Publications by authors named "David P Dixon"

36 Publications

A Photoaffinity-Based Fragment-Screening Platform for Efficient Identification of Protein Ligands.

Angew Chem Int Ed Engl 2020 11 7;59(47):21096-21105. Epub 2020 Sep 7.

GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.

Advances in genomic analyses enable the identification of new proteins that are associated with disease. To validate these targets, tool molecules are required to demonstrate that a ligand can have a disease-modifying effect. Currently, as tools are reported for only a fraction of the proteome, platforms for ligand discovery are essential to leverage insights from genomic analyses. Fragment screening offers an efficient approach to explore chemical space. Presented here is a fragment-screening platform, termed PhABits (PhotoAffinity Bits), which utilizes a library of photoreactive fragments to covalently capture fragment-protein interactions. Hits can be profiled to determine potency and the site of crosslinking, and subsequently developed as reporters in a competitive displacement assay to identify novel hit matter. The PhABit platform is envisioned to be widely applicable to novel protein targets, identifying starting points in the development of therapeutics.
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http://dx.doi.org/10.1002/anie.202008361DOI Listing
November 2020

A Qualified Success: Discovery of a New Series of ATAD2 Bromodomain Inhibitors with a Novel Binding Mode Using High-Throughput Screening and Hit Qualification.

J Med Chem 2019 08 9;62(16):7506-7525. Epub 2019 Aug 9.

GlaxoSmithKline Tres Cantos , 28760 Tres Cantos , Madrid , Spain.

The bromodomain of ATAD2 has proved to be one of the least-tractable proteins within this target class. Here, we describe the discovery of a new class of inhibitors by high-throughput screening and show how the difficulties encountered in establishing a screening triage capable of finding progressible hits were overcome by data-driven optimization. Despite the prevalence of nonspecific hits and an exceptionally low progressible hit rate (0.001%), our optimized hit qualification strategy employing orthogonal biophysical methods enabled us to identify a single active series. The compounds have a novel ATAD2 binding mode with noncanonical features including the displacement of all conserved water molecules within the active site and a halogen-bonding interaction. In addition to reporting this new series and preliminary structure-activity relationship, we demonstrate the value of diversity screening to complement the knowledge-based approach used in our previous ATAD2 work. We also exemplify tactics that can increase the chance of success when seeking new chemical starting points for novel and less-tractable targets.
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http://dx.doi.org/10.1021/acs.jmedchem.9b00673DOI Listing
August 2019

Protein-Ligand Fishing for Biologically Active Natural Products Using Glutathione Transferases.

Front Plant Sci 2018 15;9:1659. Epub 2018 Nov 15.

Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.

Screening for natural products which bind to proteins has been used to identify ligands of the plant-specific glutathione transferase (GST) tau (U) and phi (F) classes, that are present in large gene families in crops and weeds, but have largely undefined functions. When expressed as recombinant proteins in these proteins have been found to tightly bind a diverse range of natural product ligands, with fatty acid-and porphyrinogen-derivatives associated with GSTUs and a range of heterocyclic compounds with GSTFs. With an interest in detecting the natural binding partners of these proteins , we have expressed the two best characterized GSTs from (), GSTF2 and GSTU19, as -tagged fusion proteins Following transient and stable expression in Nicotiana and Arabidopsis, respectively, the GSTs were recovered using Strep-Tactin affinity chromatography and the bound ligands desorbed and characterized by LC-MS. GSTF2 predominantly bound phenolic derivatives including -glutathionylated lignanamides and methylated variants of the flavonols kaempferol and quercetin. GSTU19 captured glutathionylated conjugates of oxylipins, indoles, and lignanamides. Whereas the flavonols and oxylipins appeared to be authentic ligands, the glutathione conjugates of the lignanamides and indoles were artifacts formed during extraction. When tested for their binding characteristics, the previously undescribed indole conjugates were found to be particularly potent inhibitors of GSTU19. Such ligand fishing has the potential to both give new insight into protein function as well as identifying novel classes of natural product inhibitors of enzymes of biotechnological interest such as GSTs.
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http://dx.doi.org/10.3389/fpls.2018.01659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6253249PMC
November 2018

Glutathione transferases catalyze recycling of auto-toxic cyanogenic glucosides in sorghum.

Plant J 2018 06 19;94(6):1109-1125. Epub 2018 May 19.

VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.

Cyanogenic glucosides are nitrogen-containing specialized metabolites that provide chemical defense against herbivores and pathogens via the release of toxic hydrogen cyanide. It has been suggested that cyanogenic glucosides are also a store of nitrogen that can be remobilized for general metabolism via a previously unknown pathway. Here we reveal a recycling pathway for the cyanogenic glucoside dhurrin in sorghum (Sorghum bicolor) that avoids hydrogen cyanide formation. As demonstrated in vitro, the pathway proceeds via spontaneous formation of a dhurrin-derived glutathione conjugate, which undergoes reductive cleavage by glutathione transferases of the plant-specific lambda class (GSTLs) to produce p-hydroxyphenyl acetonitrile. This is further metabolized to p-hydroxyphenylacetic acid and free ammonia by nitrilases, and then glucosylated to form p-glucosyloxyphenylacetic acid. Two of the four GSTLs in sorghum exhibited high stereospecific catalytic activity towards the glutathione conjugate, and form a subclade in a phylogenetic tree of GSTLs in higher plants. The expression of the corresponding two GSTLs co-localized with expression of the genes encoding the p-hydroxyphenyl acetonitrile-metabolizing nitrilases at the cellular level. The elucidation of this pathway places GSTs as key players in a remarkable scheme for metabolic plasticity allowing plants to reverse the resource flow between general and specialized metabolism in actively growing tissue.
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http://dx.doi.org/10.1111/tpj.13923DOI Listing
June 2018

Structure-Based Optimization of Naphthyridones into Potent ATAD2 Bromodomain Inhibitors.

