For other phages in the L1 cluster, similar results would be expected since phages in the same sub-cluster have at least 70-75% similarity. For phages outside of the L cluster, the phage characterization and genome could be vastly different, so it is hard to tell.
I would not expect for there to be a correlation between the SD score and the life cycle of a phage. The SD score indicates how likely a ribosome would bind to the ribosome binding site of a gene, which in turn can help us understand translational efficiency. However it does not really tell us anything about whether the phage is lytic or temperate. Btw, the particular phage for this study was temperate!
For now, genes 95-100 have unknown functions. When we put the DNA sequence for each gene into BLAST and HHPred, which are tools for comparing protein sequences that give potential functions, they all came up as no known function.
I hypothesize that the score difference indicates different levels of translation. A lower score means that the ribosome does not bind to the RBS as often as it would if there was a higher score. If the ribosome does not bind well to the Shine-Dalgarno sequence, less protein is made, and therefore influences gene expression.
If you looked at other L1 phages in the cluster did you see any that you would want to compare in terms of scoring to your work on this poster? Also wanted to comment that I really like your idea of observing protein expression during real phage infection. I think that would be so interesting.
I found that phages Halena, LeBron, and Appletree2, which are all L1 cluster phages had high similarities to Enceladus. I think these phages would be interesting to compare!
Was the phage lytic or temperate, and do you think that if you were to sequence a phage of the opposite type you would see the same SD score? Were the genes studied phage-type specific (e.g integrase or holin)?
The phage was temperate. I don’t think in general that the SD score would differ very much depending on the type of phage. The genes studied were not phage-type specific.
For your future directions, would you expect that the results would be the same for other phages? Why or why not?
For other phages in the L1 cluster, similar results would be expected since phages in the same sub-cluster have at least 70-75% similarity. For phages outside of the L cluster, the phage characterization and genome could be vastly different, so it is hard to tell.
Do you think there is a correlation between the SD score and the tendency for a phage to undergo the lytic or lysogenic cycle?
I would not expect for there to be a correlation between the SD score and the life cycle of a phage. The SD score indicates how likely a ribosome would bind to the ribosome binding site of a gene, which in turn can help us understand translational efficiency. However it does not really tell us anything about whether the phage is lytic or temperate. Btw, the particular phage for this study was temperate!
What functions do you suspect genes 95-100 have given that they are likely not essential genes?
For now, genes 95-100 have unknown functions. When we put the DNA sequence for each gene into BLAST and HHPred, which are tools for comparing protein sequences that give potential functions, they all came up as no known function.
In regards to your future directions, what kinds of experiments would you use to observe protein expression during real phage infection?
Immunoprecipitation, which can be used to isolate particular proteins.
Why did the genes at the end have a lower score compared to the ones at the beginning of the gene?
I hypothesize that the score difference indicates different levels of translation. A lower score means that the ribosome does not bind to the RBS as often as it would if there was a higher score. If the ribosome does not bind well to the Shine-Dalgarno sequence, less protein is made, and therefore influences gene expression.
how are the gene scores determined in the first place?
The gene scores are determined through algorithmic matrices in a bioinformatic tool called DNA Master.
The scores are determined through algorithmic matrices in the bioinformatics tool, DNA Master.
If you looked at other L1 phages in the cluster did you see any that you would want to compare in terms of scoring to your work on this poster? Also wanted to comment that I really like your idea of observing protein expression during real phage infection. I think that would be so interesting.
I found that phages Halena, LeBron, and Appletree2, which are all L1 cluster phages had high similarities to Enceladus. I think these phages would be interesting to compare!
Why did genes 4-9 have a higher SD scores than genes 95-100?
Genes 4-9 most likely are essential genes that have been preserved through viral evolution. genes 95-100, however, are not as highly expressed.
Was the phage lytic or temperate, and do you think that if you were to sequence a phage of the opposite type you would see the same SD score? Were the genes studied phage-type specific (e.g integrase or holin)?
The phage was temperate. I don’t think in general that the SD score would differ very much depending on the type of phage. The genes studied were not phage-type specific.
Great presentation! If you were to carry out the experiments mentioned in the future directions, do you expect that the scores would be similar?