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Bettendorff L. Update on Thiamine Triphosphorylated Derivatives and Metabolizing Enzymatic Complexes. Biomolecules 2021; 11:biom11111645. [PMID: 34827643 PMCID: PMC8615392 DOI: 10.3390/biom11111645] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/12/2022] Open
Abstract
While the cellular functions of the coenzyme thiamine (vitamin B1) diphosphate (ThDP) are well characterized, the triphosphorylated thiamine derivatives, thiamine triphosphate (ThTP) and adenosine thiamine triphosphate (AThTP), still represent an intriguing mystery. They are present, generally in small amounts, in nearly all organisms, bacteria, fungi, plants, and animals. The synthesis of ThTP seems to require ATP synthase by a mechanism similar to ATP synthesis. In E. coli, ThTP is synthesized during amino acid starvation, while in plants, its synthesis is dependent on photosynthetic processes. In E. coli, ThTP synthesis probably requires oxidation of pyruvate and may play a role at the interface between energy and amino acid metabolism. In animal cells, no mechanism of regulation is known. Cytosolic ThTP levels are controlled by a highly specific cytosolic thiamine triphosphatase (ThTPase), coded by thtpa, and belonging to the ubiquitous family of the triphosphate tunnel metalloenzymes (TTMs). While members of this protein family are found in nearly all living organisms, where they bind organic and inorganic triphosphates, ThTPase activity seems to be restricted to animals. In mammals, THTPA is ubiquitously expressed with probable post-transcriptional regulation. Much less is known about the recently discovered AThTP. In E. coli, AThTP is synthesized by a high molecular weight protein complex from ThDP and ATP or ADP in response to energy stress. A better understanding of these two thiamine derivatives will require the use of transgenic models.
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Affiliation(s)
- Lucien Bettendorff
- Laboratory of Neurophysiology, GIGA Neurosciences, University of Liège, 4000 Liège, Belgium
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2
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Vogt MS, Ngouoko Nguepbeu RR, Mohr MKF, Albers SV, Essen LO, Banerjee A. The archaeal triphosphate tunnel metalloenzyme SaTTM defines structural determinants for the diverse activities in the CYTH protein family. J Biol Chem 2021; 297:100820. [PMID: 34029589 PMCID: PMC8233210 DOI: 10.1016/j.jbc.2021.100820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022] Open
Abstract
CYTH proteins make up a large superfamily that is conserved in all three domains of life. These enzymes have a triphosphate tunnel metalloenzyme (TTM) fold, which typically results in phosphatase functions, e.g., RNA triphosphatase, inorganic polyphosphatase, or thiamine triphosphatase. Some CYTH orthologs cyclize nucleotide triphosphates to 3′,5′-cyclic nucleotides. So far, archaeal CYTH proteins have been annotated as adenylyl cyclases, although experimental evidence to support these annotations is lacking. To address this gap, we characterized a CYTH ortholog, SaTTM, from the crenarchaeote Sulfolobus acidocaldarius. Our in silico studies derived ten major subclasses within the CYTH family implying a close relationship between these archaeal CYTH enzymes and class IV adenylyl cyclases. However, initial biochemical characterization reveals inability of SaTTM to produce any cyclic nucleotides. Instead, our structural and functional analyses show a classical TTM behavior, i.e., triphosphatase activity, where pyrophosphate causes product inhibition. The Ca2+-inhibited Michaelis complex indicates a two-metal-ion reaction mechanism analogous to other TTMs. Cocrystal structures of SaTTM further reveal conformational dynamics in SaTTM that suggest feedback inhibition in TTMs due to tunnel closure in the product state. These structural insights combined with further sequence similarity network–based in silico analyses provide a firm molecular basis for distinguishing CYTH orthologs with phosphatase activities from class IV adenylyl cyclases.
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Affiliation(s)
- Marian S Vogt
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | | | - Michael K F Mohr
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany; Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany.
| | - Ankan Banerjee
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany; Department of Genetics, Philipps-Universität Marburg, Marburg, Germany.