J Med Chem 2015 Aug 31;58(15):6151-78. Epub 2015 Jul 31.

∥Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

ATAD2 is a bromodomain-containing protein whose overexpression is linked to poor outcomes in a number of different cancer types. To date, no potent and selective inhibitors of the bromodomain have been reported. This article describes the structure-based optimization of a series of naphthyridones from micromolar leads with no selectivity over the BET bromodomains to inhibitors with sub-100 nM ATAD2 potency and 100-fold BET selectivity.
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http://dx.doi.org/10.1021/acs.jmedchem.5b00773DOI Listing
August 2015

Fragment-Based Discovery of Low-Micromolar ATAD2 Bromodomain Inhibitors.

J Med Chem 2015 Jul 9;58(14):5649-73. Epub 2015 Jul 9.

∥Drug Metabolism and Pharmacokinetics (DMPK), GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom.

Overexpression of ATAD2 (ATPase family, AAA domain containing 2) has been linked to disease severity and progression in a wide range of cancers, and is implicated in the regulation of several drivers of cancer growth. Little is known of the dependence of these effects upon the ATAD2 bromodomain, which has been categorized as among the least tractable of its class. The absence of any potent, selective inhibitors limits clear understanding of the therapeutic potential of the bromodomain. Here, we describe the discovery of a hit from a fragment-based targeted array. Optimization of this produced the first known micromolar inhibitors of the ATAD2 bromodomain.
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http://dx.doi.org/10.1021/acs.jmedchem.5b00772DOI Listing
July 2015

Excessive folate synthesis limits lifespan in the C. elegans: E. coli aging model.

BMC Biol 2012 Jul 31;10:67. Epub 2012 Jul 31.

School of Biological and Biomedical Sciences, Durham University, UK.

Background: Gut microbes influence animal health and thus, are potential targets for interventions that slow aging. Live E. coli provides the nematode worm Caenorhabditis elegans with vital micronutrients, such as folates that cannot be synthesized by animals. However, the microbe also limits C. elegans lifespan. Understanding these interactions may shed light on how intestinal microbes influence mammalian aging.

Results: Serendipitously, we isolated an E. coli mutant that slows C. elegans aging. We identified the disrupted gene to be aroD, which is required to synthesize aromatic compounds in the microbe. Adding back aromatic compounds to the media revealed that the increased C. elegans lifespan was caused by decreased availability of para-aminobenzoic acid, a precursor to folate. Consistent with this result, inhibition of folate synthesis by sulfamethoxazole, a sulfonamide, led to a dose-dependent increase in C. elegans lifespan. As expected, these treatments caused a decrease in bacterial and worm folate levels, as measured by mass spectrometry of intact folates. The folate cycle is essential for cellular biosynthesis. However, bacterial proliferation and C. elegans growth and reproduction were unaffected under the conditions that increased lifespan.

Conclusions: In this animal:microbe system, folates are in excess of that required for biosynthesis. This study suggests that microbial folate synthesis is a pharmacologically accessible target to slow animal aging without detrimental effects.
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http://dx.doi.org/10.1186/1741-7007-10-67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583181PMC
July 2012

The maize benzoxazinone DIMBOA reacts with glutathione and other thiols to form spirocyclic adducts.

Phytochemistry 2012 May 17;77:171-8. Epub 2012 Feb 17.

Biophysical Sciences Institute, Durham University, Durham DH1 3LE, UK.

Maize, wheat and other grasses synthesise large quantities of benzoxazinones and their glucosides, which act as antifeedant and allelopathic agents. These activities are probably due to the electrophilic nature of the aglycones, however, the mechanism of their action is unclear. In biological systems, glutathione (GSH) is the major electrophile-reactive compound so the reaction of the major maize benzoxazinone DIMBOA with GSH was studied. GSH reacts with DIMBOA to form eight isomeric mono-conjugates and eight isomeric di-conjugates. Through NMR studies with the model thiol 2-mercaptoethanol, these were structurally elucidated as unusual spirocycles. Similar reactivity was observed with proteins, with cysteinyl thiols being modified by DIMBOA. The thioether bonds formed were stable and not easily reduced to the parent thiol. DIMBOA can therefore readily deplete GSH levels and irreversibly inactivate enzymes with active-site cysteine residues, with clear implications for potentially toxic effects when young grasses are ingested, whether by insect pests or humans.
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http://dx.doi.org/10.1016/j.phytochem.2012.01.019DOI Listing
May 2012

Roles for glutathione transferases in antioxidant recycling.

Plant Signal Behav 2011 Aug 1;6(8):1223-7. Epub 2011 Aug 1.

Biophysical Sciences Institute, Durham University, Durham, UK.

