Bioinformatic Characterization of Y Cluster Mycobacteriophage Bipper

Samantha M Gatt, Zachary B Osking, Carolyn M Barcellona, Kendra D Dozier, Jennifer M Faust, Asjah J Fedrick, Lara E Gagliardi, Patrick S Gleason, Eleisia A Gomez, Ashley M Hoffman, Meagan M Jenkins, Mackenzie J Jones, Joseph F Lang, Shinesse M Lequay, Phatima J Mars, Nino Mtchedlidze, Lauren M Paul, Alec N Pica, Michael D Robison, Danay Rodriguez, Kimberly A Rosales, Lauren E Saravis, Brittany M Sisson, Amanda L Tan, Rudeline Voltaire, Scott F Michael, Sharon Isern

Our Virology class at Florida Gulf Coast University adopted mycobacterium phage Bipper from the University of Pittsburgh in the fall of 2015. Bipper was considered a singleton when we began the annotation process. We found that Bipper had 135 open reading frames (ORFs) and one methionine (cat) tRNA. Fifty seven percent of its phams were orphams. Synteny was followed with the structural genes. There was a striking abundance of long stretches of overlapping ORFs. As many as 8 consecutive ORFs overlapped by exactly 4 bp. A stretch of 36 ORFs [gp75 to gp110] encompassing 16634 bp only had a single small gap (2 bp). About 6% of ORFs contained transmembrane domains. The smallest protein had no known function and was 108 bp long, while the tape measure protein was the longest at 4,686 bp. The start site preferred by Bipper was ATG. This site was used 55% of the time while GTG was used 44%. Only one ORF used TTG as the start site. The average GC% content was 67.3% and was almost identical to that of Mycobacterium smegmatis, 67.4%, suggesting the two have co-evolved for a significant period of time. We found several interesting repeat elements using MEME. One motif was particularly long (50 bp) and had 5 occurrences in locations correlating to large gaps in the genome. Seven putative Sigma-70 promoters were found throughout its genome, two of which were directly upstream of an operon; while six rho-independent transcriptional terminators were predicted within open reading frames and six more were in noncoding regions. Bipper’s attachment site for integration was located in its immunity repressor gene. The 35 bp sequence corresponded to its host’s attachment site at the 3’ end of M. smegmatis Arg tRNA, as expected for phage with tyrosine integrases. Overall, we found that Bipper displayed many of the common characteristics shared by bacteriophage that infect M. smegmatis. Bipper was published in GenBank on 22 March 2016. Its accession number is KU728633.1.