Field of research: Bioinformatics
Lab: Weigang Qiu
School: Manhattan Hunter Science High School
Year: 10th/11th Grade
Synteny Analysis of Pfam54 Genes in 25 Borrelia burgdorferi Genomes
I worked in the Evolutionary Bioinformatics Lab researching the paralogous superfamily's molecular phylogeny for the BbCRASP gene in Borrelia burgdorferi using various computational tools, the Linux operating system, SQL databases and the Perl programming language.
Borrelia burgdorferi is a class of bacteria called spirochetes, where the B31 strain is known to be responsible for Lyme disease. The Borrelia lp54 plasmid contains the Pfam54 superfamily of surface proteins termed CRASPs,which have previously been identified for their affinity for human Factor H (FH) and Factor H Like (FHL) proteins. FH and FHL are part of the complement system that assist with clearing pathogens from the host; B31 strain,however, inactivates the complement system, and its BBA68 gene ,in particular, is suspected of that role.
With the use of a phylogenetic species tree and the Pfam54 gene tree of paralogs, I grouped unclassified genes from various strains into ortholog, or functional families. After, I retrieved the amino acid sequences from the lab database and arranged them using multiple sequence alignment program ClustalW--aligns amino acid sequences by similarity. With the aid of lp54's synteny map that depicts the relative order and the gene's location, I was able to conclusively see that BBA68 and its functional orthologs were present in all the genomes. Despite the presence of BBA68 CRASP orthologs in all the genomes, this work highlights BBA68 's distinctiveness in B31 and its role in Lyme disease.