Uniquely among the plant glutathione transferases, two classes possess a catalytic cysteine capable of performing glutathione-dependent reductions. These are the dehydroascorbate reductases (DHARs) and the lambda-class glutathione transferases (GSTLs). Using immobilized GSTLs probed with crude plant extracts we have identified flavonols as high affinity ligands and subsequently demonstrated a novel glutathione-dependent role for these enzymes in recycling oxidized quercetin. By comparing the activities of DHARs and GSTLs we now propose a unified catalytic mechanism that suggests oxidized anthocyanidins and tocopherols may be alternative polyphenolic substrates of GSTLs.
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http://dx.doi.org/10.4161/psb.6.8.16253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260729PMC
August 2011

Xenobiotic responsiveness of Arabidopsis thaliana to a chemical series derived from a herbicide safener.

J Biol Chem 2011 Sep 21;286(37):32268-76. Epub 2011 Jul 21.

School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom.

Plants respond to synthetic chemicals by eliciting a xenobiotic response (XR) that enhances the expression of detoxifying enzymes such as glutathione transferases (GSTs). In agrochemistry, the ability of safeners to induce an XR is used to increase herbicide detoxification in cereal crops. Based on the responsiveness of the model plant Arabidopsis thaliana to the rice safener fenclorim (4,6-dichloro-2-phenylpyrimidine), a series of related derivatives was prepared and tested for the ability to induce GSTs in cell suspension cultures. The XR in Arabidopsis could be divided into rapid and slow types depending on subtle variations in the reactivity (electrophilicity) and chemical structure of the derivatives. In a comparative microarray study, Arabidopsis cultures were treated with closely related compounds that elicited rapid (fenclorim) and slow (4-chloro-6-methyl-2-phenylpyrimidine) XRs. Both chemicals induced major changes in gene expression, including a coordinated suppression in cell wall biosynthesis and an up-regulation in detoxification pathways, whereas only fenclorim selectively induced sulfur and phenolic metabolism. These transcriptome studies suggested several linkages between the XR and oxidative and oxylipin signaling. Confirming links with abiotic stress signaling, suppression of glutathione content enhanced GST induction by fenclorim, whereas fatty acid desaturase mutants, which were unable to synthesize oxylipins, showed an attenuated XR. Examining the significance of these studies to agrochemistry, only those fenclorim derivatives that elicited a rapid XR proved effective in increasing herbicide tolerance (safening) in rice.
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http://dx.doi.org/10.1074/jbc.M111.252726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173150PMC
September 2011

The Arabidopsis phi class glutathione transferase AtGSTF2: binding and regulation by biologically active heterocyclic ligands.

Biochem J 2011 Aug;438(1):63-70

Centre for Bioactive Chemistry, School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK.

The plant-specific phi class of glutathione transferases (GSTFs) are often highly stress-inducible and expressed in a tissue-specific manner, suggestive of them having important protective roles. To date, these functions remain largely unknown, although activities associated with the binding and transport of reactive metabolites have been proposed. Using a sensitive and selective binding screen, we have probed the Arabidopsis thaliana GSTFs for natural product ligands from bacteria and plants. Uniquely, when overexpressed in bacteria, family members GSTF2 and GSTF3 bound a series of heterocyclic compounds, including lumichrome, harmane, norharmane and indole-3-aldehyde. When screened against total metabolite extracts from A. thaliana, GSTF2 also selectively bound the indole-derived phytoalexin camalexin, as well as the flavonol quercetin-3-O-rhamnoside. In each case, isothermal titration calorimetry revealed high-affinity binding (typically Kd<1 μM), which was enhanced in the presence of glutathione and by the other heterocyclic ligands. With GSTF2, these secondary ligand associations resulted in an allosteric enhancement in glutathione-conjugating activity. Together with the known stress responsiveness of GSTF2 and its association with membrane vesicles, these results are suggestive of roles in regulating the binding and transport of defence-related compounds in planta.
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http://dx.doi.org/10.1042/BJ20101884DOI Listing
August 2011

Multiple roles for plant glutathione transferases in xenobiotic detoxification.

Drug Metab Rev 2011 May 22;43(2):266-80. Epub 2011 Mar 22.

Center for Bioactive Chemistry, Durham University, Durham, United Kingdom.

Discovered 40 years ago, plant glutathione transferases (GSTs) now have a well-established role in determining herbicide metabolism and selectivity in crops and weeds. Within the GST superfamily, the numerous and plant-specific phi (F) and tau (U) classes are largely responsible for catalyzing glutathione-dependent reactions with xenobiotics, notably conjugation leading to detoxification and, more rarely, bioactivating isomerizations. In total, the crystal structures of 10 plant GSTs have been solved and a highly conserved N-terminal glutathione binding domain and structurally diverse C-terminal hydrophobic domain identified, along with key coordinating residues. Unlike drug-detoxifying mammalian GSTs, plant enzymes utlilize a catalytic serine in place of a tyrosine residue. Both GSTFs and GSTUs undergo changes in structure during catalysis indicative of an induced fit mechanism on substrate binding, with an understanding of plant GST structure/function allowing these proteins to be engineered for novel functions in detoxification and ligand recognition. Several major crops produce alternative thiols, with GSTUs shown to use homoglutathione in preference to glutathione, in herbicide detoxification reactions in soybeans. Similarly, hydroxymethylglutathione is used, in addition to glutathione in detoxifying the herbicide fenoxaprop in wheat. Following GST action, plants are able to rapidly process glutathione conjugates by at least two distinct pathways, with the available evidence suggesting these function in an organ- and species-specific manner. Roles for GSTs in endogenous metabolism are less well defined, with the enzymes linked to a diverse range of functions, including signaling, counteracting oxidative stress, and detoxifying and transporting secondary metabolites.
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http://dx.doi.org/10.3109/03602532.2011.552910DOI Listing
May 2011

Roles for stress-inducible lambda glutathione transferases in flavonoid metabolism in plants as identified by ligand fishing.

