Evolution of substrate recognition across a multigene family of glycosyltransferases in Arabidopsis

Eng-Kiat Lim3, Sandie Baldauf4, Yi Li3, Luisa Elias3, Dawn Worrall2,3, Steven P. Spencer3, Rosamond G. Jackson3, Goro Taguchi5, Joe Ross3 and Dianna J. Bowles1,3

3 Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
4 Department of Biology, University of York, York YO10 5DD, United Kingdom
5 Gene Research Center, Shinshu University, Ueda, Nagano 386-8567, Japan

Received on April 19, 2002; revised on September 24, 2002; accepted on September 24, 2002


    Abstract
 Top
 Abstract
 Introduction
 Results
 Discussion
 Materials and methods
 References
 
The complete sequence of the Arabidopsis genome enables definitive characterization of multigene families and analysis of their phylogenetic relationships. Using a consensus sequence previously defined for glycosyltransferases that use small-molecular-weight acceptors, 107 gene sequences were identified in the Arabidopsis genome and used to construct a phylogenetic tree. Screening recombinant proteins for their catalytic activities in vitro has revealed enzymes active toward physiologically important substrates, including hormones and secondary metabolites. The aim of this study has been to use the phylogenetic relationships across the entire family to explore the evolution of substrate recognition and regioselectivity of glucosylation. Hydroxycoumarins have been used as the model substrates for the analysis in which 90 sequences have been assayed and 48 sequences shown to recognize these compounds. The study has revealed activity in 6 of the 14 phylogenetic groups of the multigene family, suggesting that basic features of substrate recognition are retained across substantial evolutionary periods.

Key words: Arabidopsis / glucosyltransferases / hydroxycoumarins / phylogeny / plant secondary metabolites


    Introduction
 Top
 Abstract
 Introduction
 Results
 Discussion
 Materials and methods
 References
 
Glycosyltransferases (UGTs) involved in the synthesis and modification of glycoconjugates have been classified on the basis of their protein sequence similarity into 56 distinct families. In Arabidopsis thaliana, a model plant species used extensively to explore gene function, representatives of 28 of these families have been identified in the completed genome (http://afmb.cnrs-mrs.fr/~cazy/CAZY/index.html, last updated March 1, 2002). The largest of these families is Family 1, and within that group there are 107 UGT sequences known to possess a consensus identified in plant enzymes typically transferring glucose from UDP-glucose to small-molecular-weight acceptors (Hughes and Hughes, 1994Go; Ross et al., 2001Go). The same consensus is found in the family of mammalian UDP-glucuronosyltransferases involved in detoxification and cellular homeostasis (reviewed in Mackenzie, 1990Go, 1995Go). In plants, many of the major families of secondary metabolites, such as the phenylpropanoids, flavonoids, and benzoates, are known to exist in glycosylated form (reviewed in Hösel, 1981Go), as well as the major classes of hormones, including glycosylated metabolites of auxins, cytokinins, gibberellins, and abscisic acid (reviewed in Kleczkowski and Schell, 1995Go). Plant UGTs have also been shown to recognize xenobiotics, playing a role in detoxification of both pesticides and herbicides (Wetzel and Sandermann, 1994Go; Davis et al., 1991Go).

Interestingly, the action of UGTs can result in the formation of either a glucose ester or a glucoside. The former is a high-energy compound acting as biosynthetic intermediate in which the aglycone can be further transferred onto a second acceptor. The classic example of this event is the glucosylation of sinapic acid, yielding sinapoylglucose, which acts as an intermediate in the formation of sinapoylmalate and sinapoylcholine (Tkotz and Strack, 1980Go; Strack et al., 1983Go). Similarly, the coumaroyl moiety of 1-O-p-coumaroylglucose is transferred to quinic acid, forming p-coumaroylquinic acid (Kojima and Villegas, 1984Go). However, for many glucose esters, the second acceptor remains unknown. In contrast to the biosynthetic role of glucose esters, most glucosides are thought to represent detoxification compounds, although monolignol glucosides have long been thought to represent precursors of lignin (reviewed in Whetten et al., 1998Go). Whether the glucose ester or the glucoside is formed, both modifications are considered to provide access to membrane-bound transporters and exit pathways from the cytosol, such as to the cell wall or to the vacuole (reviewed in Jones and Vogt, 2001Go).

