CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus

Dorota Skotnicka,Ian T Cadby,Gert Bange,Dobromir Szadkowski,Wieland Steinchen,Andrew L Lovering,Lotte Søgaard-Andersen

doi:10.1038/s41467-020-15628-8

Abstract

Cyclic di-GMP (c-di-GMP) is a second messenger that modulates multiple responses to environmental and cellular signals in bacteria. Here we identify CdbA, a DNA-binding protein of the ribbon-helix-helix family that binds c-di-GMP in Myxococcus xanthus. CdbA is essential for viability, and its depletion causes defects in chromosome organization and segregation leading to a block in cell division. The protein binds to the M. xanthus genome at multiple sites, with moderate sequence specificity; however, its depletion causes only modest changes in transcription. The interactions of CdbA with c-di-GMP and DNA appear to be mutually exclusive and residue substitutions in CdbA regions important for c-di-GMP binding abolish binding to both c-di-GMP and DNA, rendering these protein variants non-functional in vivo. We propose that CdbA acts as a nucleoid-associated protein that contributes to chromosome organization and is modulated by c-di-GMP, thus revealing a link between c-di-GMP signaling and chromosome biology.

Highlights

Cyclic di-GMP (c-di-GMP) is a second messenger that modulates multiple responses to environmental and cellular signals in bacteria
We focused on MXAN_4361 and MXAN_4362, which were enriched in the experimental samples compared to the controls, due to their lack of homology to known c-di-GMP receptors and because in vivo analyses demonstrated that CdbA is essential
We confirmed the interaction with c-di-GMP employing purified CdbA and CdbB proteins in a differential radial capillary action of ligand assay (DRaCALA)[36], where both C-terminally His6-tagged CdbA and CdbB bound 32P-labeled c-di-GMP (Fig. 1b), i.e., binding was outcompeted by excess unlabeled c-di-GMP, but not by unlabeled GTP (Fig. 1b)

Summary

Introduction

Cyclic di-GMP (c-di-GMP) is a second messenger that modulates multiple responses to environmental and cellular signals in bacteria. The protein binds to the M. xanthus genome at multiple sites, with moderate sequence specificity; its depletion causes only modest changes in transcription. The number of DGCs and PDEs often exceeds that of known c-di-GMP receptors impeding a complete understanding of the biological functions of c-di-GMP signaling and how effects of c-di-GMP are implemented. These observations support that additional functions of c-di-GMP regulation remain to be uncovered.

Methods

Results

Conclusion