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Phaila
Phaila
The first phage we annotated was Phaila, found in 2023 by a student at Spelman College. It has a genome that is 55,645 base pairs long. We manually annotated its genome, finding that has 93 genes. Its DNA sequence shows that it is similar to other phages with the same bacterial host (Arthrobacter globiformis), classified as subcluster AU6 phages. Phaila is a siphovirus, which is a phage composed of an icosahedral head, double-stranded DNA, and a long non-contractile tail.
NyleyClemson
NyleyClemson
The second phage we annotated was NyleyClemson, isolated by a student at Spelman College in 2023. It has a genome with a length of 69,900 base pairs and approximately 127 genes. We are still working to annotate all of the genes for this phage. Its DNA sequence shows similarities to other phages with the same bacterial host (Arthrobacter globiformis), classified as subcluster AP2 phages. NyleyClemson is also a siphovirus.
Phage Types
Phage Types
Phages can be classified based on their tail lengths. Both Phaila and NyleyClemson are siphoviruses (right). Phaila is a part of the AU6 subcluster, and NyleyClemson is a part of the AP2 subcluster.
Genomic Conclusions
Genomic Conclusions
Phaila's genome is very similar to other AU6 phages, such as Navi1117 and Argan; however, multiple genes throughout Phaila are not shared with any other phages. Genes 36, 39, and 49 all code for proteins unique to Phaila that are not present in any other known organism. Gene 72 of Phaila is interesting because of its protein function as a PnuC-like nicotinamide ribosomal transporter, a protein used for the uptake of nicotinamide which is a precusor for cofactor NAD+ used by many enzymes.
HNH Endonuclease
HNH Endonuclease
HNH endonucleases are enzyme that are involved in DNA splicing and packaging within bacteriophage genomes. HNH endonucleases cut DNA at specific loci. Phaila was found to contain six genes (3, 73, 79, 82, 84, and 89) that appear to code for HNH endonucleases. NyleyClemson was found to have one gene (83) that coded for an HNH endonuclease.
Novel Genes
Novel Genes
AlphaFold3 is a program used to create 3D images of proteins using their amino acid sequence. We used that program to create a confident model of the protein product from gene 36 of Phaila that is shown below.
PnuC-like Nicotinamide Riboside Transporter
More information is needed to determine the function of PnuC-like nicotinamide riboside transporter in Phaila. However, the PnuC-like nicotinamide riboside transporter gene is generally involved in production of NAD+ to overcome bacterial defenses against the phages.
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