The MocR/GabR subfamily of chimeric proteins is widespread in bacteria and regulates a variety of biological processes. All members of this subfamily are typically composed of a winged helix-turn-helix (HTH) DNA-binding domain and a putative aminotransferase domain (AAT), belonging to the superfamily of the pyridoxal-5’-phosphate (PLP) enzymes of fold type I. The HTH-containing regions of these proteins vary from 60 to 120 residues in lenght and are similar to the winged HTH regions of bacterial transcriptional regulators of the broad GntR family. Little is known about the function of the AAT domain and about its ability to retain some catalytic activity. Moreover, the transcriptional regulatory pathways in which the MocR proteins might be involved are not known. So far, only a few MocR regulators have been characterized experimentally. One of these, PdxR is involved in the regulation of the divergently oriented pdxST operon, coding for the subunits of pyridoxal-5’-phosphate synthase in Corynebacterium glutamicum. Our research projects are aimed at the characterization of this regulator family through the following sub-tasks: -give an overview of the distribution of MocR factors among the different taxonomical bacterial divisions; -try to assess the degree of conservation of the main structural features of the AAT domain and compare them to those of the freestanding PLP enzymes; -predict which genes are controlled by these regulators; -identify, in the intergenic regions, the transcription factor binding sites (TFBSs). Methods: An ad-hoc Profile-HMM was built from a multiple sequence alignment of MocR proteins. HMM searches were carried out on the complete proteomes of each phylum reported in the taxonomy division of UniProt databank to collect most of the members of the MocR family. A Python script was used to extract information about the location, into the genome, of gene coding MocR and their neighbors genes. All sequences of neighboring genes were compared against the Pfam database to locate known domains. Pfam domain frequency was calculated as the fraction of the proteins having that particular Pfam domain. This frequency was calculated for each Pfam domain for all proteins in the dataset. Based on these frequencies and knowledge available in the literature, a subset of convergently transcribed pairs was selected. Pattern search and comparative genomics methods were used to detect direct and inverted repeat sequences in the intergenic regions between MocR and neighbors genes. Homology modelling techniques were applied to predict the three-dimensional structure of representative MocR members based on the B. subtilis GabR with PDB code 4MGR. The most interesting regulators will be selected for experimental characterization.
Transcription factors of the MocR family: in silico comparative analysis / Milano, Teresa; Pascarella, Stefano. - STAMPA. - (2014), pp. 183-184. (Intervento presentato al convegno BITS annual meeting 2014 tenutosi a Roma).
Transcription factors of the MocR family: in silico comparative analysis
MILANO, TERESA;PASCARELLA, Stefano
2014
Abstract
The MocR/GabR subfamily of chimeric proteins is widespread in bacteria and regulates a variety of biological processes. All members of this subfamily are typically composed of a winged helix-turn-helix (HTH) DNA-binding domain and a putative aminotransferase domain (AAT), belonging to the superfamily of the pyridoxal-5’-phosphate (PLP) enzymes of fold type I. The HTH-containing regions of these proteins vary from 60 to 120 residues in lenght and are similar to the winged HTH regions of bacterial transcriptional regulators of the broad GntR family. Little is known about the function of the AAT domain and about its ability to retain some catalytic activity. Moreover, the transcriptional regulatory pathways in which the MocR proteins might be involved are not known. So far, only a few MocR regulators have been characterized experimentally. One of these, PdxR is involved in the regulation of the divergently oriented pdxST operon, coding for the subunits of pyridoxal-5’-phosphate synthase in Corynebacterium glutamicum. Our research projects are aimed at the characterization of this regulator family through the following sub-tasks: -give an overview of the distribution of MocR factors among the different taxonomical bacterial divisions; -try to assess the degree of conservation of the main structural features of the AAT domain and compare them to those of the freestanding PLP enzymes; -predict which genes are controlled by these regulators; -identify, in the intergenic regions, the transcription factor binding sites (TFBSs). Methods: An ad-hoc Profile-HMM was built from a multiple sequence alignment of MocR proteins. HMM searches were carried out on the complete proteomes of each phylum reported in the taxonomy division of UniProt databank to collect most of the members of the MocR family. A Python script was used to extract information about the location, into the genome, of gene coding MocR and their neighbors genes. All sequences of neighboring genes were compared against the Pfam database to locate known domains. Pfam domain frequency was calculated as the fraction of the proteins having that particular Pfam domain. This frequency was calculated for each Pfam domain for all proteins in the dataset. Based on these frequencies and knowledge available in the literature, a subset of convergently transcribed pairs was selected. Pattern search and comparative genomics methods were used to detect direct and inverted repeat sequences in the intergenic regions between MocR and neighbors genes. Homology modelling techniques were applied to predict the three-dimensional structure of representative MocR members based on the B. subtilis GabR with PDB code 4MGR. The most interesting regulators will be selected for experimental characterization.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
