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František Potužník J, Nešuta O, Škríba A, Voleníková B, Mititelu MB, Mancini F, Serianni V, Fernandez H, Spustová K, Trylčová J, Vopalensky P, Cahová H. Diadenosine Tetraphosphate (Ap 4 A) Serves as a 5' RNA Cap in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202314951. [PMID: 37934413 DOI: 10.1002/anie.202314951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/08/2023]
Abstract
The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase modifications, 7-methylguanosine was long thought to be the only eukaryotic RNA cap. However, the discovery of non-canonical RNA caps in eukaryotes revealed a new niche of previously undetected RNA chemical modifications. We are the first to report the existence of a new non-canonical RNA cap, diadenosine tetraphosphate (Ap4 A), in human and rat cell lines. Ap4 A is the most abundant dinucleoside polyphosphate in eukaryotic cells and can be incorporated into RNA by RNA polymerases as a non-canonical initiating nucleotide (NCIN). Using liquid chromatography-mass spectrometry (LC-MS), we show that the amount of capped Ap4 A-RNA is independent of the cellular concentration of Ap4 A. A decapping enzyme screen identifies two enzymes cleaving Ap4 A-RNA,NUDT2 and DXO, both of which also cleave other substrate RNAs in vitro. We further assess the translatability and immunogenicity of Ap4 A-RNA and show that although it is not translated, Ap4 A-RNA is recognized as self by the cell and does not elicit an immune response, making it a natural component of the transcriptome. Our findings open a previously unexplored area of eukaryotic RNA regulation.
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Affiliation(s)
- Jiří František Potužník
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Ondřej Nešuta
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Anton Škríba
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Barbora Voleníková
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Maria-Bianca Mititelu
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Flaminia Mancini
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Valentina Serianni
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Henri Fernandez
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Kristína Spustová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Jana Trylčová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Pavel Vopalensky
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Hana Cahová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
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2
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Krahn N, Söll D, Vargas-Rodriguez O. Diversification of aminoacyl-tRNA synthetase activities via genomic duplication. Front Physiol 2022; 13:983245. [PMID: 36060688 PMCID: PMC9437257 DOI: 10.3389/fphys.2022.983245] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Intricate evolutionary events enabled the emergence of the full set of aminoacyl-tRNA synthetase (aaRS) families that define the genetic code. The diversification of aaRSs has continued in organisms from all domains of life, yielding aaRSs with unique characteristics as well as aaRS-like proteins with innovative functions outside translation. Recent bioinformatic analyses have revealed the extensive occurrence and phylogenetic diversity of aaRS gene duplication involving every synthetase family. However, only a fraction of these duplicated genes has been characterized, leaving many with biological functions yet to be discovered. Here we discuss how genomic duplication is associated with the occurrence of novel aaRSs and aaRS-like proteins that provide adaptive advantages to their hosts. We illustrate the variety of activities that have evolved from the primordial aaRS catalytic sites. This precedent underscores the need to investigate currently unexplored aaRS genomic duplications as they may hold a key to the discovery of exciting biological processes, new drug targets, important bioactive molecules, and tools for synthetic biology applications.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- *Correspondence: Oscar Vargas-Rodriguez,
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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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4
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Despotović D, Brandis A, Savidor A, Levin Y, Fumagalli L, Tawfik DS. Diadenosine tetraphosphate (Ap4A) - an E. coli alarmone or a damage metabolite? FEBS J 2017; 284:2194-2215. [PMID: 28516732 DOI: 10.1111/febs.14113] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 05/15/2017] [Indexed: 12/21/2022]
Abstract
Under stress, metabolism is changing: specific up- or down-regulation of proteins and metabolites occurs as well as side effects. Distinguishing specific stress-signaling metabolites (alarmones) from side products (damage metabolites) is not trivial. One example is diadenosine tetraphosphate (Ap4A) - a side product of aminoacyl-tRNA synthetases found in all domains of life. The earliest observations suggested that Ap4A serves as an alarmone for heat stress in Escherichia coli. However, despite 50 years of research, the signaling mechanisms associated with Ap4A remain unknown. We defined a set of criteria for distinguishing alarmones from damage metabolites to systematically classify Ap4A. In a nutshell, no indications for a signaling cascade that is triggered by Ap4A were found; rather, we found that Ap4A is efficiently removed in a constitutive, nonregulated manner. Several fold perturbations in Ap4A concentrations have no effect, yet accumulation at very high levels is toxic due to disturbance of zinc homeostasis, and also because Ap4A's structural overlap with ATP can result in spurious binding and inactivation of ATP-binding proteins. Overall, Ap4A met all criteria for a damage metabolite. While we do not exclude any role in signaling, our results indicate that the damage metabolite option should be considered as the null hypothesis when examining Ap4A and other metabolites whose levels change upon stress.
