Abolhassani,, N., Iyama,, T., Tsuchimoto,, D., Sakumi,, K., Ohno,, M., Behmanesh,, M., & Nakabeppu,, Y. (2010). NUDT16 and ITPA play a dual protective role in maintaining chromosome stability and cell growth by eliminating dIDP/IDP and dITP/ITP from nucleotide pools in mammals. Nucleic Acids Research, 38(9), 2891–2903. http://doi.org/10.1093/nar/gkp1250
Adams,, J. M., & Cory,, S. (1975). Modified nucleosides and bizarre 5′‐termini in mouse myeloma mRNA. Nature, 255(5503), 28–33.
Adl,, S. M., Simpson,, A. G. B., Lane,, C. E., Lukes,, J., Bass,, D., Bowser,, S. S., et al. (2012). The revised classification of eukaryotes. The Journal of Eukaryotic Microbiology, 59(5), 429–493. http://doi.org/10.1111/j.1550-7408.2012.00644.x
Andreeva,, A. V., & Kutuzov,, M. A. (2004). Widespread presence of “bacterial‐like” PPP phosphatases in eukaryotes. BMC Evolutionary Biology, 4, 47. http://doi.org/10.1186/1471-2148-4-47
Arkhipova,, V., Stolboushkina,, E., Kravchenko,, O., Kljashtorny,, V., Gabdulkhakov,, A., Garber,, M., … Nikonov,, O. (2015). Binding of the 5′‐triphosphate end of mRNA to the γ‐subunit of translation initiation factor 2 of the Crenarchaeon Sulfolobus solfataricus. Journal of Molecular Biology, 427(19), 3086–3095. http://doi.org/10.1016/j.jmb.2015.07.020
Aslett,, M., Aurrecoechea,, C., Berriman,, M., Brestelli,, J., Brunk,, B. P., Carrington,, M., … Wang,, H. (2010). TriTrypDB: A functional genomic resource for the Trypanosomatidae. Nucleic Acids Research, 38(Database issue), D457–D462. http://doi.org/10.1093/nar/gkp851
Bail,, S., & Kiledjian,, M. (2008). DcpS, a general modulator of cap‐binding protein‐dependent processes? RNA Biology, 5(4), 216–219.
Bangs,, J. D., Crain,, P. F., Hashizume,, T., McCloskey,, J. A., & Boothroyd,, J. C. (1992). Mass spectrometry of mRNA cap 4 from trypanosomatids reveals two novel nucleosides. The Journal of Biological Chemistry, 267(14), 9805–9815.
Bannerman,, B. P., Kramer,, S., Dorrell,, R. G., & Carrington,, M. (2018). Multispecies reconstructions uncover widespread conservation, and lineage‐specific elaborations in eukaryotic mRNA metabolism. PLoS One, 13(3), e0192633–e0192623. http://doi.org/10.1371/journal.pone.0192633
Barnes,, L. D., Garrison,, P. N., Siprashvili,, Z., Guranowski,, A., Robinson,, A. K., Ingram,, S. W., … Huebner,, K. (1996). Fhit, a putative tumor suppressor in humans, is a dinucleoside 5″,5″‐P1,P3‐triphosphate hydrolase. Biochemistry, 35(36), 11529–11535. http://doi.org/10.1021/bi961415t
Barton,, G. J., Cohen,, P. T., & Barford,, D. (1994). Conservation analysis and structure prediction of the protein serine/threonine phosphatases. Sequence similarity with diadenosine tetraphosphatase from Escherichia coli suggests homology to the protein phosphatases. European Journal of Biochemistry / FEBS, 220(1), 225–237.
Bessman,, M. J., Frick,, D. N., & O`Handley,, S. F. (1996). The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, “housecleaning” enzymes. The Journal of Biological Chemistry, 271(41), 25059–25062.
Bessman,, M. J., Walsh,, J. D., Dunn,, C. A., Swaminathan,, J., Weldon,, J. E., & Shen,, J. (2001). The gene ygdP, associated with the invasiveness of Escherichia coli K1, designates a Nudix hydrolase, Orf176, active on adenosine (5″)‐pentaphospho‐(5″)‐adenosine (Ap5A). The Journal of Biological Chemistry, 276(41), 37834–37838. http://doi.org/10.1074/jbc.M107032200
Bird,, J. G., Zhang,, Y., Tian,, Y., Panova,, N., Barvík,, I., Greene,, L., … Nickels,, B. E. (2016). The mechanism of RNA 5′ capping with NAD+, NADH and desphospho‐CoA. Nature, 535(7612), 444–447. http://doi.org/10.1038/nature18622
Bojarska,, E., Kraciuk,, R., Wierzchowski,, J., Wieczorek,, Z., Stepinski,, J., Jankowska,, M., et al. (1999). Hydrolysis of some mRNA 5′‐cap analogs catalyzed by the human Fhit protein‐‐and lupin ApppA hydrolases. Nucleosides %26 Nucleotides, 18(4–5), 1125–1126. http://doi.org/10.1080/15257779908041666
Bossé,, G. D., Rüegger,, S., Ow,, M. C., Vasquez‐Rifo,, A., Rondeau,, E. L., Ambros,, V. R., … Simard,, M. J. (2013). The decapping scavenger enzyme DCS‐1 controls microRNA levels in Caenorhabditis elegans. Molecular Cell, 50(2), 281–287. http://doi.org/10.1016/j.molcel.2013.02.023
Brenner,, C. (2002). Hint, Fhit, and GalT: Function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases. Biochemistry, 41(29), 9003–9014.