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3
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Świeżawska B, Duszyn M, Kwiatkowski M, Jaworski K, Pawełek A, Szmidt‐Jaworska A. Brachypodium distachyon
triphosphate tunnel metalloenzyme 3 is both a triphosphatase and an adenylyl cyclase upregulated by mechanical wounding. FEBS Lett 2020; 594:1101-1111. [DOI: 10.1002/1873-3468.13701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Brygida Świeżawska
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Maria Duszyn
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Mateusz Kwiatkowski
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Krzysztof Jaworski
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Agnieszka Pawełek
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
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4
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Vušurović J, Breuker K. Relative Strength of Noncovalent Interactions and Covalent Backbone Bonds in Gaseous RNA-Peptide Complexes. Anal Chem 2019; 91:1659-1664. [PMID: 30614682 PMCID: PMC6335609 DOI: 10.1021/acs.analchem.8b05387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Interactions of ribonucleic acids (RNA) with basic ligands such as proteins or aminoglycosides play a key role in fundamental biological processes. Native top-down mass spectrometry (MS) has recently been extended to binding site mapping of RNA-ligand interactions by collisionally activated dissociation, without the need for laborious sample preparation procedures. The technique relies on the preservation of noncovalent interactions at energies that are sufficiently high to cause RNA backbone cleavage. In this study, we address the question of how many and what types of noncovalent interactions allow for binding site mapping by top-down MS. We show that proton transfer from protonated ligand to deprotonated RNA within salt bridges initiates loss of the ligand, but that proton transfer becomes energetically unfavorable in the presence of additional hydrogen bonds such that the noncovalent interactions remain stronger than the covalent RNA backbone bonds.
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Affiliation(s)
- Jovana Vušurović
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) , Universität Innsbruck , Innrain 80-82 , 6020 Innsbruck , Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) , Universität Innsbruck , Innrain 80-82 , 6020 Innsbruck , Austria
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5
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Inorganic polyphosphate hydrolysis catalyzed by skeletal muscular actomyosin complexes is uncoupled with motility. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1224-1231. [DOI: 10.1016/j.bbapap.2018.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/10/2018] [Accepted: 09/29/2018] [Indexed: 11/22/2022]
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6
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Ung H, Karia P, Ebine K, Ueda T, Yoshioka K, Moeder W. Triphosphate Tunnel Metalloenzyme Function in Senescence Highlights a Biological Diversification of This Protein Superfamily. PLANT PHYSIOLOGY 2017; 175:473-485. [PMID: 28733390 PMCID: PMC5580764 DOI: 10.1104/pp.17.00700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/15/2017] [Indexed: 05/06/2023]
Abstract
The triphosphate tunnel metalloenzyme (TTM) superfamily comprises a group of enzymes that hydrolyze organophosphate substrates. They exist in all domains of life, yet the biological role of most family members is unclear. Arabidopsis (Arabidopsis thaliana) encodes three TTM genes. We have previously reported that AtTTM2 displays pyrophosphatase activity and is involved in pathogen resistance. Here, we report the biochemical activity and biological function of AtTTM1 and diversification of the biological roles between AtTTM1 and 2 Biochemical analyses revealed that AtTTM1 displays pyrophosphatase activity similar to AtTTM2, making them the only TTMs characterized so far to act on a diphosphate substrate. However, knockout mutant analysis showed that AtTTM1 is not involved in pathogen resistance but rather in leaf senescence. AtTTM1 is transcriptionally up-regulated during leaf senescence, and knockout mutants of AtTTM1 exhibit delayed dark-induced and natural senescence. The double mutant of AtTTM1 and AtTTM2 did not show synergistic effects, further indicating the diversification of their biological function. However, promoter swap analyses revealed that they functionally can complement each other, and confocal microscopy revealed that both proteins are tail-anchored proteins that localize to the mitochondrial outer membrane. Additionally, transient overexpression of either gene in Nicotiana benthamiana induced senescence-like cell death upon dark treatment. Taken together, we show that two TTMs display the same biochemical properties but distinct biological functions that are governed by their transcriptional regulation. Moreover, this work reveals a possible connection of immunity-related programmed cell death and senescence through novel mitochondrial tail-anchored proteins.