J Biol Chem 2010 Nov 14;285(47):36322-9. Epub 2010 Sep 14.

Centre for Bioactive Chemistry, School of Biological & Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom.

The glutathione transferases (GSTs) of plants are a superfamily of abundant enzymes whose roles in endogenous metabolism are largely unknown. For example, the lambda class of GSTs (GSTLs) have members that are selectively induced by chemical stress treatments and based on their enzyme chemistry are predicted to have roles in redox homeostasis. However, using conventional approaches these functions have yet to be determined. To address this, recombinant GSTLs from wheat and Arabidopsis were tagged with a Strep tag and after affinity-immobilization, incubated with extracts from Arabidopsis, tobacco, and wheat. Bound ligands were then recovered by solvent extraction and identified by mass spectrometry (MS). With the wheat enzyme TaGSTL1, the ligand profiles obtained with in vitro extracts from tobacco closely matched those observed after the protein had been expressed in planta, demonstrating that these associations were physiologically representative. The stress-inducible TaGSTL1 was found to selectively recognize flavonols (e.g. taxifolin; K(d) = 25 nM), with this binding being dependent upon S-glutathionylation of an active site cysteine. In the case of the wheat extracts, this selectivity in ligand recognitions lead to the detection of flavonols that had not been previously described in this cereal. Subsequent in vitro assays showed that the co-binding of flavonols, such as quercetin, to the thiolated TaGSTL1 represented an intermediate step in the reduction of the respective S-glutathionylated quinone derivatives to yield free flavonols. These results suggest a novel role for GSTLs in maintaining the flavonoid pool under stress conditions.
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http://dx.doi.org/10.1074/jbc.M110.164806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978560PMC
November 2010

Fluorescence quenched quinone methide based activity probes--a cautionary tale.

Org Biomol Chem 2010 Apr 10;8(7):1610-8. Epub 2010 Feb 10.

Centre for Bioactive Chemistry, Department of Chemistry, University of Durham, Sciences Laboratories, South Road, Durham, UK DH1 3LE.

A carbamate linked quenching group coupled with a pro-quinone methide reactive core provides an effective tool for studying enzyme function without problems associated with background fluorescence from unreacted probe. However, the relatively slow fragmentation of the carbamate linkage in such a strategy may cause problems of loss of signal or a decoupling of enzyme activity and labelling.
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http://dx.doi.org/10.1039/b920443aDOI Listing
April 2010

Roles for glutathione transferases in plant secondary metabolism.

Phytochemistry 2010 Mar 14;71(4):338-50. Epub 2010 Jan 14.

Centre for Bioactive Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK.

Plant glutathione transferases (GSTs) are classified as enzymes of secondary metabolism, but while their roles in catalysing the conjugation and detoxification of herbicides are well known, their endogenous functions are largely obscure. Thus, while the presence of GST-derived S-glutathionylated xenobiotics have been described in many plants, there is little direct evidence for the accumulation of similarly conjugated natural products, despite the presence of a complex and dichotomous metabolic pathway which processes these reaction products. The conservation in glutathione conjugating and processing pathways, the co-regulation of GSTs with inducible plant secondary metabolism and biochemical studies showing the potential of these enzymes to conjugate reactive natural products are all suggestive of important endogenous functions. As a framework for addressing these enigmatic functions we postulate that either: (a) the natural reaction products of GSTs are unstable and undergo reversible S-glutathionylation; (b) the conjugation products of GSTs are very rapidly processed to derived metabolites; (c) GSTs do not catalyse conventional conjugation reactions but instead use glutathione as a cofactor rather than co-substrate; or (d) GSTs are non-catalytic and function as transporter proteins for secondary metabolites and their unstable intermediates. In this review, we describe how enzyme biochemistry and informatics are providing clues as to GST function allowing for the critical evaluation of each of these hypotheses. We also present evidence for the involvement of GSTs in the synthesis of sulfur-containing secondary metabolites such as volatiles and glucosinolates, and the conjugation, transport and storage of reactive oxylipins, phenolics and flavonoids.
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http://dx.doi.org/10.1016/j.phytochem.2009.12.012DOI Listing
March 2010

Glutathione transferases.

Arabidopsis Book 2010 8;8:e0131. Epub 2010 May 8.

The 55 Arabidopsis glutathione transferases (GSTs) are, with one microsomal exception, a monophyletic group of soluble enzymes that can be divided into phi, tau, theta, zeta, lambda, dehydroascorbate reductase (DHAR) and TCHQD classes. The populous phi and tau classes are often highly stress inducible and regularly crop up in proteomic and transcriptomic studies. Despite much study on their xenobiotic-detoxifying activities their natural roles are unclear, although roles in defence-related secondary metabolism are likely. The smaller DHAR and lambda classes are likely glutathione-dependent reductases, the zeta class functions in tyrosine catabolism and the theta class has a putative role in detoxifying oxidised lipids. This review describes the evidence for the functional roles of GSTs and the potential for these enzymes to perform diverse functions that in many cases are not "glutathione transferase" activities. As well as biochemical data, expression data from proteomic and transcriptomic studies are included, along with subcellular localisation experiments and the results of functional genomic studies.
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http://dx.doi.org/10.1199/tab.0131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244946PMC
August 2012

Selective binding of glutathione conjugates of fatty acid derivatives by plant glutathione transferases.