Although the number of glucosylated small-molecular-weight compounds in plants is vast and their roles in cellular function are well recognized, progress on the identification and characterization of the enzymes involved is slow. Often the proteins are nonabundant, and purification to homogeneity has proven difficult to achieve. This has hampered the cloning of their respective genes using traditional approaches. Genome sequencing programs have provided a new opportunity to solve these problems, because the databases can be searched for sequences that contain motifs characteristic of proteins with particular properties. Cloning these sequences and expressing recombinant proteins in vitro enables a large-scale screen of catalytic activities to be undertaken, thereby rapidly identifying enzymes of importance.

Using this genomic approach, a number of UGTs previously intractable to biochemical analyses have been identified for the first time and characterized for their in vitro activity. This includes UGTs for the monolignols, coniferyl and sinapyl alcohol, as well as those for the sinapoylglucose intermediate (Lim et al., 2001Go). Similarly, the Arabidopsis gene encoding an enzyme glucosylating indole-3-acetic acid has been characterized (Jackson et al., 2001Go, 2002Go), and two enzymes specific for salicylic acid have been identified (Lim et al., 2002Go).

The availability of such a large, multigene family of UGT sequences can provide the basis for a structural genomic approach in which three-dimensional structures across the family can be compared to their catalytic activities. As yet, however, no structure for any of the enzymes in this family has been elucidated. Nevertheless, the phylogenetic tree established through linear sequence comparison (Li et al., 2001Go) does provide some basis from which to explore molecular evolution of the gene family. This study addresses substrate recognition and regioselectivity of glycosylation by the UGTs using model hydroxycoumarin subtrates.


    Results
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 Abstract
 Introduction
 Results
 Discussion
 Materials and methods
 References
 
The substrates and products
The two hydroxycoumarins, scopoletin and esculetin, were used as substrates to screen 90 recombinant UGTs. The reaction mix was analyzed by reverse-phase high-pressure liquid chromatography (HPLC) and the identity of the products confirmed through comparison of retention times and photo-diode array profile with authentic compounds. The three possible products of the reactions are shown in Figure 1. Scopoletin can only be glucosylated at the 7-hydroxyl group (OH) to form scopolin, whereas esculetin can be glucosylated at either the 6- or the 7-OH position, giving rise to esculin and cichoriin, respectively. No known compound exists naturally in which both the 6- and 7-OH on esculetin are glucosylated, nor was this compound ever detected in this study. All three glucosides have been found in a range of plant species (Betry et al., 1995Go; Fliniaux et al., 1997Go; Taguchi et al., 2000Go; Ito et al., 2000Go; Rees and Harborne, 1985Go; Brown et al., 1975Go; Satô and Hasegawa, 1972Go; Bramwell and Dakshini, 1971Go) but have not been reported in Arabidopsis.



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Fig. 1. Chemical structure of esculetin, scopoletin, and their glucosides.

 
Catalytic activities found in the major groups of UGTs
Phylogenetic analysis of the amino acid sequences from the Arabidopsis UGT superfamily has defined an unrooted phylogenetic tree with a total number of 14 distinct groups (Ross et al., 2001Go). Members of six different groups within the phylogenetic tree were found to display activity toward the hydroxycoumarins tested. The results are shown within the context of the phylogenetic tree in Figures 2GoGo5 and summarized in Figure 6. Of the UGTs analyzed, all members of two major groups, D and E, were found to glucosylate both hydroxycoumarins, with the exception of only one enzyme. The detailed data from group D are shown in Figure 2. Throughout the group, all the UGTs with activity can glucosylate scopoletin and prefer the 7-OH position of esculetin. UGT73D1 was inactive, suggesting a loss of catalytic activity toward the hydroxycoumarins during evolution. However, because no other substrate for this enzyme has as yet been identified, it is also possible that the protein is inactive.



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Fig. 2. The in vitro activity of group D UGTs toward esculetin and scopoletin. The unrooted phylogenetic tree of Arabidopsis UGTs is adopted from the previous report (Ross et al., 2001Go). Bootstrap values over 60% are indicated above the nodes, with the number on the left indicating neighbor-joining value and that on the right indicating parsimony. Hypothetical intron gain and loss are indicated by diamonds (for details, see Li et al., 2001Go). The UGT that did not display activity is shown as a dotted line. UGT73C7 produced the same level of esculin and cichoriin under the standard reaction conditions. The possible loss of function event is indicated by an arrow.