Burroughs,, A. M., Balaji,, S., Iyer,, L. M., & Aravind,, L. (2007). Small but versatile: The extraordinary functional and structural diversity of the beta‐grasp fold. Biology Direct, 2(1), 18. http://doi.org/10.1186/1745-6150-2-18
Buschmann,, J., Moritz,, B., Jeske,, M., Lilie,, H., Schierhorn,, A., & Wahle,, E. (2013). Identification of drosophila and human 7‐methyl GMP‐specific nucleotidases. Journal of Biological Chemistry, 288(4), 2441–2451. http://doi.org/10.1074/jbc.M112.426700
Cahová,, H., Winz,, M.‐L., Höfer,, K., Nübel,, G., & Jäschke,, A. (2015). NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature, 519(7543), 374–377. http://doi.org/10.1038/nature14020
Cartwright,, J. L., Safrany,, S. T., Dixon,, L. K., Darzynkiewicz,, E., Stepinski,, J., Burke,, R., & McLennan,, A. G. (2002). The g5R (D250) gene of African swine fever virus encodes a Nudix hydrolase that preferentially degrades diphosphoinositol polyphosphates. Journal of Virology, 76(3), 1415–1421. http://doi.org/10.1128/JVI.76.3.1415-1421.2002
Chang,, J. H., Jiao,, X., Chiba,, K., Oh,, C., Martin,, C. E., Kiledjian,, M., & Tong,, L. (2012). Dxo1 is a new type of eukaryotic enzyme with both decapping and 5″‐3″ exoribonuclease activity. Nature Structural %26 Molecular Biology, 19(10), 1011–1017. http://doi.org/10.1038/nsmb.2381
Chen,, N., Walsh,, M. A., Liu,, Y., Parker,, R., & Song,, H. (2005). Crystal structures of human DcpS in ligand‐free and m7GDP‐bound forms suggest a dynamic mechanism for scavenger mRNA decapping. Journal of Molecular Biology, 347(4), 707–718. http://doi.org/10.1016/j.jmb.2005.01.062
Chen,, Y. G., Kowtoniuk,, W. E., Agarwal,, I., Shen,, Y., & Liu,, D. R. (2009). LC/MS analysis of cellular RNA reveals NAD‐linked RNA. Nature Chemical Biology, 5(12), 879–881. http://doi.org/10.1038/nchembio.235
Clayton,, C. E. (2016). ScienceDirectGene expression in Kinetoplastids. Current Opinion in Microbiology, 32, 46–51. http://doi.org/10.1016/j.mib.2016.04.018
Clouet‐d`Orval,, B., Batista,, M., Bouvier,, M., Quentin,, Y., Fichant,, G., Marchfelder,, A., & Maier,, L.‐K. (2018). Insights into RNA processing pathways and associated‐RNA degrading enzymes in Archaea. FEMS Microbiology Reviews, 42, 579–613. http://doi.org/10.1093/femsre/fuy016
Cohen,, L. S., Mikhli,, C., Friedman,, C., Jankowska‐Anyszka,, M., Stepinski,, J., Darzynkiewicz,, E., & Davis,, R. E. (2004). Nematode m7GpppG and m3(2,2,7)GpppG decapping: Activities in Ascaris embryos and characterization of C. elegans scavenger DcpS. RNA (New York, NY), 10(10), 1609–1624. http://doi.org/10.1261/rna.7690504
Daffis,, S., Szretter,, K. J., Schriewer,, J., Li,, J., Youn,, S., Errett,, J., … Diamond,, M. S. (2010). 2′‐O methylation of the viral mRNA cap evades host restriction by IFIT family members. Nature, 468(7322), 452–456. http://doi.org/10.1038/nature09489
Deana,, A., Celesnik,, H., & Belasco,, J. G. (2008). The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature, 451(7176), 355–358. http://doi.org/10.1038/nature06475
Despotović,, D., Brandis,, A., Savidor,, A., Levin,, Y., Fumagalli,, L., & Tawfik,, D. S. (2017). Diadenosine tetraphosphate (Ap4A) ‐ an E. coli alarmone or a damage metabolite? The FEBS Journal, 284(14), 2194–2215. http://doi.org/10.1111/febs.14113
Devarkar,, S. C., Wang,, C., Miller,, M. T., Ramanathan,, A., Jiang,, F., Khan,, A. G., … Marcotrigiano,, J. (2016). Structural basis for m7G recognition and 2`‐O‐methyl discrimination in capped RNAs by the innate immune receptor RIG‐I. Proceedings of the National Academy of Sciences of the United States of America, 113(3), 596–601. http://doi.org/10.1073/pnas.1515152113
Dieci,, G., Preti,, M., & Montanini,, B. (2009). Eukaryotic snoRNAs: A paradigm for gene expression flexibility. Genomics, 94(2), 83–88. http://doi.org/10.1016/j.ygeno.2009.05.002
Dunckley,, T., & Parker,, R. (1999). The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. The EMBO Journal, 18(19), 5411–5422. http://doi.org/10.1093/emboj/18.19.5411
Edelstein,, P. H., Hu,, B., Shinzato,, T., Edelstein,, M. A. C., Xu,, W., & Bessman,, M. J. (2005). Legionella pneumophila NudA is a Nudix hydrolase and virulence factor. Infection and Immunity, 73(10), 6567–6576. http://doi.org/10.1128/IAI.73.10.6567-6576.2005
Edery,, I., & Sonenberg,, N. (1985). Cap‐dependent RNA splicing in a HeLa nuclear extract. Proceedings of the National Academy of Sciences of the United States of America, 82(22), 7590–7594.
Erben,, E. D., Fadda,, A., Lueong,, S., Hoheisel,, J. D., & Clayton,, C. E. (2014). A genome‐wide tethering screen reveals novel potential post‐transcriptional regulators in Trypanosoma brucei. PLoS Pathogens, 10(6), e1004178. http://doi.org/10.1371/journal.ppat.1004178
Filipowicz,, W., & Pogacić,, V. (2002). Biogenesis of small nucleolar ribonucleoproteins. Current Opinion in Cell Biology, 14(3), 319–327.
Fisher,, D. I., & McLennan,, A. G. (2008). Correlation of intracellular diadenosine triphosphate (Ap3A) with apoptosis in Fhit‐positive HEK293 cells. Cancer Letters, 259(2), 186–191. http://doi.org/10.1016/j.canlet.2007.10.007
Foley,, P. L., Hsieh,, P.‐K., Luciano,, D. J., & Belasco,, J. G. (2015). Specificity and evolutionary conservation of the Escherichia coli RNA pyrophosphohydrolase RppH. Journal of Biological Chemistry, 290(15), 9478–9486. http://doi.org/10.1074/jbc.M114.634659
Frick,, D. N., & Bessman,, M. J. (1995). Cloning, purification, and properties of a novel NADH pyrophosphatase. Evidence for a nucleotide pyrophosphatase catalytic domain in MutT‐like enzymes. The Journal of Biological Chemistry, 270(4), 1529–1534.
