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Williams BT, Cowles K, Bermejo Martínez A, Curson ARJ, Zheng Y, Liu J, Newton-Payne S, Hind AJ, Li CY, Rivera PPL, Carrión O, Liu J, Spurgin LG, Brearley CA, Mackenzie BW, Pinchbeck BJ, Peng M, Pratscher J, Zhang XH, Zhang YZ, Murrell JC, Todd JD. Bacteria are important dimethylsulfoniopropionate producers in coastal sediments. Nat Microbiol 2019; 4:1815-1825. [PMID: 31427729 DOI: 10.1038/s41564-019-0527-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) and its catabolite dimethyl sulfide (DMS) are key marine nutrients1,2 that have roles in global sulfur cycling2, atmospheric chemistry3, signalling4,5 and, potentially, climate regulation6,7. The production of DMSP was previously thought to be an oxic and photic process that is mainly confined to the surface oceans. However, here we show that DMSP concentrations and/or rates of DMSP and DMS synthesis are higher in surface sediment from, for example, saltmarsh ponds, estuaries and the deep ocean than in the overlying seawater. A quarter of bacterial strains isolated from saltmarsh sediment produced DMSP (up to 73 mM), and we identified several previously unknown producers of DMSP. Most DMSP-producing isolates contained dsyB8, but some alphaproteobacteria, gammaproteobacteria and actinobacteria used a methionine methylation pathway independent of DsyB that was previously only associated with higher plants. These bacteria contained a methionine methyltransferase gene (mmtN)-a marker for bacterial synthesis of DMSP through this pathway. DMSP-producing bacteria and their dsyB and/or mmtN transcripts were present in all of the tested seawater samples and Tara Oceans bacterioplankton datasets, but were much more abundant in marine surface sediment. Approximately 1 × 108 bacteria g-1 of surface marine sediment are predicted to produce DMSP, and their contribution to this process should be included in future models of global DMSP production. We propose that coastal and marine sediments, which cover a large part of the Earth's surface, are environments with high levels of DMSP and DMS productivity, and that bacteria are important producers of DMSP and DMS within these environments.
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Affiliation(s)
- Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kasha Cowles
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ana Bermejo Martínez
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yanfen Zheng
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jingli Liu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Simone Newton-Payne
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew J Hind
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Chun-Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peter Paolo L Rivera
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ornella Carrión
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ji Liu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Benjamin J Pinchbeck
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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Whitfield H, Gilmartin M, Baker K, Riley AM, Godage HY, Potter BVL, Hemmings AM, Brearley CA. A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase. J Med Chem 2018; 61:8838-8846. [PMID: 30160967 DOI: 10.1021/acs.jmedchem.8b01022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inositol pentakisphosphate 2-kinase catalyzes the phosphorylation of the axial 2-OH of myo-inositol 1,3,4,5,6-pentakisphosphate for de novo synthesis of myo-inositol hexakisphosphate. Disruption of inositol pentakisphosphate 2-kinase profoundly influences cellular processes, from nuclear mRNA export and phosphate homeostasis in yeast and plants to establishment of left-right asymmetry in zebrafish. We elaborate an active site fluorescent probe that allows high throughput screening of Arabidopsis inositol pentakisphosphate 2-kinase. We show that the probe has a binding constant comparable to the Km values of inositol phosphate substrates of this enzyme and can be used to prospect for novel substrates and inhibitors of inositol phosphate kinases. We identify several micromolar Ki inhibitors and validate this approach by solving the crystal structure of protein in complex with purpurogallin. We additionally solve structures of protein in complexes with epimeric higher inositol phosphates. This probe may find utility in characterization of a wide family of inositol phosphate kinases.
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Affiliation(s)
- Hayley Whitfield
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
| | - Megan Gilmartin
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
| | - Kendall Baker
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
| | - Andrew M Riley
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , U.K
| | - H Y Godage
- Medicinal Chemistry, Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , U.K
| | - Barry V L Potter
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , U.K.,Medicinal Chemistry, Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , U.K
| | - Andrew M Hemmings
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
| | - Charles A Brearley
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K
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3
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Bosch D, Saiardi A. Arginine transcriptional response does not require inositol phosphate synthesis. J Biol Chem 2012; 287:38347-55. [PMID: 22992733 PMCID: PMC3488103 DOI: 10.1074/jbc.m112.384255] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 09/17/2012] [Indexed: 12/25/2022] Open
Abstract
Inositol phosphates are key signaling molecules affecting a large variety of cellular processes. Inositol-polyphosphate multikinase (IPMK) is a central component of the inositol phosphate biosynthetic routes, playing essential roles during development. IPMK phosphorylates inositol 1,4,5-trisphosphate to inositol tetrakisphosphate and subsequently to inositol pentakisphosphate and has also been described to function as a lipid kinase. Recently, a catalytically inactive mammalian IPMK was reported to be involved in nutrient signaling by way of mammalian target of rapamycin and AMP-activated protein kinase. In yeast, the IPMK homologue, Arg82, is the sole inositol-trisphosphate kinase. Arg82 has been extensively studied as part of the transcriptional complex regulating nitrogen sensing, in particular arginine metabolism. Whether this role requires Arg82 catalytic activity has long been a matter of contention. In this study, we developed a novel method for the real time study of promoter strength in vivo and used it to demonstrate that catalytically inactive Arg82 fully restored the arginine-dependent transcriptional response. We also showed that expression in yeast of catalytically active, but structurally very different, mammalian or plant IPMK homologue failed to restore arginine regulation. Our work indicates that inositol phosphates do not regulate arginine-dependent gene expression.
