Global Control of Cysteine Metabolism by CymR inBacillus subtilis

Abstract

YrzC has previously been identified as a repressor controlling ytmI expression via its regulation of YtlI activator synthesis in Bacillus subtilis. We identified YrzC as a master regulator of sulfur metabolism. Gene expression profiles of B. subtilis ⌬yrzC mutant and wild-type strains grown in minimal medium with sulfate as the sole sulfur source were compared. In the mutant, increased expression was observed for 24 genes previously identified as repressed in the presence of sulfate. Since several genes involved in the pathways leading to cysteine formation were found, we propose to rename YrzC CymR, for "cysteine metabolism repressor." A CymR-dependent binding to the promoter region of the ytlI, ssuB, tcyP, yrrT, yxeK, cysK, or ydbM gene was demonstrated using gel shift experiments. A potential CymR target site, TAAWNCN 2 ANTWNAN 3 ATMGGAA TTW, was found in the promoter region of these genes. In a DNase footprint experiment, the protected region in the ytlI promoter region contained this consensus sequence. Partial deletion or introduction of point mutations in this sequence confirmed its involvement in ytlI, yrrT, and yxeK regulation. The addition of O-acetylserine in gel shift experiments prevented CymR-dependent binding to DNA for all of the targets characterized. Transcriptome analysis of a ⌬cymR mutant and the wild-type strain also brought out significant changes in the expression level of a large set of genes related to stress response or to transition toward anaerobiosis.

Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism

“…In gram-negative bacteria, this regulation often utilizes regulatory proteins that control transcription initiation in response to amino acid availability as well as leader regions that mediate transcription attenuation via leader peptide coding region translation, which is sensitive to the availability of specific charged tRNAs (116,117). In gram-positive bacteria, regulatory proteins are also used to sense amino acids (29,97,98). For example, in B. subtilis and its close relatives, the biosynthetic genes of the trp operon are regulated by tryptophan (Trp) and the TRAP RNA binding protein, which regulates transcription termination (5, VOL.…”

Various checkpoints prevent the synthesis ofStaphylococcus aureuspeptidoglycan hydrolase LytM in the stationary growth phase

“…RNA extractions were performed as previously described, 65 followed by a DNase I treatment with the TURBO DNA-free reagent (Ambion, Austin, TX) to eliminate residual genomic DNA. cDNAs (cDNAs) were synthesized using the iScript cDNA synthesis kit (Bio-Rad, Hercules, CA), in a 20 ml reaction volume containing 1 mg total RNA.…”

An Rrf2-Type Transcriptional Regulator Is Required for Expression of psaAB Genes in the Cyanobacterium Synechocystis sp. PCC 6803

“…Many of them, such as tlr0503 in Thermosynechococcus elongatus, are tandemly arranged in the genome with cysK, which encodes Cys synthase (tlr0504). These findings suggest that the second group of Rrf2 in cyanobacteria may have a role homologous to CymR that regulates expression of CysK and other enzymes in the Cys metabolism in B. subtilis (Even et al, 2006). It is of note that this group of genes is absent in the Synechocystis genome.…”

“…For example, the redox sensor IscR of E. coli possesses Cys residues for coordination of a redox-responsive iron-sulfur center in the C-terminal region. Some Rrf2 proteins bind a small molecule for transcriptional regulation (O-acetylserine for Bacillus CymR [Even et al, 2006] and nitric oxide Figure 5. Fluorescence emission spectra of the wild type (solid line) and Dslr0846 mutant (dashed line) cells grown under high-light conditions (100 mmol m 22 s 21 ) for 48 h. After dark adaptation, cells were frozen and the spectra were recorded at 77 K with excitation at 435 nm.…”

“…The Slr0846 belongs to the Rrf2 family, which includes putative bacterial transcriptional regulators such as Rrf2 in Desulfovibrio vulgaris (Rossi et al, 1993), IscR in Escherichia coli, NsrR in Nitrosomonas europaea (Beaumont et al, 2004), CymR in Bacillus subtilis (Even et al, 2006), etc. Slr0846 of Synechocystis appears to be a distant homolog of IscR of E. coli that regulates expression of an isc operon involved in assembly of iron-sulfur clusters (Schwartz et al, 2001).…”