DNA binding by Corynebacterium glutamicum TetR-type transcription regulator AmtR

Abstract

Background: The TetR family member AmtR is the central regulator of nitrogen starvation response in Corynebacterium glutamicum. While the AmtR regulon was physiologically characterized in great detail up to now, mechanistic questions of AmtR binding were not addressed. This study presents a characterization of functionally important amino acids in the DNA binding domain of AmtR and of crucial nucleotides in the AmtR recognition motif.

Caracterización de la proteína transductora de señal AmtR

“…(Muhl, 2009 The alignment of TetR with AmtR using the algorithm blastp (protein-protein BLAST) in a matrix BLOSUM62, it confirmed that Both proteins share a sequence identity of 37% in the DNA binding domain (Muhl, 2009) (Figure 3). …”

“…Some amino acids in special tyrosine's, experimented electrostatic repulsion located in its special role by virtue of the phenol functionality, also some amino acid are in a specific structural position in the binding site that permits to interact with only one phosphate group located in only one nucleotide ( Figure 20). Therefore all written above maybe reaffirms the existence of a specific DNA sequence where the AmtR protein binds (Muhl, 2009;Beckers et al, 2005;Burkovski, 2007;Walter, Hänssler, Kalinowski, & Burkovski, 2007). The Figure 20 corresponds to the PDB average taken to the stable zone in a simulation time of 100 ns, it shows six amino acids directly responsible for creating CNN will hydrogen bonds, between DNA-Protein.…”

“…An attempt to explain this interaction by the analysis of a static three-dimensional model of AmtR-DNA binding domain revealed several amino acids, which are directly implicated in DNA binding, while others have more structural function. Still the mechanism, by which the protein stabilization or destabilization will reduce or increase DNA binding affinity, cannot unambiguously be determined from the static model structure (Muhl, 2009).…”

“…Therefore, prokaryotes have developed sophisticated mechanisms to provide an optimal nitrogen supply for metabolism and to surpass and survive situations of nitrogen limitation (Muhl, 2009;Hasselt et al, 2009;Beckers et al, 2005). In the case of nitrogen control in Corynebacterium glutamicum, a Gram-Positive soil bacterium used for the industrial production of amino acids (Takors et al, 2007) (see above), the transcription of genes in answer to nitrogen limitation is governed by the master regulator of nitrogen control, called AmtR, which blocks transcription of diverse genes during growth in nitrogen-rich medium (Muhl, 2009). …”

“…Nowadays the amino acids industry is developing methods to increase the production yield. This development has integrated understanding of the elaborated mechanisms to provide an optimal nitrogen supply for metabolism and to overcome and survive situations of nitrogen limitation (Muhl, 2009;Hasselt, Sevvana, Burkovski, & Muller, 2009;Beckers et al, 2005). In this way the master regulator of nitrogen control called AmtR is responsible to block transcription of various genes when nitrogen is present in surplus.…”