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Affiliation(s)
- Dragana Despotović
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Laura Fumagalli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Italy
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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Abstract
Understanding and exploiting molecular mechanisms in biology is central to chemical biology. Chemical biology studies of biological macromolecules are now in a perfect continuum with molecular level and nanomolecular level mechanistic studies involving whole organisms. The potential opportunity presented by such studies is the design and creation of genuine precision active pharmaceutical ingredients (APIs; including DNA, siRNA, smaller-molecule bioactives) that demonstrate exceptional levels of disease target specificity and selectivity. This article covers the best of my personal and collaborative academic research work using an organic chemistry and chemical biology approach towards understanding biological molecular recognition processes, work that appears to be leading to the generation of novel precision APIs with genuine potential for the treatments of major chronic diseases that afflict globally.
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Oka M, Takegawa K, Kimura Y. Lysyl-tRNA synthetase from Myxococcus xanthus catalyzes the formation of diadenosine penta- and hexaphosphates from adenosine tetraphosphate. Arch Biochem Biophys 2016; 604:152-8. [PMID: 27392456 DOI: 10.1016/j.abb.2016.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/23/2016] [Accepted: 07/02/2016] [Indexed: 11/18/2022]
Abstract
Myxococcus xanthus lysyl-tRNA synthetase (LysS) produces diadenosine tetraphosphate (Ap4A) from ATP in the presence of Mn(2+); in the present study, it also generated Ap4 from ATP and triphosphate. When ATP and Ap4 were incubated with LysS and pyrophosphatase, first Ap4A, Ap5A, and ADP, and then Ap5, Ap6A, and Ap3A were generated. The results suggest that in the first step, LysS can form lysyl-AMP and lysyl-ADP intermediates from Ap4 and release triphosphate and diphosphate, respectively, whereas in the second step, it can produce Ap5 from lysyl-ADP with triphosphate, and Ap6A from lysyl-ADP with Ap4. In addition, in the presence of Ap4 and pyrophosphatase, but absence of ATP, LysS also generates diadenosine oligophosphates (ApnAs: n = 3-6). These results indicate that LysS has the ability to catalyze the formation of various ApnAs from Ap4 in the presence of pyrophosphatase. Furthermore, the formation of Ap4A by LysS was inhibited by tRNA(Lys) in the presence of 1 mM ATP. To the best of our knowledge, this is the first report of Ap5A and Ap6A synthesis by lysyl-tRNA synthetase.
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Affiliation(s)
- Manami Oka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Kyusyu University, Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan.
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Marriott AS, Vasieva O, Fang Y, Copeland NA, McLennan AG, Jones NJ. NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes. PLoS One 2016; 11:e0154674. [PMID: 27144453 PMCID: PMC4856261 DOI: 10.1371/journal.pone.0154674] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/18/2016] [Indexed: 01/04/2023] Open
Abstract
Regulation of gene expression is one of several roles proposed for the stress-induced nucleotide diadenosine tetraphosphate (Ap4A). We have examined this directly by a comparative RNA-Seq analysis of KBM-7 chronic myelogenous leukemia cells and KBM-7 cells in which the NUDT2 Ap4A hydrolase gene had been disrupted (NuKO cells), causing a 175-fold increase in intracellular Ap4A. 6,288 differentially expressed genes were identified with P < 0.05. Of these, 980 were up-regulated and 705 down-regulated in NuKO cells with a fold-change ≥ 2. Ingenuity® Pathway Analysis (IPA®) was used to assign these genes to known canonical pathways and functional networks. Pathways associated with interferon responses, pattern recognition receptors and inflammation scored highly in the down-regulated set of genes while functions associated with MHC class II antigens were prominent among the up-regulated genes, which otherwise showed little organization into major functional gene sets. Tryptophan catabolism was also strongly down-regulated as were numerous genes known to be involved in tumor promotion in other systems, with roles in the epithelial-mesenchymal transition, proliferation, invasion and metastasis. Conversely, some pro-apoptotic genes were up-regulated. Major upstream factors predicted by IPA® for gene down-regulation included NFκB, STAT1/2, IRF3/4 and SP1 but no major factors controlling gene up-regulation were identified. Potential mechanisms for gene regulation mediated by Ap4A and/or NUDT2 disruption include binding of Ap4A to the HINT1 co-repressor, autocrine activation of purinoceptors by Ap4A, chromatin remodeling, effects of NUDT2 loss on transcript stability, and inhibition of ATP-dependent regulatory factors such as protein kinases by Ap4A. Existing evidence favors the last of these as the most probable mechanism. Regardless, our results suggest that the NUDT2 protein could be a novel cancer chemotherapeutic target, with its inhibition potentially exerting strong anti-tumor effects via multiple pathways involving metastasis, invasion, immunosuppression and apoptosis.
