Coevolution of the bacterial pheromone ComS and sensor ComR fine-tunes natural transformation in streptococci

Felipe Viela,Laura Ledesma-García,Patrice Soumillion,Yves F Dufrêne,Pascal Hols,Denis Dereinne,Sylvie Nessler,Imke Ensinck,Johann Mignolet

doi:10.1016/j.jbc.2021.101346

Abstract

Competence for natural transformation extensively contributes to genome evolution and the rapid adaptability of bacteria dwelling in challenging environments. In most streptococci, this process is tightly controlled by the ComRS signaling system, which is activated through the direct interaction between the (R)RNPP-type ComR sensor and XIP pheromone (mature ComS). The overall mechanism of activation and the basis of pheromone selectivity have been previously reported in Gram-positive salivarius streptococci; however, detailed 3D-remodeling of ComR leading up to its activation remains only partially understood. Here, we identified using a semirational mutagenesis approach two residues in the pheromone XIP that bolster ComR sensor activation by interacting with two aromatic residues of its XIP-binding pocket. Random and targeted mutagenesis of ComR revealed that the interplay between these four residues remodels a network of aromatic–aromatic interactions involved in relaxing the sequestration of the DNA-binding domain. Based on these data, we propose a comprehensive model for ComR activation based on two major conformational changes of the XIP-binding domain. Notably, the stimulation of this newly identified trigger point by a single XIP substitution resulted in higher competence and enhanced transformability, suggesting that pheromone-sensor coevolution counter-selects for hyperactive systems in order to maintain a trade-off between competence and bacterial fitness. Overall, this study sheds new light on the ComRS activation mechanism and how it could be exploited for biotechnological and biomedical purposes.

Highlights

Bacteria have developed diverse horizontal gene transfer mechanisms that favor their adaptation and survival to a fluctuating and competitive ecological niche (1)
Besides ~40% of mutants that contained point mutations in residues involved in HTH-domain sequestration (e.g. E118, E146, D147 or neighboring residues) (Fig. 4A and Fig. S3B), ~60% of them displayed the substitution F171L in ComR α10 helix. These results strongly suggest that residue F171 is pivotal for the activating conformational change of the ComR tetratricopeptide repeat (TPR) domain, which corroborates previous observations of F171Y174 interactions with XIP-1/5 in the activation mechanism (29)
We propose a refined model of the ComRS activation mechanism where the TPR domain is double-locked for its conformational change (Fig. 8, Movies S1 and S2)

Summary

INTRODUCTION

Bacteria have developed diverse horizontal gene transfer mechanisms that favor their adaptation and survival to a fluctuating and competitive ecological niche (1). In the case of ComR, the HTHdomain is composed of 5 α-helices while the TPR-domain encompasses 5 pairs of anti-parallel αhelices (forming 5 TPR-subdomains) and a single C-terminal CAP helix (capping helix α16) (27, 29) These detailed structure-function studies revealed that all (R)RNPPs undergo various conformational changes upon pheromone interaction that result in very diverse regulatory mechanisms (24, 26). While apo-ComR displays a sequestered HTH domain fasten by the TPR domain, XIP binding induces conformational changes resulting in dimerization of the TPR domain and allosteric release of the two DNA-binding domains (29, 30) This idiosyncratic molecular mechanism ensures locking of the transcriptional regulator in absence of its specific inducing pheromone. A detailed reciprocal investigation of ComR-XIP interacting residues revealed an underestimated critical step of the ComRS activation mechanism

RESULTS

DISCUSSION

Conflict of interests