The function of KptA/Tpt1 gene – a minor review
Shiquan Yang A , Gaoyi Qu A , Bixia Fu A , Feng Yang A , Weixian Zeng A , Yunzhang Cai A , Tao Ye A , Youzhen Yang , Xiangwen Deng C , Wenhua Xiang A B C , Dan Peng A B D and Bo Zhou
A B C D E G
+ Author Affiliations
- Author Affiliations
A Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China.
B Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China.
C National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha, Hunan, 410004, China.
D Forestry Biotechnology Hunan Key Laboratories, Changsha, Hunan, 410004, China.
E Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China.
F State Administration of Ying Zui Jie National Nature Reserve, Huitong, Hunan, 418000, China.
G Corresponding author. Email: zhoubo8888899999@163.com
Functional Plant Biology 47(7) 577-591 https://doi.org/10.1071/FP19159
Submitted: 6 June 2019 Accepted: 6 February 2020 Published: 22 May 2020
Abstract
Rapid response of uni- and multicellular organisms to environmental changes and their own growth is achieved through a series of molecular mechanisms, often involving modification of macromolecules, including nucleic acids, proteins and lipids. The ADP-ribosylation process has ability to modify these different macromolecules in cells, and is closely related to the biological processes, such as DNA replication, transcription, signal transduction, cell division, stress, microbial aging and pathogenesis. In addition, tRNA plays an essential role in the regulation of gene expression, as effector molecules, no-load tRNA affects the overall gene expression level of cells under some nutritional stress. KptA/Tpt1 is an essential phosphotransferase in the process of pre-tRNA splicing, releasing mature tRNA and participating in ADP-ribose. The objective of this review is concluding the gene structure, the evolution history and the function of KptA/Tpt1 from prokaryote to eukaryote organisms. At the same time, the results of promoter elements analysis were also shown in the present study. Moreover, the problems in the function of KptA/Tpt1 that have not been clarified at the present time are summarised, and some suggestions to solve those problems are given. This review presents no only a summary of clear function of KptA/Tpt1 in the process of tRNA splicing and ADP-ribosylation of organisms, but also gives some proposals to clarify unclear problems of it in the future.
Additional keywords: ADP-ribosylation, tRNA splicing.
References
Abelson J, Trotta CR, Li H (1998) tRNA splicing. Journal of Biological Chemistry 273, 12685–12688.| tRNA splicing.Crossref | GoogleScholarGoogle Scholar | 9582290PubMed |
Akama K, Naß A, Junker V, Beier H (1997) Characterization of nuclear tRNA Tyr introns: their evolution from red algae to higher plants. FEBS Letters 417, 213–218.
| Characterization of nuclear tRNA Tyr introns: their evolution from red algae to higher plants.Crossref | GoogleScholarGoogle Scholar | 9395298PubMed |
Akama K, Junker V, Yukawa Y, Sugiura M, Beier H (2000) Splicing of Arabidopsis tRNA Met precursors in tobacco cell and wheat germ extracts. Plant Molecular Biology 44, 155–165.
| Splicing of Arabidopsis tRNA Met precursors in tobacco cell and wheat germ extracts.Crossref | GoogleScholarGoogle Scholar | 11117259PubMed |
Anantharaman V, Iyer LM, Aravind L (2010) Presence of a classical RRM-fold palm domain in Thg1-type 3′-5′ nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. Biology Direct 5, 43
| Presence of a classical RRM-fold palm domain in Thg1-type 3′-5′ nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains.Crossref | GoogleScholarGoogle Scholar | 20591188PubMed |
Andree H, Thiele H, Fähling M, Schmidt I, Thiele BJ (2006) Expression of the human TPT1 gene coding for translationally controlled tumor protein (TCTP) is regulated by CREB transcription factors. Gene 380, 95–103.
| Expression of the human TPT1 gene coding for translationally controlled tumor protein (TCTP) is regulated by CREB transcription factors.Crossref | GoogleScholarGoogle Scholar | 16859841PubMed |
Aravind L, Iyer LM, Anantharaman V (2003) The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism. Genome Biology 4, R64
| The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.Crossref | GoogleScholarGoogle Scholar | 14519199PubMed |
Aravind L, Zhang D, de Souza RF, Anand S, Iyer LM (2014) The natural history of ADP-ribosyltransferases and the ADP-ribosylation system. In ‘Endogenous ADP-ribosylation’. (Ed F Koch-Nolte) pp. 3–32. (Springer: Cham, Germany)
Banerjee A, Munir A, Abdullahu L, Damha MJ, Goldgur Y, Shuman S (2019) Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2′-PO4 recognition and ADP-ribosylation. Nature Communications 10, 218
| Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2′-PO4 recognition and ADP-ribosylation.Crossref | GoogleScholarGoogle Scholar | 30644400PubMed |
Barkauskaite E, Jankevicius G, Ahel I (2015) Structures and mechanisms of enzymes employed in the synthesis and degradation of parp-dependent protein ADP-ribosylation. Molecular Cell 58, 935–946.