Fritz,, M., Vanselow,, J., Sauer,, N., Lamer,, S., Goos,, C., Siegel,, T. N., … Kramer,, S. (2015). Novel insights into RNP granules by employing the trypanosome`s microtubule skeleton as a molecular sieve. Nucleic Acids Research, 43(16), 8013–8032. http://doi.org/10.1093/nar/gkv731
Furuichi,, Y., LaFiandra,, A., & Shatkin,, A. J. (1977). 5′‐terminal structure and mRNA stability. Nature, 266(5599), 235–239.
Furuichi,, Y., Morgan,, M., Shatkin,, A. J., Jelinek,, W., Salditt‐Georgieff,, M., & Darnell,, J. E. (1975). Methylated, blocked 5 termini in HeLa cell mRNA. Proceedings of the National Academy of Sciences of the United States of America, 72(5), 1904–1908.
Gabelli,, S. B., Bianchet,, M. A., Bessman,, M. J., & Amzel,, L. M. (2001). The structure of ADP‐ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family. Nature Structural Biology, 8(5), 467–472. http://doi.org/10.1038/87647
Gao,, A., Vasilyev,, N., Luciano,, D. J., Levenson‐Palmer,, R., Richards,, J., Marsiglia,, W. M., … Serganov,, A. (2018). Structural and kinetic insights into stimulation of RppH‐dependent RNA degradation by the metabolic enzyme DapF. sNucleic Acids Research, 46, 6841–6856. http://doi.org/10.1093/nar/gky327
Garneau,, N. L., Wilusz,, J., & Wilusz,, C. J. (2007). The highways and byways of mRNA decay. Nature Reviews Molecular Cell Biology, 8(2), 113–126. http://doi.org/10.1038/nrm2104
Ghosh,, T., Peterson,, B., Tomasevic,, N., & Peculis,, B. A. (2004). Xenopus U8 snoRNA binding protein is a conserved nuclear decapping enzyme. Molecular Cell, 13(6), 817–828.
Grudzien‐Nogalska,, E., Jiao,, X., Song,, M.‐G., Hart,, R. P., & Kiledjian,, M. (2016). Nudt3 is an mRNA decapping enzyme that modulates cell migration. RNA (New York, NY), 22(5), 773–781. http://doi.org/10.1261/rna.055699.115
Grudzien‐Nogalska,, E., & Kiledjian,, M. (2017). New insights into decapping enzymes and selective mRNA decay. WIREs RNA, 8(1), e1379. http://doi.org/10.1002/wrna.1379
Grzela,, R., Nasilowska,, K., Lukaszewicz,, M., Tyras,, M., Stepinski,, J., Jankowska‐Anyszka,, M., … Darzynkiewicz,, E. (2018). Hydrolytic activity of human Nudt16 enzyme on dinucleotide cap analogs and short capped oligonucleotides. RNA (New York, NY), 24(5), 633–642. http://doi.org/10.1261/rna.065698.118
Gu,, M., Fabrega,, C., Liu,, S.‐W., Liu,, H., Kiledjian,, M., & Lima,, C. D. (2004). Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity. Molecular Cell, 14(1), 67–80.
Guranowski,, A. (2000). Specific and nonspecific enzymes involved in the catabolism of mononucleoside and dinucleoside polyphosphates. Pharmacology %26 Therapeutics, 87(2–3), 117–139.
Hamm,, J., & Mattaj,, I. W. (1990). Monomethylated cap structures facilitate RNA export from the nucleus. Cell, 63(1), 109–118.
Han,, G. W., Schwarzenbacher,, R., McMullan,, D., Abdubek,, P., Ambing,, E., Axelrod,, H., … Wilson,, I. A. (2005). Crystal structure of an Apo mRNA decapping enzyme (DcpS) from mouse at 1.83 a resolution. Proteins: Structure, Function, and Bioinformatics, 60(4), 797–802. http://doi.org/10.1002/prot.20467
Hasenöhrl,, D., Lombo,, T., Kaberdin,, V., Londei,, P., & Bläsi,, U. (2008). Translation initiation factor a/eIF2(−gamma) counteracts 5″ to 3″ mRNA decay in the archaeon Sulfolobus solfataricus. Proceedings of the National Academy of Sciences of the United States of America, 105(6), 2146–2150. http://doi.org/10.1073/pnas.0708894105
Höfer,, K., Li,, S.s., Abele,, F., Frindert,, J., Schlotthauer,, J., Grawenhoff,, J., … Jäschke,, A. (2016). Structure and function of the bacterial decapping enzyme NudC. Nature Chemical Biology, 12(9), 730–734. http://doi.org/10.1038/nchembio.2132
Hsieh,, P.‐K., Richards,, J., Liu,, Q., & Belasco,, J. G. (2013). Specificity of RppH‐dependent RNA degradation in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America, 110(22), 8864–8869. http://doi.org/10.1073/pnas.1222670110
Hsu,, C. L., & Stevens,, A. (1993). Yeast cells lacking 5′→3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Molecular and Cellular Biology, 13(8), 4826–4835.
