Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis.

Sophie Blinker,Jocelyne Vreede,Stanley Brul,Peter Setlow

doi:10.3390/ijms22073793

Abstract

Bacillus subtilis forms dormant spores upon nutrient depletion. Germinant receptors (GRs) in spore’s inner membrane respond to ligands such as L-alanine, and trigger spore germination. In B. subtilis spores, GerA is the major GR, and has three subunits, GerAA, GerAB, and GerAC. L-Alanine activation of GerA requires all three subunits, but which binds L-alanine is unknown. To date, how GRs trigger germination is unknown, in particular due to lack of detailed structural information about B subunits. Using homology modelling with molecular dynamics (MD) simulations, we present structural predictions for the integral membrane protein GerAB. These predictions indicate that GerAB is an -helical transmembrane protein containing a water channel. The MD simulations with free L-alanine show that alanine binds transiently to specific sites on GerAB. These results provide a starting point for unraveling the mechanism of L-alanine mediated signaling by GerAB, which may facilitate early events in spore germination.

Highlights

Germination of spores of the bacterium Bacillus subtilis can be induced by exposure to a variety of sugars, amino acids and cationic ions [1,2]
Clustering of Germinant receptors (GRs) in a germinosome appears to greatly increase GR function and downstream signaling which eventually lead to spore germination and outgrowth [1]
The SWISS-model search resulted in the first potential template to model the structure of GerAB, GkApcT (PDB code 6F34) [26]. 6F34 was identified as the best suitable template because the model showed the best QMEAN score [34] (13.99% sequence identity, sequence similarity of 0.28, QMEAN = −5.57)

Summary

Introduction

Germination of spores of the bacterium Bacillus subtilis can be induced by exposure to a variety of sugars, amino acids and cationic ions [1,2]. The current view is that once GRs sense germinants such as L-alanine, they undergo a conformational change, most likely in at least a region of a GR subunit in spores’ IM, which results in increased IM permeability to small molecules [1,3,15]. This latter change commits a spore to germinate and leads first to the intake of some water and the release of core monovalent cations and small amounts of the core’s huge pool of Ca-dipicolinic acid (CaDPA), which constitute 25% of spore dry core.

Methods

Results

Conclusion