| Structures and mechanisms of enzymes employed in the synthesis and degradation of parp-dependent protein ADP-ribosylation.Crossref | GoogleScholarGoogle Scholar | 26091342PubMed |
Bazan JF, Koch-Nolte F (1997) Sequence and structural links between distant ADP-ribosyltransferase families. In ‘ADP-ribosylation in animal tissues.’ (Eds F Haag, F Koch-Nolte) pp. 99–107. (Springer: Boston, MA, USA)
Belenky P, Bogan KL, Brenner C (2007) NAD+ metabolism in health and disease. Trends in Biochemical Sciences 32, 12–19.
| NAD+ metabolism in health and disease.Crossref | GoogleScholarGoogle Scholar | 17161604PubMed |
Bell CE, Eisenberg D (1996) Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Biochemistry 35, 1137–1149.
| Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide.Crossref | GoogleScholarGoogle Scholar | 8573568PubMed |
Berg JM, Tymoczko JL, Stryer L (2012) ‘Oxidative phosphorylation. Biochemistry.’ (WH Freeman: New York, NY, USA)
Boyd EF (2012) Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions. Advances in Virus Research 82, 91–118.
| Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions.Crossref | GoogleScholarGoogle Scholar | 22420852PubMed |
Burroughs AM, Iyer LM, Aravind L (2009) Natural history of the E1‐like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation proteins Structure, Function, and Bioinformatics 75, 895–910.
| Natural history of the E1‐like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation proteinsCrossref | GoogleScholarGoogle Scholar |
Butepage M, Eckei L, Verheugd P, Lüscher B (2015) Intracellular mono-ADP-ribosylation in signaling and disease. Cells 4, 569–595.
| Intracellular mono-ADP-ribosylation in signaling and disease.Crossref | GoogleScholarGoogle Scholar | 26426055PubMed |
Cambronne XA, Stewart ML, Kim D, Jones-Brunette AM, Morgan RK, Farrens DL, Goodman RH (2016) Biosensor reveals multiple sources for mitochondrial NAD+. Science 352, 1474–1477.
| Biosensor reveals multiple sources for mitochondrial NAD+.Crossref | GoogleScholarGoogle Scholar | 27313049PubMed |
Carter-O’Connell I, Jin H, Morgan RK, Zaja R, David LL, Ahel I, Cohen MS (2016) Identifying family-member-specific targets of mono-ARTDs by using a chemical genetics approach. Cell reports 14, 621–631.
| Identifying family-member-specific targets of mono-ARTDs by using a chemical genetics approach.Crossref | GoogleScholarGoogle Scholar | 26774478PubMed |
Chambon P, Weill JD, Mandel P (1963) Nicotinamide mononucleotide activation of a new DNA-dependent polyadenylic acid synthesizing nuclear enzyme. Biochemical and Biophysical Research Communications 11, 39–43.
| Nicotinamide mononucleotide activation of a new DNA-dependent polyadenylic acid synthesizing nuclear enzyme.Crossref | GoogleScholarGoogle Scholar | 14019961PubMed |
Chen C, Xia R, Chen H, He Y (2018) TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface. bioRxiv 289660,
| TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface.Crossref | GoogleScholarGoogle Scholar |
Cohen-Armon M, Visochek L, Katzoff A, Levitan D, Susswein AJ, Klein R, Schwartz JH (2004) Long-term memory requires poly ADP-ribosylation. Science 304, 1820–1822.
| Long-term memory requires poly ADP-ribosylation.Crossref | GoogleScholarGoogle Scholar | 15205535PubMed |
Collier R, Pappenheimer A (1964) Studies on the mode of action of diphtheria toxin. II. Effect of toxin on amino acid incorporation in cell-free systems. Journal of Experimental Medicine 120, 1019–1039.
| Studies on the mode of action of diphtheria toxin. II. Effect of toxin on amino acid incorporation in cell-free systems.Crossref | GoogleScholarGoogle Scholar | 14238922PubMed |
Corda D, Di Girolamo M (2003) Functional aspects of protein mono-ADP-ribosylation. EMBO Journal 22, 1953–1958.
| Functional aspects of protein mono-ADP-ribosylation.Crossref | GoogleScholarGoogle Scholar | 12727863PubMed |
Cozzi A, Cipriani G, Fossati S, Faraco G, Formentini L, Min W, Chiarugi A (2006) Poly (ADP-ribose) accumulation and enhancement of postischemic brain damage in 110-kDa poly (ADP-ribose) glycohydrolase null mice. Journal of Cerebral Blood Flow and Metabolism 26, 684–695.
