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McCombe CL, Catanzariti AM, Greenwood JR, Desai AM, Outram MA, Yu DS, Ericsson DJ, Brenner SE, Dodds PN, Kobe B, Jones DA, Williams SJ. A rust-fungus Nudix hydrolase effector decaps mRNA in vitro and interferes with plant immune pathways. THE NEW PHYTOLOGIST 2023; 239:222-239. [PMID: 36631975 DOI: 10.1111/nph.18727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/02/2023] [Indexed: 06/02/2023]
Abstract
To infect plants, pathogenic fungi secrete small proteins called effectors. Here, we describe the catalytic activity and potential virulence function of the Nudix hydrolase effector AvrM14 from the flax rust fungus (Melampsora lini). We completed extensive in vitro assays to characterise the enzymatic activity of the AvrM14 effector. Additionally, we used in planta transient expression of wild-type and catalytically dead AvrM14 versions followed by biochemical assays, phenotypic analysis and RNA sequencing to unravel how the catalytic activity of AvrM14 impacts plant immunity. AvrM14 is an extremely selective enzyme capable of removing the protective 5' cap from mRNA transcripts in vitro. Homodimerisation of AvrM14 promoted biologically relevant mRNA cap cleavage in vitro and this activity was conserved in related effectors from other Melampsora spp. In planta expression of wild-type AvrM14, but not the catalytically dead version, suppressed immune-related reactive oxygen species production, altered the abundance of some circadian-rhythm-associated mRNA transcripts and reduced the hypersensitive cell-death response triggered by the flax disease resistance protein M1. To date, the decapping of host mRNA as a virulence strategy has not been described beyond viruses. Our results indicate that some fungal pathogens produce Nudix hydrolase effectors with in vitro mRNA-decapping activity capable of interfering with plant immunity.
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Affiliation(s)
- Carl L McCombe
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ann-Maree Catanzariti
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Julian R Greenwood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Anna M Desai
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Megan A Outram
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel S Yu
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3168, Australia
| | - Steven E Brenner
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld, 4072, Australia
| | - David A Jones
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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2
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Sun Y, Shen W, Hu S, Lyu Q, Wang Q, Wei T, Zhu W, Zhang J. METTL3 promotes chemoresistance in small cell lung cancer by inducing mitophagy. J Exp Clin Cancer Res 2023; 42:65. [PMID: 36932427 PMCID: PMC10022264 DOI: 10.1186/s13046-023-02638-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/05/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer. Although most patients are initially sensitive to first-line combination chemotherapy with cisplatin and etoposide, chemotherapy drug resistance easily develops and quickly leads to tumour progression. Therefore, understanding the mechanisms of chemotherapy drug resistance and how to reverse it is key to improving the prognosis of patients with SCLC. Moreover, N6-methyladenosine (m6A) is the most abundant mRNA modification and is catalysed by the methyltransferase complex, in which methyltransferase-like 3 (METTL3) is the sole catalytic subunit. METHODS The effects of METTL3 on chemoresistance in SCLC cells were determined using qRT-PCR, Western blotting, immunohistochemistry, cell counting kit (CCK-8) assays, flow cytometry, and tumorigenicity experiments. Methylated RNA immunoprecipitation sequencing (MeRIP-seq), MeRIP qPCR, immunofluorescence, and drug inhibitor experiments were performed to confirm the molecular mechanism of Decapping Protein 2 (DCP2), which is involved in the chemoresistance of SCLC. RESULTS In the present study, we found that METTL3 is a marker for poor SCLC prognosis, and it is highly expressed in chemoresistant SCLC cells. METTL3 promotes SCLC chemoresistance by positively regulating mitophagy. METTL3 induces m6A methylation of DCP2 and causes the degradation of DCP2, which promotes mitochondrial autophagy through the Pink1-Parkin pathway, leading to chemotherapy resistance. We also found that STM2457, a novel METTL3 inhibitor, can reverse SCLC chemoresistance. CONCLUSIONS The m6A methyltransferase METTL3 regulates Pink1-Parkin pathway-mediated mitophagy and mitochondrial damage in SCLC cells by targeting DCP2, thereby promoting chemotherapy resistance in patients with SCLC.