Huh,, W.‐K., Falvo,, J. V., Gerke,, L. C., Carroll,, A. S., Howson,, R. W., Weissman,, J. S., & O`Shea,, E. K. (2003). Global analysis of protein localization in budding yeast. Nature, 425(6959), 686–691. http://doi.org/10.1038/nature02026
Hui,, M. P., Foley,, P. L., & Belasco,, J. G. (2014). Messenger RNA degradation in bacterial cells. Annual Review of Genetics, 48(1), 537–559. http://doi.org/10.1146/annurev-genet-120213-092340
Ignatochkina,, A. V., Takagi,, Y., Liu,, Y., Nagata,, K., & Ho,, C. K. (2015). The messenger RNA decapping and recapping pathway in Trypanosoma. Proceedings of the National Academy of Sciences of the United States of America, 112(22), 6967–6972. http://doi.org/10.1073/pnas.1424909112
Ismail,, T. M., Hart,, C. A., & McLennan,, A. G. (2003). Regulation of dinucleoside polyphosphate pools by the YgdP and ApaH hydrolases is essential for the ability of salmonella enterica serovar typhimurium to invade cultured mammalian cells. The Journal of Biological Chemistry, 278(35), 32602–32607. http://doi.org/10.1074/jbc.M305994200
Jäschke,, A., Höfer,, K., Nübel,, G., & Frindert,, J. (2016). Cap‐like structures in bacterial RNA and epitranscriptomic modification. Current Opinion in Microbiology, 30, 44–49. http://doi.org/10.1016/j.mib.2015.12.009
Jiao,, X., Chang,, J. H., Kilic,, T., Tong,, L., & Kiledjian,, M. (2013). A mammalian pre‐mRNA 5′ end capping quality control mechanism and an unexpected link of capping to pre‐mRNA processing. Molecular Cell, 50(1), 104–115. http://doi.org/10.1016/j.molcel.2013.02.017
Jiao,, X., Doamekpor,, S. K., Bird,, J. G., Nickels,, B. E., Tong,, L., Hart,, R. P., & Kiledjian,, M. (2017). 5′ end nicotinamide adenine dinucleotide cap in human cells promotes RNA decay through DXO‐mediated deNADding. Cell, 168(6), 1015–1027.e10. http://doi.org/10.1016/j.cell.2017.02.019
Jiao,, X., Xiang,, S., Oh,, C., Martin,, C. E., Tong,, L., & Kiledjian,, M. (2010). Identification of a quality‐control mechanism for mRNA 5′‐end capping. Nature, 467(7315), 608–611. http://doi.org/10.1038/nature09338
Jurado,, A. R., Tan,, D., Jiao,, X., Kiledjian,, M., & Tong,, L. (2014). Structure and function of pre‐mRNA 5″‐end capping quality control and 3″‐end processing. Biochemistry, 53(12), 1882–1898. http://doi.org/10.1021/bi401715v
Kerk,, D., Templeton,, G., & Moorhead,, G. B. G. (2008). Evolutionary radiation pattern of novel protein phosphatases revealed by analysis of protein data from the completely sequenced genomes of humans, green algae, and higher plants. Plant Physiology, 146(2), 351–367. http://doi.org/10.1104/pp.107.111393
Kiledjian,, M. (2018). Eukaryotic RNA 5′‐end NAD+ capping and DeNADding. Trends in Cell Biology, 28(6), 454–464. http://doi.org/10.1016/j.tcb.2018.02.005
Kiss,, D. L., Baez,, W., Huebner,, K., Bundschuh,, R., & Schoenberg,, D. R. (2017). Impact of FHIT loss on the translation of cancer‐associated mRNAs. Molecular Cancer, 16(1), 179. http://doi.org/10.1186/s12943-017-0749-x
Kiss,, D. L., Waters,, C. E., Ouda,, I. M., Saldivar,, J. C., Karras,, J. R., Amin,, Z. A., … Huebner,, K. (2017). Identification of Fhit as a post‐transcriptional effector of thymidine kinase 1 expression. Biochimica et Biophysica Acta, 1860(3), 374–382. http://doi.org/10.1016/j.bbagrm.2017.01.005
Konarska,, M. M., Padgett,, R. A., & Sharp,, P. A. (1984). Recognition of cap structure in splicing in vitro of mRNA precursors. Cell, 38(3), 731–736.
Koonin,, E. V. (1993a). A highly conserved sequence motif defining the family of MutT‐related proteins from eubacteria, eukaryotes and viruses. Nucleic Acids Research, 21(20), 4847.
Koonin,, E. V. (1993b). Bacterial and bacteriophage protein phosphatases. Molecular Microbiology, 8(4), 785–786.
Kowtoniuk,, W. E., Shen,, Y., Heemstra,, J. M., Agarwal,, I., & Liu,, D. R. (2009). A chemical screen for biological small molecule‐RNA conjugates reveals CoA‐linked RNA. Proceedings of the National Academy of Sciences of the United States of America, 106(19), 7768–7773. http://doi.org/10.1073/pnas.0900528106
Kramer,, S. (2017). The ApaH‐like phosphatase TbALPH1 is the major mRNA decapping enzyme of trypanosomes. PLoS Pathogens, 13(6), e1006456. http://doi.org/10.1371/journal.ppat.1006456
Kramer,, S., Piper,, S., Estevez,, A. M., & Carrington,, M. (2016). Polycistronic trypanosome mRNAs are a target for the exosome. Molecular and Biochemical Parasitology, 205(1–2), 1–5. http://doi.org/10.1016/j.molbiopara.2016.02.009
Kramer,, S., Queiroz,, R., Ellis,, L., Webb,, H., Hoheisel,, J. D., Clayton,, C. E., & Carrington,, M. (2008). Heat shock causes a decrease in polysomes and the appearance of stress granules in trypanosomes independently of eIF2(alpha) phosphorylation at Thr169. Journal of Cell Science, 121(Pt 18), 3002–3014. http://doi.org/10.1242/jcs.031823
Lamond,, A. L. (1990). The trimethyl‐guanosine cap is a nuclear targeting signal for snRNPs. Trends in Biochemical Sciences, 15(12), 451–452.
Lee,, C.‐R., Kim,, M., Park,, Y.‐H., Kim,, Y.‐R., & Seok,, Y.‐J. (2014). RppH‐dependent pyrophosphohydrolysis of mRNAs is regulated by direct interaction with DapF in Escherichia coli. Nucleic Acids Research, 42(20), 12746–12757. http://doi.org/10.1093/nar/gku926
Lévĕque,, F., Blanchin‐Roland,, S., Fayat,, G., Plateau,, P., & Blanquet,, S. (1990). Design and characterization of Escherichia coli mutants devoid of Ap4N‐hydrolase activity. Journal of Molecular Biology, 212(2), 319–329.
