Annotation of Mycobacteriophage Dr. PhinkDaddy

Waller, Tamia, Jonathan S. Finkel, and Jacob D. Kagey

For centuries, human viruses such as the common cold, influenza, chickenpox, HIV, and Ebola have plagued the nation. Certain bacteria have been previously associated with these viruses. The relative ability of bacteria to cause disease is described in terms of virulence and antibiotic resistance. Bacteriophage, however, can penetrate the walls of the resistant bacteria, allowing them to function as intelligent antibiotics. Discovery of unique bacteriophage can lead to many advancements in medicine for virus treatments. Mycobacteriophage Dr. PhinkDaddy was isolated using Mycobacterium M. smegmatis as a host from the University of Detroit Mercy’s campus in the fall of 2017. A portion of Dr. PhinkDaddy’s DNA sequence was annotated and compared to the DNA sequences of previously annotated, well-known bacteriophages. Gene annotation involves describing different fragments of a DNA sequence with the intention of revealing which sections of that sequence are in fact genes. In short, annotation ultimately reveals the location and coding regions of all genes within a specific genome. Although there are many different approaches that could be taken to do the following, the process used in the case of Dr. PhinkDaddy included prediction based methods (which led to the discovery of genes/gene structures based on nucleotide sequence) and sequence similarity methods (which included the alignment of DNA with other sequences and proteins from different or similar species for comparison). A combination of software informers was used to annotate, including the freeware DNA sequence editor DNA Master and the online program, Phamerator. Synchronized use of the two programs led to the separation of the phage’s DNA sequence into various components and the generation of genome maps that incorporated nucleotide and amino acid sequence relationships. This project involved the annotation of 150 of the 234 genes that make up Dr. PhinkDaddy, which in turn revealed coding regions, gene location, and clues to gene functionality.