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Affiliation(s)
- Yueqin Sun
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Weitao Shen
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shulu Hu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qiong Lyu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qiongyao Wang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Wei
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Weiliang Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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3
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A Hypothesis on How the Azolla Symbiosis Mitigates Nitrous Oxide Based on In Silico Analyses. J 2022. [DOI: 10.3390/j5010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nitrous oxide is a long-lived greenhouse gas that exists for 114 years in the atmosphere and is 298-fold more potent than carbon dioxide in its global warming potential. Two recent studies showcased the utility of Azolla plants for a lesser footprint in nitrous oxide production from urea and other supplements to the irrigated ecosystem, which mandates exploration since there is still no clear solution to nitrous oxide in paddy fields or in other ecosystems. Here, we propose a solution based on the evolution of a single cytochrome oxidase subunit II protein (WP_013192178.1) from the cyanobiont Trichormus azollae that we hypothesize to be able to quench nitrous oxide. First, we draw attention to a domain in the candidate protein that is emerging as a sensory periplasmic Y_Y_Y domain that is inferred to bind nitrous oxide. Secondly, we draw the phylogeny of the candidate protein showcasing the poor bootstrap support of its position in the wider clade showcasing its deviation from the core function. Thirdly, we show that the NtcA protein, the apical N-effecting transcription factor, can putatively bind to a promoter sequence of the gene coding for the candidate protein (WP_013192178.1), suggesting a function associated with heterocysts and N-metabolism. Our fourth point involves a string of histidines at the C-terminal extremity of the WP_013192178.1 protein that is missing on all other T. azollae cytochrome oxidase subunit II counterparts, suggesting that such histidines are perhaps involved in forming a Cu center. As the fifth point, we showcase a unique glycine-183 in a lengthy linker region containing multiple glycines that is absent in all proximal Nostocales cyanobacteria, which we predict to be a DNA binding residue. We propose a mechanism of action for the WP_013192178.1 protein based on our in silico analyses. In total, we hypothesize the incomplete and rapid conversion of a likely heterocystous cytochrome oxidase subunit II protein to an emerging nitrous oxide sensing/quenching subunit based on bioinformatics analyses and past literature, which can have repercussions to climate change and consequently, future human life.
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Kago G, Parrish S. The Mimivirus L375 Nudix enzyme hydrolyzes the 5' mRNA cap. PLoS One 2021; 16:e0245820. [PMID: 34582446 PMCID: PMC8478210 DOI: 10.1371/journal.pone.0245820] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/10/2021] [Indexed: 11/19/2022] Open
Abstract
The giant Mimivirus is a member of the nucleocytoplasmic large DNA viruses (NCLDV), a group of diverse viruses that contain double-stranded DNA (dsDNA) genomes that replicate primarily in eukaryotic hosts. Two members of the NCLDV, Vaccinia Virus (VACV) and African Swine Fever Virus (ASFV), both synthesize Nudix enzymes that have been shown to decap mRNA, a process thought to accelerate viral and host mRNA turnover and promote the shutoff of host protein synthesis. Mimivirus encodes two Nudix enzymes in its genome, denoted as L375 and L534. Importantly, L375 exhibits sequence similarity to ASFV-DP and eukaryotic Dcp2, two Nudix enzymes shown to possess mRNA decapping activity. In this work, we demonstrate that recombinant Mimivirus L375 cleaves the 5' m7GpppN mRNA cap, releasing m7GDP as a product. L375 did not significantly cleave mRNAs containing an unmethylated 5'GpppN cap, indicating that this enzyme specifically hydrolyzes methylated-capped transcripts. A point mutation in the L375 Nudix motif completely eliminated cap hydrolysis, showing that decapping activity is dependent on this motif. Addition of uncapped RNA significantly reduced L375 decapping activity, suggesting that L375 may recognize its substrate through interaction with the RNA body.
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Affiliation(s)
- Grace Kago
- Department of Biology, McDaniel College, Westminster, Maryland, United States of America
| | - Susan Parrish
- Department of Biology, McDaniel College, Westminster, Maryland, United States of America
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5
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Pietrowska-Borek M, Dobrogojski J, Sobieszczuk-Nowicka E, Borek S. New Insight into Plant Signaling: Extracellular ATP and Uncommon Nucleotides. Cells 2020; 9:E345. [PMID: 32024306 PMCID: PMC7072326 DOI: 10.3390/cells9020345] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
New players in plant signaling are described in detail in this review: extracellular ATP (eATP) and uncommon nucleotides such as dinucleoside polyphosphates (NpnN's), adenosine 5'-phosphoramidate (NH2-pA), and extracellular NAD+ and NADP+ (eNAD(P)+). Recent molecular, physiological, and biochemical evidence implicating concurrently the signaling role of eATP, NpnN's, and NH2-pA in plant biology and the mechanistic events in which they are involved are discussed. Numerous studies have shown that they are often universal signaling messengers, which trigger a signaling cascade in similar reactions and processes among different kingdoms. We also present here, not described elsewhere, a working model of the NpnN' and NH2-pA signaling network in a plant cell where these nucleotides trigger induction of the phenylpropanoid and the isochorismic acid pathways yielding metabolites protecting the plant against various types of stresses. Through these signals, the plant responds to environmental stimuli by intensifying the production of various compounds, such as anthocyanins, lignin, stilbenes, and salicylic acid. Still, more research needs to be performed to identify signaling networks that involve uncommon nucleotides, followed by omic experiments to define network elements and processes that are controlled by these signals.