 


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Fig. 3. (A) The in vitro activity of group E UGTs toward esculetin and scopoletin. The UGTs that prefer the 7-OH position of esculetin are shown in green. The UGTs that prefer the 6-OH position of esculetin are shown in blue. The UGTs that have not been purified successfully as soluble recombinant proteins are shown in black. The possible regioselectivity switching events are indicated by arrows. (B) and (C) show the other two possible phylogenetic placements of the UGT71 and UGT72 families and UGT88A1 in group E.

 


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Fig. 4. The in vitro activity of group H UGTs toward esculetin and scopoletin. The UGTs that did not display activity or have not been purified successfully as soluble proteins are shown as dotted lines. The possible loss or gain of function events are indicated by arrows.

 


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Fig. 5. The in vitro activity of group L UGTs toward esculetin and scopoletin. The UGTs that did not display activity or have not been purified successfully as soluble proteins are shown by dotted lines. The possible loss of function events are indicated by arrows.

 


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Fig. 6. An overview of the in vitro activity of Arabidopsis UGTs toward esculetin and scopoletin. Similar to Figures 2GoGo5, the UGTs that prefer the 7-OH position of esculetin are shown in green and the UGTs that prefer the 6-OH position of esculetin are shown in blue. The UGTs that did not show activity are shown in red. The UGTs that have not been purified successfully as soluble recombinant proteins are shown in gray.

 
Results from group E are shown in Figure 3A. All the UGTs analyzed could glucosylate scopoletin. However, when esculetin was used as the substrate, a regioselectivity within the group was found with respect to the 6- and 7-OH positions. UGT71 family and UGT72B3 glucosylated position 7-OH of esculetin, producing esculin, whereas all other members of UGT72 family only glucosylated position 6-OH, producing cichoriin. Viewed within the context of the phylogeny, two regioselectivity switching events must have occurred. One of these events occurred early in the evolution of group E after the UGT71 family split from its common ancestor with UGT88A1. If this were the case, the common ancestor of group E would probably have had a regioselectivity to the 6-OH of esculetin because most of the deep branches in this group glucosylate esculetin at the 6-OH position.

However, due to the highly divergent nature of the UGT88A1 sequence and the inconclusive bootstrap support for its placement (79/65, neighbor joining/parsimony), two other possibilities cannot be ruled out. One alternative is that UGT88A1 branched off before the split of the UGT72 and UGT71 families, making it the outgroup to both. In this case, the interpretation of the tree is similar to that already discussed, except that the regioselectivity switching event would have occurred after the split of the two families (Figure 3B). Alternatively, UGT88A1 could belong to the branch with the UGT72 family; the regioselectivity switching event would then have occurred shortly after the branch including the UGT72 family and UGT88A1 separated from UGT71 family, with the ancestor's regioselectivity towardesculetin unknown (Figure 3C).

Regardless of the timing of the first switching event, the second regioselectivity switching event in group E happened either in the common ancestor of UGT72B2 and UGT72B3 or at some stage along the unique line leading to UGT72B3, as indicated in Figure 3A. This event switched the regioselectivity of UGT72B3 from the 6-OH position to the 7-OH position of esculetin. The exact interpretation depends on the regioselectivity of UGT72B2, which has not been obtained in soluble form. The availability of UGT72B2 will help confirm the regioselectivity switching event in this branch.

Data from groups H and L are shown in Figures 4 and 5. When activity was observed toward the model substrates, the UGTs were found to glucosylate scopoletin and esculetin only at the 7-OH position. Interpretation of negative results in group H is difficult because no other catalytic activity of these proteins has as yet been observed. However, in group L, there is clear evidence for loss of activity toward hydroxycoumarins in at least one evolutionary event leading to UGT84A2 (Figure 5), because this enzyme has known activity toward phenylpropanoids (Lim et al., 2001Go).


