Detecting ADP-Ribosylation in RNA.
ADP-ribosylation
PARPs
RNA
TRPT1
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
4
6
2021
pubmed:
5
6
2021
medline:
23
6
2021
Statut:
ppublish
Résumé
ADP-ribosylation is a widespread reversible chemical modification of macromolecular targets. Protein ADP-ribosylation has been widely studied and plays a vital role in the regulation of several biological processes. In recent years there has been increasing interest in alternative ADP-ribosylation targets such as nucleic acids-DNA and RNA. Here we report different methods to detect ADP-ribosylation of RNA substrates.
Identifiants
pubmed: 34085249
doi: 10.1007/978-1-0716-1374-0_15
doi:
Substances chimiques
RNA
63231-63-0
DNA
9007-49-2
Poly(ADP-ribose) Polymerases
EC 2.4.2.30
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
231-243Subventions
Organisme : Wellcome Trust
ID : 101794
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 210634
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R007195/1
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C35050/A22284
Pays : United Kingdom
Références
Gibson BA, Kraus WL (2012) New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs. Nat Rev Mol Cell Biol 13:411–424
doi: 10.1038/nrm3376
Vyas S, Matic I, Uchima L, Rood J, Zaja R, Hay RT, Ahel I, Chang P (2014) Family-wide analysis of poly(ADP-ribose) polymerase activity. Nat Commun 5:4426
doi: 10.1038/ncomms5426
Crawford K, Bonfiglio JJ, Mikoč A, Matic I, Ahel I (2018) Specificity of reversible ADP-ribosylation and regulation of cellular processes. Crit Rev Biochem Mol Biol 53:64–82
doi: 10.1080/10409238.2017.1394265
Cohen MS, Chang P (2018) Insights into the biogenesis, function, and regulation of ADP-ribosylation. Nat Chem Biol 14:236–243
doi: 10.1038/nchembio.2568
Gupte R, Liu Z, Kraus WL (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev 31:101–126
doi: 10.1101/gad.291518.116
Palazzo L, Mikoč A, Ahel I (2017) ADP-ribosylation: new facets of an ancient modification. FEBS J 284:2932–2946
doi: 10.1111/febs.14078
Rack JGM, Morra R, Barkauskaite E, Kraehenbuehl R, Ariza A, Qu Y, Ortmayer M, Leidecker O, Cameron DR, Matic I et al (2015) Identification of a class of protein ADP-ribosylating sirtuins in microbial pathogens. Mol Cell 59:309–320
doi: 10.1016/j.molcel.2015.06.013
Choi J-E, Mostoslavsky R (2014) Sirtuins, metabolism, and DNA repair. Curr Opin Genet Dev 26:24–32
doi: 10.1016/j.gde.2014.05.005
Barkauskaite E, Jankevicius G, Ahel I (2015) Structures and mechanisms of enzymes employed in the synthesis and degradation of PARP-dependent protein ADP-ribosylation. Mol Cell 58:935–946
doi: 10.1016/j.molcel.2015.05.007
Eisemann T, Pascal JM (2020) Poly(ADP-ribose) polymerase enzymes and the maintenance of genome integrity. Cell Mol Life Sci 77:19–33
doi: 10.1007/s00018-019-03366-0
Kim D-S, Challa S, Jones A, Kraus WL (2020) PARPs and ADP-ribosylation in RNA biology: from RNA expression and processing to protein translation and proteostasis. Genes Dev 34:302–320
doi: 10.1101/gad.334433.119
Rack JGM, Palazzo L, Ahel I (2020) (ADP-ribosyl)hydrolases: structure, function, and biology. Genes Dev 34:263–284
doi: 10.1101/gad.334631.119
Slade D, Dunstan MS, Barkauskaite E, Weston R, Lafite P, Dixon N, Ahel M, Leys D, Ahel I (2011) The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase. Nature 477:616–620
doi: 10.1038/nature10404
Oka S, Kato J, Moss J (2006) Identification and characterization of a mammalian 39-kDa poly(ADP-ribose) glycohydrolase. J Biol Chem 281:705–713
doi: 10.1074/jbc.M510290200
Lin W, Amé J-C, Aboul-Ela N, Jacobson EL, Jacobson MK (1997) Isolation and characterization of the cDNA encoding bovine poly(ADP-ribose) glycohydrolase. J Biol Chem 272:11895–11901
doi: 10.1074/jbc.272.18.11895
Sharifi R, Morra R, Appel CD, Tallis M, Chioza B, Jankevicius G, Simpson MA, Matic I, Ozkan E, Golia B et al (2013) Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease. EMBO J 32:1225–1237
doi: 10.1038/emboj.2013.51