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MESH Headings
- Cell Line, Tumor
- Dinucleoside Phosphates/metabolism
- Down-Regulation
- Gene Expression Profiling
- Gene Knockout Techniques
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Phosphoric Monoester Hydrolases/deficiency
- Phosphoric Monoester Hydrolases/genetics
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Affiliation(s)
- Andrew S. Marriott
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Olga Vasieva
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Yongxiang Fang
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Nikki A. Copeland
- Division of Biomedical and Life Sciences, University of Lancaster, Lancaster, Lancashire, United Kingdom
| | - Alexander G. McLennan
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, United Kingdom
- * E-mail: (AGM); (NJJ)
| | - Nigel J. Jones
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, United Kingdom
- * E-mail: (AGM); (NJJ)
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Anashkin VA, Salminen A, Tuominen HK, Orlov VN, Lahti R, Baykov AA. Cystathionine β-Synthase (CBS) Domain-containing Pyrophosphatase as a Target for Diadenosine Polyphosphates in Bacteria. J Biol Chem 2015; 290:27594-603. [PMID: 26400082 DOI: 10.1074/jbc.m115.680272] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Indexed: 11/06/2022] Open
Abstract
Among numerous proteins containing pairs of regulatory cystathionine β-synthase (CBS) domains, family II pyrophosphatases (CBS-PPases) are unique in that they generally contain an additional DRTGG domain between the CBS domains. Adenine nucleotides bind to the CBS domains in CBS-PPases in a positively cooperative manner, resulting in enzyme inhibition (AMP or ADP) or activation (ATP). Here we show that linear P(1),P(n)-diadenosine 5'-polyphosphates (ApnAs, where n is the number of phosphate residues) bind with nanomolar affinity to DRTGG domain-containing CBS-PPases of Desulfitobacterium hafniense, Clostridium novyi, and Clostridium perfringens and increase their activity up to 30-, 5-, and 7-fold, respectively. Ap4A, Ap5A, and Ap6A bound noncooperatively and with similarly high affinities to CBS-PPases, whereas Ap3A bound in a positively cooperative manner and with lower affinity, like mononucleotides. All ApnAs abolished kinetic cooperativity (non-Michaelian behavior) of CBS-PPases. The enthalpy change and binding stoichiometry, as determined by isothermal calorimetry, were ~10 kcal/mol nucleotide and 1 mol/mol enzyme dimer for Ap4A and Ap5A but 5.5 kcal/mol and 2 mol/mol for Ap3A, AMP, ADP, and ATP, suggesting different binding modes for the two nucleotide groups. In contrast, Eggerthella lenta and Moorella thermoacetica CBS-PPases, which contain no DRTGG domain, were not affected by ApnAs and showed no enthalpy change, indicating the importance of the DTRGG domain for ApnA binding. These findings suggest that ApnAs can control CBS-PPase activity and hence affect pyrophosphate level and biosynthetic activity in bacteria.
