Active bacterial modification of the host environment through RNA polymerase II inhibition
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
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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Research Article Inflammation Microbiology

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 3

Inhibition of Pol II phosphorylation by E. coli 83972 single gene mutants.

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Inhibition of Pol II phosphorylation by E. coli 83972 single gene mutant...
(A) Schematic of genomic changes detected in the E. coli SN25 genome (red lines) compared with the ancestral strain E. coli 83972 (black lines) (n = 48). Genes with mutations leading to amino acid changes or frame shifts (fs) are indicated in red. (B and C) Pol II inhibition by E. coli 83972 single gene deletion mutants. Human kidney epithelial cells were infected for 4 hours, stained with antibodies against Pol II phosphorylated on Ser2 (Pol II-p), and analyzed by (B) confocal microscopy or (C) flow cytometry. The inhibitory phenotype of E. coli 83972 was attenuated after deletion of lldD, lldR, nlpD, rfaH, or cysE. (D) Pol II inhibition by supernatants from E. coli 83972 single gene deletion mutants. The ΔlldD, ΔlldR, ΔnlpD, or ΔrfaH deletions (red) attenuated Pol II inhibition, reproducing the E. coli SN25 phenotype. Scale bars: 10 μm. Data are presented as mean ± SEM (n = 2–10 experiments). *P < 0.05, **P < 0.01, ***P < 0.001 compared with E. coli 83972 by Kruskal-Wallis test with Dunn’s multiple-comparison test.