Jankevicius G, Hassler M, Golia B, Rybin V, Zacharias M, Timinszky G, Ladurner AG (2013) A family of macrodomain proteins reverses cellular mono-ADP-ribosylation. Nat Struct Mol Biol 20:508–514
doi: 10.1038/nsmb.2523
Chen D, Vollmar M, Rossi MN, Phillips C, Kraehenbuehl R, Slade D, Mehrotra PV, von Delft F, Crosthwaite SK, Gileadi O et al (2011) Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J Biol Chem 286:13261–13271
doi: 10.1074/jbc.M110.206771
Ono T, Kasamatsu A, Oka S, Moss J (2006) The 39-kDa poly(ADP-ribose) glycohydrolase ARH3 hydrolyzes O-acetyl-ADP-ribose, a product of the Sir2 family of acetyl-histone deacetylases. Proc Natl Acad Sci U S A 103:16687–16691
doi: 10.1073/pnas.0607911103
Kato J, Zhu J, Liu C, Moss J (2007) Enhanced sensitivity to cholera toxin in ADP-ribosylarginine hydrolase-deficient mice. Mol Cell Biol 27:5534–5543
doi: 10.1128/MCB.00302-07
Palazzo L, Thomas B, Jemth A-S, Colby T, Leidecker O, Feijs KLH, Zaja R, Loseva O, Puigvert JC, Matic I et al (2015) Processing of protein ADP-ribosylation by Nudix hydrolases. Biochem J 468:293–301
doi: 10.1042/BJ20141554
Palazzo L, Daniels CM, Nettleship JE, Rahman N, McPherson RL, Ong S-E, Kato K, Nureki O, Leung AKL, Ahel I (2016) ENPP1 processes protein ADP-ribosylation in vitro. FEBS J 283:3371–3388
doi: 10.1111/febs.13811
Takamura-Enya T, Watanabe M, Totsuka Y, Kanazawa T, Matsushima-Hibiya Y, Koyama K, Sugimura T, Wakabayashi K (2001) Mono(ADP-ribosyl)ation of 2'-deoxyguanosine residue in DNA by an apoptosis-inducing protein, pierisin-1, from cabbage butterfly. Proc Natl Acad Sci U S A 98:12414–12419
doi: 10.1073/pnas.221444598
Nakano T, Takahashi-Nakaguchi A, Yamamoto M, Watanabe M (2015) In: Koch-Nolte F (ed) Endogenous ADP-ribosylation. Springer, Cham, pp 127–149
Nakano T, Matsushima-Hibiya Y, Yamamoto M, Enomoto S, Matsumoto Y, Totsuka Y, Watanabe M, Sugimura T, Wakabayashi K (2006) Purification and molecular cloning of a DNA ADP-ribosylating protein, CARP-1, from the edible clam Meretrix lamarckii. Proc Natl Acad Sci U S A 103:13652–13657
doi: 10.1073/pnas.0606140103
Jankevicius G, Ariza A, Ahel M, Ahel I (2016) The toxin-antitoxin system DarTG catalyzes reversible ADP-ribosylation of DNA. Mol Cell 64:1109–1116
doi: 10.1016/j.molcel.2016.11.014
Lawarée E, Jankevicius G, Cooper C, Ahel I, Uphoff S, Tang CM (2020) DNA ADP-ribosylation stalls replication and is reversed by RecF-mediated homologous recombination and nucleotide excision repair. Cell Rep 30:1373–1384
doi: 10.1016/j.celrep.2020.01.014
Talhaoui I, Lebedeva NA, Zarkovic G, Saint-Pierre C, Kutuzov MM, Sukhanova MV, Matkarimov BT, Gasparutto D, Saparbaev MK, Lavrik OI et al (2016) Poly(ADP-ribose) polymerases covalently modify strand break termini in DNA fragments in vitro. Nucleic Acids Res 44:9279–9295
pmcid: 5100588
Munnur D, Ahel I (2017) Reversible mono-ADP-ribosylation of DNA breaks. FEBS J 284:4002–4016
doi: 10.1111/febs.14297
Zarkovic G, Belousova EA, Talhaoui I, Saint-Pierre C, Kutuzov MM, Matkarimov BT, Biard D, Gasparutto D, Lavrik OI, Ishchenko AA (2018) Characterization of DNA ADP-ribosyltransferase activities of PARP2 and PARP3: new insights into DNA ADP-ribosylation. Nucleic Acids Res 46:2417–2431
doi: 10.1093/nar/gkx1318
Belousova EA, Ishchenko A, Lavrik OI (2018) DNA is a new target of Parp3. Sci Rep 8:4176–4176
doi: 10.1038/s41598-018-22673-3
Agnew T, Munnur D, Crawford K, Palazzo L, Mikoč A, Ahel I (2018) MacroD1 is a promiscuous ADP-Ribosyl hydrolase localized to mitochondria. Front Microbiol 9:20–20
doi: 10.3389/fmicb.2018.00020
Munir A, Banerjee A, Shuman S (2018) NAD+-dependent synthesis of a 5'-phospho-ADP-ribosylated RNA/DNA cap by RNA 2'-phosphotransferase Tpt1. Nucleic Acids Res 46:9617–9624
doi: 10.1093/nar/gky792
Munnur D, Bartlett E, Mikolčević P, Kirby IT, Matthias Rack JG, Mikoč A, Cohen MS, Ahel I (2019) Reversible ADP-ribosylation of RNA. Nucleic Acids Res 47:5658–5669
doi: 10.1093/nar/gkz305
Kleine H, Poreba E, Lesniewicz K, Hassa PO, Hottiger MO, Litchfield DW, Shilton BH, Lüscher B (2008) Substrate-assisted catalysis by PARP10 limits its activity to mono-ADP-Ribosylation. Mol Cell 32:57–69
doi: 10.1016/j.molcel.2008.08.009