{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/115323"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/115323","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"RNA regulation of polysaccharide metabolism in human gut Bacteroidetes","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-11 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled &#x27;Open Access&#x27;. The submission was exported from vireo on 2022-11-11 without embargo terms","abstract_has_math":false,"creators":["Adams, Amanda Nichole Danielle"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Microbiology","degree_department":null,"school":null,"contributors":["Vanderpool, Carin K","Cann, Isaac","Kehl-Fie, Thomas","Olsen, Gary"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-05","date_published":"2022-05","updated_at":"2026-07-22T22:24:54Z","subjects":["human microbiome","Bacteroidetes","polysaccharide metabolism","RNA regulation"],"languages":["en","eng"],"rights":["Copyright 2022 Amanda Adams"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/115323","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Vanderpool, Carin K","Cann, Isaac","Kehl-Fie, Thomas","Olsen, Gary"]},{"key":"dc:creator","label":"Author","values":["Adams, Amanda Nichole Danielle"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-05","2022-01-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Microbiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["human microbiome","Bacteroidetes","polysaccharide metabolism","RNA regulation"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2022 Amanda Adams"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/115323"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-11 without embargo terms","The student, Amanda Adams, accepted the attached license on 2022-01-03 at 10:01.","The student, Amanda Adams, submitted this Dissertation for approval on 2022-01-03 at 10:01.","This Dissertation was approved for publication on 2022-01-05 at 16:21.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17471 on 2022-11-11 at 13:04:03","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."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["RNA regulation of polysaccharide metabolism in human gut Bacteroidetes"]}]}],"canonical_facts":{"dc:contributor":["Vanderpool, Carin K","Cann, Isaac","Kehl-Fie, Thomas","Olsen, Gary"],"dc:creator":["Adams, Amanda Nichole Danielle"],"dc:date":["2022-05","2022-01-05"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-11 without embargo terms","The student, Amanda Adams, accepted the attached license on 2022-01-03 at 10:01.","The student, Amanda Adams, submitted this Dissertation for approval on 2022-01-03 at 10:01.","This Dissertation was approved for publication on 2022-01-05 at 16:21.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17471 on 2022-11-11 at 13:04:03","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."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/115323"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Amanda Adams"],"dc:subject":["human microbiome","Bacteroidetes","polysaccharide metabolism","RNA regulation"],"dc:title":["RNA regulation of polysaccharide metabolism in human gut Bacteroidetes"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Microbiology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:54Z"}