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Affiliation(s)
- Viktor A Anashkin
- From the Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland and the Belozersky Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Anu Salminen
- From the Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland and
| | - Heidi K Tuominen
- From the Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland and
| | - Victor N Orlov
- the Belozersky Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Reijo Lahti
- From the Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland and
| | - Alexander A Baykov
- the Belozersky Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
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Enzymatic characterization of a class II lysyl-tRNA synthetase, LysS, from Myxococcus xanthus. Arch Biochem Biophys 2015; 579:33-9. [PMID: 26048731 DOI: 10.1016/j.abb.2015.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/21/2022]
Abstract
Lysyl-tRNA synthetases efficiently produce diadenosine tetraphosphate (Ap4A) from lysyl-AMP with ATP in the absence of tRNA. We characterized recombinant class II lysyl-tRNA synthetase (LysS) from Myxococcus xanthus and found that it is monomeric and requires Mn(2+) for the synthesis of Ap4A. Surprisingly, Zn(2+) inhibited enzyme activity in the presence of Mn(2+). When incubated with ATP, Mn(2+), lysine, and inorganic pyrophosphatase, LysS first produced Ap4A and ADP, then converted Ap4A to diadenosine triphosphate (Ap3A), and finally converted Ap3A to ADP, the end product of the reaction. Recombinant LysS retained Ap4A synthase activity without lysine addition. Additionally, when incubated with Ap4A (minus pyrophosphatase), LysS converted Ap4A mainly ATP and AMP, or ADP in the presence or absence of lysine, respectively. These results demonstrate that M. xanthus LysS has different enzymatic properties from class II lysyl-tRNA synthetases previously reported.
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10
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Azhar MA, Wright M, Kamal A, Nagy J, Miller AD. Biotin-c10-AppCH2ppA is an effective new chemical proteomics probe for diadenosine polyphosphate binding proteins. Bioorg Med Chem Lett 2014; 24:2928-33. [PMID: 24852122 DOI: 10.1016/j.bmcl.2014.04.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/14/2014] [Accepted: 04/21/2014] [Indexed: 02/04/2023]
Abstract
Here we report on the synthesis of a synthetic, stable biotin-c10-AppCH2ppA conjugate involving an unusual Cannizzaro reaction step. This conjugate is used to bind prospective Ap4A binding proteins from Escherichia coli bacterial cell lyzates. Following binding, identities of these proteins are then determined smoothly by a process of magnetic bio-panning and electrospray mass spectrometry. Protein hits appear to be a definitive set of stress protein related targets. While this hit list may not be exclusive, and may vary with the nature of sampling conditions and organism status, nevertheless hits do appear to correspond with bona fide Ap4A-binding proteins. Therefore these hits represent a sound basis on which to construct new hypotheses concerning the cellular importance of Ap4A to bacterial cells and the potential biological significance of Ap4A-protein binding interactions.
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Affiliation(s)
- M Ameruddin Azhar
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London SW7 2AZ,UK; Division of Organic Chemistry, Indian Institute of Chemical Technology, Hyderabad, India
| | - Michael Wright
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London SW7 2AZ,UK; Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Waterloo Campus, 150 Stamford Street, London SE1 9NH,UK
| | - Ahmed Kamal
- Division of Organic Chemistry, Indian Institute of Chemical Technology, Hyderabad, India
| | - Judith Nagy
- Institute of Biomedical Engineering, Armstrong Road, Imperial College London, London SW7 2AZ,UK
| | - Andrew D Miller
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London SW7 2AZ,UK; Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Waterloo Campus, 150 Stamford Street, London SE1 9NH,UK.
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11
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Wright M, Azhar MA, Kamal A, Miller AD. Syntheses of stable, synthetic diadenosine polyphosphate analogues using recombinant histidine-tagged lysyl tRNA synthetase (LysU). Bioorg Med Chem Lett 2014; 24:2346-52. [PMID: 24736113 DOI: 10.1016/j.bmcl.2014.03.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 11/18/2022]
Abstract
Recombinant Escherichia coli lysyl-tRNA synthase (LysU) has been previously utilised in the production of stabile, synthetic diadenosine polyphosphate (ApnA) analogues. Here we report on the extended use of a new recombinant histidine residue-tagged LysU as a tool for highly controlled phosphatephosphate bond formation between nucleotides, avoiding the need for complex protecting group chemistries. Resulting high yielding tandem LysU-based biosynthetic-synthetic/synthetic-biosynthetic strategies emerge for the preparation of varieties of ApnA analogues directly from inexpensive natural nucleotides and nucleosides. Analogues so formed make a useful small library with which to probe ApnA activities in vitro and in vivo leading to the discovery of new, potentially potent biopharmaceuticals active against chronic pain and other chronic, high-burden disease states.