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Affiliation(s)
- Huoi Ung
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Purva Karia
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Kazuo Ebine
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Keiko Yoshioka
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Wolfgang Moeder
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
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7
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Zhang Y, Agrebi R, Bellows LE, Collet JF, Kaever V, Gründling A. Evolutionary Adaptation of the Essential tRNA Methyltransferase TrmD to the Signaling Molecule 3',5'-cAMP in Bacteria. J Biol Chem 2017; 292:313-327. [PMID: 27881678 PMCID: PMC5217690 DOI: 10.1074/jbc.m116.758896] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/21/2016] [Indexed: 11/06/2022] Open
Abstract
The nucleotide signaling molecule 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) plays important physiological roles, ranging from carbon catabolite repression in bacteria to mediating the action of hormones in higher eukaryotes, including human. However, it remains unclear whether 3',5'-cAMP is universally present in the Firmicutes group of bacteria. We hypothesized that searching for proteins that bind 3',5'-cAMP might provide new insight into this question. Accordingly, we performed a genome-wide screen and identified the essential Staphylococcus aureus tRNA m1G37 methyltransferase enzyme TrmD, which is conserved in all three domains of life as a tight 3',5'-cAMP-binding protein. TrmD enzymes are known to use S-adenosyl-l-methionine (AdoMet) as substrate; we have shown that 3',5'-cAMP binds competitively with AdoMet to the S. aureus TrmD protein, indicating an overlapping binding site. However, the physiological relevance of this discovery remained unclear, as we were unable to identify a functional adenylate cyclase in S. aureus and only detected 2',3'-cAMP but not 3',5'-cAMP in cellular extracts. Interestingly, TrmD proteins from Escherichia coli and Mycobacterium tuberculosis, organisms known to synthesize 3',5'-cAMP, did not bind this signaling nucleotide. Comparative bioinformatics, mutagenesis, and biochemical analyses revealed that the highly conserved Tyr-86 residue in E. coli TrmD is essential to discriminate between 3',5'-cAMP and the native substrate AdoMet. Combined with a phylogenetic analysis, these results suggest that amino acids in the substrate binding pocket of TrmD underwent an adaptive evolution to accommodate the emergence of adenylate cyclases and thus the signaling molecule 3',5'-cAMP. Altogether this further indicates that S. aureus does not produce 3',5'-cAMP, which would otherwise competitively inhibit an essential enzyme.
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Affiliation(s)
- Yong Zhang
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rym Agrebi
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium, and
| | - Lauren E Bellows
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium, and
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Angelika Gründling
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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8
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 458] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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9
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Martinez J, Truffault V, Hothorn M. Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. J Biol Chem 2015. [PMID: 26221030 PMCID: PMC4641920 DOI: 10.1074/jbc.m115.674473] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Triphosphate tunnel metalloenzymes (TTMs) are present in all kingdoms of life and catalyze diverse enzymatic reactions such as mRNA capping, the cyclization of adenosine triphosphate, the hydrolysis of thiamine triphosphate, and the synthesis and breakdown of inorganic polyphosphates. TTMs have an unusual tunnel domain fold that harbors substrate- and metal co-factor binding sites. It is presently poorly understood how TTMs specifically sense different triphosphate-containing substrates and how catalysis occurs in the tunnel center. Here we describe substrate-bound structures of inorganic polyphosphatases from Arabidopsis and Escherichia coli, which reveal an unorthodox yet conserved mode of triphosphate and metal co-factor binding. We identify two metal binding sites in these enzymes, with one co-factor involved in substrate coordination and the other in catalysis. Structural comparisons with a substrate- and product-bound mammalian thiamine triphosphatase and with previously reported structures of mRNA capping enzymes, adenylate cyclases, and polyphosphate polymerases suggest that directionality of substrate binding defines TTM catalytic activity. Our work provides insight into the evolution and functional diversification of an ancient enzyme family.
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Affiliation(s)
- Jacobo Martinez
- From the Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and
| | - Vincent Truffault
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Michael Hothorn
- From the Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and
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10
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Ung H, Moeder W, Yoshioka K. Arabidopsis triphosphate tunnel metalloenzyme2 is a negative regulator of the salicylic acid-mediated feedback amplification loop for defense responses. PLANT PHYSIOLOGY 2014; 166:1009-21. [PMID: 25185123 PMCID: PMC4213072 DOI: 10.1104/pp.114.248757] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The triphosphate tunnel metalloenzyme (TTM) superfamily represents a group of enzymes that is characterized by their ability to hydrolyze a range of tripolyphosphate substrates. Arabidopsis (Arabidopsis thaliana) encodes three TTM genes, AtTTM1, AtTTM2, and AtTTM3. Although AtTTM3 has previously been reported to have tripolyphosphatase activity, recombinantly expressed AtTTM2 unexpectedly exhibited pyrophosphatase activity. AtTTM2 knockout mutant plants exhibit an enhanced hypersensitive response, elevated pathogen resistance against both virulent and avirulent pathogens, and elevated accumulation of salicylic acid (SA) upon infection. In addition, stronger systemic acquired resistance compared with wild-type plants was observed. These enhanced defense responses are dependent on SA, PHYTOALEXIN-DEFICIENT4, and NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1. Despite their enhanced pathogen resistance, ttm2 plants did not display constitutively active defense responses, suggesting that AtTTM2 is not a conventional negative regulator but a negative regulator of the amplification of defense responses. The transcriptional suppression of AtTTM2 by pathogen infection or treatment with SA or the systemic acquired resistance activator benzothiadiazole further supports this notion. Such transcriptional regulation is conserved among TTM2 orthologs in the crop plants soybean (Glycine max) and canola (Brassica napus), suggesting that TTM2 is involved in immunity in a wide variety of plant species. This indicates the possible usage of TTM2 knockout mutants for agricultural applications to generate pathogen-resistant crop plants.
