Catalytic properties of glutathione-binding residues in a tau class glutathione transferase (PtGSTU1) from Pinus tabulaeformis

Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches

Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes.

Effects of conserved Arg20, Glu74 and Asp77 on the structure and function of a tau class glutathione S-transferase in rice

The relative position of domains is critical for enzymatic properties of tau class glutathione S-transferases, and altering the position of linker far away from the active center affects catalytic property. Glutathione S-transferases (GSTs) are a family of phase II detoxification enzymes whose main function is to improve plant resistance to stresses. To understand the structural effects of tau class GSTs on their function, using OsGSTU17 as an example, we predicted the residues involved in the interactions between its domains and linker region. We further detected the structural changes in mutants and the corresponding changes in terms of substrate activity and kinetic parameters. Four pairs of residues, including Ala14 and Trp165, Arg20 and Tyr154, Glu74 and Arg98, Asp77 and Met87, forming hydrogen bonds and salt bridges were found to play important roles in maintaining the relative position between the domains and linker region inside the protein. The hydrogen bond between Trp165 and Ala14 affected the structural stability has been demonstrated in our previous study. The mutant R20A lost almost all catalytic activity. Interestingly, the mutant E74A exhibited a significant decrease in activity towards 7-chloro-4-nitrobenzo-2-oxa-1, 3-diazole, 1-chloro-2, 4-dinitrobenzene and 4-nitrobenzyl chloride, while its activity towards substrate cumene hydroperoxide remained unchanged. Compared with other mutants, the mutant D77A exhibited decreased affinity to its substrates and increased activity towards 1-chloro-2, 4-dinitrobenzene and cumene hydroperoxide, but its thermodynamic stability did not change significantly. The relative position of individual domain was critical for enzymatic properties, and the linker which is far away from the active site could change the enzymatic properties of GSTs via altering the relative position of the individual domain. Our results provide insights into the relationship between structure and function of tau class GSTs.

Biochemical Functions of Glutathione S-Transferase Family of Salix babylonica

Glutathione S-transferases (GSTs) are ubiquitous enzymes that are encoded by a large gene family, and they contribute to the detoxification of endogenous or xenobiotic compounds and oxidative stress metabolism in plants. Although the GSTs gene family has been reported in many land plants, our knowledge of the evolution and function of the willow GSTs is still limited. In this study, 22 full-length GST genes were cloned from Salix babylonica and divided into three classes based on the conserved domain analysis, phylogenetic tree and gene structure: tau, phi and DHAR. The tissue-specific expression patterns were substantially different among the tau and phi GSTs. The Salix GST proteins showed functional divergences in the substrate specificities, substrate activities and kinetic characteristics. The site-directed mutagenesis studies revealed that a single amino acid mutation (Ile/Val53→Thr53) resulted in the lowest activity of SbGSTU7 among the Salix GSTs. These results suggest that non-synonymous substitution of an amino acid at the putative glutathione-binding site may play an important role in the divergence of enzymatic functions of Salix GST family.

Effects of Substrate-Binding Site Residues on the Biochemical Properties of a Tau Class Glutathione S-Transferase from Oryza sativa

Glutathione S-transferases (GSTs)—an especially plant-specific tau class of GSTs—are key enzymes involved in biotic and abiotic stress responses. To improve the stress resistance of crops via the genetic modification of GSTs, we predicted the amino acids present in the GSH binding site (G-site) and hydrophobic substrate-binding site (H-site) of OsGSTU17, a tau class GST in rice. We then examined the enzyme activity, substrate specificity, enzyme kinetics and thermodynamic stability of the mutant enzymes. Our results showed that the hydrogen bonds between Lys42, Val56, Glu68, and Ser69 of the G-site and glutathione were essential for enzyme activity and thermal stability. The hydrophobic side chains of amino acids of the H-site contributed to enzyme activity toward 4-nitrobenzyl chloride but had an inhibitory effect on enzyme activity toward 1-chloro-2,4-dinitrobenzene and cumene hydroperoxide. Different amino acids of the H-site had different effects on enzyme activity toward a different substrate, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. Moreover, Leu112 and Phe162 were found to inhibit the catalytic efficiency of OsGSTU17 to 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole, while Pro16, Leu112, and Trp165 contributed to structural stability. The results of this research enhance the understanding of the relationship between the structure and function of tau class GSTs to improve the abiotic stress resistance of crops.

