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Faculty of Graduate Studies

Bernadette Alvarez

  • BSc (Vancouver Island University, 2019)
Notice of the Final Oral Examination for the Degree of Doctor of Philosophy

Topic

In vitro characterization of polysaccharide utilization locus 25 from Bacteroides caccae

Department of Biochemistry and Microbiology

Date & location

  • Wednesday, August 27, 2025
  • 12:00 P.M.
  • Clearihue Building, Room B017

Examining Committee

Supervisory Committee

  • Dr. Alisdair Boraston, Department of Biochemistry & Microbiology, University of Victoria (Supervisor)
  • Dr. Lisa Reynolds, Department of Biochemistry & Microbiology, UVic (Member)
  • Dr. John Burke, Department of Biochemistry & Microbiology, UVic (Member)
  • Dr. Bob Chow, Department of Biology, UVic (Outside Member)

External Examiner

  • Dr. Nicole Koropatkin, Department of Microbiology & Immunology, University of Michigan

Chair of Oral Examination

  • Dr. Reuven Gordon, Department of Electrical and Computer Engineering, UVic

Abstract

The human gut microbiota (HGM) plays a significant role in maintaining our overall health through its dynamic composition, ability to degrade recalcitrant nutrient sources, and production of metabolites that enable host-gut microbiota crosstalk. However, many aspects of HGM function remain poorly understood. Despite the highly diverse nature of the human diet, our understanding on how the HGM metabolises the glycan and peptide components of glycoproteins is limited. Here, we investigate how polysaccharide utilization locus 25 from Bacteroides caccae (BcPUL25) targets the glycosaminoglycan (GAG) and peptide components of aggrecan, a major dietary proteoglycan. Through structure-function analyses of its encoded carbohydrate-active enzymes (CAZymes), we show that BcPUL25 targets desulfated CS, or chondroitin, through a unique pathway that uses a carbohydrate dehydratase to prime saturated reducing end β-glucuronic acid residues for cleavage, allowing for more efficient GAG degradation by this PUL. Similarly, biochemical assessment of both BcM60_F and BcM60_G using mucin-specific FRET substrates revealed that BcM60_G can accommodate numerous glycan structures, whereas BcM60_F exhibited more stringent peptide specificity than its counterpart and could only bind to linear glycan moieties. All tested mucin O-glycan structures have been observed to decorate the aggrecan peptide backbone. Collectively, these findings establish B. caccae as a potential glycoprotein specialist and provides the molecular framework for exploring glycoprotein metabolism by the HGM. Overall, this research contributes toward our understanding of the molecular interplay within the trifecta of microbial composition, nutrient availability, and metabolite production. In the future, studies such as this will eventually result in the development of therapeutics that will alleviate HGM-influenced disease states.

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