Active bacterial modification of the host environment through RNA polymerase II inhibition
Inès Ambite, … , Ulrich Dobrindt, Catharina Svanborg
Inès Ambite, … , Ulrich Dobrindt, Catharina Svanborg
Published December 15, 2020
Citation Information: J Clin Invest. 2021;131(4):e140333. https://doi.org/10.1172/JCI140333.
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Active bacterial modification of the host environment through RNA polymerase II inhibition

Abstract

Unlike pathogens, which attack the host, commensal bacteria create a state of friendly coexistence. Here, we identified a mechanism of bacterial adaptation to the host niche, where they reside. Asymptomatic carrier strains were shown to inhibit RNA polymerase II (Pol II) in host cells by targeting Ser2 phosphorylation, a step required for productive mRNA elongation. Assisted by a rare, spontaneous loss-of-function mutant from a human carrier, the bacterial NlpD protein was identified as a Pol II inhibitor. After internalization by host cells, NlpD was shown to target constituents of the Pol II phosphorylation complex (RPB1 and PAF1C), attenuating host gene expression. Therapeutic efficacy of a recombinant NlpD protein was demonstrated in a urinary tract infection model, by reduced tissue pathology, accelerated bacterial clearance, and attenuated Pol II–dependent gene expression. The findings suggest an intriguing, evolutionarily conserved mechanism for bacterial modulation of host gene expression, with a remarkable therapeutic potential.

Authors

Inès Ambite, Nina A. Filenko, Elisabed Zaldastanishvili, Daniel S.C. Butler, Thi Hien Tran, Arunima Chaudhuri, Parisa Esmaeili, Shahram Ahmadi, Sanchari Paul, Björn Wullt, Johannes Putze, Swaine L. Chen, Ulrich Dobrindt, Catharina Svanborg

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Figure 7

Complementation of nlpD and rpoS expression in E. coli SN25.

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Complementation of nlpD and rpoS expression in E. coli SN25. (A) NlpD le...
(A) NlpD levels in the supernatant of E. coli SN25-pRH320, complemented with the nlpD-rpoS operon from E. coli 83972. E. coli SN25-pBR322 carrying the empty vector served as a negative control (35, 36). (B) Inhibition by E. coli SN25-pRH320 of Pol II-p and PAF1C in infected cells. Nuclei were counterstained with DRAQ5. Fluorescence intensity was quantified by confocal microscopy, normalized against uninfected cells. Data are representative of 3 independent experiments and are presented as mean ± SEM (n = 50 cells). Scale bars: 20 μm. ***P < 0.001 compared with PBS by Kruskal-Wallis test with Dunn’s multiple-comparison test. (C–E) Whole genome transcriptomic analysis of the cellular response to infection (1 × 108 CFU/mL, 4 hours). (C) Reduced transcriptional activity in cells infected with E. coli SN25-pRH320. Heatmap: FC > 2.0 compared with uninfected cells. (D) Antiinflammatory effect of E. coli SN25-pRH320 defined by the inhibition of specific cytokine genes. (E) Principal component analysis of gene expression profiles in cells infected with E. coli SN25-pRH320 or E. coli 83972, compared with SN25 and uninfected controls.