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Affiliation(s)
- Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Jędrzej Dobrogojski
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (E.S.-N.); (S.B.)
| | - Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (E.S.-N.); (S.B.)
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Nyikó T, Auber A, Bucher E. Functional and molecular characterization of the conserved Arabidopsis PUMILIO protein, APUM9. PLANT MOLECULAR BIOLOGY 2019; 100:199-214. [PMID: 30868544 PMCID: PMC6513901 DOI: 10.1007/s11103-019-00853-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/01/2019] [Indexed: 05/08/2023]
Abstract
Here we demonstrate that the APUM9 RNA-binding protein and its co-factors play a role in mRNA destabilization and how this activity might regulate early plant development. APUM9 is a conserved PUF RNA-binding protein (RBP) under complex transcriptional control mediated by a transposable element (TE) that restricts its expression in Arabidopsis. Currently, little is known about the functional and mechanistic details of the plant PUF regulatory system and the biological relevance of the TE-mediated repression of APUM9 in plant development and stress responses. By combining a range of transient assays, we show here, that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunit of the decapping complex and DCP2 overexpression induces rapid decay of APUM9 targeted mRNAs. We show that APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated control of APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions.
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Affiliation(s)
- Tünde Nyikó
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS-INRA), 42 rue Georges Morel, 24, 49071, Beaucouzé, France
- Agricultural Biotechnology Institute, Szent-Györgyi Albert 4, Gödöllő, 2100, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi Albert 4, Gödöllő, 2100, Hungary
| | - Etienne Bucher
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS-INRA), 42 rue Georges Morel, 24, 49071, Beaucouzé, France.
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7
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Tsuzuki M, Motomura K, Kumakura N, Takeda A. Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants. JOURNAL OF PLANT RESEARCH 2017; 130:211-226. [PMID: 28197782 DOI: 10.1007/s10265-017-0906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.
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Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kazuki Motomura
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Naoyoshi Kumakura
- Center for Sustainable Resource Science, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
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8
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Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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9
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Tanaka H, Maruta T, Ogawa T, Tanabe N, Tamoi M, Yoshimura K, Shigeoka S. Identification and characterization of Arabidopsis AtNUDX9 as a GDP-d-mannose pyrophosphohydrolase: its involvement in root growth inhibition in response to ammonium. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5797-808. [PMID: 26049160 PMCID: PMC4566977 DOI: 10.1093/jxb/erv281] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
GDP-d-mannose (GDP-d-Man) is an important intermediate in ascorbic acid (AsA) synthesis, cell wall synthesis, protein N-glycosylation, and glycosylphosphatidylinositol-anchoring in plants. Thus, the modulation of intracellular levels of GDP-d-Man could be important for maintaining various cellular processes. Here an Arabidopsis GDP-d-Man pyrophosphohydrolase, AtNUDX9 (AtNUDT9; At3g46200), which hydrolysed GDP-d-Man to GMP and mannose 1-phosphate, was identified. The K m and V max values for GDP-d-Man of AtNUDX9 were 376±24 μM and 1.61±0.15 μmol min(-1) mg(-1) protein, respectively. Among various tissues, the expression levels of AtNUDX9 and the total activity of GDP-d-Man pyrophosphohydrolase were the highest in the roots. The GDP-d-Man pyrophosphohydrolase activity was increased in the root of plants grown in the presence of ammonium. No difference was observed in the levels of AsA in the leaf and root tissues of the wild-type and knockout-nudx9 (KO-nudx9) plants, whereas a marked increase in N-glycoprotein levels and enhanced growth were detected in the roots of KO-nudx9 plants in the presence of ammonium. These results suggest that AtNUDX9 is involved in the regulation of GDP-d-Man levels affecting ammonium sensitivity via modulation of protein N-glycosylation in the roots.