| Poly (ADP-ribose) accumulation and enhancement of postischemic brain damage in 110-kDa poly (ADP-ribose) glycohydrolase null mice.Crossref | GoogleScholarGoogle Scholar | 16177811PubMed |
Culbertson MR, Winey M (1989) Split tRNA genes and their products: a paradigm for the study of cell function and evolution. Yeast 5, 405–427.
| Split tRNA genes and their products: a paradigm for the study of cell function and evolution.Crossref | GoogleScholarGoogle Scholar | 2694676PubMed |
Culver GM, McCraith SM, Zillmann M, Kierzek R, Michaud N, LaReau RD, Phizicky EM (1993) An NAD derivative produced during transfer RNA splicing: ADP-ribose 1″-2″ cyclic phosphate. Science 261, 206–208.
| An NAD derivative produced during transfer RNA splicing: ADP-ribose 1″-2″ cyclic phosphate.Crossref | GoogleScholarGoogle Scholar | 8392224PubMed |
Culver GM, McCraith SM, Consaul SA, Stanford DR, Phizicky EM (1997) A 2′-phosphotransferase implicated in tRNA splicing is essential in Saccharomyces cerevisiae. Journal of Biological Chemistry 272, 13203–13210.
| A 2′-phosphotransferase implicated in tRNA splicing is essential in Saccharomyces cerevisiae.Crossref | GoogleScholarGoogle Scholar | 9148937PubMed |
Daniels CM, Ong SE, Leung AK (2015) The promise of proteomics for the study of ADP-ribosylation. Molecular Cell 58, 911–924.
| The promise of proteomics for the study of ADP-ribosylation.Crossref | GoogleScholarGoogle Scholar | 26091340PubMed |
de Souza RF, Aravind L (2012) Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions. Molecular BioSystems 8, 1661–1677.
| Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions.Crossref | GoogleScholarGoogle Scholar | 22399070PubMed |
Dunstan MS, Barkauskaite E, Lafite P, Knezevic CE, Brassington A, Ahe M (2012) Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase. Nature Communications 3, 878
| Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase.Crossref | GoogleScholarGoogle Scholar | 22673905PubMed |
Englert M, Beier H (2005) Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Research 33, 388–399.
| Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins.Crossref | GoogleScholarGoogle Scholar | 15653639PubMed |
Englert M, Latz A, Becker D (2007) Plant pre-tRNA splicing enzymes are targeted to multiple cellular compartments. Biochimie 89, 1351–1365.
| Plant pre-tRNA splicing enzymes are targeted to multiple cellular compartments.Crossref | GoogleScholarGoogle Scholar | 17698277PubMed |
Fedoroff NV, Battisti DS, Beachy RN (2010) Radically rethinking agriculture for the 21st century. Science 327, 833–834.
| Radically rethinking agriculture for the 21st century.Crossref | GoogleScholarGoogle Scholar | 20150494PubMed |
Ferat JL, Michel F (1993) Group II self-splicing introns in bacteria. Nature 364, 358
| Group II self-splicing introns in bacteria.Crossref | GoogleScholarGoogle Scholar | 7687328PubMed |
Fickett JW, Hatzigeorgiou AG (1997) Eukaryotic promoter recognition. Genome Research 7, 861–878.
| Eukaryotic promoter recognition.Crossref | GoogleScholarGoogle Scholar | 9314492PubMed |
Fieldhouse RJ, Turgeon Z, White D, Merrill AR (2010) Cholera-and anthrax-like toxins are among several new ADP-ribosyltransferases. PLoS Computational Biology 6, e1001029
| Cholera-and anthrax-like toxins are among several new ADP-ribosyltransferases.Crossref | GoogleScholarGoogle Scholar | 21170356PubMed |
Filipowicz W, Shatkin AJ (1983) Origin of splice junction phosphate in tRNAs processed by HeLa cell extract. Cell 32, 547–557.
| Origin of splice junction phosphate in tRNAs processed by HeLa cell extract.Crossref | GoogleScholarGoogle Scholar | 6186399PubMed |
Fu H, Feng J, Liu Q, Sun F, Tie Y, Zhu J, Zheng X (2009) Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Letters 583, 437–442.
| Stress induces tRNA cleavage by angiogenin in mammalian cells.Crossref | GoogleScholarGoogle Scholar | 19114040PubMed |
Gazzaniga F, Stebbins R, Chang SZ, McPeek MA, Brenner C (2009) Microbial NAD metabolism: lessons from comparative genomics. Microbiology and Molecular Biology Reviews 73, 529–541.