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Affiliation(s)
- Daniel Bosch
- From the Cell Biology Unit, Medical Research Council Laboratory for Molecular Cell Biology, and Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Adolfo Saiardi
- From the Cell Biology Unit, Medical Research Council Laboratory for Molecular Cell Biology, and Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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Cooper SJ, Finney GL, Brown SL, Nelson SK, Hesselberth J, MacCoss MJ, Fields S. High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. Genome Res 2010; 20:1288-96. [PMID: 20610602 DOI: 10.1101/gr.105825.110] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The measurement of small molecule metabolites on a large scale offers the opportunity for a more complete understanding of cellular metabolism. We developed a high-throughput method to quantify primary amine-containing metabolites in the yeast Saccharomyces cerevisiae by the use of capillary electrophoresis in combination with fluorescent derivatization of cell extracts. We measured amino acid levels in the yeast deletion collection, a set of approximately 5000 strains each lacking a single gene, and developed a computational pipeline for data analysis. Amino acid peak assignments were validated by mass spectrometry, and the overall approach was validated by the result that expected pathway intermediates accumulate in mutants of the arginine biosynthetic pathway. Global analysis of the deletion collection was carried out using clustering methods. We grouped strains based on their metabolite profiles, revealing clusters of mutants enriched for genes encoding mitochondrial proteins, urea cycle enzymes, and vacuolar ATPase functions. One of the most striking profiles, common among several strains lacking ribosomal protein genes, accumulated lysine and a lysine-related metabolite. Mutations in the homologous ribosomal protein genes in the human result in Diamond-Blackfan anemia, demonstrating that metabolite data may have potential value in understanding disease pathology. This approach establishes metabolite profiling as capable of characterizing genes in a large collection of genetic variants.
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Affiliation(s)
- Sara J Cooper
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition. Proc Natl Acad Sci U S A 2010; 107:9608-13. [PMID: 20453199 DOI: 10.1073/pnas.0912979107] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Inositol phosphates (InsPs) are signaling molecules with multiple roles in cells. In particular (InsP(6)) is involved in mRNA export and editing or chromatin remodeling among other events. InsP(6) accumulates as mixed salts (phytate) in storage tissues of plants and plays a key role in their physiology. Human diets that are exclusively grain-based provide an excess of InsP(6) that, through chelation of metal ions, may have a detrimental effect on human health. Ins(1,3,4,5,6)P(5) 2-kinase (InsP(5) 2-kinase or Ipk1) catalyses the synthesis of InsP(6) from InsP(5) and ATP, and is the only enzyme that transfers a phosphate group to the axial 2-OH of the myo-inositide. We present the first structure for an InsP(5) 2-kinase in complex with both substrates and products. This enzyme presents a singular structural region for inositide binding that encompasses almost half of the protein. The key residues in substrate binding are identified, with Asp368 being responsible for recognition of the axial 2-OH. This study sheds light on the unique molecular mechanism for the synthesis of the precursor of inositol pyrophosphates.
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Zhu JQ, Zhang JT, Tang RJ, Lv QD, Wang QQ, Yang L, Zhang HX. Molecular characterization of ThIPK2, an inositol polyphosphate kinase gene homolog from Thellungiella halophila, and its heterologous expression to improve abiotic stress tolerance in Brassica napus. PHYSIOLOGIA PLANTARUM 2009; 136:407-425. [PMID: 19470090 DOI: 10.1111/j.1399-3054.2009.01235.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Inositol polyphosphate kinases play important roles in diverse cellular processes. In this study, the function of an inositol polyphosphate kinase gene homolog named ThIPK2 from a dicotyledonous halophyte Thellungiella halophila was investigated. The deduced translation product (ThIPK2) shares 85% identity with the Arabidopsis inositol polyphosphate kinase AtIPK2beta. Transient expression of ThIPK2-YFP fusion protein in tobacco (Nicotiana tabacum) protoplasts indicates that the protein is localized to the nucleus and plasma membrane, with a minor localization to the cytosol. Heterologous expression of ThIPK2 in ipk2Delta (also known as arg82Delta), a yeast mutant strain that lacks inositol polyphosphate multikinase (Ipk2) activity, rescued the mutant's salt-, osmotic- and temperature-sensitive growth defects. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed ubiquitous expression of ThIPK2 in various tissues, including roots, rosette leaves, cauline leaves, stem, flowers and siliques, and shoot ThIPK2 transcript was strongly induced by NaCl or mannitol in T. halophila as exhibited by real-time PCR analysis. Transgenic expression of ThIPK2 in Brassica napus led to significantly improved salt-, dehydration- and oxidative stress resistance. Furthermore, the transcripts of various stress responsive marker genes increased in ThIPK2 transgenic plants under salt stress condition. These results suggest that ThIPK2 is involved in plant stress responses, and for the first time demonstrate that ThIPK2 could be a useful candidate gene for improving drought and salt tolerance in important crop plants by genetic transformation.
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Affiliation(s)
- Jin-Qi Zhu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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