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Affiliation(s)
- Hiroyuki Tanaka
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Takanori Maruta
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Takahisa Ogawa
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Noriaki Tanabe
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Masahiro Tamoi
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Kazuya Yoshimura
- Department of Food and Nutritional Science, College of Bioscience and Biotechnology, Chubu University,1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Shigeru Shigeoka
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
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Trésaugues L, Lundbäck T, Welin M, Flodin S, Nyman T, Silvander C, Gräslund S, Nordlund P. Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate. PLoS One 2015; 10:e0131507. [PMID: 26121039 PMCID: PMC4485890 DOI: 10.1371/journal.pone.0131507] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022] Open
Abstract
Human NUDT16 is a member of the NUDIX hydrolase superfamily. After having been initially described as an mRNA decapping enzyme, recent studies conferred it a role as an “housecleaning” enzyme specialized in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. Here we present the crystal structure of human NUDT16 both in its apo-form and in complex with its product inosine monophosphate (IMP). NUDT16 appears as a dimer whose formation generates a positively charged trench to accommodate substrate-binding. Complementation of the structural data with detailed enzymatic and biophysical studies revealed the determinants of substrate recognition and particularly the importance of the substituents in position 2 and 6 on the purine ring. The affinity for the IMP product, harboring a carbonyl in position 6 on the base, compared to purine monophosphates lacking a H-bond acceptor in this position, implies a catalytic cycle whose rate is primarily regulated by the product-release step. Finally, we have also characterized a phenomenon of inhibition by the product of the reaction, IMP, which might exclude non-deleterious nucleotides from NUDT16-mediated hydrolysis regardless of their cellular concentration. Taken together, this study details structural and regulatory mechanisms explaining how substrates are selected for hydrolysis by human NUDT16.
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Affiliation(s)
- Lionel Trésaugues
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (PN); (LT)
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratories, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Flodin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Nyman
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Silvander
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (PN); (LT)
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Muthuramalingam M, Zeng X, Iyer NJ, Klein P, Mahalingam R. A GCC-box motif in the promoter of nudix hydrolase 7 (AtNUDT7) gene plays a role in ozone response of Arabidopsis ecotypes. Genomics 2015; 105:31-8. [PMID: 25451743 DOI: 10.1016/j.ygeno.2014.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/15/2014] [Accepted: 10/29/2014] [Indexed: 01/01/2023]
Abstract
Arabidopsis nudix hydrolase 7 (AtNudt7) plays an important role in regulating redox homeostasis during stress/defense signaling and seed germination. The early responsiveness of AtNudt7 provides a useful marker especially during oxidative cell death in plants. Nuclear run-on assays demonstrate that AtNudt7 is transcriptionally regulated. AtNUDT7 promoter-GUS transgenic plants show rapid inducibility in response to ozone and pathogens. A 16-bp insertion containing a GCC-box motif was identified in the promoter of a Ws-2 ecotype and was absent in Col-0. The 16-bp sequence was identified in 5% of the Arabidopsis ecotypes used in the 1001 genome sequencing project. The kinetics of expression of Ethylene Response Factor 1 (ERF1), a GCC-box binding factor is in synchrony with expression of AtNudt7 in response to ozone stress. ERF1 protein binds to the GCC-box motif in the AtNUDT7 promoter. In silico analysis of erf1 mutant and overexpressor lines supports a role for this protein in regulating AtNUDT7 expression.
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Affiliation(s)
| | - Xin Zeng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Niranjani J Iyer
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Peter Klein
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Ramamurthy Mahalingam
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
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12
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Yoshimura K, Shigeoka S. Versatile physiological functions of the Nudix hydrolase family in Arabidopsis. Biosci Biotechnol Biochem 2014; 79:354-66. [PMID: 25483172 DOI: 10.1080/09168451.2014.987207] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nudix hydrolases are widely distributed in all kingdoms of life and have the potential to hydrolyze a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, nucleotide coenzymes, nucleotide sugars, and RNA caps. However, except for E. coli MutT and its orthologs in other organisms that sanitize oxidized nucleotides to prevent DNA and RNA mutations, the functions of Nudix hydrolases had largely remained unclear until recently, because many members of this enzyme family exhibited broad substrate specificities. There is now increasing evidence to show that their functions extend into many aspects of the regulation of cellular responses. This review summarizes current knowledge on the molecular and enzymatic properties as well as physiological functions of Arabidopsis Nudix hydrolases. The information presented here may provide novel insights into the physiological roles of these enzymes in not only plant species, but also other organisms.