Li,, C.‐H., Irmer,, H., Gudjonsdottir‐Planck,, D., Freese,, S., Salm,, H., Haile,, S., … Clayton,, C. (2006). Roles of a Trypanosoma brucei 5″→3″ exoribonuclease homolog in mRNA degradation. RNA (New York, NY), 12(12), 2171–2186. http://doi.org/10.1261/rna.291506
Li,, Y., Ho,, E. S., Gunderson,, S. I., & Kiledjian,, M. (2009). Mutational analysis of a Dcp2‐binding element reveals general enhancement of decapping by 5′‐end stem‐loop structures. Nucleic Acids Research, 37(7), 2227–2237. http://doi.org/10.1093/nar/gkp087
Li,, Y., & Kiledjian,, M. (2010). Regulation of mRNA decapping. WIREs RNA, 1(2), 253–265. http://doi.org/10.1002/wrna.15
Li,, Y., Song,, M., & Kiledjian,, M. (2011). Differential utilization of decapping enzymes in mammalian mRNA decay pathways. RNA (New York, NY), 17(3), 419–428. http://doi.org/10.1261/rna.2439811
Li,, Y., Song,, M.‐G., & Kiledjian,, M. (2008). Transcript‐specific decapping and regulated stability by the human Dcp2 decapping protein. Molecular and Cellular Biology, 28(3), 939–948. http://doi.org/10.1128/MCB.01727-07
Lima,, C. D., Klein,, M. G., & Hendrickson,, W. A. (1997). Structure‐based analysis of catalysis and substrate definition in the HIT protein family. Science (New York, N.Y.), 278(5336), 286–290.
Liu,, H., & Kiledjian,, M. (2005). Scavenger decapping activity facilitates 5″ to 3″ mRNA decay. Molecular and Cellular Biology, 25(22), 9764–9772. http://doi.org/10.1128/MCB.25.22.9764-9772.2005
Liu,, H., Rodgers,, N. D., Jiao,, X., & Kiledjian,, M. (2002). The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. The EMBO Journal, 21(17), 4699–4708. http://doi.org/10.1093/emboj/cdf448
Liu,, Q., Liang,, X.‐H., Uliel,, S., Belahcen,, M., Unger,, R., & Michaeli,, S. (2004). Identification and functional characterization of lsm proteins in Trypanosoma brucei. The Journal of Biological Chemistry, 279(18), 18210–18219. http://doi.org/10.1074/jbc.M400678200
Liu,, S.‐W., Jiao,, X., Liu,, H., Gu,, M., Lima,, C. D., & Kiledjian,, M. (2004). Functional analysis of mRNA scavenger decapping enzymes. RNA (New York, NY), 10(9), 1412–1422. http://doi.org/10.1261/rna.7660804
Lu,, G., Zhang,, J., Li,, Y., Li,, Z., Zhang,, N., Xu,, X., … Yan,, J. (2011). hNUDT16: A universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA. Protein %26 Cell, 2(1), 64–73. http://doi.org/10.1007/s13238-011-1009-2
Luciano,, D. J., Vasilyev,, N., Richards,, J., Serganov,, A., & Belasco,, J. G. (2017). A novel RNA phosphorylation state enables 5′ end‐dependent degradation in Escherichia coli. Molecular Cell, 67(1), 44–54.e6. http://doi.org/10.1016/j.molcel.2017.05.035
Luciano,, D. J., Vasilyev,, N., Richards,, J., Serganov,, A., & Belasco,, J. G. (2018). Importance of a diphosphorylated intermediate for RppH‐dependent RNA degradation. RNA Biology, 15(6), 703–706. http://doi.org/10.1080/15476286.2018.1460995
Lueong,, S., Merce,, C., Fischer,, B., Hoheisel,, J. D., & Erben,, E. D. (2016). Gene expression regulatory networks in Trypanosoma brucei: Insights into the role of the mRNA‐binding proteome. Molecular Microbiology, 100(3), 457–471. http://doi.org/10.1111/mmi.13328
Lykke‐Andersen,, J. (2002). Identification of a human Decapping complex associated with hUpf proteins in nonsense‐mediated decay. Molecular and Cellular Biology, 22(23), 8114–8121. http://doi.org/10.1128/MCB.22.23.8114-8121.2002
Mackie,, G. A. (1998). Ribonuclease E is a 5′‐end‐dependent endonuclease. Nature, 395(6703), 720–723. http://doi.org/10.1038/27246
Maize,, K. M., Wagner,, C. R., & Finzel,, B. C. (2013). Structural characterization of human histidine triad nucleotide‐binding protein 2, a member of the histidine triad superfamily. The FEBS Journal, 280(14), 3389–3398. http://doi.org/10.1111/febs.12330
Malys,, N., Carroll,, K., Miyan,, J., Tollervey,, D., & McCarthy,, J. E. G. (2004). The “scavenger” m7GpppX pyrophosphatase activity of Dcs1 modulates nutrient‐induced responses in yeast. Nucleic Acids Research, 32(12), 3590–3600. http://doi.org/10.1093/nar/gkh687
Malys,, N., & McCarthy,, J. E. G. (2006). Dcs2, a novel stress‐induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies. Journal of Molecular Biology, 363(2), 370–382. http://doi.org/10.1016/j.jmb.2006.08.015
Manful,, T., Fadda,, A., & Clayton,, C. E. (2011). The role of the 5″‐3″ exoribonuclease XRNA in transcriptome‐wide mRNA degradation. RNA (New York, NY), 17(11), 2039–2047. http://doi.org/10.1261/rna.2837311
Marriott,, A. S., Vasieva,, O., Fang,, Y., Copeland,, N. A., McLennan,, A. G., & Jones,, N. J. (2016). NUDT2 disruption elevates Diadenosine Tetraphosphate (Ap4A) and Down‐regulates immune response and cancer promotion genes. PLoS One, 11(5), e0154674. http://doi.org/10.1371/journal.pone.0154674
Martin,, J., St‐Pierre,, M. V., & Dufour,, J.‐F. (2011). Hit proteins, mitochondria and cancer. Biochimica et Biophysica Acta, 1807(6), 626–632. http://doi.org/10.1016/j.bbabio.2011.02.001
Mauer,, J., Luo,, X., Blanjoie,, A., Jiao,, X., Grozhik,, A. V., Patil,, D. P., … Jaffrey,, S. R. (2017). Reversible methylation of m6Am in the 5′ cap controls mRNA stability. Nature, 541(7637), 371–375. http://doi.org/10.1038/nature21022
McLennan,, A. G. (2000). Dinucleoside polyphosphates‐friend or foe? Pharmacology %26 Therapeutics, 87(2–3), 73–89.
McLennan,, A. G. (2006). The Nudix hydrolase superfamily. Cellular and Molecular Life Sciences, 63(2), 123–143. http://doi.org/10.1007/s00018-005-5386-7
McLennan,, A. G. (2007). Decapitation: Poxvirus makes RNA lose its head. Trends in Biochemical Sciences, 32(7), 297–299. http://doi.org/10.1016/j.tibs.2007.05.001
McLennan,, A. G. (2012). Substrate ambiguity among the nudix hydrolases: Biologically significant, evolutionary remnant, or both? Cellular and Molecular Life Sciences, 70(3), 373–385. http://doi.org/10.1007/s00018-012-1210-3
Meziane,, O., Piquet,, S., Bossé,, G. D., Gagné,, D., Paquet,, E., Robert,, C., … Simard,, M. J. (2015). The human decapping scavenger enzyme DcpS modulates microRNA turnover. Scientific Reports, 5(1), 16688. http://doi.org/10.1038/srep16688
Milac,, A. L., Bojarska,, E., & del Nogal,, A. W. (2014). Decapping scavenger (DcpS) enzyme: Advances in its structure, activity and roles in the cap‐dependent mRNA metabolism. BBA ‐ Gene Regulatory Mechanisms, 1839(6), 452–462. http://doi.org/10.1016/j.bbagrm.2014.04.007
Mildvan,, A. S., Xia,, Z., Azurmendi,, H. F., Saraswat,, V., Legler,, P. M., Massiah,, M. A., … Amzel,, L. M. (2005). Structures and mechanisms of Nudix hydrolases. Archives of Biochemistry and Biophysics, 433(1), 129–143. http://doi.org/10.1016/j.abb.2004.08.017
Milone,, J., Wilusz,, J., & Bellofatto,, V. (2002). Identification of mRNA decapping activities and an ARE‐regulated 3″ to 5″ exonuclease activity in trypanosome extracts. Nucleic Acids Research, 30(18), 4040–4050.
Monecke,, T., Buschmann,, J., Neumann,, P., Wahle,, E., & Ficner,, R. (2014). Crystal structures of the novel cytosolic 5′‐nucleotidase IIIB explain its preference for m7GMP. PLoS One, 9(3), e90915. http://doi.org/10.1371/journal.pone.0090915
Mukherjee,, C., Bakthavachalu,, B., & Schoenberg,, D. R. (2014). The cytoplasmic capping complex assembles on adapter protein nck1 bound to the proline‐rich C‐terminus of mammalian capping enzyme. PLoS Biology, 12(8), e1001933. http://doi.org/10.1371/journal.pbio.1001933
Mukherjee,, C., Patil,, D. P., Kennedy,, B. A., Bakthavachalu,, B., Bundschuh,, R., & Schoenberg,, D. R. (2012). Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Reports, 2(3), 674–684. http://doi.org/10.1016/j.celrep.2012.07.011
Otsuka,, Y., Kedersha,, N. L., & Schoenberg,, D. R. (2009). Identification of a cytoplasmic complex that adds a cap onto 5′‐monophosphate RNA. Molecular and Cellular Biology, 29(8), 2155–2167. http://doi.org/10.1128/MCB.01325-08
Pace,, H. C., Garrison,, P. N., Robinson,, A. K., Barnes,, L. D., Draganescu,, A., Rösler,, A., et al. (1998). Genetic, biochemical, and crystallographic characterization of Fhit‐substrate complexes as the active signaling form of Fhit. Proceedings of the National Academy of Sciences of the United States of America, 95(10), 5484–5489.
Parker,, R. (2012). RNA degradation in saccharomyces cerevisae. Genetics, 191(3), 671–702. http://doi.org/10.1534/genetics.111.137265
Parrish,, S., Hurchalla,, M., Liu,, S.‐W., & Moss,, B. (2009). The African swine fever virus g5R protein possesses mRNA decapping activity. Virology, 393(1), 177–182. http://doi.org/10.1016/j.virol.2009.07.026
Parrish,, S., & Moss,, B. (2007). Characterization of a second vaccinia virus mRNA‐decapping enzyme conserved in poxviruses. Journal of Virology, 81(23), 12973–12978. http://doi.org/10.1128/JVI.01668-07
Perry,, K. L., Watkins,, K. P., & Agabian,, N. (1987). Trypanosome mRNAs have unusual “cap 4” structures acquired by addition of a spliced leader. Proceedings of the National Academy of Sciences of the United States of America, 84(23), 8190–8194.
Picard‐Jean,, F., Brand,, C., Tremblay‐Létourneau,, M., Allaire,, A., Beaudoin,, M. C., Boudreault,, S., … Bisaillon,, M. (2018). 2`‐O‐methylation of the mRNA cap protects RNAs from decapping and degradation by DXO. PLoS One, 13(3), e0193804. http://doi.org/10.1371/journal.pone.0193804
Piton,, J., Larue,, V., Thillier,, Y., Dorléans,, A., Pellegrini,, O., Li de la Sierra‐Gallay,, I., et al. (2013). Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates. Proceedings of the National Academy of Sciences of the United States of America, 110(22), 8858–8863. http://doi.org/10.1073/pnas.1221510110
Preusser,, C., Jaé,, N., & Bindereif,, A. (2012). mRNA splicing in trypanosomes. International Journal of Medical Microbiology, 302(4–5), 221–224. http://doi.org/10.1016/j.ijmm.2012.07.004
Ramanathan,, A., Robb,, G. B., & Chan,, S.‐H. (2016). mRNA capping: Biological functions and applications. Nucleic Acids Research, 44(16), 7511–7526. http://doi.org/10.1093/nar/gkw551
Richards,, J., Liu,, Q., Pellegrini,, O., Celesnik,, H., Yao,, S., Bechhofer,, D. H., … Belasco,, J. G. (2011). An RNA pyrophosphohydrolase triggers 5′‐exonucleolytic degradation of mRNA in Bacillus subtilis. Molecular Cell, 43(6), 940–949. http://doi.org/10.1016/j.molcel.2011.07.023
Sachs,, A. B. (1993). Messenger RNA degradation in eukaryotes. Cell, 74(3), 413–421.
Safrany,, S. T., Ingram,, S. W., Cartwright,, J. L., Falck,, J. R., McLennan,, A. G., Barnes,, L. D., & Shears,, S. B. (1999). The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the human diphosphoinositol polyphosphate phosphohydrolase. Overlapping substrate specificities in a MutT‐type protein. The Journal of Biological Chemistry, 274(31), 21735–21740.
Schwede,, A., Ellis,, L., Luther,, J., Carrington,, M., Stoecklin,, G., & Clayton,, C. E. (2008). A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells. Nucleic Acids Research, 36(10), 3374–3388. http://doi.org/10.1093/nar/gkn108
Séraphin,, B. (1992). The HIT protein family: A new family of proteins present in prokaryotes, yeast and mammals. DNA Sequence : the Journal of DNA Sequencing and Mapping, 3(3), 177–179.
Shen,, V., Liu,, H., Liu,, S.‐W., Jiao,, X., & Kiledjian,, M. (2008). DcpS scavenger decapping enzyme can modulate pre‐mRNA splicing. RNA (New York, NY), 14(6), 1132–1142. http://doi.org/10.1261/rna.1008208
Silverman,, R. H. (2015). Caps off to poxviruses. Cell Host %26 Microbe, 17(3), 287–289. http://doi.org/10.1016/j.chom.2015.02.013
Sinturel,, F., Bréchemier‐Baey,, D., Kiledjian,, M., Condon,, C., & Bénard,, L. (2012). Activation of 5″‐3″ exoribonuclease Xrn1 by cofactor Dcs1 is essential for mitochondrial function in yeast. Proceedings of the National Academy of Sciences of the United States of America, 109(21), 8264–8269. http://doi.org/10.1073/pnas.1120090109
Sonenberg,, N., Rupprecht,, K. M., Hecht,, S. M., & Shatkin,, A. J. (1979). Eukaryotic mRNA cap binding protein: Purification by affinity chromatography on sepharose‐coupled m7GDP. Proceedings of the National Academy of Sciences of the United States of America, 76(9), 4345–4349.
Song,, M.‐G., Bail,, S., & Kiledjian,, M. (2013). Multiple Nudix family proteins possess mRNA decapping activity. RNA (New York, NY), 19(3), 390–399. http://doi.org/10.1261/rna.037309.112
Song,, M.‐G., Li,, Y., & Kiledjian,, M. (2010). Multiple mRNA decapping enzymes in mammalian cells. Molecular Cell, 40(3), 423–432. http://doi.org/10.1016/j.molcel.2010.10.010
Srouji,, J. R., Xu,, A., Park,, A., Kirsch,, J. F., & Brenner,, S. E. (2017). The evolution of function within the Nudix homology clan. Proteins: Structure, Function, and Bioinformatics, 85(5), 775–811. http://doi.org/10.1002/prot.25223
Stevens,, A., & Poole,, T. L. (1995). 5″‐Exonuclease‐2 of Saccharomyces cerevisiae. Purification and features of ribonuclease activity with comparison to 5‐″exonuclease‐1. The Journal of Biological Chemistry, 270(27), 16063–16069.
Taverniti,, V., & Séraphin,, B. (2015). Elimination of cap structures generated by mRNA decay involves the new scavenger mRNA decapping enzyme Aph1/FHIT together with DcpS. Nucleic Acids Research, 43(1), 482–492. http://doi.org/10.1093/nar/gku1251
Taylor,, M. J., & Peculis,, B. A. (2008). Evolutionary conservation supports ancient origin for Nudt16, a nuclear‐localized, RNA‐binding, RNA‐decapping enzyme. Nucleic Acids Research, 36(18), 6021–6034. http://doi.org/10.1093/nar/gkn605
Tkacz,, I. D., Cohen,, S., Salmon‐Divon,, M., & Michaeli,, S. (2008). Identification of the heptameric Lsm complex that binds U6 snRNA in Trypanosoma brucei. Molecular and Biochemical Parasitology, 160(1), 22–31. http://doi.org/10.1016/j.molbiopara.2008.03.003
Trésaugues,, L., Lundbäck,, T., Welin,, M., Flodin,, S., Nyman,, T., Silvander,, C., … Nordlund,, P. (2015). Structural basis for the specificity of human NUDT16 and its regulation by Inosine monophosphate. PLoS One, 10(6), e0131507. http://doi.org/10.1371/journal.pone.0131507
Uhrig,, R. G., Kerk,, D., & Moorhead,, G. B. (2013). Evolution of bacterial‐like phosphoprotein phosphatases in photosynthetic eukaryotes features ancestral mitochondrial or archaeal origin and possible lateral gene transfer. Plant Physiology, 163(4), 1829–1843. http://doi.org/10.1104/pp.113.224378
Uhrig,, R. G., Labandera,, A.‐M., & Moorhead,, G. B. (2013). Arabidopsis PPP family of serine/threonine protein phosphatases: Many targets but few engines. Trends in Plant Science, 18(9), 505–513. http://doi.org/10.1016/j.tplants.2013.05.004
Uhrig,, R. G., & Moorhead,, G. B. (2011). Two ancient bacterial‐like PPP family phosphatases from Arabidopsis are highly conserved plant proteins that possess unique properties. Plant Physiology, 157(4), 1778–1792. http://doi.org/10.1104/pp.111.182493
Valkov,, E., Jonas,, S., & Weichenrieder,, O. (2017). Mille viae in eukaryotic mRNA decapping. Current Opinion in Structural Biology, 47, 40–51. http://doi.org/10.1016/j.sbi.2017.05.009
van Dijk,, E., Cougot,, N., Meyer,, S., Babajko,, S., Wahle,, E., & Séraphin,, B. (2002). Human Dcp2: A catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. The EMBO Journal, 21(24), 6915–6924.