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Affiliation(s)
- Michael Wright
- Imperial College Genetic Therapies Centre, Department of Chemistry, Imperial College London, Flowers Building, Armstrong Road, London SW7 2AZ, UK; Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Waterloo Campus, 150 Stamford Street, London SE1 9NH, UK
| | - M Ameruddin Azhar
- Imperial College Genetic Therapies Centre, Department of Chemistry, Imperial College London, Flowers Building, Armstrong Road, London SW7 2AZ, UK; Organic-I Division, Indian Institute of Chemical Technology, Habsigida, Hyderabad, India
| | - Ahmed Kamal
- Organic-I Division, Indian Institute of Chemical Technology, Habsigida, Hyderabad, India
| | - Andrew D Miller
- Imperial College Genetic Therapies Centre, Department of Chemistry, Imperial College London, Flowers Building, Armstrong Road, London SW7 2AZ, UK; Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Waterloo Campus, 150 Stamford Street, London SE1 9NH, UK.
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12
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Boonyalai N, Pullen JR, Abdul Wahab MF, Wright M, Miller AD. Escherichia coli LysU is a potential surrogate for human lysyl tRNA synthetase in interactions with the C-terminal domain of HIV-1 capsid protein. Org Biomol Chem 2013. [DOI: 10.1039/c2ob26499d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Chen X, Boonyalai N, Lau C, Thipayang S, Xu Y, Wright M, Miller AD. Multiple catalytic activities of Escherichia coli lysyl-tRNA synthetase (LysU) are dissected by site-directed mutagenesis. FEBS J 2012; 280:102-14. [PMID: 23121660 DOI: 10.1111/febs.12053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 10/24/2012] [Accepted: 10/29/2012] [Indexed: 11/28/2022]
Abstract
The heat-inducible lysyl-tRNA synthetase from Escherichia coli (LysU; EC6/1/1/6.html) converts ATP to diadenosine tri- and tetraphosphates (Ap(3)A/Ap(4)A) in the presence of L-lysine/Mg(2+)/Zn(2+). To understand LysU in more detail, 26 mutants were prepared: six of E264, four of R269 and sixteen mutants by alanine-scanning of the inner shell/motif 2 loop. In the presence of glycerol and absence of exogenously added Zn(2+)/L-lysine, we unexpectedly found that E264K catalysed the production of glycerol-3-phosphate, powered by ATP turnover to ADP. E264Q and E264N are also capable of this activity, but all three show little formation of Ap(4)A/Ap(3)A under normal conditions (additional Zn(2+)/L-lysine/Mg(2+)). By contrast, wild-type LysU has a weaker glycerol kinase-like capability in the absence of Zn(2+) and is dominated by Ap(4)A/Ap(3)A synthesis in its presence. Kinetic and isothermal titration calorimetry results suggest that E264 is a crucial residue for Zn(2+) promotion of Ap(4)A/Ap(3)A synthesis. This is consistent with the hypothesis that E264 provides an anchor point for a Zn(2+) ion complexed to the active site, with simultaneous coordination to the enzyme bound lysyl-adenylate intermediate and secondary substrate ATP/ADP. The glycerol kinase-like activity is uncovered on disruption of this specific coordination.
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Affiliation(s)
- Xiaolong Chen
- Zhejiang California International NanoSystems Institute, Zhejiang University, Hangzhou, China
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14
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Wright M, Miller AD. Quantification of diadenosine polyphosphates in blood plasma using a tandem boronate affinity-ion exchange chromatography system. Anal Biochem 2012; 432:103-5. [PMID: 23046945 DOI: 10.1016/j.ab.2012.09.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 09/27/2012] [Accepted: 09/28/2012] [Indexed: 10/27/2022]
Abstract
Endogenous diadenosine polyphosphates (Ap(n)As) have been associated with a variety of biological effects but quantifying their concentration in blood is difficult. We report on the development of a tandem affinity-ion exchange high-performance liquid chromatography (HPLC) system that employs boronate affinity upstream of ion exchange chromatography for automated rapid (45-min) resolution and extraction of Ap(n)As from human plasma. This system obviates previous requirements for multiple column separations and handling steps, so it is ideally set up for time- and cost-efficient screening of blood samples for Ap(n)A pharmacokinetic and biodistribution studies.