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Affiliation(s)
- Kazuya Yoshimura
- a Department of Food and Nutritional Science , College of Bioscience and Biotechnology, Chubu University , Kasugai , Japan
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Enzymatic and molecular characterization of Arabidopsis ppGpp pyrophosphohydrolase, AtNUDX26. Biosci Biotechnol Biochem 2012; 76:2236-41. [PMID: 23221701 DOI: 10.1271/bbb.120523] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Not only in bacteria but also in plant cells, guanosine-3',5'-tetraphosphate (ppGpp) is an important signaling molecule, that affects various cellular processes. In this study, we identified nucleoside diphosphates linked to some moiety X (Nudix) hydrolases, AtNUDX11, 15, 25, and 26, having ppGpp pyrophosphohydrolase activity from Arabidopsis plants. Among these, AtNUDX26 localized in chloroplasts had the highest Vmax and kcat values, leading to high catalytic efficiency, kcat/Km. The activity of AtNUDX26 required Mg2+ or Mn2+ ions as cofactor and was optimal at pH 9.0 and 50 °C. The expression of AtNUDX26 and of ppGpp metabolism-associated genes was regulated by various types of stress, suggesting that AtNUDX26 regulates cellular ppGpp levels in response to stress and impacts gene expression in chloroplasts. This is the first report on the molecular properties of ppGpp pyrophosphohydrolases in plants.
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Thran M, Link K, Sonnewald U. The Arabidopsis DCP2 gene is required for proper mRNA turnover and prevents transgene silencing in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:368-77. [PMID: 22639932 DOI: 10.1111/j.1365-313x.2012.05066.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Post-transcriptional gene silencing often limits the over-expression of transgenes in transgenic plants. It involves RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), which recognizes aberrant transcripts, such as inaccurately processed or uncapped mRNA, and triggers silencing of target transcripts. Here, we describe the isolation and characterization of an Arabidopsis mutant displaying increased transgene silencing (its1). Reduced accumulation of transgene mRNA in the its1 mutant background was accompanied by accumulation of transgene-specific siRNAs and was overcome by potyvirus infection. We therefore speculated that ITS1 is a suppressor of post-transcriptional gene silencing. Map-based cloning and subsequent complementation revealed that ITS1 encodes DECAPPING 2 (DCP2), which is crucial for decapping, a prerequisite for mRNA degradation. In agreement with the proposed function of DCP2, we found a reduced accumulation of uncapped mRNA in the its1 mutant. Furthermore, silencing in the its1 mutant was dependent on RDR6 function, suggesting that reduced decapping leads to accumulation of aberrant capped mRNA. Hence, we provide evidence for a class of aberrant mRNA that accumulates upon impaired mRNA decapping and triggers post-transcriptional gene silencing in Arabidopsis. As DCP2 knockouts cause post-embryo lethality, we isolated a hypomorphic dcp2 allele, providing insights into mRNA degradation and its interplay with post-transcriptional gene silencing.
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Affiliation(s)
- Moritz Thran
- Department of Biology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
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Motomura K, Le QT, Kumakura N, Fukaya T, Takeda A, Watanabe Y. The role of decapping proteins in the miRNA accumulation in Arabidopsis thaliana. RNA Biol 2012; 9:644-52. [PMID: 22614834 DOI: 10.4161/rna.19877] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Decapping 1 (DCP1), Decapping 2 (DCP2) and VARICOSE (VCS) are components of the decapping complex that removes the 7-methyl-guanosine 5'-diphosphate from the 5' end of mRNAs. In animals, the decapping proteins are involved in miRNA-mediated gene silencing, whereas in plants the roles of the decapping proteins in the miRNA pathway are not well understood. Here we demonstrated that the accumulation of miRNAs decreased in dcp1, dcp2 and vcs mutants, indicating that DCP1, DCP2 and VCS are important for the miRNA pathway in Arabidopsis thaliana. The primary miRNAs (pri-miRNAs) did not increase and miRNA biogenesis components did not decrease in these mutants, suggesting that the miRNA decrease in decapping mutants is not due to the defect of pri-miRNA processing. We showed that the accumulation of miRNA targets increased concomitantly with the decrease of miRNA in the decapping mutants. Our results suggested that the seedling lethal phenotypes in the dcp1, dcp2 and vcs mutants are caused not only by the defect in decapping, but also by the disruption of miRNA-mediated gene regulation.