| Microbial NAD metabolism: lessons from comparative genomics.Crossref | GoogleScholarGoogle Scholar | 19721089PubMed |
Gelfand MS (1995) Prediction of function in DNA sequence analysis. Journal of Computational Biology 2, 87–115.
| Prediction of function in DNA sequence analysis.Crossref | GoogleScholarGoogle Scholar | 7497122PubMed |
Genschik P, Hall J, Filipowicz W (1997) Cloning and characterization of the Arabidopsis cyclic phosphodiesterase which hydrolyzes ADP-ribose 1″, 2″-cyclic phosphate and nucleoside 2, -cyclic phosphates. Journal of Biological Chemistry 272, 13211–13219.
| Cloning and characterization of the Arabidopsis cyclic phosphodiesterase which hydrolyzes ADP-ribose 1″, 2″-cyclic phosphate and nucleoside 2, -cyclic phosphates.Crossref | GoogleScholarGoogle Scholar | 9148938PubMed |
Gibson BA, Kraus WL (2012) New insights into the molecular and cellular functions of poly (ADP-ribose) and PARPs. Nature Reviews. Molecular Cell Biology 13, 411
| New insights into the molecular and cellular functions of poly (ADP-ribose) and PARPs.Crossref | GoogleScholarGoogle Scholar | 22713970PubMed |
Gomes I, Gupta R (1997) RNA splicing ligase activity in the Archaeon Haloferax volcanii. Biochemical and Biophysical Research Communications 237, 588–594.
| RNA splicing ligase activity in the Archaeon Haloferax volcanii.Crossref | GoogleScholarGoogle Scholar | 9299409PubMed |
Gupte R, Liu Z, Kraus WL (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes & Development 31, 101–126.
| PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes.Crossref | GoogleScholarGoogle Scholar |
Haikarainen T, Krauss S, Lehtio L (2014) Tankyrases: structure, function and therapeutic implications in cancer. Current Pharmaceutical Design 20, 6472–6488.
| Tankyrases: structure, function and therapeutic implications in cancer.Crossref | GoogleScholarGoogle Scholar | 24975604PubMed |
Haiser HJ, Karginov FV, Hannon GJ, Elliot MA (2008) Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor. Nucleic Acids Research 36, 732–741.
| Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor.Crossref | GoogleScholarGoogle Scholar | 18084030PubMed |
Harding HP, Lackey JG, Hsu HC, Zhang Y, Deng J, Xu RM, Ron D (2007) An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation. RNA 14, 225–232.
| An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation.Crossref | GoogleScholarGoogle Scholar | 18094117PubMed |
Hassa PO, Haenni SS, Elser M, Hottiger MO (2006) Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiology and Molecular Biology Reviews 70, 789–829.
| Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going?Crossref | GoogleScholarGoogle Scholar | 16959969PubMed |
Hayashi S, Mori S, Suzuki T, Suzuki T, Yoshihisa T (2019) Impact of intron removal from tRNA genes on Saccharomyces cerevisiae. Nucleic Acids Research 47, 5936–5949.
| Impact of intron removal from tRNA genes on Saccharomyces cerevisiae.Crossref | GoogleScholarGoogle Scholar | 30997502PubMed |
Hopper AK, Nostramo RT (2019) tRNA biogenesis and subcellular trafficking proteins multitask in pathways for other RNAs. Frontiers in Genetics 10, 96
| tRNA biogenesis and subcellular trafficking proteins multitask in pathways for other RNAs.Crossref | GoogleScholarGoogle Scholar | 30842788PubMed |
Hottiger MO (2015) Nuclear ADP-ribosylation and its role in chromatin plasticity, cell differentiation, and epigenetics. Annual Review of Biochemistry 84, 227–263.
| Nuclear ADP-ribosylation and its role in chromatin plasticity, cell differentiation, and epigenetics.Crossref | GoogleScholarGoogle Scholar | 25747399PubMed |
Hottiger MO, Hassa PO, Lüscher B (2010) Toward a unified nomenclature for mammalian ADP-ribosyltransferases Trends in Biochemical Sciences 35, 208–219.
| Toward a unified nomenclature for mammalian ADP-ribosyltransferasesCrossref | GoogleScholarGoogle Scholar | 20106667PubMed |
Hu QD, Lu H, Huo K, Ying K, Li J, Xie Y, Li YY (2003) A human homolog of the yeast gene encoding tRNA 2′-phosphotransferase: cloning, characterization and complementation analysis. Cellular and Molecular Life Sciences CMLS 60, 1725–1732.
| A human homolog of the yeast gene encoding tRNA 2′-phosphotransferase: cloning, characterization and complementation analysis.Crossref | GoogleScholarGoogle Scholar | 14504659PubMed |
Iyer LM, Anantharaman V, Wolf MY, Aravind L (2008) Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. International Journal for Parasitology 38, 1–31.
| Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes.Crossref | GoogleScholarGoogle Scholar | 17949725PubMed |
James DI, Smith KM, Jordan AM, Fairweather EE, Griffiths LA, Hamilton NS, McGonagle AE (2016) First-in-class chemical probes against poly (ADP-ribose) glycohydrolase (PARG) inhibit DNA repair with differential pharmacology to olaparib. ACS Chemical Biology 11, 3179–3190.
| First-in-class chemical probes against poly (ADP-ribose) glycohydrolase (PARG) inhibit DNA repair with differential pharmacology to olaparib.Crossref | GoogleScholarGoogle Scholar | 27689388PubMed |
Jankevicius G, Ariza A, Ahel M (2016) The toxin-antitoxin system DarTG catalyzes reversible ADP-ribosylation of DNA. Molecular Cell 64, 1109–1116.
| The toxin-antitoxin system DarTG catalyzes reversible ADP-ribosylation of DNA.Crossref | GoogleScholarGoogle Scholar | 27939941PubMed |
Jöchl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl , Hüttenhofer A (2008) Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Research 36, 2677–2689.
| Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis.Crossref | GoogleScholarGoogle Scholar | 18346967PubMed |
Jwa M, Chang P (2012) PARP16 is a tail-anchored endoplasmic reticulum protein required for the PERK-and IRE1α-mediated unfolded protein response. Nature Cell Biology 14, 1223
| PARP16 is a tail-anchored endoplasmic reticulum protein required for the PERK-and IRE1α-mediated unfolded protein response.Crossref | GoogleScholarGoogle Scholar | 23103912PubMed |
Kato-Murayama M, Bessho Y, Shirouzu M, Yokoyama S (2005) Crystal structure of the RNA 2′-phosphotransferase from Aeropyrum pernix K1. Journal of Molecular Biology 348, 295–305.
| Crystal structure of the RNA 2′-phosphotransferase from Aeropyrum pernix K1.Crossref | GoogleScholarGoogle Scholar | 15811369PubMed |
Kauder F, Ludewig F, Heineke D (2000) Ontogenetic changes of potato plants during acclimation to elevated carbon dioxide. Journal of Experimental Botany 51, 429–437.
| Ontogenetic changes of potato plants during acclimation to elevated carbon dioxide.Crossref | GoogleScholarGoogle Scholar | 10938851PubMed |
Kilian O, Kroth PG (2004) Presequence acquisition during secondary endocytobiosis and the possible role of introns. Journal of Molecular Evolution 58, 712–721.
| Presequence acquisition during secondary endocytobiosis and the possible role of introns.Crossref | GoogleScholarGoogle Scholar | 15461428PubMed |
Kistemaker HA, Lameijer LN, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV (2015) Synthesis of well‐defined adenosine diphosphate ribose oligomers. Angewandte Chemie International Edition 54, 4915–4918.
| Synthesis of well‐defined adenosine diphosphate ribose oligomers.Crossref | GoogleScholarGoogle Scholar | 25704172PubMed |
Kistemaker HA, Nardozza AP, Overkleeft HS, Van dMGA, Ladurner AG, Filippov DV (2016) Synthesis and macrodomain binding of mono‐ADP‐ribosylated peptides. Angewandte Chemie International Edition in English 55, 10634–10638.
| Synthesis and macrodomain binding of mono‐ADP‐ribosylated peptides.Crossref | GoogleScholarGoogle Scholar |
Koch-Nolte F, Kernstock S, Mueller-Dieckmann C, Weiss MS, Haag F (2008) Mammalian ADP-ribosyltransferases and ADP-ribosylhydrolases Frontiers in bioscience: a journal and virtual library 13, 6716–6729.
| Mammalian ADP-ribosyltransferases and ADP-ribosylhydrolasesCrossref | GoogleScholarGoogle Scholar |
Konarska M, Filipowicz W, Domdey H, Gross HJ (1981) Formation of a 2′-phosphomonoester, 3′, 5′-phosphodiester linkage by a novel RNA ligase in wheat germ. Nature 293, 112
| Formation of a 2′-phosphomonoester, 3′, 5′-phosphodiester linkage by a novel RNA ligase in wheat germ.Crossref | GoogleScholarGoogle Scholar | 7266664PubMed |
Lambrecht MJ, Brichacek M, Barkauskaite E, Ariza A, Ahelbb I, Hergenrother PJ (2015) Synthesis of dimeric ADP-ribose and its structure with human poly (ADP-ribose) glycohydrolase. Journal of the American Chemical Society 137, 3558–3564.
| Synthesis of dimeric ADP-ribose and its structure with human poly (ADP-ribose) glycohydrolase.Crossref | GoogleScholarGoogle Scholar | 25706250PubMed |
Laski FA, Fire AZ, RajBhandary UL, Sharp PA (1983) Characterization of tRNA precursor splicing in mammalian extracts. Journal of Biological Chemistry 258, 11974–11980.
