scholarly journals Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs

2020 ◽  
Vol 48 (12) ◽  
pp. 6788-6798 ◽  
Author(s):  
Sunny Sharma ◽  
Ewa Grudzien-Nogalska ◽  
Keith Hamilton ◽  
Xinfu Jiao ◽  
Jun Yang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nicotinamide Adenine Dinucleotide ◽  
Mammalian Cells ◽  
Flavin Adenine Dinucleotide ◽  
Nicotinamide Adenine ◽  
Nudix Hydrolase ◽  
Decapping Enzymes ◽  
Hydrolysis Of ◽  
In Cells

Abstract We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5′caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

scholarly journals Extensive 5′-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yaqing Zhang ◽  
David Kuster ◽  
Tobias Schmidt ◽  
Daniel Kirrmaier ◽  
Gabriele Nübel ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Nicotinamide Adenine Dinucleotide ◽  
Transcription Initiation ◽  
Budding Yeast ◽  
Nicotinamide Adenine ◽  
Core Motif ◽  
Ribonucleic Acids ◽  
Decapping Enzymes

Abstract The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5′-ends. The modification percentage of transcripts is low (<5%). NAD incorporation occurs mainly during transcription initiation by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3′-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs are not translatable in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be disadvantageous to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

scholarly journals The human silent information regulator (Sir)2 homologue hSIRT3 is a mitochondrial nicotinamide adenine dinucleotide–dependent deacetylase

2002 ◽  
Vol 158 (4) ◽  
pp. 647-657 ◽  
Author(s):  
Björn Schwer ◽  
Brian J. North ◽  
Roy A. Frye ◽  
Melanie Ott ◽  
Eric Verdin
Keyword(s):  
Nicotinamide Adenine Dinucleotide ◽  
Mammalian Cells ◽  
Latent Class ◽  
Trichostatin A ◽  
Hydrolysis Product ◽  
Nicotinamide Adenine ◽  
Mitochondrial Matrix ◽  
Class Iii ◽  
Α Helix

The yeast silent information regulator (Sir)2 protein links cellular metabolism and transcriptional silencing through its nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylase activity. We report that mitochondria from mammalian cells contain intrinsic NAD-dependent deacetylase activity. This activity is inhibited by the NAD hydrolysis product nicotinamide, but not by trichostatin A, consistent with a class III deacetylase. We identify this deacetylase as the nuclear-encoded human Sir2 homologue hSIRT3, and show that hSIRT3 is located within the mitochondrial matrix. Mitochondrial import of hSIRT3 is dependent on an NH2-terminal amphipathic α-helix rich in basic residues. hSIRT3 is proteolytically processed in the mitochondrial matrix to a 28-kD product. This processing can be reconstituted in vitro with recombinant mitochondrial matrix processing peptidase (MPP) and is inhibited by mutation of arginines 99 and 100. The unprocessed form of hSIRT3 is enzymatically inactive and becomes fully activated in vitro after cleavage by MPP. These observations demonstrate the existence of a latent class III deacetylase that becomes catalytically activated upon import into the human mitochondria.

scholarly journals Methylation of deoxyribonucleic acid in cultured mammalian cells by N-methyl-N′-nitro-N-nitrosoguanidine. The influence of cellular thiol concentrations on the extent of methylation and the 6-oxygen atom of guanine as a site of methylation

1970 ◽  
Vol 116 (4) ◽  
pp. 693-707 ◽  
Author(s):  
P. D. Lawley ◽  
Carolyn J. Thatcher
Keyword(s):  
Oxygen Atom ◽  
Nucleic Acids ◽  
Mammalian Cells ◽  
Dimethyl Sulphate ◽  
Biological Effects ◽  
Methylation Of Dna ◽  
Thiol Content ◽  
Cellular Thiol ◽  
In Cells