J Biol Chem 2009 Aug 11;284(32):21249-56. Epub 2009 Jun 11.

Centre for Bioactive Chemistry, School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom.

Proteomic studies with Arabidopsis thaliana have revealed that the plant-specific Tau (U) class glutathione transferases (GSTs) are selectively retained by S-hexylglutathione affinity supports. Overexpression of members of the Arabidopsis GST superfamily in Escherichia coli showed that 25 of the complement of 28 GSTUs caused the aberrant accumulation of acylated glutathione thioesters in vivo, a perturbation that was not observed with other GST classes. Each GSTU caused a specific group of fatty acyl derivatives to accumulate, which varied in chain length (C(6) to C(18)), additional oxygen content (0 or 1), and desaturation (0 or 1). Thioesters bound tightly to recombinant GSTs (K(d) approximately 1 microm), explaining their accumulation. Transient expression of GSTUs in Nicotiana benthamiana followed by recovery by Strep-tag affinity chromatography allowed the respective plant ligands to be extracted and characterized. Again, each GST showed a distinct profile of recovered metabolites, notably glutathionylated oxophytodienoic acid and related oxygenated fatty acids. Similarly, the expression of the major Tau protein GSTU19 in the endogenous host Arabidopsis led to the selective binding of the glutathionylated oxophytodienoic acid-glutathione conjugate, with the enzyme able to catalyze the conjugation reaction. Additional ligands identified in planta included other fatty acid derivatives including divinyl ethers and glutathionylated chlorogenic acid. The strong and specific retention of various oxygenated fatty acids by each GSTU and the conservation in binding observed in the different hosts suggest that these proteins have selective roles in binding and conjugating these unstable metabolites in vivo.
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http://dx.doi.org/10.1074/jbc.M109.020107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755848PMC
August 2009

An efficient method for 15N-labeling of chitin in fungi.

Biomacromolecules 2009 Apr;10(4):793-7

Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom.

To permit facile (15)N solid-state NMR (ssNMR) analysis of the degree of acetylation (DA) of chitinous materials in fungi a method for the introduction of a (15)N isotopic label has been developed. Using Penicillium chrysogenum as a model system, a series of (15)N-based media were surveyed for their abilities to support mycelial growth, and a rich medium supplemented with ((15)NH(4))(2)SO(4) supported good growth. Uptake of label into chitin extracted from mycelia grown in the rich ((15)NH(4))(2)SO(4)-based media was monitored by mass spectrometry, with approximately 1 g/L of ((15)NH(4))(2)SO(4) leading to approximately 65% incorporation. The labeled chitin was studied by ssNMR to determine its DA, and the (15)N label permitted measurement of DA to within 0.5% with acquisition times of on the order of half an hour. Similar studies validated the method for DA measurements on chitin from cultures of Aspergillus niger and Mucor rouxii.
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http://dx.doi.org/10.1021/bm8012814DOI Listing
April 2009

Enzyme activities and subcellular localization of members of the Arabidopsis glutathione transferase superfamily.

J Exp Bot 2009 27;60(4):1207-18. Epub 2009 Jan 27.

School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK.

Enzyme screens with Strep-tagged recombinant proteins and expression studies with the respective green fluorescent protein (GFP) fusions have been employed to examine the functional activities and subcellular localization of members of the Arabidopsis glutathione transferase (GST) superfamily. Fifty-one of 54 GST family members were transcribed and 41 found to express as functional glutathione-dependent enzymes in Escherichia coli. Functional redundancy was observed and in particular three theta (T) class GSTs showed conserved activities as hydroperoxide-reducing glutathione peroxidases (GPOXs). When expressed in tobacco as GFP fusions, all three GSTTs localized to the peroxisome, where their GPOX activity could prevent membrane damage arising from fatty acid oxidation. Through alternative splicing, two of these GSTTs form fusions with Myb transcription factor-like domains. Examination of one of these variants showed discrete localization within the nucleus, possibly serving a role in reducing nucleic acid hydroperoxides or in signalling. Based on this unexpected differential sub-cellular localization, 15 other GST family members were expressed as GFP fusions in tobacco. Most accumulated in the cytosol, but GSTU12 localized to the nucleus, a family member resembling a bacterial tetrachlorohydroquinone dehalogenase selectively associated with the plasma membrane, and a lambda GSTL2 was partially directed to the peroxisome after removal of a putative chloroplast transit peptide. Based on the results obtained with the GSTTs, it was concluded that these proteins can exert identical protective functions in differing subcellular compartments.
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http://dx.doi.org/10.1093/jxb/ern365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657551PMC
May 2009

Getting the most out of publicly available T-DNA insertion lines.

Plant J 2008 Nov 4;56(4):665-77. Epub 2008 Jul 4.

School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK.

In the course of several different projects, we came to realize that there is a significant amount of untapped potential in the publicly available T-DNA insertion lines. In addition to the GABI-Kat lines, which were designed specifically for activation tagging, lines from the SAIL and FLAGdb collections are also useful for this purpose. As well as the 35S promoter chosen for activation tagging in GABI-Kat lines, we found that the 1'2' bidirectional promoter is capable of activating expression of flanking genomic sequences in both GABI-Kat and SAIL lines. Thus these lines have added potential for activation tagging. We also show that these lines are capable of generating antisense transcripts and so have the potential to be used for suppression (loss/reduction of function) studies. By virtue of weak terminator sequences in some T-DNA constructs, transcript read-through from selectable markers is also possible, which again has the potential to be exploited in activation/suppression studies. Finally, we show that, by selecting and characterizing lines in which the T-DNA insertions are present specifically within introns of a target gene, an allelic series of mutants with varying levels of reduced expression can be generated, due to differences in efficiency of intron splicing. Taken together, our analyses demonstrate that there is a wealth of untapped potential within existing insertion lines for studies on gene function, and the effective exploitation of these resources is discussed.
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http://dx.doi.org/10.1111/j.1365-313X.2008.03608.xDOI Listing
November 2008

Binding and glutathione conjugation of porphyrinogens by plant glutathione transferases.

