Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism.

Besides its function as an essential redox cofactor, nicotinamide adenine dinucleotide (NAD) also serves as a consumable substrate for several reactions with broad impact on many cellular processes. NAD homeostasis appears to be tightly controlled, but the mechanism of its regulation is little understood. Here we demonstrate that a previously predicted bacterial transcriptional regulator, NrtR, represses the transcription of NAD biosynthetic genes in vitro. The NAD metabolite ADP-ribose functions as an activator suppressing NrtR repressor activity. The presence of high ADP-ribose levels in the cell is indicative of active NAD turnover in bacteria, which could signal the activation of NAD biosynthetic gene expression via inhibiting the repressor function of NrtR. By comparing the crystal structures of NrtR in complex with DNA and with ADP-ribose, we identified a "Nudix switch" element that likely plays a critical role in the allosteric regulation of DNA binding and repressor function of NrtR.

[1]  L. Amzel,et al.  Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase. , 2002, Biochemistry.

[2]  C. G. Goff.  Chemical structure of a modification of the Escherichia coli ribonucleic acid polymerase alpha polypeptides induced by bacteriophage T4 infection. , 1974, The Journal of biological chemistry.

[3]  P. Dorrestein,et al.  The biosynthesis of nicotinamide adenine dinucleotides in bacteria. , 2001, Vitamins and hormones.

[4]  J. Day,et al.  Bacterial DNA ligases , 2001, Molecular microbiology.

[5]  K. Ochi,et al.  ADP-ribosylation of proteins in Bacillus subtilis and its possible importance in sporulation , 1996, Journal of bacteriology.

[6]  R. Marmorstein,et al.  Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli. , 2004, Journal of molecular biology.

[7]  D. Cervantes-Laurean,et al.  Glycation of proteins by ADP-ribose , 1994, Molecular and Cellular Biochemistry.

[8]  C. Sander,et al.  Dali: a network tool for protein structure comparison. , 1995, Trends in biochemical sciences.

[9]  Mikhail S. Gelfand,et al.  Evolution of the Nadr Regulon in Enterobacteriaceae , 2005, J. Bioinform. Comput. Biol..

[10]  V. Ramakrishnan,et al.  Crystal structure of globular domain of histone H5 and its implications for nucleosome binding , 1993, Nature.

[11]  C. Mueller-Dieckmann,et al.  Mammalian ADP-ribosyltransferases and ADP-ribosylhydrolases. , 2008, Frontiers in bioscience : a journal and virtual library.

[12]  R. Marmorstein.  Structure and chemistry of the Sir2 family of NAD+-dependent histone/protein deactylases. , 2004, Biochemical Society transactions.

[13]  C. Brenner,et al.  Nicotinamide Riboside and Nicotinic Acid Riboside Salvage in Fungi and Mammals , 2009, Journal of Biological Chemistry.

[14]  Hon Cheung Lee,et al.  Physiological functions of cyclic ADP-ribose and NAADP as calcium messengers. , 2001, Annual review of pharmacology and toxicology.

[15]  Mikhail S. Gelfand,et al.  Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon , 2008, Nucleic acids research.

[16]  J. Foster,et al.  Regulation of NAD biosynthesis in Salmonella typhimurium: expression of nad-lac gene fusions and identification of a nad regulatory locus. , 1985, Journal of general microbiology.

[17]  G. Archer,et al.  Crystal Structures of the BlaI Repressor from Staphylococcus aureus and Its Complex with DNA: Insights into Transcriptional Regulation of the bla and mec Operons , 2005, Journal of bacteriology.

[18]  J. Roth,et al.  Regulation of NAD Synthesis by the Trifunctional NadR Protein of Salmonella enterica , 2005, Journal of bacteriology.

[19]  W. Ying.  NAD+ and NADH in brain functions, brain diseases and brain aging. , 2007, Frontiers in bioscience : a journal and virtual library.

[20]  Z Dauter,et al.  Novel approach to phasing proteins: derivatization by short cryo-soaking with halides. , 2000, Acta crystallographica. Section D, Biological crystallography.

[21]  K. E. Everse,et al.  The pyridine nucleosidases from Bacillus subtilis and Neurospora crassa. Isolation and structural properties. , 1975, Archives of biochemistry and biophysics.