1. In neutral aqueous solution N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) yields salts of nitrocyanamide as u.v.-absorbing products. With cysteine, as found independently by Schulz & McCalla (1969), the principal product is 2-nitràminothiazoline-4-carboxylic acid. Both these reactions liberate the methylating species; thiols enhance the rate markedly at neutral pH values. An alternative reaction with thiols gives cystine, presumably via the unstable S-nitrosocysteine. 2. Thiols (glutathione or N-acetylcysteine) in vitro at about the concentration found in mammalian cells enhance the rate of methylation of DNA markedly over that in neutral solution. 3. Treatment of cultured mammalian cells with MNNG results in rapid methylation of nucleic acids, the extent being greater the higher the thiol content of the cells. Rodent embryo cells are more extensively methylated than mouse L-cells of the same thiol content. Cellular thiol concentrations are decreased by MNNG. Proteins are less methylated by MNNG than are nucleic acids. 4. Methylation of cells by dimethyl sulphate does not depend on cellular thiol content and protein is not less methylated than nucleic acids. Methylation by MNNG may therefore be thiol-stimulated in cells. 5. Both in vitro and in cells about 7% of the methylation of DNA by MNNG occurs at the 6-oxygen atom of guanine. The major products 7-methylguanine and 3-methyladenine are given by both MNNG and dimethyl sulphate, but dimethyl sulphate does not yield O6-methylguanine. Possible reaction mechanisms to account for this difference between these methylating agents and its possible significance as a determinant of their biological effects are discussed.

NAD(P)H oxidase–dependent platelet superoxide anion release increases platelet recruitment

Blood ◽  
2002 ◽  
Vol 100 (3) ◽  
pp. 917-924 ◽  
Author(s):  
Florian Krötz ◽  
Hae Young Sohn ◽  
Torsten Gloe ◽  
Stefan Zahler ◽  
Tobias Riexinger ◽  
...  
Keyword(s):  
Nicotinamide Adenine Dinucleotide ◽  
Thrombus Formation ◽  
Nicotinamide Adenine Dinucleotide Phosphate ◽  
Human Platelets ◽  
Nicotinamide Adenine ◽  
Irreversible Aggregation ◽  
Reduced Nicotinamide Adenine Dinucleotide ◽  
Specific Peptide

Abstract Platelets, although not phagocytotic, have been suggested to release O2−. Since O2−-producing reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) oxidases can be specifically activated by certain agonists and are found in several nonphagocytotic tissues, we investigated whether such an enzyme is the source of platelet-derived O2−. We further studied which agonists cause platelet O2−release and whether platelet-derived O2− influences thrombus formation in vitro. Collagen, but not adenosine 5′-diphosphate (ADP) or thrombin, increased O2− formation in washed human platelets. This was a reduced nicotinamide adenine dinucleotide (NADH)–dependent process, as shown in platelet lysates. Consistent with a role of a platelet, NAD(P)H oxidase expression of its subunits p47phox and p67phoxand inhibition of platelet O2− formation by diphenylene-iodoniumchloride (DPI) and by the specific peptide-antagonist gp91ds-tat were observed. Whereas platelet-derived O2− did not influence initial aggregation, platelet recruitment to a preformed thrombus following collagen stimulation was significantly attenuated by superoxide dismutase (SOD) or DPI. It was also inhibited when ADP released during aggregation was cleaved by the ectonucleotidase apyrase. ADP in supernatants of collagen-activated platelets was decreased in the presence of SOD, resulting in lower ADP concentrations available for recruitment of further platelets. Exogenous O2−increased ADP- concentrations in supernatants of collagen-stimulated platelets and induced irreversible aggregation when platelets were stimulated with otherwise subthreshold concentrations of ADP. These results strongly suggest that collagen activation induces NAD(P)H oxidase–dependent O2− release in platelets, which in turn enhances availability of released ADP, resulting in increased platelet recruitment.

scholarly journals Minireview: NAD+, a Circadian Metabolite with an Epigenetic Twist

Endocrinology ◽  
2012 ◽  
Vol 153 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Paolo Sassone-Corsi
Keyword(s):  
Circadian Clock ◽  
Nicotinamide Adenine Dinucleotide ◽  
Mammalian Cells ◽  
Feedback Loop ◽  
Large Fraction ◽  
Sirtuin 1 ◽  
Nicotinamide Adenine ◽  
Dynamic Changes ◽  
Metabolic Functions ◽  
Transcriptional Feedback

Abstract A wide variety of endocrine, physiological, and metabolic functions follow daily oscillations. Most of these regulations are controlled at the level of gene expression by the circadian clock and, a remarkably coordinated transcription-translation machinery that exerts its function in virtually all mammalian cells. A large fraction of the genome is under control of the circadian clock, a regulation that is achieved through dynamic changes in chromatin states. Recent findings have demonstrated intimate connections between the circadian clock and epigenetic control. The case of nicotinamide adenine dinucleotide, which modulates the circadian activity of the deacetylase sirtuin 1, constitutes a paradigmatic example of the link between cyclic cellular metabolism and chromatin remodeling. Indeed, the clock transcriptional feedback loop is interlocked with the enzymatic loop of the nicotinamide adenine dinucleotide salvage pathway.

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