Hyperevolution of trypanosome Variant Surface Glycoprotein genes

Plenderleith, Lindsey J. (2013) Hyperevolution of trypanosome Variant Surface Glycoprotein genes. PhD thesis, University of Glasgow.

Abstract

The African sleeping sickness parasite Trypanosoma brucei evades the immune system of its mammalian host by periodically switching the variant surface glycoprotein (VSG) that forms its cell-surface coat. This process of antigenic variation utilises a large archive of VSG genes, which are primarily subtelomeric and appear to evolve rapidly. Subtelomeres are the location of multi-member, variable gene families in many organisms, and often seem to have an elevated rate of mutation. The VSG archive is a particularly striking example of an organism taking advantage of this environment to promote hyperevolution. The aim of this project was to investigate the changes that occur in VSG evolution. In collaboration with researchers at the Sanger Institute, genomes from two time-separated isolates of the same trypanosome strain were sequenced and assembled. The quality of the genome assemblies was assessed, and the genomes concluded to be of sufficient quality for further analysis. Chromosome core genes and VSG N-terminal domain (NTD) genes and pseudogenes were annotated in each genome, and mutations between the genomes in each gene were catalogued. VSG NTDs had a significantly higher mutation frequency than core genes, and the specific patterns of mutations differed significantly between the two genome regions. These results together implied that VSG are subject to different mutational processes from core genes. However, mutation frequency did not appear to differ between VSG NTDs and other subtelomeric sequence, indicating that it is the subtelomeres in general that are subject to elevated mutational activity. Further examination of the VSG NTDs within each new genome reinforced published observations in the reference genome strain VSG archive of extensive substructuring and abundance of pseudogenes. Finally, to address the question of which mechanisms may be involved in elevating the mutation rate in subtelomeres, an attempt was made to characterise two members of a gene family predicted to encode error-prone lesion bypass DNA polymerases, a class of enzymes that have been suggested to have a role in the systematic generation of mutations. Such results as were obtained suggested that the genes examined may not encode active polymerases, and the results did not provide any evidence for a role for these polymerases in VSG hyperevolution. Overall, however, the project has uncovered considerable detail of how hypermutation proceeds in this highly variable gene family.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Keywords: trypanosome, VSG, hyperevolution, antigenic variation, subtelomere, parasitology
• Subjects: Q Science > QH Natural history > QH301 Biology; Q Science > QH Natural history > QH426 Genetics
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Parasitology
• Supervisor's Name: Barry, Prof. J. David
• Date of Award: 2013
• Depositing User: Lindsey J Plenderleith
• Unique ID: glathesis:2013-4557
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 03 Sep 2013 15:03
• Last Modified: 11 Aug 2015 10:50
• URI: https://theses.gla.ac.uk/id/eprint/4557