Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis

Ramses Gallegos-Monterrosa,Anna Dragoš,Mathilde Nordgaard Christensen,Ákos T Kovács,Sonja Koppenhöfer,Tino Barchewitz,Paul J Kempen,Balázs Bálint,Gergely Maróti,B Priyadarshini

doi:10.1038/s42003-021-01983-9

Abstract

Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.

Highlights

Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth
We were interested in systematically determining the impact that each regulator aspartylphosphate (Rap) system (Fig. 1a) has on the population fitness of B. subtilis, on sporulation within biofilms, and how absence or presence of different Rap phosphatases would affect the adaptability of B. subtilis to different growth conditions
We have examined how variability in the number and function of Rap–Phr pairs allows B. subtilis to adapt to certain selection pressures

Summary

Introduction

Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Even when grown in liquid mixed cultures, where environmental conditions are assumed to be homogeneous, B. subtilis cells can be found as single flagellated cells or as nonflagellated chained cells due to stochastic variation in the expression of motility-related genes[3] This population heterogeneity further increases when B. subtilis develops a biofilm, i.e., cells commit to particular functions, such as biofilm matrix production, exoenzyme secretion, or spore formation[1,4]. B. subtilis possesses a complex regulatory network that leads the cells within the biofilm to generate a phenotypically heterogeneous population This network is described to be mainly controlled by the master transcriptional regulators Spo0A, DegU, and ComA. The Rap proteins are, in turn, inhibited by their cognate Phr peptides, which are produced as pre-Phr proteins that are exported to the extracellular milieu and cleaved to produce mature five to six amino acid Phr peptides

Methods

Results

Conclusion