Identification of additional TnrA‐regulated genes of Bacillus subtilis associated with a TnrA box

Abstract

SummaryBacillus subtilis TnrA is a global regulator that responds to the availability of nitrogen sources and both activates and represses many genes during nitrogen-limited growth. In order to obtain a holistic view of the gene regulation depending on TnrA, we performed a genome-wide screening for TnrAregulated genes associated with a TnrA box. A combination of DNA microarray hybridization and a genome-wide search for TnrA boxes allowed us to find 36 TnrA-regulated transcription units associated with a putative TnrA box. Gel retardation assaying, using probes carrying at least one putative TnrA box and the deletion derivatives of each box, indicated that 17 out of 36 transcription units were likely TnrA targets associated with the TnrA boxes, two of which ( nasA and nasBCDEF ) possessed a common TnrA box. The sequences of these TnrA boxes contained a consensus one, TGTNANAWWWTMTNACA. The TnrA targets detected in this study were nrgAB , pucJKLM , gln-QHMP , nasDEF , oppABCDF , nasA , nasBCDEF and ywrD for positive regulation, and gltAB , pel , ywdIJK , yycCB , yttA , yxkC , ywlFG , yodF and alsT for negative regulation, nrgAB and gltAB being well-studied TnrA targets. It was unexpected that the negatively regulated TnrA targets were as many as the positively regulated targets. The physiological role of the TnrA regulon is discussed.

Bacillus subtilisLmrA Is a Repressor of thelmrABandyxaGHOperons: Identification of Its Binding Site and Functional Analysis oflmrBandyxaGH

“…To screen for additional LmrA targets, we employed a strategy analogous to that used in a previous study involving combined DNA microarray and gel retardation analyses (26). DNA microarray analysis was performed as described previously (26).…”

“…To screen for additional LmrA targets, we employed a strategy analogous to that used in a previous study involving combined DNA microarray and gel retardation analyses (26). DNA microarray analysis was performed as described previously (26). B. subtilis strains PLR2 and 168 were grown in LB liquid medium, and then the cells were harvested in the middle of the logarithmic phase at an optical density at 600 nm of 0.5 and disrupted to extract total RNA by vigorous shaking with glass beads in the presence of sodium dodecyl sulfate and phenol (25).…”

Interaction of the Membrane-bound GlnK-AmtB Complex with the Master Regulator of Nitrogen Metabolism TnrA in Bacillus subtilis

“…29), its own gene (tnrA; see Ref. 23), and other genes of nitrogen assimilation (30). Moreover, TnrA acts as a repressor for the genes gltAB and glnRA (31) as well as some other genes (30).…”

“…23), and other genes of nitrogen assimilation (30). Moreover, TnrA acts as a repressor for the genes gltAB and glnRA (31) as well as some other genes (30). Concerning the mechanism of control of TnrA activity, it could be shown that feedback-inhibited GS directly interacts with TnrA and blocks its DNA binding activity under conditions of good ammonium supply (32).…”

Genetic Requirements for Potassium Ion-Dependent Colony Spreading inBacillus subtilis

“…It is known that expression of glutamine synthetase (GlnA) is necessary for function of the transcription factor TnrA, which is a global regulator of nitrogen metabolism genes (34). When bound to feedback inhibitors, GlnA binds to TnrA and prevents its DNA from binding to genes regulated by a TnrA box sequence (34,35). To determine if the surface growth effects seen with the glnA mutant were a result of disruption of controls of TnrA, we constructed a tnrA mutant strain (MH11) in the 3610 genetic background.…”