Functional and structural profiles of GST gene family from three Populus species reveal the sequence-function decoupling of orthologous genes

A common assumption in comparative genomics is that orthologous genes are functionally more similar than paralogous genes. However, the validity of this assumption needs to be assessed using robust experimental data. We conducted tissue-specific gene expression and protein function analyses of orthologous groups within the glutathione S-transferase (GST) gene family in three closely related Populus species: Populus trichocarpa, Populus euphratica and Populus yatungensis. This study identified 21 GST orthologous groups in the three Populus species. Although the sequences of the GST orthologous groups were highly conserved, the divergence in enzymatic functions was prevalent. Through site-directed mutagenesis of orthologous proteins, this study revealed that nonsynonymous substitutions at key amino acid sites played an important role in the divergence of enzymatic functions. In particular, a single amino acid mutation (Arg39→Trp39) contributed to P. euphratica PeGSTU30 possessing high enzymatic activity via increasing the hydrophobicity of the active cavity. This study provided experimental evidence showing that orthologues belonging to the gene family have functional divergences. The nonsynonymous substitutions at a few amino acid sites resulted in functional divergence of the orthologous genes. Our findings provide new insights into the evolution of orthologous genes in closely related species.

Evolution and Function of the Populus SABATH Family Reveal That a Single Amino Acid Change Results in a Substrate Switch

Evolutionary mechanisms of substrate specificities of enzyme families remain poorly understood. Plant SABATH methyltransferases catalyze methylation of the carboxyl group of various low molecular weight metabolites. Investigation of the functional diversification of the SABATH family in plants could shed light on the evolution of substrate specificities in this enzyme family. Previous studies identified 28 SABATH genes from the Populus trichocarpa genome. In this study, we re-annotated the Populus SABATH gene family, and performed molecular evolution, gene expression and biochemical analyses of this large gene family. Twenty-eight Populus SABATH genes were divided into three classes with distinct divergences in their gene structure, expression responses to abiotic stressors and enzymatic properties of encoded proteins. Populus class I SABATH proteins converted IAA to methyl-IAA, class II SABATH proteins converted benzoic acid (BA) and salicylic acid (SA) to methyl-BA and methyl-SA, while class III SABATH proteins converted farnesoic acid (FA) to methyl-FA. For Populus class II SABATH proteins, both forward and reverse mutagenesis studies showed that a single amino acid switch between PtSABATH4 and PtSABATH24 resulted in substrate switch. Our findings provide new insights into the evolution of substrate specificities of enzyme families.

Recent advances in protein engineering and biotechnological applications of glutathione transferases

Glutathione transferases (GSTs, EC 2.5.1.18) are a widespread family of enzymes that play a central role in the detoxification, metabolism, and transport or sequestration of endogenous or xenobiotic compounds. During the last two decades, delineation of the important structural and catalytic features of GSTs has laid the groundwork for engineering GSTs, involving both rational and random approaches, aiming to create new variants with new or altered properties. These approaches have expanded the usefulness of native GSTs, not only for understanding the fundamentals of molecular detoxification mechanisms, but also for the development medical, analytical, environmental, and agricultural applications. This review article attempts to summarize successful examples and current developments on GST engineering, highlighting in parallel the recent knowledge gained on their phylogenetic relationships, structural/catalytic features, and biotechnological applications.

Insights into ligand binding to a glutathione S-transferase from mango: Structure, thermodynamics and kinetics

We studied a mango glutathione S-transferase (GST) (Mangifera indica) bound to glutathione (GSH) and S-hexyl glutathione (GSX). This GST Tau class (MiGSTU) had a molecular mass of 25.5 kDa. MiGSTU Michaelis-Menten kinetic constants were determined for their substrates obtaining a Km, Vmax and kcat for CDNB of 0.792 mM, 80.58 mM min-1 and 68.49 s-1 respectively and 0.693 mM, 105.32 mM min-1 and 89.57 s-1, for reduced GSH respectively. MiGSTU had a micromolar affinity towards GSH (5.2 μM) or GSX (7.8 μM). The crystal structure of the MiGSTU in apo or bound to GSH or GSX generated a model that explains the thermodynamic signatures of binding and showed the importance of enthalpic-entropic compensation in ligand binding to Tau-class GST enzymes.