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Affiliation(s)
- Kazuki Motomura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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Gardiner J, Overall R, Marc J. PDZ domain proteins: 'dark matter' of the plant proteome? MOLECULAR PLANT 2011; 4:933-937. [PMID: 21653283 DOI: 10.1093/mp/ssr043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PDZ domain proteins in metazoans function in diverse roles, and in conjunction with PDZ domain-binding proteins form macromolecular complexes for signaling at synapses and cell junctions. Bioinformatics approaches using the SMART tool indicate there are only a modest number of Arabidopsis PDZ proteins. However, there are hundreds of proteins predicted to possess PDZ domain-binding motifs, suggesting that there are many PDZ domain proteins not detectable by conventional bioinformatic approaches. Our Scansite analysis of PDZ domain-binding proteins indicates that PDZ domain proteins may play key roles in cytoskeletal organization including actin microfilaments, microtubules, and nuclear cytoskeletal proteins, and in the organization of macromolecular complexes involved in cell-to-cell signaling, transport, and cell wall formation.
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Affiliation(s)
- John Gardiner
- School of Biological Sciences, University of Sydney, Sydney 2006, Australia.
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Briggs AG, Bent AF. Poly(ADP-ribosyl)ation in plants. TRENDS IN PLANT SCIENCE 2011; 16:372-80. [PMID: 21482174 DOI: 10.1016/j.tplants.2011.03.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 03/07/2011] [Accepted: 03/09/2011] [Indexed: 05/03/2023]
Abstract
Poly(ADP-ribose) polymerases (PARPs) and poly(ADP-ribose) glycohydrolases (PARGs) are the main enzymes responsible for the post-translational modification known as poly(ADP-ribosyl)ation. These enzymes play important roles in genotoxic stress tolerance and DNA repair, programmed cell death, transcription, and cell cycle control in animals. Similar impacts are being discovered in plants, as well as roles in plant-specific processes. In particular, we review recent work that has revealed significant roles for poly(ADP-ribosyl)ation in plant responses to biotic and abiotic stress, as well as roles for ADP-ribose pyrophosphatases (a subset of the nucleoside diphosphate linked to some moiety-X or NUDX hydrolases). Future challenges include identification of poly(ADP-ribosyl)ation targets and interacting proteins, improved use of inhibitors and plant mutants, and field-based studies with economically valuable plant species.
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Affiliation(s)
- Amy G Briggs
- Program in Cellular and Molecular Biology, University of Wisconsin - Madison, WI, USA
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Soulière MF, Perreault JP, Bisaillon M. Insights into the molecular determinants involved in cap recognition by the vaccinia virus D10 decapping enzyme. Nucleic Acids Res 2010; 38:7599-610. [PMID: 20639534 PMCID: PMC2995054 DOI: 10.1093/nar/gkq628] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Decapping enzymes are required for the removal of the 5′-end m7GpppN cap of mRNAs to allow their decay in cells. While many cap-binding proteins recognize the cap structure via the stacking of the methylated guanosine ring between two aromatic residues, the precise mechanism of cap recognition by decapping enzymes has yet to be determined. In order to get insights into the interaction of decapping enzymes with the cap structure, we studied the vaccinia virus D10 decapping enzyme as a model to investigate the important features for substrate recognition by the enzyme. We demonstrate that a number of chemically modified purines can competitively inhibit the decapping reaction, highlighting the molecular features of the cap structure that are required for recognition by the enzyme, such as the nature of the moiety at positions 2 and 6 of the guanine base. A 3D structural model of the D10 protein was generated which suggests amino acids implicated in cap binding. Consequently, we expressed 17 mutant proteins with amino acid substitutions in the active site of D10 and found that eight are critical for the decapping activity. These data underscore the functional features involved in the non-canonical cap-recognition by the vaccinia virus D10 decapping enzyme.
