University of Illinois Urbana-Champaign

RNA regulation of polysaccharide metabolism in human gut Bacteroidetes

Adams, Amanda Nichole Danielle

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ADAMS-DISSERTATION-2022.pdf

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https://hdl.handle.net/2142/115323

Description

Title
RNA regulation of polysaccharide metabolism in human gut Bacteroidetes
Author(s)
Adams, Amanda Nichole Danielle
Issue Date
2022-01-05
Director of Research (if dissertation) or Advisor (if thesis)
Vanderpool, Carin K
Doctoral Committee Chair(s)
Vanderpool, Carin K
Committee Member(s)
  • Cann, Isaac
  • Kehl-Fie, Thomas
  • Olsen, Gary
Department of Study
Microbiology
Discipline
Microbiology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
  • human microbiome
  • Bacteroidetes
  • polysaccharide metabolism
  • RNA regulation
Abstract
The human gut microbiome influences many aspects of host health from dietary nutrient acquisition, immune system development, and vitamin biosynthesis to hormone metabolism and circadian rhythm regulation. One of the primary drivers of gut microbial community composition and function is the diet. Members of the prominent phylum Bacteroidetes can readily switch between host-associated and dietary polysaccharides as they become available, thereby allowing them to persist in the host for long periods of time. To accomplish this, Bacteroides encode dozens of substrate specific Polysaccharide Utilization Loci (PULs) that allow for sensing, uptake, and metabolism of dietary polysaccharides. Despite the importance of Bacteroides polysaccharide metabolism in governing gut microbiome function, the molecular mechanisms underlying production and regulation of these systems remain poorly defined. In this work, we seek to fill this gap by identifying RNA-mediated regulatory mechanisms controlling polysaccharide metabolism. We identify and characterize a family of RNA Recognition Motif (RRM-1) RNA Binding Proteins (RBPs) that are commonly found in the Bacteroidetes of the human gut. These RBPs are small (<10 kDa) proteins, occur in multiple copies per genome, and are abundantly expressed in vivo and in culture. Characterization in the model organism Bacteroides thetaiotaomicron reveals that RBPs are important for carbohydrate utilization and production through the regulation of PULs and capsular polysaccharide (CPS) loci. We demonstrate that the B. thetaiotaomicron RBP, RbpB, is a ssRNA binding protein, and mutants of rbpB are defective for growth on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs) due to decreased expression of an essential melibiase, BT1871. We further evaluate the role of RbpB in regulation of BT1871 and discover that a previously unidentified duplication of BT1871 in the B. thetaiotaomicron wild-type strain is lost in ∆rbpB mutant strains. Duplication loss is widespread in strains that are mutant derivatives of the wild-type strain. We show experimentally that the duplication is stable in genomes of B. thetaiotaomicron strains that are cultured through serial passage but is sporadically lost in strains that are genetically manipulated. Loss of the duplication broadly contributes to fitness defects on RFOs in a manner that does not depend on rbpB. This work describes and highlights the importance of RNA regulation and genomic plasticity in mediating polysaccharide metabolism in Bacteroidetes of the human gut.
Graduation Semester
2022-05
Type of Resource
Thesis
Handle URL
https://hdl.handle.net/2142/115323
Copyright and License Information
Copyright 2022 Amanda Adams

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Graduate Dissertations and Theses at Illinois PRIMARY
Graduate Theses and Dissertations at Illinois