The conserved mosaic prophage protein paratox inhibits the natural competence regulator ComR in Streptococcus

Lauren Mashburn-Warren,Steven D Goodman,Gerd Prehna,Michael J Federle

doi:10.1038/s41598-018-34816-7

Lauren Mashburn-Warren, Steven D Goodman + Show 2 more

Open Access

https://doi.org/10.1038/s41598-018-34816-7

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Abstract

Horizontal gene transfer is an important means of bacterial evolution. This includes natural genetic transformation, where bacterial cells become “competent” and DNA is acquired from the extracellular environment. Natural competence in many species of Streptococcus, is regulated by quorum sensing via the ComRS receptor-signal pair. The ComR-XIP (mature ComS peptide) complex induces expression of the alternative sigma factor SigX, which targets RNA polymerase to CIN-box promoters to activate genes involved in DNA uptake and recombination. In addition, the widely distributed Streptococcus prophage gene paratox (prx) also contains a CIN-box, and here we demonstrate it to be transcriptionally activated by XIP. In vitro experiments demonstrate that Prx binds ComR directly and prevents the ComR-XIP complex from interacting with DNA. Mutations of prx in vivo caused increased expression of the late competence gene ssb when induced with XIP as compared to wild-type, and Prx orthologues are able to inhibit ComR activation by XIP in a reporter strain which lacks an endogenous prx. Additionally, an X-ray crystal structure of Prx reveals a unique fold that implies a novel molecular mechanism to inhibit ComR. Overall, our results suggest Prx functions to inhibit the acquisition of new DNA by Streptococcus.

Highlights

Horizontal gene transfer is an important means of bacterial evolution
In our efforts to study the regulation of natural competence in Streptococcus spp. by ComRS based quorum sensing, we discovered that prx genes contain a perfect CIN-box within their promoter region for recognition by the SigX core-RNA-polymerase complex, and that transcription of prx is induced by XIP
We confirmed that the majority of genes induced by XIP were known genes involved in natural transformation of well-characterized model systems; we discovered a small subset of genes that have not been described as being a part of the competence regulon

Summary

Introduction

Horizontal gene transfer is an important means of bacterial evolution. This includes natural genetic transformation, where bacterial cells become “competent” and DNA is acquired from the extracellular environment. The ComR-XIP (mature ComS peptide) complex induces expression of the alternative sigma factor SigX, which targets RNA polymerase to CIN-box promoters to activate genes involved in DNA uptake and recombination. SigX recognizes a specific DNA sequence (TACGAATA) known as a CIN-box, which directs the core-RNA polymerase to initiate transcription of several genes having a CIN-box within their promoter region These genes are known as “late” competence genes and include those that encode the DNA uptake machinery and enzymes used in recombination of acquired DNA6–8. Upon uptake into the cell, XIP binds and activates ComR10,12, which induces a significant conformational change and dimerization that allows for the recognition of the comS (XIP) and sigX promoter regions[13,14].

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