    Discussion
 Top
 Abstract
 Introduction
 Results
 Discussion
 Materials and methods
 References
 
Recent studies have shown that plant genomes contain a great diversity of gene sequences predicted to be involved in glycan synthesis and modification (Campbell et al., 1997Go; Henrissat and Davies, 2000Go). In this context, it is possible that these high numbers of UGTs glycosylating small-molecular-weight acceptors reflects the plasticity of plant development and plant metabolism. Because plants are sedentary organisms, their survival depends on rapid adaptation to a changing biotic and abiotic environment. One likely evolutionary consequence is the vast diversity of secondary metabolites, such as those involved in protection against oxidative stress and those involved in interactions between plants and other organisms. Glycosylation of these metabolites is a common occurrence and is thought to play a key role in cellular homeostasis.

We use a genomic approach to study this multigene family of UGTs in Arabidopsis. The sequences have been cloned, expressed as recombinant proteins in Escherichia coli, and used to screen for catalytic activity in vitro toward substrates of importance. This has led to the identification of genes encoding UGTs specific for hydroxycinnamates, benzoates, and plant hormones (Lim et al., 2001Go, 2002Go; Jackson et al., 2001Go). Despite the recent successes, substrates for only ~18 UGTs out of the 107 have been identified so far. Interestingly, from these limited studies, there are data showing that linear sequence homology correlates with similarity in substrate recognition. For example, the four UGTs 84A1–A4 all recognize the carboxyl group of cinnamic acids and form a long deep branch in group L (Lim et al., 2001Go). Similarly, UGT74F1 and UGT74F2, again forming a long deep branch in group L, are the only two enzymes that recognize salicylic acid (Lim et al., 2002Go). Although both of these enzymes recognize the same substrate, they exhibit different regioselectivity of glucosylation with UGT74F1 glucosylating the 2-OH of salicylic acid to form an O-glucoside, whereas UGT74F2 transfers glucose onto the carboxyl group to produce a glucose ester.

To explore the molecular evolution of substrate recognition and regioselectivity of glucosylation in more depth, this study uses model substrates with features recognized by many different UGTs spread across the entire family. Earlier work had shown that a number of UGTs could recognize the hydroxycoumarin scopoletin (Lim et al., 2001Go). This suggested that scopoletin could be a useful model substrate. Esculetin, another hydroxycoumarin, has one additional OH group, making it possible to analyze both substrate recognition and regioselectivity on the ring. Surprisingly, as summarized in Figure 6, as many as three major phylogenetic groups (groups D, E, and L) all show activity toward the two hydroxycoumarins. It is unlikely that all of these UGTs will catalyze the glucosylation of these compounds in vivo. However, the results of this study imply that there are at least three ancestral UGTs that once recognized substrates with features common to hydroxycoumarins. During evolution, new sequences evolved to recognize structurally related metabolites. Although we know that these include the monolignols, hydroxycinnamates, benzoates, and auxins (Lim et al., 2001Go, 2002Go; Jackson et al., 2001Go), the precise identity of other endogenous metabolites is yet to be revealed.

Conclusions on the correlation between sequence similarities and substrate recognition have been drawn from positive results. Negative results are more difficult to interpret because there are at least two possible explanations. Individuals of an entire group may be all catalytically inactive. Alternatively, the group members simply may not recognize the features of hydroxycoumarins, but instead recognize quite different compounds. It may be relevant that all of the compounds we have analyzed so far are metabolites on the shikimate pathway.

In addition to overall substrate recognition, an interesting observation has emerged concerning regioselectivity of glucosylation in group E. Following an ancestral change in regioselectivity between 6- and 7-OH glucosylation, all individuals of the two separate branches retain the different regioselectivity. In a much more recent evolutionary event, another switching event has occurred once (Figures 3 and 6).

Data gained in this study of a multigene family in Arabidopsis show a correlation between phylogenetic relatedness and substrate recognition. The question arises as to whether there is a similar correlation when UGTs from different plant species are analyzed. Two recent reviews have summarized plant UGTs and their catalytic activities (reviewed in Jones and Vogt, 2001Go; Keegstra and Raikhel, 2001Go). When these sequences are included in the Arabidopsis phylogenetic tree, the eight UGTs known to recognize substrates structurally similar to the hydroxycoumarins are all located in the same three major groups D, E, and L (Li et al., 2001Go; Ross et al., 2001Go). It will be interesting to examine UGTs from rice, of which the genome has been sequenced (Yu et al., 2002Go; Goff et al., 2002Go), to determine whether substrate recognition again remains conserved across the major phylogenetic groups.