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Affiliation(s)
- Huoi Ung
- Department of Cell and Systems Biology (H.U., W.M., K.Y.) andCenter for the Analysis of Genome Evolution and Function (K.Y.), University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Wolfgang Moeder
- Department of Cell and Systems Biology (H.U., W.M., K.Y.) andCenter for the Analysis of Genome Evolution and Function (K.Y.), University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Keiko Yoshioka
- Department of Cell and Systems Biology (H.U., W.M., K.Y.) andCenter for the Analysis of Genome Evolution and Function (K.Y.), University of Toronto, Toronto, Ontario, Canada M5S 3B2
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11
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Albi T, Serrano A. Two exopolyphosphatases with distinct molecular architectures and substrate specificities from the thermophilic green-sulfur bacterium Chlorobium tepidum TLS. Microbiology (Reading) 2014; 160:2067-2078. [DOI: 10.1099/mic.0.080952-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The genome of the thermophilic green-sulfur bacterium Chlorobium tepidum TLS possesses two genes encoding putative exopolyphosphatases (PPX; EC 3.6.1.11), namely CT0099 (ppx1, 993 bp) and CT1713 (ppx2, 1557 bp). The predicted polypeptides of 330 and 518 aa residues are Ppx-GppA phosphatases of different domain architectures – the largest one has an extra C-terminal HD domain – which may represent ancient paralogues. Both ppx genes were cloned and overexpressed in Escherichia coli BL21(DE3). While CtPPX1 was validated as a monomeric enzyme, CtPPX2 was found to be a homodimer. Both PPX homologues were functional, K+-stimulated phosphohydrolases, with an absolute requirement for divalent metal cations and a marked preference for Mg2+. Nevertheless, they exhibited remarkably different catalytic specificities with regard to substrate classes and chain lengths. Even though both enzymes were able to hydrolyse the medium-size polyphosphate (polyP) P13–18 (polyP mix with mean chain length of 13–18 phosphate residues), CtPPX1 clearly reached its highest catalytic efficiency with tripolyphosphate and showed substantial nucleoside triphosphatase (NTPase) activity, while CtPPX2 preferred long-chain polyPs (>300 Pi residues) and did not show any detectable NTPase activity. These catalytic features, taken together with the distinct domain architectures and molecular phylogenies, indicate that the two PPX homologues of Chl. tepidum belong to different Ppx-GppA phosphatase subfamilies that should play specific biochemical roles in nucleotide and polyP metabolisms. In addition, these results provide an example of the remarkable functional plasticity of the Ppx-GppA phosphatases, a family of proteins with relatively simple structures that are widely distributed in the microbial world.
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Affiliation(s)
- Tomás Albi
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, CSIC-Universidad de Sevilla, Spain
| | - Aurelio Serrano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, CSIC-Universidad de Sevilla, Spain
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12
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Moeder W, Garcia-Petit C, Ung H, Fucile G, Samuel MA, Christendat D, Yoshioka K. Crystal structure and biochemical analyses reveal that the Arabidopsis triphosphate tunnel metalloenzyme AtTTM3 is a tripolyphosphatase involved in root development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:615-26. [PMID: 24004165 DOI: 10.1111/tpj.12325] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 08/23/2013] [Accepted: 08/30/2013] [Indexed: 05/15/2023]
Abstract
The Arabidopsis protein AtTTM3 belongs to the CYTH superfamily named after its two founding members, the CyaB adenylate cyclase from Aeromonas hydrophila and the mammalian thiamine triphosphatase. In this study we report the three-dimensional structure of a plant CYTH domain protein, AtTTM3, determined at 1.9 Å resolution. The crystal structure revealed the characteristic tunnel architecture of CYTH proteins, which specialize in the binding of nucleotides and other organic phosphates and in phosphoryl transfer reactions. The β barrel is composed of eight antiparallel β strands with a cluster of conserved inwardly facing acidic and basic amino acid residues. Mutagenesis of these residues in the catalytic core led to an almost complete loss of enzymatic activity. We established that AtTTM3 is not an adenylate cyclase. Instead, the enzyme displayed weak NTP phosphatase as well as strong tripolyphosphatase activities similar to the triphosphate tunnel metalloenzyme proteins from Clostridium thermocellum (CthTTM) and Nitrosomonas europaea (NeuTTM). AtTTM3 is most highly expressed in the proximal meristematic zone of the plant root. Furthermore, an AtTTM3 T-DNA insertion knockout line displayed a delay in root growth as well as reduced length and number of lateral roots, suggesting a role for AtTTM3 in root development.