J Biol Chem 2008 Jul 20;283(29):20268-76. Epub 2008 May 20.

Centre for Bioactive Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham, UK.

Overexpression in Escherichia coli of a tau (U) class glutathione transferase (GST) from maize (Zea mays L.), termed ZmGSTU1, caused a reduction in heme levels and an accumulation of porphyrin precursors. This disruption was highly specific, with the expression of the closely related ZmGSTU2 or other maize GSTs having little effect. Expression in E. coli of a series of chimeric ZmGSTU1/ZmGSTU2 proteins identified domains responsible for disrupting porphyrin metabolism. In addition to known heme precursors, expression of ZmGSTU1 led to the accumulation of a novel glutathione conjugate of harderoporphyrin(ogen) (2,7,12,18-tetramethyl-3-vinylporphyrin-8,13,17-tripropionic acid). Using the related protoporphyrinogen as a substrate, conjugation could be shown to occur on one vinyl group and was actively catalyzed by the ZmGSTU. In plant transgenesis studies, the ZmGSTUs did not perturb porphyrin metabolism when expressed in the cytosol of Arabidopsis or tobacco. However, expression of a ZmGSTU1-ZmGSTU2 chimera in the chloroplasts of tobacco resulted in the accumulation of the harderoporphyrin(ogen)-glutathione conjugate observed in the expression studies in bacteria. Our results show that the well known ability of GSTs to act as ligand binding (ligandin) proteins of porphyrins in vitro results in highly specific interactions with porphyrinogen intermediates, which can be demonstrated in both plants and bacteria in vivo.
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http://dx.doi.org/10.1074/jbc.M802026200DOI Listing
July 2008

Enzymes of tyrosine catabolism in Arabidopsis thaliana.

Plant Sci 2006 Sep 16;171(3):360-6. Epub 2006 May 16.

School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK.

Tyrosine catabolism is an essential pathway in animals, but its role in plants is unclear. The first steps of tyrosine degradation lead to the formation of homogentisate. In animals this is then sequentially acted on by homogentisate dioxygenase (HGO), maleylacetoacetate isomerase (MAAI) and fumarylacetoacetate hydrolase (FAH) to generate fumarate and acetoacetate. In plants, homogentisate is used to generate the essential redox metabolites tocopherol and plastoquinone, which effectively act as an alternative metabolic fate for tyrosine. Having determined that a zeta class glutathione transferase from Arabidopsis thaliana is a functional MAAI, we have looked for evidence that the mammalian degradation pathway could also operate in plants. Based on array and quantitative PCR experiments, the A. thaliana homologues AtHGO, AtMAAI and AtFAH could be shown to be expressed, with AtHGO and AtMAAI showing evidence of co-regulation. cDNAs encoding AtHGO, AtMAAI and AtFAH were cloned in Escherichia coli and shown to represent a fully functional catabolic pathway when combined in vitro. The significance of this pathway, including increased transcription of the associated enzymes in senescing tissue, compartmentalisation and impact on flux into synthesis of Vitamin E and other tocopherols of biotechnological interest is discussed.
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http://dx.doi.org/10.1016/j.plantsci.2006.04.008DOI Listing
September 2006

Cloning and characterization of a theta class glutathione transferase from the potato pathogen Phytophthora infestans.

Phytochemistry 2006 Jul 23;67(14):1427-34. Epub 2006 Jun 23.

School of Biological and Biomedical Sciences, Crop Protection Group, Durham University, South Road, Durham DH1 3LE, UK.

A glutathione transferase (GST) related to the theta (T) class of enzymes found in plants and animals has been cloned from the potato pathogen Phytophthora infestans. The cDNA encoded a 25kDa polypeptide termed PiGSTT1 which was expressed in E. coli as the native protein. The purified recombinant enzyme behaved as a dimer (PiGSTT1-1) and while being unable to catalyse the glutathione conjugation of 1-chloro-2,4-dintrobenzene, was highly active as a glutathione peroxidase with organic hydroperoxide substrates. In addition to reducing the synthetic substrate cumene hydroperoxide, PiGSTT1-1 was shown to be highly active toward 9(S)-hydroperoxy-(10E,12Z,15Z)-octadecatrienoic acid=9(S)-HPOT, which is formed in potato plants during infection by P. infestans as a precursor of the antifungal oxylipin colnelenic acid. An antiserum was raised to PiGSTT1-1 and used to demonstrate that the respective enzyme was abundantly expressed in P. infestans both cultured on pea agar and during the infection of potato plants.
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http://dx.doi.org/10.1016/j.phytochem.2006.05.012DOI Listing
July 2006

Plant glutathione transferases.

Methods Enzymol 2005 ;401:169-86

Centre for Bioactive Chemistry, School of Biological and Biomedical Sciences, Durham University, United Kingdom.