Lee SR, Collins K (2005) Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. Journal of Biological Chemistry 280, 42744–42749.
| Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila.Crossref | GoogleScholarGoogle Scholar | 16272149PubMed |
Li Y, Luo J, Zhou H, Liao JY, Ma LM, Chen YQ, Qu LH (2008) Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia. Nucleic Acids Research 36, 6048–6055.
| Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia.Crossref | GoogleScholarGoogle Scholar | 18820301PubMed |
Li L, Siebrands CC, Yang Z (2010) Novel nucleobase-simplified cyclic ADP-ribose analogue: a concise synthesis and Ca2+-mobilizing activity in T-lymphocytes. Organic & Biomolecular Chemistry 8, 1843–1848.
| Novel nucleobase-simplified cyclic ADP-ribose analogue: a concise synthesis and Ca2+-mobilizing activity in T-lymphocytes.Crossref | GoogleScholarGoogle Scholar |
Li L, Degardin M, Lavergne T (2013) Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications. Journal of the American Chemical Society 136, 826–829.
| Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications.Crossref | GoogleScholarGoogle Scholar | 24152106PubMed |
Marck C, Grosjean H (2003) Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA 9, 1516–1531.
| Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications.Crossref | GoogleScholarGoogle Scholar | 14624007PubMed |
Martello R, Leutert M, Jungmichel S, Bilan V, Larsen SC, Young C, Nielsen ML (2016) Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue. Nature Communications 7, 12917
| Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue.Crossref | GoogleScholarGoogle Scholar | 27686526PubMed |
Masutani M, Fujimori H (2013) Poly (ADP-ribosyl) ation in carcinogenesis. Molecular Aspects of Medicine 34, 1202–1216.
| Poly (ADP-ribosyl) ation in carcinogenesis.Crossref | GoogleScholarGoogle Scholar | 23714734PubMed |
Mazumder R, Iyer LM, Vasudevan S, Aravind L (2002) Detection of novel members, structure–function analysis and evolutionary classification of the 2H phosphoesterase superfamily. Nucleic Acids Research 30, 5229–5243.
| Detection of novel members, structure–function analysis and evolutionary classification of the 2H phosphoesterase superfamily.Crossref | GoogleScholarGoogle Scholar | 12466548PubMed |
McCraith SM, Phizicky EM (1990) A highly specific phosphatase from Saccharomyces cerevisiae implicated in tRNA splicing. Molecular and Cellular Biology 10, 1049–1055.
| A highly specific phosphatase from Saccharomyces cerevisiae implicated in tRNA splicing.Crossref | GoogleScholarGoogle Scholar | 2154680PubMed |
Mi GQ, Liu LY, Dang JW, Zhang ZX, Ren HZ (2008) Identification of low-light induced genes in cucumber (Cucumis sativus) seedlings by suppression subtractive hybridization. Scientia Horticulturae 117, 89–94.
| Identification of low-light induced genes in cucumber (Cucumis sativus) seedlings by suppression subtractive hybridization.Crossref | GoogleScholarGoogle Scholar |
Mohseni M, Cidado J, Croessmann S, Cravero K, Cimino-Mathews A, Wong HY, Wang GM (2014) MACROD2 overexpression mediates estrogen independent growth and tamoxifen resistance in breast cancers. Proceedings of the National Academy of Sciences of the United States of America 111, 17606–17611.
| MACROD2 overexpression mediates estrogen independent growth and tamoxifen resistance in breast cancers.Crossref | GoogleScholarGoogle Scholar | 25422431PubMed |
Moyle PM, Muir TW (2010) Method for the synthesis of mono-ADP-ribose conjugated peptides. Journal of the American Chemical Society 132, 15878–15880.
| Method for the synthesis of mono-ADP-ribose conjugated peptides.Crossref | GoogleScholarGoogle Scholar | 20968292PubMed |
Munir A, Abdullahu L, Banerjee A, Damha MJ, Shuman S (2019) NAD+-dependent RNA terminal 2′ and 3′ phosphomonoesterase activity of a sub-set of Tpt1 enzymes. RNA 25, 783–792.
| NAD+-dependent RNA terminal 2′ and 3′ phosphomonoesterase activity of a sub-set of Tpt1 enzymes.Crossref | GoogleScholarGoogle Scholar | 31019096PubMed |
Nakano TTakahashi-Nakaguchi AYamamoto M2015
Ogawa T, Tomita K, Ueda T, Watanabe K, Uozumi T, Masaki H (1999) A cytotoxic ribonuclease targeting specific transfer RNA anticodons. Science 283, 2097–2100.
