Year

2023

Degree Name

Doctor of Philosophy

Department

School of Chemistry and Molecular Biosciences

Abstract

The single-strand annealing homologous recombination (SSA) is one of the dsDNA break repair pathways, and albeit its importance from bacteria to bacteriophages, its molecular function is still unknown. The SSA reaction is catalysed by the enzyme complexes known as Exonuclease Annealase Two-component Recombinase (EATRs). The RecT and ORF6 proteins are single-stranded DNA-binding and annealing proteins expressed in E. coli and Kaposi’s sarcoma-associated herpesvirus (KSHV), respectively. RecT has already been shown to catalyse the SSA reaction. Although ORF6 has been shown to bind to ssDNA, further experimental evidence is needed to solidify its annealase activity. Since structure can dictate the function, this thesis aimed to determine the structure of the annealases RecT and ORF6 using a state-in-art cryo-electron microscopy technique. Furthermore, the shadow-casting EM technique has been established by optimising it for the equipment available at UOW, which is helpful for imaging the substrate DNA intermediates and the nucleoprotein complexes formed during SSA to better understand the molecular mechanistic details of this reaction.

This thesis includes the details about RecT and ORF6 proteins’ cloning, expression, and purification, which were further optimised for purity and homogeneity for cryo-electron microscopy with the help of negative staining electron microscopy (NSEM). Additionally, based on several NSEM analyses, the C-terminal His-tag containing RecT (RecTCH) oligomerisation on ssDNA was studied, and a general mechanism of its oligomerisation is described. Unfortunately, during the RecTCH protein’s cryo-EM sample optimisation, the LiRecT structure was published by another group. Therefore, work on that project was ceased at that point.

Several novel findings on ORF6 are reported in this thesis. Primarily, the concentration of the purified protein was increased 3 times more than the reports in the literature. Based on the NSEM and preliminary cryo-EM map of ORF6, it is shown that the ORF6 structure overall resembles the HSV1-ICP8 protein. Further, based on the steady-state and time-resolved fluorescence resonance energy transfer (FRET) experiments, a model for the ORF6 annealing mechanism is suggested. Towards generating a high-resolution structure, ORF6 monomers and filaments were optimised and imaged by using cryo-EM.

Processing a data set obtained from a monomeric ORF6 sample showed the presence of conformational heterogeneity in the particles, which was expected as the ORF6 AlphaFold model shows that the N-terminal and C-terminal domains are connected by an 18 amino acids long loop, allowing C-terminal domain to be relatively flexible to move around. Processing of another data set obtained from a sample containing ORF6 filaments generated 2-dimensional averages that look promising for generating a high-resolution structure.

This thesis also shows the details related to the installation and optimisation of the shadowing technique using a modern material, graphene oxide (GO), as a support film. This technique involves optimising both sample preparation and instrumentation for metal evaporation and deposition. For sample preparation, GO was deposited on cryo-EM holey grids, on which the sample was mounted. For instrumentation optimisation, a DENTON brand evaporator was used. The grid stage was re-engineered using AutoCAD to achieve the finest metal evaporation, and parameters such as amperage, vacuum, metal thickness, and angles were optimised. The optimised parameters were used to shadow-cast different lengths of DNA and their complexes with proteins, and good contrast images were acquired for qualitative and quantitative analyses.

Overall, this thesis presents two main novel findings. First, RecTCH monomers oligomerise into an open ring-shaped structure, which stacks together to generate short filaments. Second, to anneal two complementary ssDNA strands, ORF6 first forms filaments with both ssDNA, which then come in contact with each other rapidly to anneal the complementary strands. Once the annealing finishes, the annealed dsDNA is released from the filaments as the filaments fall apart into monomers. We also found that ORF6 monomers oligomerise to form the helical and non-helical filaments in the presence of DTT+Mg2+ and DTT-containing buffer, respectively.

FoR codes (2008)

0601 BIOCHEMISTRY AND CELL BIOLOGY, 0604 GENETICS, 0605 MICROBIOLOGY, 0915 INTERDISCIPLINARY ENGINEERING

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Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong.