Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity

Jason Saba, Katia Flores, Bailey Marshall, Michael D. Engstrom, Yikai Peng, Atharv S. Garje, Laurie E. Comstock and Robert Landick ()
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Jason Saba: University of Wisconsin–Madison
Katia Flores: University of Chicago
Bailey Marshall: University of Wisconsin–Madison
Michael D. Engstrom: University of Wisconsin–Madison
Yikai Peng: University of Wisconsin–Madison
Atharv S. Garje: University of Wisconsin–Madison
Laurie E. Comstock: University of Chicago
Robert Landick: University of Wisconsin–Madison

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract The genomes of human gut bacteria in the genus Bacteroides include numerous operons for biosynthesis of diverse capsular polysaccharides (CPSs). The first two genes of each CPS operon encode a locus-specific paralog of transcription elongation factor NusG (called UpxY), which enhances transcript elongation, and a UpxZ protein that inhibits noncognate UpxYs. This process, together with promoter inversions, ensures that a single CPS operon is transcribed in most cells. Here, we use in-vivo nascent-RNA sequencing and promoter-less in-vitro transcription (PIVoT) to show that UpxY recognizes a paused RNA polymerase via sequences in both the exposed non-template DNA and the upstream duplex DNA. UpxY association is aided by ‘pause-then-escape’ nascent RNA hairpins. UpxZ binds non-cognate UpxYs to directly inhibit UpxY association. This UpxY-UpxZ hierarchical regulatory program allows Bacteroides to generate subpopulations of cells producing diverse CPSs for optimal fitness.

Date: 2024
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DOI: 10.1038/s41467-024-55215-9

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