| A cytotoxic ribonuclease targeting specific transfer RNA anticodons.Crossref | GoogleScholarGoogle Scholar | 10092236PubMed |
Palazzo L, Thomas B, Jemth AS, Colby T, Leidecker O, Feijs KL, Helleday T (2015) Processing of protein ADP-ribosylation by Nudix hydrolases. The Biochemical Journal 468, 293–301.
| Processing of protein ADP-ribosylation by Nudix hydrolases.Crossref | GoogleScholarGoogle Scholar | 25789582PubMed |
Palazzo L, Mikoč A, Ahel I (2017) ADP-ribosylation: new facets of an ancient modification. The FEBS Journal 284, 2932–2946.
| ADP-ribosylation: new facets of an ancient modification.Crossref | GoogleScholarGoogle Scholar | 28383827PubMed |
Paushkin SV, Patel M, Furia BS, Peltz SW, Trotta CR (2004) Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3′ end formation. Cell 117, 311–321.
| Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3′ end formation.Crossref | GoogleScholarGoogle Scholar | 15109492PubMed |
Perina D, Mikoč A, Ahel J, Ćetković H, Žaja R, Ahel I (2014) Distribution of protein poly (ADP-ribosyl) ation systems across all domains of life. DNA Repair 23, 4–16.
| Distribution of protein poly (ADP-ribosyl) ation systems across all domains of life.Crossref | GoogleScholarGoogle Scholar | 24865146PubMed |
Qi J, Isupov MN, Littlechild JA, Anderson LE (2001) Chloroplast glyceraldehyde-3-phosphate dehydrogenase contains a single disulfide bond located in the C-terminal extension to the B subunit. Journal of Biological Chemistry 276, 35247–35252.
| Chloroplast glyceraldehyde-3-phosphate dehydrogenase contains a single disulfide bond located in the C-terminal extension to the B subunit.Crossref | GoogleScholarGoogle Scholar | 11438534PubMed |
Reinhold-Hurek B, Shub DA (1992) Self-splicing introns in tRNA genes of widely divergent bacteria. Nature 357, 173
| Self-splicing introns in tRNA genes of widely divergent bacteria.Crossref | GoogleScholarGoogle Scholar | 1579169PubMed |
Sawaya R, Schwer B, Shuman S (2005) Structure–function analysis of the yeast NAD+-dependent tRNA 2′-phosphotransferase Tpt1. RNA 11, 107–113.
| Structure–function analysis of the yeast NAD+-dependent tRNA 2′-phosphotransferase Tpt1.Crossref | GoogleScholarGoogle Scholar | 15611301PubMed |
Schneider A, Häusler RE, Kolukisaoglu Ü, Kunze R, Van Der Graaff E, Schwacke R, Flügge UI (2002) An Arabidopsis thaliana knock‐out mutant of the chloroplast triose phosphate/phosphate translocator is severely compromised only when starch synthesis, but not starch mobilisation is abolished. The Plant Journal 32, 685–699.
| An Arabidopsis thaliana knock‐out mutant of the chloroplast triose phosphate/phosphate translocator is severely compromised only when starch synthesis, but not starch mobilisation is abolished.Crossref | GoogleScholarGoogle Scholar | 12472685PubMed |
Sharifi R, Morra R, Appel CD, Tallis M, Chioza B, Jankevicius G, Schellenberg MJ (2013) Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease. EMBO Journal 32, 1225–1237.
| Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease.Crossref | GoogleScholarGoogle Scholar | 23481255PubMed |
Söding J (2005) Protein homology detection by HMM–HMM comparison. Bioinformatics 21, 951–960.
| Protein homology detection by HMM–HMM comparison.Crossref | GoogleScholarGoogle Scholar | 15531603PubMed |
Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids research 33, W244–W248.
| The HHpred interactive server for protein homology detection and structure prediction.Crossref | GoogleScholarGoogle Scholar | 15980461PubMed |
Sorci L, Kurnasov OV, Rodionov DA, Osterman A (2010) Genomics and enzymology of NAD biosynthesis. In ‘Comprehensive natural products II’. (Eds LN Mander, HW Lui) pp. 213–257. (Elsevier: Oxford, UK)
Spinelli SL, Consaul SA, Phizicky EM (1997) A conditional lethal yeast phosphotransferase (Tpt1) mutant accumulates tRNAs with a 2′-phosphate and an under modified base at the splice junction. RNA (New York, N.Y.) 3, 1388–1400.