Substrate specificities of two tau class glutathione transferases inducible by 2,4,6-trinitrotoluene in poplar

BACKGROUND

The genome of poplar (Populus trichocarpa) encodes 81 glutathione transferases (GSTs) annotated in eight distinct classes. The tau class is considered the most versatile in the biotransformation of xenobiotics and is composed of 58 GSTs. Two of the enzymes, GSTU16 and GSTU45, have particular interest since their expression is induced by exposure of poplar tissues to 2,4,6-trinitrotoluene (TNT) and could potentially be involved in the metabolism of this toxic environmental contaminant.

RESULTS

DNA encoding these GSTs was synthesized and the proteins were heterologously expressed in Escherichia coli and the purified enzymes were characterized.

MAJOR CONCLUSIONS

GSTU16 assayed with a number of conventional GST substrates showed the highest specific activity (60μmolmin⁻¹ mg⁻¹) with phenethyl isothiocyanate, 150-fold higher than that with CDNB. By contrast, GSTU45 showed CDNB as the most active substrate (3.3μmolmin⁻¹ mg⁻¹) whereas all of the 16 alternative substrates tested yielded significantly lower activities. Homology modeling suggested that the aromatic residues Phe10 and Tyr107 in the active site of GSTU16 are promoting the high activity with PEITC and other substrates with aromatic side-chains. Nonetheless, TNT was a poor substrate for GSTU16 as well as for GSTU45 with a specific activity of 0.05nmolmin⁻¹ mg⁻¹ for both enzymes.

GENERAL SIGNIFICANCE

GSTU16 and GSTU45 do not play a major role in the degradation of TNT in poplar.

Plant GSTome: structure and functional role in xenome network and plant stress response

Glutathione transferases (GSTs) represent a major group of detoxification enzymes. All plants possess multiple cytosolic GSTs, each of which displays distinct catalytic as well as non-catalytic binding properties. The progress made in recent years in the fields of genomics, proteomics and protein crystallography of GSTs, coupled with studies on their molecular evolution, diversity and substrate specificity has provided new insights into the function of these enzymes. In plants, GSTs appear to be implicated in an array of different functions, including detoxification of xenobiotics and endobiotics, primary and secondary metabolism, stress tolerance, and cell signalling. This review focuses on plant GSTome and attempts to give an overview of its catalytic and functional role in xenome and plant stress regulatory networks.

Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family

Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families.

Biochemical functions of the glutathione transferase supergene family of Larix kaempferi

Glutathione transferases (GSTs), which are ubiquitous in plants, play a major role in the detoxification of xenobiotics and oxidative stress metabolism. Due to their role in herbicide detoxification, previous studies of plant GSTs have mainly focused on agricultural plants. In contrast, functional information regarding gymnosperm GSTs is scarce. In this study, we cloned 27 full-length GST genes from the deciduous conifer Larix kaempferi, which is widely distributed across the cooler regions of the northern hemisphere. As with the angiosperm GST gene family, Larix GSTs are divided into eight classes, and tau class GSTs are the most numerous. Compared to the other seven classes of GSTs, Larix tau GST genes show substantially more variation in their expression patterns. The purified Larix GST proteins showed different substrate specificities, substrate activities, and kinetic characteristics. The pH and temperature profiles of purified Larix GST proteins showed broad optimum pH and temperature ranges for enzymatic activity, suggesting that Larix GSTs have evolutionary adaptations to various adverse environments. Taken together, this study provides comprehensive insight into the gymnosperm GST gene family.

Structural and functional evolution of positively selected sites in pine glutathione S-transferase enzyme family

Phylogenetic analyses have identified positive selection as an important driver of protein evolution, both structural and functional. However, the lack of appropriate combined functional and structural assays has generally hindered attempts to elucidate patterns of positively selected sites and their effects on enzyme activity and substrate specificity. In this study we investigated the evolutionary divergence of the glutathione S-transferase (GST) family in Pinus tabuliformis, a pine that is widely distributed from northern to central China, including cold temperate and drought-stressed regions. GSTs play important roles in plant stress tolerance and detoxification. We cloned 44 GST genes from P. tabuliformis and found that 26 of the 44 belong to the largest (Tau) class of GSTs and are differentially expressed across tissues and developmental stages. Substitution models identified five positively selected sites in the Tau GSTs. To examine the functional significance of these positively selected sites, we applied protein structural modeling and site-directed mutagenesis. We found that four of the five positively selected sites significantly affect the enzyme activity and specificity; thus their variation broadens the GST family substrate spectrum. In addition, positive selection has mainly acted on secondary substrate binding sites or sites close to (but not directly at) the primary substrate binding site; thus their variation enables the acquisition of new catalytic functions without compromising the protein primary biochemical properties. Our study sheds light on selective aspects of the functional and structural divergence of the GST family in pine and other organisms.