Soluble plant glutathione transferases (GSTs) consist of seven distinct classes, six of which have been functionally characterized. The phi and tau class GSTs are specific to plants and the most numerous and abundant of these enzymes. Both have classic conjugating activities toward a diverse range of xenobiotics, including pesticides, where they are major determinants of herbicide selectivity in crops and weeds. In contrast, the zeta and theta class GSTs are conserved in animals and plants and have very restricted activities toward xenobiotics. Theta GSTs function as glutathione peroxidases, reducing organic hydroperoxides produced during oxidative stress. Zeta GSTs act as glutathione-dependent isomerases, catalyzing the conversion of maleylacetoacetate to fumarylacetoacetate, the penultimate step in tyrosine degradation. The other two classes of plant GSTs, the dehydroascorbate reductases (DHARs) and lambda GSTs, differ from phi, tau, zeta, and theta enzymes in being monomers rather than dimers and possessing a catalytic cysteine rather than serine in the active site. Both can function as thioltransferases, with the DHARs having a specialized function in reducing dehydroascorbate to ascorbic acid. The determination of the diverse plant-specific functions of the differing GST classes is described.
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http://dx.doi.org/10.1016/S0076-6879(05)01011-6DOI Listing
February 2006

Stress-induced protein S-glutathionylation in Arabidopsis.

Plant Physiol 2005 Aug 29;138(4):2233-44. Epub 2005 Jul 29.

School of Biological and Biomedical Sciences, University of Durham, Durham DH1 3LE, United Kingdom.

S-Glutathionylation (thiolation) is a ubiquitous redox-sensitive and reversible modification of protein cysteinyl residues that can directly regulate their activity. While well established in animals, little is known about the formation and function of these mixed disulfides in plants. After labeling the intracellular glutathione pool with [35S]cysteine, suspension cultures of Arabidopsis (Arabidopsis thaliana ecotype Columbia) were shown to undergo a large increase in protein thiolation following treatment with the oxidant tert-butylhydroperoxide. To identify proteins undergoing thiolation, a combination of in vivo and in vitro labeling methods utilizing biotinylated, oxidized glutathione (GSSG-biotin) was developed to isolate Arabidopsis proteins/protein complexes that can be reversibly glutathionylated. Following two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry proteomics, a total of 79 polypeptides were identified, representing a mixture of proteins that underwent direct thiolation as well as proteins complexed with thiolated polypeptides. The mechanism of thiolation of five proteins, dehydroascorbate reductase (AtDHAR1), zeta-class glutathione transferase (AtGSTZ1), nitrilase (AtNit1), alcohol dehydrogenase (AtADH1), and methionine synthase (AtMetS), was studied using the respective purified recombinant proteins. AtDHAR1, AtGSTZ1, and to a lesser degree AtNit1 underwent spontaneous thiolation with GSSG-biotin through modification of active-site cysteines. The thiolation of AtADH1 and AtMetS required the presence of unidentified Arabidopsis proteins, with this activity being inhibited by S-modifying agents. The potential role of thiolation in regulating metabolism in Arabidopsis is discussed and compared with other known redox regulatory systems operating in plants.
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http://dx.doi.org/10.1104/pp.104.058917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1183410PMC
August 2005

Dynamic interaction of NtMAP65-1a with microtubules in vivo.

J Cell Sci 2005 Jul;118(Pt 14):3195-201

The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, University of Durham, South Road, Durham, DH1 3LE, UK.

Plant microtubules are intrinsically more dynamic than those from animals. We know little about the dynamics of the interaction of plant microtubule-associated proteins (MAPs) with microtubules. Here, we have used tobacco and Arabidopsis MAPs with relative molecular mass 65 kDa (NtMAP65-1a and AtMAP65-1), to study their interaction with microtubules in vivo. Using fluorescence recovery after photobleaching we report that the turnover of both NtMAP65-1a and AtMAP65-1 bound to microtubules is four- to fivefold faster than microtubule treadmilling (13 seconds compared with 56 seconds, respectively) and that the replacement of NtMAP65-1a on microtubules is by random association rather than by translocation along microtubules. MAP65 will only bind polymerised microtubules and not its component tubulin dimers. The turnover of NtMAP65-1a and AtMAP65-1 on microtubules is similar in the interphase cortical array, the preprophase band and the phragmoplast, strongly suggesting that their role in these arrays is the same. NtMAP65-1a and AtMAP65-1 are not observed to bind microtubules in the metaphase spindle and their rate of recovery is consistent with their cytoplasmic localisation. In addition, the dramatic reappearance of NtMAP65-1a on microtubules at the spindle midzone in anaphase B suggests that NtMAP65-1a is controlled post-translationally. We conclude that the dynamic properties of these MAPs in vivo taken together with the fact that they have been shown not to effect microtubule polymerisation in vitro, makes them ideally suited to a role in crossbridging microtubules that need to retain spatial organisation in rapidly reorganising microtubule arrays.
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http://dx.doi.org/10.1242/jcs.02433DOI Listing
July 2005

Differential induction of glutathione transferases and glucosyltransferases in wheat, maize and Arabidopsis thaliana by herbicide safeners.

Z Naturforsch C J Biosci 2005 Mar-Apr;60(3-4):307-16

School of Biological & Biomedical Sciences, University of Durham, UK.