Spinelli SL, Malik HS, Consaul SA, Phizicky EM (1998) A functional homolog of a yeast tRNA splicing enzyme is conserved in higher eukaryotes and in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 95, 14136–14141.
| A functional homolog of a yeast tRNA splicing enzyme is conserved in higher eukaryotes and in Escherichia coli.Crossref | GoogleScholarGoogle Scholar | 9826666PubMed |
Spinelli SL, Kierzek R, Turner DH (1999) Transient ADP-ribosylation of a 2″-phosphate implicated in its removal from ligated tRNA during splicing in yeast. Journal of Biological Chemistry 274, 2637–2644.
| Transient ADP-ribosylation of a 2″-phosphate implicated in its removal from ligated tRNA during splicing in yeast.Crossref | GoogleScholarGoogle Scholar | 9915792PubMed |
Sugimura T, Miwa M (1994) Poly (ADP-ribose) historical perspective. Molecular and Cellular Biochemistry 138, 5–12.
| Poly (ADP-ribose) historical perspective.Crossref | GoogleScholarGoogle Scholar | 7898475PubMed |
Sun YV, Boverhof DR, Burgoon LD, Fielden MR, Zacharewski TR (2004) Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences. Nucleic Acids Research 32, 4512–4523.
| Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences.Crossref | GoogleScholarGoogle Scholar | 15328365PubMed |
Talhaoui I, Lebedeva NA, Zarkovic G (2016) Poly (ADP-ribose) polymerases covalently modify strand break termini in DNA fragments in vitro. Nucleic Acids Research 44, 9279–9295.
| Poly (ADP-ribose) polymerases covalently modify strand break termini in DNA fragments in vitro.Crossref | GoogleScholarGoogle Scholar | 27471034PubMed |
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673–4680.
| CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Crossref | GoogleScholarGoogle Scholar | 7984417PubMed |
Thompson DM, Lu C, Green PJ, Parker R (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14, 2095–2103.
| tRNA cleavage is a conserved response to oxidative stress in eukaryotes.Crossref | GoogleScholarGoogle Scholar | 18719243PubMed |
Tomita K, Ogawa T, Uozumi T, Watanabe K, Masaki H (2000) A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. Proceedings of the National Academy of Sciences of the United States of America 97, 8278–8283.
| A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops.Crossref | GoogleScholarGoogle Scholar | 10880568PubMed |
Trotta CR, Miao F, Arn EA, Stevens SW, Ho CK, Rauhut R, Abelson JN (1997) The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 89, 849–858.
| The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases.Crossref | GoogleScholarGoogle Scholar | 9200603PubMed |
Tsan JT, Wang Z, Jin Y, Hwang LY, Bash RO, Baer R (1997) Mammalian cells as hosts for two-hybrid studies of protein-protein interaction In ‘The yeast two-hybrid system’. (Eds PL Bartal, S Fields) pp. 217–232. (Oxford University Press: Oxford, UK)
Ueda K, Hayaishi O (1985) ADP-ribosylation. Annual Review of Biochemistry 54, 73–100.
| ADP-ribosylation.Crossref | GoogleScholarGoogle Scholar | 3927821PubMed |
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Qureshi-Emili A (2000) A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403, 623
| A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae.Crossref | GoogleScholarGoogle Scholar | 10688190PubMed |
Walsh C (2006) ‘Posttranslational modification of proteins: expanding nature’s inventory.’ (Roberts & Co. Publishers: Bonn, Germany)
Wan R, Bai R, Yan C, Lei J, Shi Y (2019) Structures of the catalytically activated yeast spliceosome reveal the mechanism of branching. Cell
| Structures of the catalytically activated yeast spliceosome reveal the mechanism of branching.Crossref | GoogleScholarGoogle Scholar | 30879786PubMed |
Xu MQ, Kathe SD, Goodrich-Blair H, Nierzwicki-Bauer SA, Shub DA (1990) Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science 250, 1566–1570.
| Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria.Crossref | GoogleScholarGoogle Scholar | 2125747PubMed |
Zhang Y, Wang J, Ding M, Yu (2013) Site-specific characterization of the Asp-and Glu-ADP-ribosylated proteome. Nature Methods 10, 981
| Site-specific characterization of the Asp-and Glu-ADP-ribosylated proteome.Crossref | GoogleScholarGoogle Scholar | 23955771PubMed |
Zhu J-K (2016) Abiotic stress signaling and responses in plants. Cell 167, 313–324.
| Abiotic stress signaling and responses in plants.Crossref | GoogleScholarGoogle Scholar | 27716505PubMed |
Zillmann M, Gorovsky MA, Phizicky EM (1991) Conserved mechanism of tRNA splicing in eukaryotes. Molecular and Cellular Biology 11, 5410–5416.
| Conserved mechanism of tRNA splicing in eukaryotes.Crossref | GoogleScholarGoogle Scholar | 1922054PubMed |