Functional divergence of the glutathione S-transferase supergene family in Physcomitrella patens reveals complex patterns of large gene family evolution in land plants

Plant glutathione S-transferases (GSTs) are multifunctional proteins encoded by a large gene family that play major roles in the detoxification of xenobiotics and oxidative stress metabolism. To date, studies on the GST gene family have focused mainly on vascular plants (particularly agricultural plants). In contrast, little information is available on the molecular characteristics of this large gene family in nonvascular plants. In addition, the evolutionary patterns of this family in land plants remain unclear. In this study, we identified 37 GST genes from the whole genome of the moss Physcomitrella patens, a nonvascular representative of early land plants. The 37 P. patens GSTs were divided into 10 classes, including two new classes (hemerythrin and iota). However, no tau GSTs were identified, which represent the largest class among vascular plants. P. patens GST gene family members showed extensive functional divergence in their gene structures, gene expression responses to abiotic stressors, enzymatic characteristics, and the subcellular locations of the encoded proteins. A joint phylogenetic analysis of GSTs from P. patens and other higher vascular plants showed that different class GSTs had distinct duplication patterns during the evolution of land plants. By examining multiple characteristics, this study revealed complex patterns of evolutionary divergence among the GST gene family in land plants.

Conserved residues in the subunit interface of tau glutathione s-transferase affect catalytic and structural functions

The tau class glutathione S-transferases (GSTs) have important roles in stress tolerance and the detoxification of herbicides in crops and weeds. Structural investigations of a wheat tau GST (TaGSTU4) show two subunit interactions: a hydrogen bond between the Tyr93 and Pro65 from another subunit of the dimer, and two salt bridges between residues Glu78 and side chains of Arg95 and Arg99 in the opposite subunit. By investigating enzyme activities, kinetic parameters and structural characterizations, this study showed the following results: (i) the hydrogen bond interaction between the Tyr93 and Pro65 was not essential for dimerization, but contributed to the enzyme's catalytic activity, thermal stability and affinity towards substrates glutathione and 1-chloro-2, 4-dinitrobenzene; and (ii) two salt bridges mainly contributed to the protein structure stability and catalysis. The results of this study form a structural and functional basis for rational design of more selective and environmentally friendly herbicides.

Different roles of functional residues in the hydrophobic binding site of two sweet orange tau glutathione S-transferases

Glutathione S-transferases (GSTs) catalyze the conjugation of glutathione to hydrophobic compounds, contributing to the metabolism of toxic chemicals. In this study, we show that two naturally occurring tau GSTs (GSTUs) exhibit distinctive kinetic parameters towards 1-chloro-2,4-dinitrobenzene (CDNB), although they differ only in three amino acids (Arg89, Glu117 and Ile172 in GSTU1 are replaced by Pro89, Lys117 and Val172 in GSTU2). In order to understand the effects of the single mismatched residues, several mutant GSTs were generated through site-directed mutagenesis. The analysis of the kinetic parameters of the mutants led to the conclusion that Glu117 provides a critical contribution to the maintenance of a high-affinity CDNB-binding site. However, the substitution E117K gives rise to mutants showing increased k(cat) values for CDNB, suggesting that Lys117 might positively influence the formation of the transition state during catalysis. No changes in the K(m) values towards glutathione were found between the naturally occurring GSTs and mutants, except for the mutant caused by the substitution R89P in GSTU1, which showed a sharp increase in K(m). Moreover, the analysis of enzyme reactivation after denaturation showed that this R89P substitution leads to a two-fold enhancement of the refolded enzyme yield, suggesting that the insertion of proline might induce critical structural modifications. In contrast, the substitution P89R in GSTU2 does not modify the reactivation yield and does not impair the affinity of the mutant for glutathione, suggesting that all three residues investigated in this work are fundamental in the creation of enzymes characterized by unique biochemical properties.