    Materials and methods
 Top
 Abstract
 Introduction
 Results
 Discussion
 Materials and methods
 References
 
Construction of GST-UGT expression plasmids
DNA fragments corresponding to putative UGT sequences with no introns were amplified from A. thaliana Columbia genomic DNA by polymerase chain reaction (PCR) and were subcloned into the appropriate restriction sites on the multiple cloning site of the glutathione-S-transferase (GST) gene fusion vector pGEX-2T (Amersham Pharmacia Biotech, Chalfont St. Giles, UK) (Li et al., 2001Go). For those sequences containing introns, the expression plasmids were constructed either using the full-length expressed sequence tag obtained from the Arabidopsis Biological Resource Center or by removing the predicted introns described by Li et al. (2001)Go. For intron removal, specific oligonucleotide sets were designed to amplify the entire plasmids except for the predicted intron regions as described in Lim et al. (2002)Go, and the PCR reactions were set up following the conditions described previously (Lim et al., 1998Go). The PCR products were analyzed and purified from 1% (w/v) agarose gel, phosphorylated using T4 polynucleotide kinase, and self-ligated using T4 DNA ligase (Sambrook et al., 1989Go). The deletions of introns were confirmed by sequencing using appropriate oligonucleotides. The intronless coding region fragments were then subcloned into the pGEX-2T expression vector and all of the nucleotide sequences were confirmed by DNA Sequencing Services of Oxford University (UK) and Qiagen (Hilden, Germany).

Glucosyltransferase activity assay
Recombinant UGTs were purified as GST fusion proteins from E. coli carrying the expression constructs following the methods described previously (Lim et al., 2001Go). Each glucosyltransferase activity assay mix (200 µl) contained 1 µg of recombinant protein, 50 mM Tris-HCl, pH 7.0, 14 mM 2-mercaptoethanol, 5 mM UDP-glucose, and 1 mM phenolic substrate. The reaction was carried out at 30°C for 30 min and was stopped by the addition of 20 µl trichloroacetic acid (240 mg/ml), quick-frozen, and stored at -20°C prior to the reverse-phase HPLC analysis. The specific enzyme activity was expressed as nmol of phenolic compound glucosylated per second (nkat) by 1 mg of protein in 30 min of reaction time.

HPLC analysis
Reverse-phase HPLC (SpectraSYSTEM HPLC systems and UV6000LP Photodiode Array Detector, ThermoQuest, Manchester, UK) analyses were carried out using a Columbus 5 µ C18 column (250x4.6 mm, Phenomenex, Macclesfield, UK). A linear gradient of acetonitrile in H2O (all solutions contained 0.1% trifluoroacetic acid) at 1 ml/min over 20 min was used to separate the glucose conjugates from their aglycone. The HPLC methods were as follows: esculetin, {lambda}296\ nm, 10–20% acetonitrile; scopoletin, {lambda}296\ nm, 10–30% acetonitrile. The retention time (Rt) of the glucose conjugates analyzed was as follows: esculin, Rt=9.7 min; cichoriin, Rt=9.6 min; scopolin, Rt=9.9 min.


    Acknowledgements
 
The research was supported in part by the Biotechnology and Biological Sciences Research Council grant 87/97 8855 to D.J.B. and in part by funding from the Garfield Western Foundation for the Centre for Novel Agricultural Products. We thank Christine A. Williams (University of Reading) for providing authentic cichoriin and David A. Ashford for helpful discussions.


    Footnotes
 
2 Present address: Department of Biological Sciences, IENS, Lancaster University, Lancaster LA1 4YQ, United Kingdom Back

1 To whom correspondence should be addressed; e-mail:djb32{at}york.ac.uk Back


    Abbreviations
 
GST, glutathione-S-transferase; HPLC, high pressure liquid chromatography; OH, hydroxyl group; PCR, polymerase chain reaction; UGT, glycosyltransferase.


    References
 Top
 Abstract
 Introduction
 Results
 Discussion
 Materials and methods
 References
 
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