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Affiliation(s)
- Marie F Soulière
- RNA Group, Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Parrish S, Hurchalla M, Liu SW, Moss B. The African swine fever virus g5R protein possesses mRNA decapping activity. Virology 2009; 393:177-82. [PMID: 19695654 PMCID: PMC3392020 DOI: 10.1016/j.virol.2009.07.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 07/23/2009] [Indexed: 01/29/2023]
Abstract
The African Swine Fever Virus (ASFV) encodes a single Nudix enzyme in its genome, termed the g5R protein (g5Rp). Nudix phosphohydrolases cleave a variety of substrates, such as nucleotides and diphosphoinositol polyphosphates. Previously, ASFV g5Rp was shown to hydrolyze diphosphoinositol polyphosphates and GTP, but was unable to cleave methylated mRNA cap analogues. In vaccinia virus (VACV), a distant relative of ASFV, the D9 and D10 Nudix enzymes were shown to cleave the mRNA cap, but only when the cap was attached to an RNA body. Here, we show that recombinant ASFV g5Rp hydrolyzes the mRNA cap when tethered to an RNA moiety, liberating m(7)GDP as a product. Mutations in the Nudix motif abolished mRNA decapping activity, confirming that g5Rp was responsible for cap cleavage. The decapping activity of g5Rp was potently inhibited by excess uncapped RNA but not by methylated cap analogues, suggesting that substrate recognition occurs by RNA binding.
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Affiliation(s)
- Susan Parrish
- McDaniel College, 2 College Hill, Eaton Hall, Room 212, Westminster, MD 21157, USA.
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Rao S, Dinkins RD, Hunt AG. Distinctive interactions of the Arabidopsis homolog of the 30 kD subunit of the cleavage and polyadenylation specificity factor (AtCPSF30) with other polyadenylation factor subunits. BMC Cell Biol 2009; 10:51. [PMID: 19573236 PMCID: PMC2712457 DOI: 10.1186/1471-2121-10-51] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 07/02/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arabidopsis ortholog of the 30 kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor (AtCPSF30) is an RNA-binding endonuclease that is associated with other Arabidopsis CPSF subunits (orthologs of the 160, 100, and 73 kD subunits of CPSF). In order to further explore the functions of AtCPSF30, the subcellular distribution of the protein was examined by over-expressing fusion proteins containing fluorescent reporters linked to different CPSF subunits. RESULTS It was found that AtCPSF30 by itself localizes, not to the nucleus, but to the cytoplasm. AtCPSF30 could be found in the nucleus when co-expressed with AtCPSF160 or AtCPSF73(I), one of the two Arabidopsis orthologs of CPSF73. This re-directing of AtCPSF30 indicates that AtCPSF30 is retained in the nucleus via interactions with either or both of these other CPSF subunits. Co-expression of AtCSPF30 with AtCPSF100 altered the location, not of AtCPSF30, but rather of AtCPSF100, with these proteins residing in the cytoplasm. Deletion of plant-specific N- or C-terminal domains of AtCPSF30 abolished various of the interactions between AtCPSF30 and other CPSF subunits, suggesting that the plant CPSF complex assembles via novel protein-protein interactions. CONCLUSION These results suggest that the nuclear CPSF complex in plants is a dynamic one, and that the interactions between AtCPSF30 and other CPSF subunits are different from those existing in other eukaryotes.
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Affiliation(s)
- Suryadevara Rao
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
| | - Randy D Dinkins
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
- USDA-ARS, FAPRU, Lexington, KY 40546-0091 USA
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
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Gunawardana D, Likic VA, Gayler KR. A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana. Comp Funct Genomics 2009; 2009:820381. [PMID: 19590748 PMCID: PMC2707057 DOI: 10.1155/2009/820381] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 04/16/2009] [Indexed: 11/17/2022] Open
Abstract
Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily.
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Affiliation(s)
- D. Gunawardana
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
- School of Biological Sciences, University of Sydney, New South Wales 2006, Australia
| | - V. A. Likic
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - K. R. Gayler
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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Characterization of the vaccinia virus D10 decapping enzyme provides evidence for a two-metal-ion mechanism. Biochem J 2009; 420:27-35. [PMID: 19210265 DOI: 10.1042/bj20082296] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Decapping enzymes are required for the removal of the 5'-end cap of mRNAs. These enzymes exhibit a specific hydrolase activity, resulting in cleavage between the alpha- and beta-phosphates of the m7GpppN cap to generate both m7GDP and monophosphorylated RNA products. Decapping enzymes have been found in humans, plants and yeasts, and have been discovered more recently in vaccinia virus (D10 protein). Although experimental evidences are lacking, three-metal- and two-metal-ion mechanisms have been proposed so far for the decapping enzymes. In the present study, we performed a biochemical characterization of the interaction of bivalent cations with the vaccinia virus D10 protein. Synergistic activation of the enzyme was observed in the presence of Mg2+ and Mn2+ ions, suggesting the existence of two metal-ion-binding sites on the D10 protein. Moreover, dual-ligand titration experiments using fluorescence spectroscopy demonstrated the presence of two metal-ion-binding sites on the enzyme. A three-dimensional structural model of the active site of the enzyme was generated which highlighted the importance of three glutamate residues involved in the co-ordination of two metal ions and a water molecule. Mutational analyses confirmed the role of two glutamate residues for the binding of metal ions. We demonstrate that one metal ion is co-ordinated by Glu132, while the second metal ion is co-ordinated by Glu145. Taken together, these results support the proposed two-metal-ion mechanistic model for the D10 decapping enzyme.