Biochemical and physiological characterization of a tau class glutathione transferase from rice (Oryza sativa)

The classical phase II detoxification glutathione transferases (GSTs) are key metabolic enzymes that catalyze the conjugation of glutathione to various electrophilic compounds. A tau class GST gene (OsGSTU17) was cloned from rice, which encodes a protein of 223 amino acid residues with a calculated molecular mass of 25.18 kDa. The recombinant OsGSTU17 formed a homodimer protein and showed GSH-conjugating activity with various xenobiotics. Kinetic analysis with respect to NBD-Cl as substrate revealed a K(m) of 0.324 mM and V(max) of 0.219 micromol/min per mg of protein. The enzyme had a maximum activity at pH 7.5, and a high thermal stability with 81% of its initial activity at 55 degrees C for 15 min. Site-directed mutagenesis revealed that Ser15 in the N-terminal domain is a critical catalytic residue, responsible for stabilisation of the thiolate anion of enzyme-bound glutathione. OsGSTU17 mRNA was expressed in different tissues of rice, both above and below ground. The relative transcript levels of OsGSTU17 mRNA varied significantly among the tissues in response to CDNB, hydrogen peroxide and atrazine treatments, indicating the gene has diverse regulation mechanisms in response to abiotic stresses.

Plant glutathione transferases — a decade falls short

The glutathione transferase (GST) superfamily in plants has been subdivided into eight classes, seven of which (phi, tau, zeta, theta, lambda, dehydroascorbate reductase, and tetrachlorohydroquinone dehalogenase) are soluble and one is microsomal. Since their identification in plants in 1970, these enzymes have been well established as phase II detoxification enzymes that perform several other essential functions in plant growth and development. These enzymes catalyze nucleophilic conjugation of the reduced form of the tripeptide glutathione to a wide variety of hydrophobic, electrophilic, and usually cytotoxic substrates. In plants, the conjugated product is either sequestered in the vacuole or transferred to the apoplast. The GSTs of phi and tau classes, which are plant-specific and the most abundant, are chiefly involved in xenobiotic metabolism. Zeta- and theta-class GSTs have very restricted activities towards xenobiotics. Theta-class GSTs are glutathione peroxidases and are involved in oxidative-stress metabolism, whereas zeta-class GSTs act as glutathione-dependent isomerases and catalyze the glutathione-dependent conversion of maleylacetoacetate to fumarylacetoacetate. Zeta-class GSTs participate in tyrosine catabolism. Dehydroascorbate reductase- and lambda-class GSTs function as thioltransferases. Microsomal-class GSTs are members of the MAPEG (membrane-associated proteins in eicosanoid and glutathione metabolism) superfamily. A plethora of studies utilizing both proteomics and genomics approaches have greatly helped in revealing the functional diversity exhibited by these enzymes. The three-dimensional structure of some of the members of the family has been described and this has helped in elucidating the mechanism of action and active-site amino-acid residues of these enzymes. Although a large amount of information is available on this complex enzyme superfamily, more research is necessary to answer additional questions such as, why are phi- and tau-class GSTs more abundant than GSTs from other classes? What functions do phi- and tau-class GSTs perform in plant taxa other than angiosperms? Do more GST classes exist? Future studies on GSTs should focus on these aspects.

Glutamate-64, a newly identified residue of the functionally conserved electron-sharing network contributes to catalysis and structural integrity of glutathione transferases

In Anopheles dirus glutathione transferase D3-3, position 64 is occupied by a functionally conserved glutamate residue, which interacts directly with the gamma-glutamate moiety of GSH (glutathione) as part of an electron-sharing network present in all soluble GSTs (glutathione transferases). Primary sequence alignment of all GST classes suggests that Glu64 is one of a few residues that is functionally conserved in the GST superfamily. Available crystal structures as well as consideration of the property of the equivalent residue at position 64, acidic or polar, suggest that the GST electron-sharing motif can be divided into two types. Electrostatic interaction between the GSH glutamyl and carboxylic Glu64, as well as with Arg66 and Asp100, was observed to extend the electron-sharing motif identified previously. Glu64 contributes to the catalytic function of this motif and the 'base-assisted deprotonation' that are essential for GSH ionization during catalysis. Moreover, this residue also appears to affect multiple steps in the enzyme catalytic strategy, including binding of GSH, nucleophilic attack by thiolate at the electrophilic centre and product formation, probably through active-site packing effects. Replacement with non-functionally-conserved amino acids alters initial packing or folding by favouring aggregation during heterologous expression. Thermodynamic and reactivation in vitro analysis indicated that Glu64 also contributes to the initial folding pathway and overall structural stability. Therefore Glu64 also appears to impact upon catalysis through roles in both initial folding and structural maintenance.