m not sure what it is off the top of my head but I think another group in my class was using it for one of their projects. Once I do more research and make use of such a program I would be able to map phage phylogenetic relationships and then work my way backwards from Tootsieroll’s genome. I would specifically look for a common ancestor that had glycosyltransferase.
I think you’re asking about their amino acid sequence. I didn’t look at their sequences, but I used their gene projects for comparison. Generally speaking, I can say Gene 94 was a GT-2 and is much larger/longer than Gene 95 which was a GT-25 (almost twice as long)
A glycosyltransferase is an enzyme that helps synthesize sugars and other products and is involved with biogenesis. Basically, they’re involved with building membranes, cell walls, cells envelopes, etc.
In bacteria it’s been confirmed that glycosyltransferases play a role in protecting the cell from extracellular threats due to the the role they take in membrane biogenesis. More research has to be done to confirm why phage would evolve such an enzyme, but slycosyltransferases may play a similar role of protection. Tootsieroll is also a temperate phage, perhaps the enzyme is extra protection for the phage/bacterial DNA combo during the phages’ stay in order to avoid an early evacuation, if you will, due to unsavory circumstances.
Each gene contains different domains: Gene 94 contains domains GT-A, family 2, GT-2, and WcaA; Gene 95 contains domains of family 25 LPS bio synthesis protein and family 25 LOS lipo oligosaccharide biosynthesis. These families are responsible for specific folds and functions.
What are the implications of these two genes being linked?
If they are separate genes, do you think they have different functions as glycosyltransferases?
Thank you for your question, Gia.
I can only assume based on the BLASTp that if the genes were to be linked they would make an illegitimate gene, given one half of the gene is meant to perform as a GT-2 (glycosyltransferase) and the other is meant to perform as a GT-25.
Great job! You mentioned in your future directions that you want to investigate the commonality between the genes in the F1 cluster, what methods would you use to investigate those similarities?
Thank you for your question, Nathalie.
I would primarily use Phamerator and BLAST. I’ve been having a lot of issues with Tootsieroll’s genome map on Phamerator but once all the annotations are done (our class is finishing them now) it will be easier to compare and contrast other F1 cluster phages that also have glycosyltranferases. Phamerator can also tell me which phage in other clusters share this gene and BLAST can tell me other organisms that share the gene.
Very nice presentation! In your future directions you talked about investigating the ancestral history of the two genes, how could you go about that?
Thank you for your question, Leah.
I know there’s a program that helps you build phylogenetic relationships. I’m not sure what it is off the top of my head but I think another group in my class was using it for one of their projects. Once I do more research and make use of such a program I would be able to map phage phylogenetic relationships and then work my way backwards from Tootsieroll’s genome. I would specifically look for a common ancestor that had glycosyltransferase.
Were you the two proteins specifically different in one crucial or particular area or were the two sequences differnt overall?
Thank you for your question, Annalise.
I think you’re asking about their amino acid sequence. I didn’t look at their sequences, but I used their gene projects for comparison. Generally speaking, I can say Gene 94 was a GT-2 and is much larger/longer than Gene 95 which was a GT-25 (almost twice as long)
What exactly is glycosyltransferase and what is its specific function?
Thank you for your question, Alex.
A glycosyltransferase is an enzyme that helps synthesize sugars and other products and is involved with biogenesis. Basically, they’re involved with building membranes, cell walls, cells envelopes, etc.
Why do you think tootsieroll and other phages have genes for glycosyltransferase?
Thank you for your question, Nikhil.
In bacteria it’s been confirmed that glycosyltransferases play a role in protecting the cell from extracellular threats due to the the role they take in membrane biogenesis. More research has to be done to confirm why phage would evolve such an enzyme, but slycosyltransferases may play a similar role of protection. Tootsieroll is also a temperate phage, perhaps the enzyme is extra protection for the phage/bacterial DNA combo during the phages’ stay in order to avoid an early evacuation, if you will, due to unsavory circumstances.
What makes genes 94 and 95 too diverse and why?
Thank you for your question, Shelby.
Each gene contains different domains: Gene 94 contains domains GT-A, family 2, GT-2, and WcaA; Gene 95 contains domains of family 25 LPS bio synthesis protein and family 25 LOS lipo oligosaccharide biosynthesis. These families are responsible for specific folds and functions.