The YmdB Phosphodiesterase Is a Global Regulator of Late Adaptive Responses in Bacillus subtilis

Abstract

dBacillus subtilis mutants lacking ymdB are unable to form biofilms, exhibit a strong overexpression of the flagellin gene hag, and are deficient in SlrR, a SinR antagonist. Here, we report the functional and structural characterization of YmdB, and we find that YmdB is a phosphodiesterase with activity against 2=,3=-and 3=,5=-cyclic nucleotide monophosphates. The structure of YmdB reveals that the enzyme adopts a conserved phosphodiesterase fold with a binuclear metal center. Mutagenesis of a catalytically crucial residue demonstrates that the enzymatic activity of YmdB is essential for biofilm formation. The deletion of ymdB affects the expression of more than 800 genes; the levels of the D -dependent motility regulon and several sporulation genes are increased, and the levels of the SinR-repressed biofilm genes are decreased, confirming the role of YmdB in regulating late adaptive responses of B. subtilis.

Cyclic diguanylate regulation of Bacillus cereus group biofilm formation

“…For many of the B. thuringiensis 407 derivative strains, wild type B. thuringiensis 407 included, c‐di‐GMP content was below the level of detection (LOD, 0.8 ng ml −1 ; Limit of quantitation, LOQ: 3.5 ng ml −1 ). This has also been observed during vegetative growth in B. subtilis (Gao et al ., ), although detectable levels of c‐di‐GMP were identified by Diethmaier and co‐workers (Diethmaier et al ., ). However the CdgB and in particular CdgF overexpression strains showed highly increased c‐di‐GMP content, indicating that they have DGC activity under the selected experimental conditions (Table ; the full data set for all strains is described in Supporting Information Table S3).…”

Identification, Characterization, and Structure Analysis of the Cyclic di-AMP-binding PII-like Signal Transduction Protein DarA

“…The Gram-positive model organism Bacillus subtilis produces ppGpp, c-di-GMP, and c-di-AMP (9,(12)(13)(14)(15). Cyclic di-AMP can be synthesized by three different enzymes in this organism.…”

Selective Pressure for Biofilm Formation in Bacillus subtilis: Differential Effect of Mutations in the Master Regulator SinR on Bistability

“…subtilis. The phosphodiesterase activity of YmdB has already been shown to be required for the control of biofilm formation and motility (21), and the suppressor mutants might reveal the molecular target of YmdB.…”