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Affiliation(s)
- Michael Wright
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, UK
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15
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Wang J, Fang P, Schimmel P, Guo M. Side chain independent recognition of aminoacyl adenylates by the Hint1 transcription suppressor. J Phys Chem B 2012; 116:6798-805. [PMID: 22329685 PMCID: PMC3375047 DOI: 10.1021/jp212457w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Human Hint1 suppresses specific gene transcription by
interacting with the transcription factor MITF in mast cells. Hint1
activity is connected to lysyl-tRNA synthetase (LysRS), a member of
the universal aminoacyl tRNA synthetase family that catalyzes specific
aminoacylation of their cognate tRNAs, through an aminoacyl adenylate
(aa-AMP) intermediate. During immune activation, LysRS produces a
side-product diadenosine tetraphosphate (Ap4A) from the
condensation of Lys-AMP with ATP. The pleiotropic signaling molecule
Ap4A then binds Hint1 to promote activation of MITF-target
gene transcription. Earlier work showed that Hint1 can also bind and
hydrolyze Lys-AMP, possibly to constrain Ap4A production.
Because Ap4A can result from condensation of other aa-AMP's
with ATP, the specificity of the Hint1 aa-AMP–hydrolysis activity
is of interest. Here we show that Hint1 has broad specificity for
adenylate hydrolysis, whose structural basis we revealed through high-resolution
structures of Hint1 in complex with three different aa-AMP analogues.
Hint1 recognizes only the common main chain of the aminoacyl moiety,
and has no contact with the aa side chain. The α-amino group
is anchored by a cation-pi interaction with Trp123 at the C-terminus
of Hint1. These results reveal the structural basis for the remarkable
adenylate surveillance activity of Hint1, to potentially control Ap4A levels in the cell.
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Affiliation(s)
- Jing Wang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
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16
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Guo W, Azhar MA, Xu Y, Wright M, Kamal A, Miller AD. Isolation and identification of diadenosine 5',5'''-P1,P4-tetraphosphate binding proteins using magnetic bio-panning. Bioorg Med Chem Lett 2011; 21:7175-9. [PMID: 22014552 DOI: 10.1016/j.bmcl.2011.09.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/16/2011] [Accepted: 09/19/2011] [Indexed: 11/19/2022]
Abstract
We report the development of a synthetic, biotin-conjugated diadenosine tetraphosphate (Ap(4)A)-'molecular hook' attached to magnetic beads enabling the isolation of Ap(4)A-binding proteins from bacterial cells or mammalian tissue lysates. Characterisation and identification of isolated binding proteins is performed sequentially by mass spectrometry. The observation of positive controls suggests that these newly observed proteins are putative Ap(4)A-binding partners, and we have expectations that others can be found with further technical improvements in our methods.
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Affiliation(s)
- Wei Guo
- Pharmacy School of Shanghai Jiao Tong University, Shanghai, China
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17
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Fraga H, Fontes R. Enzymatic synthesis of mono and dinucleoside polyphosphates. Biochim Biophys Acta Gen Subj 2011; 1810:1195-204. [PMID: 21978831 DOI: 10.1016/j.bbagen.2011.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 09/09/2011] [Accepted: 09/19/2011] [Indexed: 01/08/2023]
Abstract
BACKGROUND Mono and dinucleoside polyphosphates (p(n)Ns and Np(n)Ns) exist in living organisms and induce diverse biological effects through interaction with intracellular and cytoplasmic membrane proteins. The source of these compounds is associated with secondary activities of a diverse group of enzymes. SCOPE OF REVIEW Here we discuss the mechanisms that can promote their synthesis at a molecular level. Although all the enzymes described in this review are able to catalyse the in vitro synthesis of Np(n)Ns (and/or p(n)N), it is not clear which ones are responsible for their in vivo accumulation. MAJOR CONCLUSIONS Despite the large amount of knowledge already available, important questions remain to be answered and a more complete understanding of p(n)Ns and Np(n)Ns synthesis mechanisms is required. With the possible exception of (GTP:GTP guanylyltransferase of Artemia), all enzymes able to catalyse the synthesis of p(n)Ns and Np(n)Ns are unspecific and the factors that can promote their synthesis relative to the canonical enzyme activities are unclear. GENERAL SIGNIFICANCE The fact that p(n)Ns and Np(n)Ns syntheses are promiscuous activities of housekeeping enzymes does not reduce its physiological or pathological importance. Here we resume the current knowledge regarding their enzymatic synthesis and point the open questions on the field.
