Insights into the substrate specificities, interactions and regulatory mechanisms of bacterial glycoconjugate biosynthesis enzymes
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Anderson-ajander-phd-bio-2023-thesis.pdf
Description
Thesis PDF
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34.39 MB
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Adobe PDF
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ef891f6e4a80f66b44f8b8e5a04dfeec
Author(s)
Anderson, Alyssa J.
Advisor(s)
Imperiali, Barbara
Date Issued
June 2023
Publisher
Massachusetts Institute of Technology
Abstract
Monotopic phosphoglycosyl transferase enzymes (MonoPGTs) are membrane-bound enzymes that initiate the assembly of prokaryotic glycoconjugates essential for bacterial survival and proliferation. MonoPGTs belong to an expansive superfamily with a diverse and richly annotated sequence space; however, limited biochemical characterization of this enzyme superfamily has been performed. To close the gap between sequence annotation and biochemical characterization of these critical enzymes, this thesis presents methods for characterizing the substrate specificities, interactions, and regulatory mechanisms of monoPGTs.
Substrate specificities of monoPGTs are largely unknown; therefore, connecting the sequences of monoPGTs to the composition of the final glycoconjugate produced remains a significant challenge. In Chapter 2, structural, sequence, and biochemical analyses are combined to identify co-conserved sequence “fingerprints” that predict the substrate specificity for a subset of monoPGTS that utilize UDP-N,N’-diacetylbacillosamine. The methodology described is generalizable and may be applied to identify sequence motifs that serve as fingerprints for monoPGTs of differing substrate specificities.
Evidence suggests glycoconjugate biosynthesis machinery forms complexes to centralize glycoconjugate production in the cell. However, the protein-protein interactions that comprise these complexes are poorly understood. In Chapter 3, I explore interactions among a subfamily of monoPGTs known as large (Lg) PGTs in near-native membrane mimetic systems. In this work, I characterize LgPGT dimerization using detergent-free solubilization and chemical crosslinking. This approach to studying protein-protein interactions of membrane-bound enzymes can be broadly applied to characterize interactions among glycoconjugate biosynthesis enzymes as a whole.
The regulatory mechanisms that govern monoPGT regulation remain enigmatic. In Chapter 4, activity-based protein profiling (ABPP) probes are implemented as protein-centric, membrane-protein compatible tools that lay the groundwork for understanding the activity and regulation of the monoPGT superfamily from a cellular proteome. Robust, covalent labeling at the active site of various representative monoPGTs from unfractionated cell membrane fractions is demonstrated using 3- phenyl-2H-azirine probes.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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