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Ogawa T, Yoshimura K, Miyake H, Ishikawa K, Ito D, Tanabe N, Shigeoka S. Molecular characterization of organelle-type Nudix hydrolases in Arabidopsis. PLANT PHYSIOLOGY 2008; 148:1412-24. [PMID: 18815383 PMCID: PMC2577243 DOI: 10.1104/pp.108.128413] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 09/22/2008] [Indexed: 05/18/2023]
Abstract
Nudix (for nucleoside diphosphates linked to some moiety X) hydrolases act to hydrolyze ribonucleoside and deoxyribonucleoside triphosphates, nucleotide sugars, coenzymes, or dinucleoside polyphosphates. Arabidopsis (Arabidopsis thaliana) contains 27 genes encoding Nudix hydrolase homologues (AtNUDX1 to -27) with a predicted distribution in the cytosol, mitochondria, and chloroplasts. Previously, cytosolic Nudix hydrolases (AtNUDX1 to -11 and -25) were characterized. Here, we conducted a characterization of organelle-type AtNUDX proteins (AtNUDX12 to -24, -26, and -27). AtNUDX14 showed pyrophosphohydrolase activity toward both ADP-ribose and ADP-glucose, although its K(m) value was approximately 100-fold lower for ADP-ribose (13.0+/-0.7 microm) than for ADP-glucose (1,235+/-65 microm). AtNUDX15 hydrolyzed not only reduced coenzyme A (118.7+/-3.4 microm) but also a wide range of its derivatives. AtNUDX19 showed pyrophosphohydrolase activity toward both NADH (335.3+/-5.4 microm) and NADPH (36.9+/-3.5 microm). AtNUDX23 had flavin adenine dinucleotide pyrophosphohydrolase activity (9.1+/-0.9 microm). Both AtNUDX26 and AtNUDX27 hydrolyzed diadenosine polyphosphates (n=4-5). A confocal microscopic analysis using a green fluorescent protein fusion protein showed that AtNUDX15 is distributed in mitochondria and AtNUDX14 -19, -23, -26, and -27 are distributed in chloroplasts. These AtNUDX mRNAs were detected ubiquitously in various Arabidopsis tissues. The T-DNA insertion mutants of AtNUDX13, -14, -15, -19, -20, -21, -25, -26, and -27 did not exhibit any phenotypical differences under normal growth conditions. These results suggest that Nudix hydrolases in Arabidopsis control a variety of metabolites and are pertinent to a wide range of physiological processes.
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Affiliation(s)
- Takahisa Ogawa
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nara 631-8505, Japan
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Jiao Y, Riechmann JL, Meyerowitz EM. Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. THE PLANT CELL 2008; 20:2571-85. [PMID: 18952771 PMCID: PMC2590717 DOI: 10.1105/tpc.108.062786] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The composition of the transcriptome is determined by a balance between mRNA synthesis and degradation. An important route for mRNA degradation produces uncapped mRNAs, and this decay process can be initiated by decapping enzymes, endonucleases, and small RNAs. Although uncapped mRNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale until recently. Here, we present an experimental method for transcriptome-wide profiling of uncapped mRNAs that can be used in any eukaryotic system. We applied the method to study the prevalence of uncapped transcripts during the early stages of Arabidopsis thaliana flower development. Uncapped transcripts were identified for the majority of expressed genes, although at different levels. By comparing uncapped RNA levels with steady state overall transcript levels, our study provides evidence for widespread mRNA degradation control in numerous biological processes involving genes of varied molecular functions, implying that uncapped mRNA levels are dynamically regulated. Sequence analyses identified structural features of transcripts and cis-elements that were associated with different levels of uncapping. These transcriptome-wide profiles of uncapped mRNAs will aid in illuminating new regulatory mechanisms of eukaryotic transcriptional networks.
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Affiliation(s)
- Yuling Jiao
- California Institute of Technology, Division of Biology 156-29, Pasadena, California 91125, USA.
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