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Affiliation(s)
- Wolfgang Moeder
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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13
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Structural determinants of specificity and catalytic mechanism in mammalian 25-kDa thiamine triphosphatase. Biochim Biophys Acta Gen Subj 2013; 1830:4513-23. [DOI: 10.1016/j.bbagen.2013.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/24/2013] [Accepted: 05/09/2013] [Indexed: 11/24/2022]
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14
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Bettendorff L, Wins P. Thiamine triphosphatase and the CYTH superfamily of proteins. FEBS J 2013; 280:6443-55. [DOI: 10.1111/febs.12498] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/01/2013] [Indexed: 11/28/2022]
Affiliation(s)
| | - Pierre Wins
- GIGA-Neuroscience; University of Liège; Belgium
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15
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Kohn G, Delvaux D, Lakaye B, Servais AC, Scholer G, Fillet M, Elias B, Derochette JM, Crommen J, Wins P, Bettendorff L. High inorganic triphosphatase activities in bacteria and mammalian cells: identification of the enzymes involved. PLoS One 2012; 7:e43879. [PMID: 22984449 PMCID: PMC3440374 DOI: 10.1371/journal.pone.0043879] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 07/30/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND We recently characterized a specific inorganic triphosphatase (PPPase) from Nitrosomonas europaea. This enzyme belongs to the CYTH superfamily of proteins. Many bacterial members of this family are annotated as predicted adenylate cyclases, because one of the founding members is CyaB adenylate cyclase from A. hydrophila. The aim of the present study is to determine whether other members of the CYTH protein family also have a PPPase activity, if there are PPPase activities in animal tissues and what enzymes are responsible for these activities. METHODOLOGY/PRINCIPAL FINDINGS Recombinant enzymes were expressed and purified as GST- or His-tagged fusion proteins and the enzyme activities were determined by measuring the release of inorganic phosphate. We show that the hitherto uncharacterized E. coli CYTH protein ygiF is a specific PPPase, but it contributes only marginally to the total PPPase activity in this organism, where the main enzyme responsible for hydrolysis of inorganic triphosphate (PPP(i)) is inorganic pyrophosphatase. We further show that CyaB hydrolyzes PPP(i) but this activity is low compared to its adenylate cyclase activity. Finally we demonstrate a high PPPase activity in mammalian and quail tissue, particularly in the brain. We show that this activity is mainly due to Prune, an exopolyphosphatase overexpressed in metastatic tumors where it promotes cell motility. CONCLUSIONS AND GENERAL SIGNIFICANCE We show for the first time that PPPase activities are widespread in bacteria and animals. We identified the enzymes responsible for these activities but we were unable to detect significant amounts of PPP(i) in E. coli or brain extracts using ion chromatography and capillary electrophoresis. The role of these enzymes may be to hydrolyze PPP(i), which could be cytotoxic because of its high affinity for Ca(2+), thereby interfering with Ca(2+) signaling.
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Affiliation(s)
- Gregory Kohn
- GIGA-Neurosciences, University of Liège, Liège, Belgium
| | - David Delvaux
- GIGA-Neurosciences, University of Liège, Liège, Belgium
| | | | - Anne-Catherine Servais
- Laboratory of Analytical Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, CIRM, University of Liège, Liège, Belgium
| | - Georges Scholer
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marianne Fillet
- Laboratory of Analytical Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, CIRM, University of Liège, Liège, Belgium
| | - Benjamin Elias
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Jacques Crommen
- Laboratory of Analytical Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, CIRM, University of Liège, Liège, Belgium
| | - Pierre Wins
- GIGA-Neurosciences, University of Liège, Liège, Belgium
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