By learning lessons from weed science we have adopted three approaches to make plants more effective in phytoremediation: (1) The application of functional genomics to identify key components involved in the detoxification of, or tolerance to, xenobiotics for use in subsequent genetic engineering/breeding programmes. (2) The rational metabolic engineering of plants through the use of forced evolution of protective enzymes, or alternatively transgenesis of detoxification pathways. (3) The use of chemical treatments which protect plants from herbicide injury. In this paper we examine the regulation of the xenome by herbicide safeners, which are chemicals widely used in crop protection due to their ability to enhance herbicide selectivity in cereals. We demonstrate that these chemicals act to enhance two major groups of phase 2 detoxification enzymes, notably the glutathione transferases and glucosyltransferases, in both cereals and the model plant Arabidopsis thaliana, with the safeners acting in a chemical- and species-specific manner. Our results demonstrate that by choosing the right combination of safener and plant it should be possible to enhance the tolerance of diverse plants to a wide range of xenobiotics including pollutants.
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http://dx.doi.org/10.1515/znc-2005-3-416DOI Listing
June 2005

Redox regulation of a soybean tyrosine-specific protein phosphatase.

Biochemistry 2005 May;44(21):7696-703

School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK.

Plant protein tyrosine phosphatases (PTPs) are important in regulating cellular responses to redox change through their reversible inactivation under oxidative conditions. Studies on the soybean (Glycine max) GmPTP have shown that, compared with its mammalian counterparts, the plant enzyme is relatively insensitive to inactivation by H2O2 but hypersensitive (k(inact) = 559 M(-1) s(-1)) to S-glutathionylation (thiolation) promoted by the presence of oxidized glutathione (GSSG). Through a combination of chemical and mutational modification studies, three of the seven cysteine residues of GmPTP have been identified by mass spectrometry as being able to inactivate the enzyme when thiolated by GSSG or alkylated with iodoacetamide. Conserved Cys 266 was shown to be essential for catalysis but surprisingly resistant to S-modification, whereas the regulatory Cys 78 and Cys 176 were readily thiolated and/or alkylated. Mutagenesis of these cysteines showed that all three residues were in proximity of each other, regulating each's reactivity to S-modifying agents. Through a combination of protein modification and kinetic experiments, we conclude that the inactivation of GmPTP by GSSG is regulated at two levels. Cys 176 appears to be required to promote the formation of the reduced form of Cys 266, which is otherwise unreactive. When thiolated, Cys 176 immediately inactivates the enzyme, and this is followed by the thiolation of Cys 78, which undergoes a slow disulfide exchange with Cys 266 giving rise to a Cys 78-Cys 266 disulfide. We speculate that this two-tiered protection is required for regulation of GmPTP under highly oxidizing conditions.
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http://dx.doi.org/10.1021/bi047324aDOI Listing
May 2005

Cloning and initial characterization of the Arabidopsis thaliana endoplasmic reticulum oxidoreductins.

Antioxid Redox Signal 2003 Aug;5(4):389-96

Department of Biological and Biomedical Sciences, University of Durham, Durham, U.K.

The oxidation and isomerization of disulfide bonds is necessary for the growth of all organisms. In yeast, the oxidative folding of secretory pathway proteins is catalyzed by protein disulfide isomerase (PDI), which requires Ero1p (endoplasmic reticulum oxidoreductin) for its own oxidation. In Homo sapiens, two homologues of Ero1p, Ero1-Lalpha and Ero1-Lbeta, have been cloned. Both Ero1-Lalpha and Ero1-Lbeta interact via disulfide bonds with PDI and support the oxidation of immunoglobulin light chains. However, the function of Ero proteins in plants has not yet been analyzed. In this article, we report the cloning of the two Ero1p homologues present in Arabidopsis thaliana, demonstrating that one of the cDNAs has a shorter terminal exon than predicted and differs from the annotated sequence found in the genome database. Sequence analysis of the Arabidopsis endoplasmic reticulum oxidoreductins (AEROs) reveals that both AERO1 and AERO2 are more closely related to each other than to either of the human Eros. Both in vitro translated AERO proteins are targeted to the endoplasmic reticulum and glycosylated. The ability to use a genetically tractable multicellular organism in combination with biochemical approaches should further our understanding of redox networks and Ero function in both plants and animals.
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http://dx.doi.org/10.1089/152308603768295122DOI Listing
August 2003

Isolation of a glucosyltransferase from Arabidopsis thaliana active in the metabolism of the persistent pollutant 3,4-dichloroaniline.

Plant J 2003 May;34(4):485-93

Crop Protection Group, School of Biological and Biomedical Sciences, University of Durham, UK.

The pollutant 3,4-dichloroaniline (DCA) was rapidly detoxified by glucosylation in Arabidopsis thaliana root cultures, with the N-beta-d-glucopyranosyl-DCA exported into the medium. The N-glucosyltransferase (N-GT) responsible for this activity was purified from Arabidopsis suspension cultures and the resulting 50 kDa polypeptide analysed by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) following tryptic digestion. The protein was identified as GT72B1. The GT was cloned and the purified recombinant enzyme shown to be highly active in conjugating DCA and 2,4,5-trichlorophenol, as well as several other chlorinated phenols and anilines, demonstrating both N-GT and O-GT activity. GT72B1 showed little activity towards natural products with the exception of the tyrosine catabolite 4-hydroxyphenylpyruvic acid. Both O-GT and N-GT activities were enhanced in both plants and cultures treated with herbicide safeners, demonstrating the chemical inducibility of this detoxification system in Arabidopsis.
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http://dx.doi.org/10.1046/j.1365-313x.2003.01742.xDOI Listing
May 2003