new member of MocR/GabR‐type PLP‐binding regulator of d‐alanyl‐d‐alanine ligase in Brevibacillus brevis

• Published in: The FEBS journal Vol. 282; no. 21; pp. 4201 - 4217
• Main Authors: Takenaka, Takashi, Ito, Tomokazu, Miyahara, Ikuko, Hemmi, Hisashi, Yoshimura, Tohru
• Format: Journal Article
• Language: English
• Published: England Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies 01.11.2015; Blackwell Publishing Ltd
• Subjects: Actinobacteria; alanine; Amino Acid Sequence; aminotransferase; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Base Sequence; Binding Sites - genetics; bioinformatics; Brevibacillus - genetics; Brevibacillus - metabolism; Brevibacillus brevis; dipeptides; Dipeptides - metabolism; DNA; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA-binding domains; d‐alanyl‐d‐alanine; genes; Genes, Bacterial; glycylglycine; Helix; Inverted Repeat Sequences; MocR/GabR family transcriptional regulator; Molecular Sequence Data; Operon; operons; Peptide Synthases - metabolism; Phylogeny; Promoter Regions, Genetic; Protein Binding; pyridoxal; pyridoxal 5′‐phosphate; Sequence Homology, Amino Acid; spectroscopy; Trans-Activators - chemistry; Trans-Activators - genetics; Trans-Activators - metabolism; transcription (genetics); transcription factors; Transcriptional Activation; aminotransferase; MocR/GabR family transcriptional regulator; glycylglycine; d-alanyl-d-alanine; pyridoxal 5′-phosphate
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/febs.13415

The Brevibacillus brevis BBR47_28440 gene (referred to as ddlR) encodes an MocR/GabR family transcriptional regulator consisting of an N‐terminal helix‐turn‐helix DNA binding domain and a C‐terminal aminotransferase‐like domain. The ddlR gene is located just upstream of the d‐alanyl‐d‐alanine ligase gene (ddl) in the B. brevis genome, and these two genes form an operon. Gel‐shift assays indicated that purified DdlR binds specifically to the DNA region that includes putative −35 and −10 regions of the ddlR promoter. A 6‐bp inverted repeat that overlaps the −10 region of the ddlR promoter was found to be important for the binding. In vivo reporter assays confirmed that DdlR is an activator of the ddlR‐ddl operon. Spectroscopic analyses indicated that purified DdlR is a pyridoxal 5′‐phosphate binding transcriptional regulator that has dipeptide binding ability for d‐alanyl‐d‐alanine, the enzymatic product of Ddl, and glycylglycine. DdlR is capable of forming a dipeptide‐pyridoxal 5′‐phosphate external aldimine, but it lacks aminotransferase activity. Bioinformatic analyses suggest that DdlR‐mediated transcriptional regulation of ddlR and ddl may occur in multiple bacterial systems such as Actinobacteria and Bacillus species.