van Dijk,, E., Le Hir,, H., & Séraphin,, B. (2003). DcpS can act in the 5′‐3′ mRNA decay pathway in addition to the 3″‐5″ pathway. Proceedings of the National Academy of Sciences of the United States of America, 100(21), 12081–12086. http://doi.org/10.1073/pnas.1635192100
Vasilyev,, N., & Serganov,, A. (2015). Structures of RNA complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5′‐end‐dependent mRNA decay. Journal of Biological Chemistry, 290(15), 9487–9499. http://doi.org/10.1074/jbc.M114.634824
Visa,, N., Izaurralde,, E., Ferreira,, J., Daneholt,, B., & Mattaj,, I. W. (1996). A nuclear cap‐binding complex binds Balbiani ring pre‐mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export. The Journal of Cell Biology, 133(1), 5–14.
Vvedenskaya,, I. O., Bird,, J. G., Zhang,, Y., Zhang,, Y., Jiao,, X., Barvík,, I., et al. (2018). CapZyme‐Seq comprehensively defines promoter‐sequence determinants for RNA 5; capping with NAD. Molecular Cell, 70(3), 553–564.e9. http://doi.org/10.1016/j.molcel.2018.03.014
Walters,, R. W., Matheny,, T., Mizoue,, L. S., Rao,, B. S., Muhlrad,, D., & Parker,, R. (2017). Identification of NAD+ capped mRNAs in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 114(3), 480–485. http://doi.org/10.1073/pnas.1619369114
Wang,, V. Y.‐F., Jiao,, X., Kiledjian,, M., & Tong,, L. (2015). Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes. Nucleic Acids Research, 43(13), 6596–6606. http://doi.org/10.1093/nar/gkv620
Wang,, Z., Jiao,, X., Carr‐Schmid,, A., & Kiledjian,, M. (2002). The hDcp2 protein is a mammalian mRNA decapping enzyme. Proceedings of the National Academy of Sciences of the United States of America, 99(20), 12663–12668. http://doi.org/10.1073/pnas.192445599
Wang,, Z., & Kiledjian,, M. (2001). Functional link between the mammalian exosome and mRNA decapping. Cell, 107(6), 751–762.
Waters,, C. E., Saldivar,, J. C., Hosseini,, S. A., & Huebner,, K. (2014). The FHIT gene product: Tumor suppressor and genome "caretaker". Cellular and Molecular Life Sciences, 71(23), 4577–4587. http://doi.org/10.1007/s00018-014-1722-0
Wei,, C., Gershowitz,, A., & Moss,, B. (1975b). N6, O2″‐dimethyladenosine a novel methylated ribonucleoside next to the 5″ terminal of animal cell and virus mRNAs. Nature, 257(5523), 251–253.
Wei,, C. M., Gershowitz,, A., & Moss,, B. (1975a). Methylated nucleotides block 5′ terminus of HeLa cell messenger RNA. Cell, 4(4), 379–386.
Wypijewska,, A., Bojarska,, E., Lukaszewicz,, M., Stepinski,, J., Jemielity,, J., Davis,, R. E., & Darzynkiewicz,, E. (2012). 7‐methylguanosine diphosphate (m(7)GDP) is not hydrolyzed but strongly bound by decapping scavenger (DcpS) enzymes and potently inhibits their activity. Biochemistry, 51(40), 8003–8013. http://doi.org/10.1021/bi300781g
Wypijewska del Nogal,, A., Surleac,, M. D., Kowalska,, J., Lukaszewicz,, M., Jemielity,, J., Bisaillon,, M., … Bojarska,, E. (2013). Analysis of decapping scavenger cap complex using modified cap analogs reveals molecular determinants for efficient cap binding. The FEBS Journal, 280(24), 6508–6527. http://doi.org/10.1111/febs.12553
Xiang,, S., Cooper‐Morgan,, A., Jiao,, X., Kiledjian,, M., Manley,, J. L., & Tong,, L. (2009). Structure and function of the 5′→3′ exoribonuclease Rat1 and its activating partner Rai1. Nature, 458(7239), 784–788. http://doi.org/10.1038/nature07731
Xue,, Y., Bai,, X., Lee,, I., Kallstrom,, G., Ho,, J., Brown,, J., … Johnson,, A. W. (2000). Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. Molecular and Cellular Biology, 20(11), 4006–4015.
Zamudio,, J. R., Mittra,, B., Campbell,, D. A., & Sturm,, N. R. (2009). Hypermethylated cap 4 maximizes Trypanosoma brucei translation. Molecular Microbiology, 72(5), 1100–1110.
Zeiner,, G. M., Sturm,, N. R., & Campbell,, D. A. (2003). The Leishmania tarentolae spliced leader contains determinants for association with polysomes. The Journal of Biological Chemistry, 278(40), 38269–38275. http://doi.org/10.1074/jbc.M304295200
Zhai,, L.‐T., & Xiang,, S. (2014). mRNA quality control at the 5′ end. Journal of Zhejiang University. Science. B, 15(5), 438–443. http://doi.org/10.1631/jzus.B1400070
Zhang,, D., Liu,, Y., Wang,, Q., Guan,, Z., Wang,, J., Liu,, J., et al. (2016). Structural basis of prokaryotic NAD‐RNA decapping by NudC. Nature Publishing Group, 26(9), 1062–1066. http://doi.org/10.1038/cr.2016.98
Zheng,, D., Chen,, C.‐Y. A., & Shyu,, A.‐B. (2011). Unraveling regulation and new components of human P‐bodies through a protein interaction framework and experimental validation. RNA (New York, NY), 17(9), 1619–1634. http://doi.org/10.1261/rna.2789611