Inducer responses of BenM, a LysR‐type transcriptional regulator from Acinetobacter baylyi ADP1

Abstract

SummaryBenM and CatM control transcription of a complex regulon for aromatic compound degradation. These Acinetobacter baylyi paralogues belong to the largest family of prokaryotic transcriptional regulators, the LysR-type proteins. Whereas BenM activates transcription synergistically in response to two effectors, benzoate and cis,cis-muconate, CatM responds only to cis,cis-muconate. Here, site-directed mutagenesis was used to determine the physiological significance of an unexpected benzoate-binding pocket in BenM discovered during structural studies. Residues in BenM were changed to match those of CatM in this hydrophobic pocket. Two BenM residues, R160 and Y293, were found to mediate the response to benzoate. Additionally, alteration of these residues caused benzoate to inhibit activation by cis,cismuconate, positioned in a separate primary effectorbinding site of BenM. The location of the primary site, in an interdomain cleft, is conserved in diverse LysRtype regulators. To improve understanding of this important family, additional regulatory mutants were analysed. The atomic-level structures were characterized of the effector-binding domains of variants that do not require inducers for activation, CatM(R156H) and BenM(R156H,T157S). These structures clearly resemble those of the wild-type proteins in their activated muconate-bound complexes. Amino acid replacements that enable activation without effectors reside at protein interfaces that may impact transcription through effects on oligomerization.

Peroxide‐Sensing Transcriptional Regulators in Bacteria

“…There are also indications of the potential involvement of a third cysteine in peroxide sensing (4). The LysR-type regulator BenM, which controls genes involved in benzoate catabolism, is known to sense two coinducers (cis,cis-muconate and benzoate) that bind to distinct sites on the protein (23). Binding of each ligand singly activates transcription, while simultaneous binding of both coinducers results in a synergistic increase in target gene transcription (11) that is not observed for all BenM target promoters (21).…”

Biochemical and Genetic Bases of Indole-3-Acetic Acid (Auxin Phytohormone) Degradation by the Plant-Growth-Promoting Rhizobacterium Paraburkholderia phytofirmans PsJN

“…In addition, IAA degradation cat genes in strain PsJN is associated with a CatR-like regulator (Fig. 1B), similar to CatM and BenM of Bz catabolism (55,56). However, participation by this regulator remains unclear because strain PsJN cat genes are regulated by IacR2 (Fig.…”

“…On the other hand, the LTTR family is a well-characterized group of transcriptional regulators, highly conserved and ubiquitous among bacteria (51), which have been involved in control of metabolism, cell division, quorum sensing, virulence, motility, and nitrogen fixation, among others (51)(52)(53)(54). A larger subgroup of LTTRs is associated with degradation of aromatic compounds, in which regulators CatM and BenM of Bz catabolism are quite well studied (55,56). It is reported here that the iacR1 and iacR2 genes are essential for P. phytofirmans IAA catabolism, whereas the lack of the iacS gene decreased catabolism of IAA.…”

The Transcription Factor AlsR Binds and Regulates the Promoter of the alsSD Operon Responsible for Acetoin Formation in Bacillus subtilis

“…This coinducer binding region comprises two distinct ␣/␤ subdomains, which are connected by two crossover regions that form a hinge or cleft (34). Previous structural studies identified the binding site for the effector lying between these subdomains of CatM and BenM (4,8). The effector binding domain of BenM was determined with and without the cognate effector (8).…”