cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• Bacteroides species are key members of the human gut microbiota, influencing host health and disease.
• Polysaccharide Utilization Loci (PULs) enable Bacteroides to metabolize complex carbohydrates, crucial for colonization and energy acquisition.
• Existing regulatory mechanisms for PULs are known, but additional controls are suspected to explain hierarchical utilization and catabolite repression.

Purpose of the Study:

• To investigate novel regulatory mechanisms controlling polysaccharide utilization in Bacteroides.
• To identify new regulatory elements impacting the expression of polysaccharide utilization loci (PULs).
• To understand the role of these novel regulators in the context of host-derived and dietary glycan utilization.

Main Methods:

• Exploratory transcriptome sequencing (RNA-seq) to identify novel regulatory elements.
• Construction and analysis of a model system using the N-glycan degradation (Don) PUL in Bacteroides fragilis.
• Comparative analysis across multiple Bacteroides species to assess conservation.

Main Results:

• Discovery of cis-encoded antisense small RNAs (sRNAs) associated with 30% of B. fragilis PULs.
• Demonstration that the donS sRNA negatively regulates the Don PUL at the transcriptional level, reducing N-glycan utilization.
• Identification of a conserved regulatory mechanism across Bacteroides species, primarily affecting PULs involved in host-derived glycan metabolism.

Conclusions:

• A previously unknown layer of regulatory control mediated by antisense sRNAs governs PUL expression in Bacteroides.
• This regulatory system contributes to the hierarchical control of glycan utilization, particularly for host-derived glycans.
• The findings provide new insights into the complex regulation of Bacteroides physiology and gut homeostasis.