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Affiliation(s)
- Hugo Fraga
- Department of Biochemistry, Universitat Autonoma de Barcelona, Spain
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18
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Park SG, Choi EC, Kim S. Aminoacyl-tRNA synthetase-interacting multifunctional proteins (AIMPs): a triad for cellular homeostasis. IUBMB Life 2010; 62:296-302. [PMID: 20306515 DOI: 10.1002/iub.324] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are highly conserved for efficient and precise translation of genetic codes. In higher eukaryotic systems, several different ARSs including glutamyl-prolyl-, isoelucyl-, leucyl-, methionyl-, glutaminyl-, lysyl-, arginyl-, and aspartyl-tRNA synthetase form a macromolecular protein complex with three nonenzymatic cofactors (AIMP1/p43, AIMP2/p38, and AIMP3/p18). Although the structure and functional implications for this complex formation are not completely understood, rapidly accumulating evidences suggest that this complex would work as a molecular hub linked to the multiple signaling pathways that involve the components of enzymes and cofactors. In this article, the roles of three nonenzymatic components of the multi-tRNA synthetase complex in the assembly of the components and in cell regulation are addressed.
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Affiliation(s)
- Sang Gyu Park
- Department of Biomedical Science, CHA University, Yeoksam-dong, Kangnam-gu, Seoul, Korea
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19
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Guo RT, Chong YE, Guo M, Yang XL. Crystal structures and biochemical analyses suggest a unique mechanism and role for human glycyl-tRNA synthetase in Ap4A homeostasis. J Biol Chem 2009; 284:28968-76. [PMID: 19710017 PMCID: PMC2781443 DOI: 10.1074/jbc.m109.030692] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aminoacyl-tRNA synthetases catalyze the attachment of amino acids to their cognate tRNAs for protein synthesis. However, the aminoacylation reaction can be diverted to produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways. The only known mechanism for Ap4A production by a tRNA synthetase is through the aminoacylation reaction intermediate aminoacyl-AMP, thus making Ap4A synthesis amino acid-dependent. Here, we demonstrate a new mechanism for Ap4A synthesis. Crystal structures and biochemical analyses show that human glycyl-tRNA synthetase (GlyRS) produces Ap4A by direct condensation of two ATPs, independent of glycine concentration. Interestingly, whereas the first ATP-binding pocket is conserved for all class II tRNA synthetases, the second ATP pocket is formed by an insertion domain that is unique to GlyRS, suggesting that GlyRS is the only tRNA synthetase catalyzing direct Ap4A synthesis. A special role for GlyRS in Ap4A homeostasis is proposed.
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Affiliation(s)
- Rey-Ting Guo
- From the Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Yeeting E. Chong
- From the Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Min Guo
- From the Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Xiang-Lei Yang
- From the Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, To whom correspondence should be addressed: Scripps Research Inst., BCC110, North Torrey Pines Rd., La Jolla, CA 92037. Tel.: 858-784-8976; Fax: 858-784-7250; E-mail:
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Kron M, Leykam J, Kopaczewski J, Matus I. Identification of diadenosine triphosphate in Brugia malayi by reverse phase high performance liquid chromatography and MALDI mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 856:234-8. [PMID: 17631429 PMCID: PMC2044565 DOI: 10.1016/j.jchromb.2007.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 05/31/2007] [Accepted: 06/10/2007] [Indexed: 11/21/2022]
Abstract
The presence of diadenosine oligophosphates (ApnA) in eukaryotic pathogens has been difficult technically to assess and thus is often overlooked. ApnA are a family of intercellular and intracellular signaling molecules and their biological activities differ relative to the number of phosphate moieties. The application of mass spectrometry to differentiate nucleotide phosphates has been limited by the high salt content in tissue extracts, enzymatic reactions or high performance liquid chromatography (HPLC) buffers, as well as the potential for sample loss when processing and desalting small biological samples. To address this problem a simple reverse phase HPLC (RP-HPLC) method using volatile organic buffers at low pH was developed to create elution profiles of adenosine and diadenosine phosphates. To test this method on a eukaryotic pathogen, small intravascular human filarial parasites (Brugia malayi) were extracted in phosphate buffered saline and a nucleotide phosphate profile was visualized by RP-HPLC. A major peak eluting at 10.4 min was analyzed directly by mass spectrometry and this confirmed the presence of significant quantities of diadenosine triphosphate, Ap3A. Application of this simplified RP-HPLC method will facilitate research on the normal and pathophysiological effects of ApnA particularly in situations when analysis of small biological samples is required.
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Affiliation(s)
- Michael Kron
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, United States.
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