Bacterial control of host gene expression through RNA polymerase II
Nataliya Lutay, … , Björn Wullt, Catharina Svanborg
Nataliya Lutay, … , Björn Wullt, Catharina Svanborg
Published May 24, 2013
Citation Information: J Clin Invest. 2013;123(6):2366-2379. https://doi.org/10.1172/JCI66451.
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Research Article

Bacterial control of host gene expression through RNA polymerase II

Abstract

The normal flora furnishes the host with ecological barriers that prevent pathogen attack while maintaining tissue homeostasis. Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation in which some patients infected with Escherichia coli develop acute pyelonephritis, while other patients with bacteriuria exhibit an asymptomatic carrier state similar to bacterial commensalism. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease-associated responses in the host. Here, we identify a new mechanism of bacterial adaptation through broad suppression of RNA polymerase II–dependent (Pol II–dependent) host gene expression. Over 60% of all genes were suppressed 24 hours after human inoculation with the prototype asymptomatic bacteriuria (ABU) strain E. coli 83972, and inhibition was verified by infection of human cells. Specific repressors and activators of Pol II–dependent transcription were modified, Pol II phosphorylation was inhibited, and pathogen-specific signaling was suppressed in cell lines and inoculated patients. An increased frequency of strains inhibiting Pol II was epidemiologically verified in ABU and fecal strains compared with acute pyelonephritis, and a Pol II antagonist suppressed the disease-associated host response. These results suggest that by manipulating host gene expression, ABU strains promote tissue integrity while inhibiting pathology. Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that potentially destructive immune activation will not occur.

Authors

Nataliya Lutay, Ines Ambite, Jenny Grönberg Hernandez, Gustav Rydström, Bryndís Ragnarsdóttir, Manoj Puthia, Aftab Nadeem, Jingyao Zhang, Petter Storm, Ulrich Dobrindt, Björn Wullt, Catharina Svanborg

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Figure 3

Suppression of RNA Pol II–dependent transcription by E. coli 83972.

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Suppression of RNA Pol II–dependent transcription by E. coli 83972. (A...
(A) Overview of the Pol II–dependent transcription cycle, with genes modified by E. coli 83972 indicated in boxes adjacent to each step (modified from Fuda et al., ref. 38). For log2 fold changes of individual genes, see Supplemental Table 3. Step 1: Chromatin opening and binding of the Pol II transcriptional complex to DNA is modified by specific activators or repressors. E. coli 83972 suppressed 6 transcriptional activators and activated 3 repressors. Step 2: Preinitiation complex formation. HSP70 interacting with GTFs was inhibited. Genes involved in steps 3 (initiation of transcription), 4 (promoter escape/clearance), and 5 (escape from pausing) were not affected. Step 6: Message elongation. Suppressed snRNA RN7SK, which binds to the transcription elongation factor P-TEFb. Step 7: Termination. Suppressed snRNA RNU6ATAC, involved in pre-mRNA splicing. See also Supplemental Figure 2 and Supplemental Table 3. (B) Heatmap of 83972-specific genes interacting with Pol II and regulating transcription. (C) Verification of the transcriptomic analysis. RT-PCR confirmed a reduction in transcript levels for genes in the Pol II cycle (FOS, LBH, HSPA6, RN7SK, and RNU6ATAC) in A498 cells infected with E. coli 83972. Data represent the means ± SEM. *P < 0.05; **P < 0.01. (D) Western blot analysis confirming suppression by E. coli 83972. Reduced levels of FOS, FOSB, LBH, and increased levels of DACH1 were detected.