The aspartate aminotransferase-like domain of Firmicutes MocR transcriptional regulators

Bacterial MocR transcriptional regulators possess an N-terminal DNA-binding domain containing a conserved helix-turn-helix module and an effector-binding and/or oligomerization domain at the C-terminus, homologous to fold type-I pyridoxal 5'-phosphate (PLP) enzymes. Since a comprehensive structural analysis of the MocR regulators is still missing, a comparisons of Firmicutes MocR sequences was undertook to contribute to the understanding of the structural characteristics of the C-terminal domain of these proteins, and to shed light on the structural and functional relationship with fold type-I PLP enzymes. Results of this work suggest the presence of at least three subgroups within the MocR sequences and provide a guide for rational site-directed mutagenesis studies aimed at deciphering the structure-function relationships in this new protein family.

[1]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[2]  Marco Ciotti,et al.  Genetic diversity of HIV type 1 in Montenegro. , 2011, AIDS research and human retroviruses.

[3]  Masaru Goto,et al.  Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5′‐phosphate‐dependent transcriptional regulator , 2015, Molecular microbiology.

[4]  S. Garcia-Vallvé,et al.  Horizontal gene transfer in bacterial and archaeal complete genomes. , 2000, Genome research.

[5]  J. Guest,et al.  A new family of bacterial regulatory proteins. , 1991, FEMS microbiology letters.

[6]  L. Aravind,et al.  The many faces of the helix-turn-helix domain: transcription regulation and beyond. , 2005, FEMS microbiology reviews.

[7]  S. Whelan,et al.  A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.

[8]  Gustavo Caetano-Anollés,et al.  A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life , 2014, Archaea.

[9]  Martin Vingron,et al.  TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing , 2002, Bioinform..

[10]  Eduardo Díaz,et al.  Identification of a Missing Link in the Evolution of an Enzyme into a Transcriptional Regulator , 2013, PloS one.

[11]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[12]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[13]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[14]  K. Strimmer,et al.  Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Riccardo Percudani,et al.  The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families , 2009, BMC Bioinformatics.

[16]  Sébastien Rigali,et al.  Chapter 1: Variation in form and function the helix-turn-helix regulators of the GntR superfamily. , 2009, Advances in applied microbiology.

[17]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[18]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[19]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[20]  Alessandro Paiardini,et al.  Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases , 2011, Proceedings of the National Academy of Sciences.

[21]  Stefano Pascarella,et al.  Conformational transitions driven by pyridoxal‐5′‐phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii , 2014, Proteins.

[22]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[23]  B. Belitsky,et al.  Role of PdxR in the activation of vitamin B6 biosynthesis in Listeria monocytogenes , 2014, Molecular microbiology.

[24]  D. Posada,et al.  Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. , 2004, Systematic biology.

[25]  G. Schneider,et al.  The manifold of vitamin B6 dependent enzymes. , 2000, Structure.

[26]  Takeo Tomita,et al.  Mechanism for multiple‐substrates recognition of α‐aminoadipate aminotransferase from Thermus thermophilus , 2009, Proteins.

[27]  C. Mcphalen,et al.  X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase. , 1993, Journal of molecular biology.

[28]  Juan Crugeiras,et al.  The PLP cofactor: lessons from studies on model reactions. , 2011, Biochimica et biophysica acta.

[29]  G. Eichele,et al.  Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure. , 1984, Journal of molecular biology.

[30]  A. Tauch,et al.  Positive transcriptional control of the pyridoxal phosphate biosynthesis genes pdxST by the MocR-type regulator PdxR of Corynebacterium glutamicum ATCC 13032. , 2011, Microbiology.

[31]  Stefano Pascarella,et al.  Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold‐type I, pyridoxal‐5′‐phosphate‐dependent enzymes , 2004, Protein science : a publication of the Protein Society.

[32]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[33]  Wei Wang,et al.  Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT , 2013, Proceedings of the National Academy of Sciences.

[34]  S Pascarella,et al.  Genomic distribution and heterogeneity of MocR-like transcriptional factors containing a domain belonging to the superfamily of the pyridoxal-5'-phosphate dependent enzymes of fold type I. , 2011, Biochemical and biophysical research communications.

[35]  B. Belitsky,et al.  Bacillus subtilis GabR, a protein with DNA-binding and aminotransferase domains, is a PLP-dependent transcriptional regulator. , 2004, Journal of molecular biology.

[36]  J. Felsenstein.  Phylogenies from molecular sequences: inference and reliability. , 1988, Annual review of genetics.

[37]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[38]  Stefano Pascarella,et al.  Type I pyridoxal 5′-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines , 2013, BMC Structural Biology.

[39]  Tal Pupko,et al.  ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids , 2010, Nucleic Acids Res..

[40]  Stefano Pascarella,et al.  PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL , 2012, BMC Bioinformatics.

[41]  John B. Anderson,et al.  CDD: a curated Entrez database of conserved domain alignments , 2003, Nucleic Acids Res..