[22]  M. Knight,et al.  A heat-stable nicotinamide-adenine dinucleotide glycohydrolase from Pseudomonas putida KB1. Partial purification and some properties of the enzyme and an inhibitory protein. , 1972, The Biochemical journal.

[23]  J. Denu.  The Sir 2 family of protein deacetylases. , 2005, Current opinion in chemical biology.

[24]  Joseph D. Kwasnoski,et al.  High-density miniaturized thermal shift assays as a general strategy for drug discovery. , 2001, Journal of biomolecular screening.

[25]  Charles Brenner,et al.  Nicotinamide Riboside Kinase Structures Reveal New Pathways to NAD+ , 2007, PLoS biology.

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

[27]  G. Magni,et al.  Enzymology of NAD+ homeostasis in man , 2003, Cellular and Molecular Life Sciences CMLS.

[28]  D. Frick,et al.  The MutT Proteins or “Nudix” Hydrolases, a Family of Versatile, Widely Distributed, “Housecleaning” Enzymes* , 1996, The Journal of Biological Chemistry.

[29]  Ehmke Pohl,et al.  Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator , 2003, Molecular microbiology.

[30]  S. Imai.  Nicotinamide phosphoribosyltransferase (Nampt): a link between NAD biology, metabolism, and diseases. , 2009, Current pharmaceutical design.

[31]  L. Amzel,et al.  The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family , 2001, Nature Structural Biology.

[32]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[33]  K. Gopinathan,et al.  Nicotinamide-adenine dinucleotide glycohydrolase of Mycobacterium tuberculosis H37Rv. , 1964, The Biochemical journal.

[34]  A. Perraud,et al.  ADP-ribose gating of the calcium-permeable LTRPC2 channel revealed by Nudix motif homology , 2001, Nature.

[35]  P. Ludden.  Reversible ADP-ribosylation as a mechanism of enzyme regulation in procaryotes , 1994, Molecular and Cellular Biochemistry.

[36]  K. Ochi,et al.  Isolation and Identification of Novel ADP-Ribosylated Proteins from Streptomyces coelicolor A3(2) , 2002, Bioscience, biotechnology and biochemistry.

[37]  A. Albertini,et al.  YrxA Is the Transcriptional Regulator That Represses De Novo NAD Biosynthesis in Bacillus subtilis , 2005, Journal of bacteriology.

[38]  A. Guse,et al.  Determination of intracellular concentrations of the TRPM2 agonist ADP-ribose by reversed-phase HPLC. , 2005, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[39]  R. Frye,et al.  Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. , 2000, Biochemical and biophysical research communications.

[40]  N. Grishin,et al.  Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism. , 2008, Structure.

[41]  Dmitry A. Rodionov,et al.  Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators , 2008, Nucleic acids research.

[42]  L. Amzel,et al.  Structure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis. , 2003, Structure.

[43]  M. Wessels,et al.  Enhancement of Streptolysin O Activity and Intrinsic Cytotoxic Effects of the Group A Streptococcal Toxin, NAD-Glycohydrolase* , 2006, Journal of Biological Chemistry.

[44]  Mathias Ziegler,et al.  The new life of a centenarian: signalling functions of NAD(P). , 2004, Trends in biochemical sciences.

[45]  Y. Yokota,et al.  Genetic and Biochemical Properties of Streptococcal NAD-glycohydrolase Inhibitor* , 2006, Journal of Biological Chemistry.

[46]  F. Kühn,et al.  TRPM2: a calcium influx pathway regulated by oxidative stress and the novel second messenger ADP-ribose , 2005, Pflügers Archiv.

[47]  P. Baker,et al.  The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms. , 2002, Structure.

[48]  J. Eisfeld,et al.  Endogenous ADP-ribose enables calcium-regulated cation currents through TRPM2 channels in neutrophil granulocytes. , 2006, The Biochemical journal.

[49]  J. Denu,et al.  Hydrolase Regulates NAD+ Metabolites and Modulates Cellular Redox , 2009, Journal of Biological Chemistry.

[50]  K. Acharya,et al.  A family of killer toxins , 2006, The FEBS journal.