Characterization of Microbacterium liquefaciencs Bacteriophages Isolated from the Local Soil Environment on the Winthrop University Campus
Poster Number
100
Session Title
Biology and Biomedical Research
College
College of Arts and Sciences
Department
Biology
Faculty Mentor
Kristi M. Westover, Ph.D., and Victoria J. Frost, Ph.D.
Abstract
In the fourth year of Winthrop University’s involvement in the HHMI SEA—PHAGES program, two new bacteriophages were discovered and annotated using the host Microbacterium liquefaciens. Bacteriophages Mercedes and Leafus were isolated from soil on the Winthrop University campus in Rock Hill, South Carolina. DNA from each phage was isolated, and restriction enzyme digests were performed. Phage structures were also described using TEM microscopy. Once isolated, the DNA was sent to the University of Pittsburgh for genomic sequencing. DNA Master software and other programs, including Glimmer, GeneMark, Phamerator, the NCBI Blast Local Alignment Search Tool, the HHPred Bioinformatics Toolkit, and Starterator, were used to annotate and identify the functions of genes by comparing the sequences to other phages. The Mercedes genome length was found to be 40,230 base pairs (bp) long in a circularly permuted organization containing an estimated 59 genes. The Leafus genome length was found to be 42,000 bp long, also in a circularly permuted pattern containing an estimated 64 genes. While Leafus is a member of the EA1 subcluster, Mercedes has not been placed into a subcluster yet. The completed annotation should be able to shed light on its phylogenetic relationship with other EA cluster phages. The two most closely related phage sequences based on nucleotide similarity and gene structure are Neferthena, and EA5 subcluster phage and Chepli, an EA6 cluster phage. SEA—PHAGES research allowing for exploration of mycobacteriophage genomes will help researchers to ultimately develop gene libraries for biomedically relevant bacteriophages.
Grant Support?
Supported by a grant from the Howard Hughes Medical Institute for the SEA-PHAGES Program
Start Date
24-4-2020 12:00 AM
Characterization of Microbacterium liquefaciencs Bacteriophages Isolated from the Local Soil Environment on the Winthrop University Campus
In the fourth year of Winthrop University’s involvement in the HHMI SEA—PHAGES program, two new bacteriophages were discovered and annotated using the host Microbacterium liquefaciens. Bacteriophages Mercedes and Leafus were isolated from soil on the Winthrop University campus in Rock Hill, South Carolina. DNA from each phage was isolated, and restriction enzyme digests were performed. Phage structures were also described using TEM microscopy. Once isolated, the DNA was sent to the University of Pittsburgh for genomic sequencing. DNA Master software and other programs, including Glimmer, GeneMark, Phamerator, the NCBI Blast Local Alignment Search Tool, the HHPred Bioinformatics Toolkit, and Starterator, were used to annotate and identify the functions of genes by comparing the sequences to other phages. The Mercedes genome length was found to be 40,230 base pairs (bp) long in a circularly permuted organization containing an estimated 59 genes. The Leafus genome length was found to be 42,000 bp long, also in a circularly permuted pattern containing an estimated 64 genes. While Leafus is a member of the EA1 subcluster, Mercedes has not been placed into a subcluster yet. The completed annotation should be able to shed light on its phylogenetic relationship with other EA cluster phages. The two most closely related phage sequences based on nucleotide similarity and gene structure are Neferthena, and EA5 subcluster phage and Chepli, an EA6 cluster phage. SEA—PHAGES research allowing for exploration of mycobacteriophage genomes will help researchers to ultimately develop gene libraries for biomedically relevant bacteriophages.
