RNA regulation of polysaccharide metabolism in human gut Bacteroidetes

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Microbiology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Adams, Amanda Nichole Danielle

Contributors dc:contributor

• Vanderpool, Carin K
• Cann, Isaac
• Kehl-Fie, Thomas
• Olsen, Gary

• human microbiome
• Bacteroidetes
• polysaccharide metabolism
• RNA regulation

Statement dc:rights

• Copyright 2022 Amanda Adams

Language dc:language

en, eng

Handle dc:identifier

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

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F115323