Dehydrogenase Attack FAD Cofactor

doi:10.1016/j.jmb.2008.05.044

J. Mol. Biol. (2008) 380, 886–899

Available online at www.sciencedirect.com

Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase Attack FAD Cofactor David Kopečný 1,2 ⁎, Marek Šebela 2 , Pierre Briozzo 3 , Lukáš Spíchal 4 , Nicole Houba-Hérin 1 , Vlastimil Mašek 5 , Nathalie Joly 3 , Catherine Madzak 6 , Pavel Anzenbacher 5 and Michel Laloue 1 1

Laboratoire de Biologie Cellulaire, INRA, Route de Saint-Cyr, F-78026 Versailles Cedex, France 2

Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 11, CZ78371 Olomouc, Czech Republic 3

UMR206 Chimie Biologique, INRA-AgroParisTech, F-78850 Thiverval-Grignon, France

4

Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, ASCR, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic

5

Department of Pharmacology, Faculty of Medicine, Palacký University, Hněvotínská 3, CZ-77215 Olomouc, Czech Republic

Cytokinin oxidases/dehydrogenases (CKOs) mediate catabolic regulation of cytokinin levels in plants. Several substrate analogs containing an unsaturated side chain were studied for their possible inhibitory effect on maize CKO (ZmCKO1) by use of various bioanalytical methods. Two allenic derivatives, N6-(buta-2,3-dienyl)adenine (HA-8) and N6-(penta-2,3-dienyl)adenine (HA-1), were identified as strong mechanism-based inhibitors of the enzyme. Despite exhaustive dialysis, the enzyme remained inhibited. Conversely, substrate analogs with a triple bond in the side chain were much weaker inactivators. The crystal structures of recombinant ZmCKO1 complexed with HA-1 or HA-8 were solved to 1.95 Å resolution. Together with Raman spectra of the inactivated enzyme, it was revealed that reactive imine intermediates generated by oxidation of the allenic inhibitors covalently bind to the flavin adenine dinucleotide (FAD) cofactor. The binding occurs at the C4a atom of the isoalloxazine ring of FAD, the planarity of which is consequently disrupted. All the compounds under study were also analyzed for binding to the Arabidopsis cytokinin receptors AHK3 and AHK4 in a bacterial receptor assay and for cytokinin activity in the Amaranthus bioassay. HA-1 and HA-8 were found to be good receptor ligands with a significant cytokinin activity. Nevertheless, due to their ability to inactivate CKO in the desired time intervals or developmental stages, they both represent attractive compounds for physiological studies, as the inhibition mechanism of HA-1 and HA-8 is mainly FAD dependent. © 2008 Elsevier Ltd. All rights reserved.

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UMR1238, Microbiologie et Génétique Moléculaire, INRACNRS-AgroParisTech, F-78850 Thiverval-Grignon, France Received 18 February 2008; received in revised form 16 May 2008; accepted 20 May 2008 Available online 24 May 2008

Edited by R. Huber

Keywords: cytokinin oxidase/dehydrogenase; cytokinin signaling; protein structure; maize; mechanism-based inhibitor

*Corresponding author. Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic. E-mail address: [email protected]. Abbreviations used: AHK, Arabidopsis histidine kinase; DCPIP, 2,6-dichlorophenol indophenol; FAD, flavin adenine dinucleotide; HA-1, N6-(penta-2,3-dienyl)adenine; HA-8, N6-(buta-2,3-dienyl)adenine; HA-10, N6-(4-methyl-penta-2,3dienyl)adenine; iP, N6-(2-isopentenyl)adenine; iPR, N6-(2-isopentenyl)adenosine; MALDI-TOF, matrix-assisted laser desorption/ionization time-of-flight; RM1, N6-(4-hydroxy-2-butynyl)adenine; RM2, N6-(4-epoxy-2-butynyl)adenine; RM3, N6-(2-propynyl)adenine; RM4, N6-(4,4-dimethoxy-2-butynyl)adenine; RM5, N6-(4,4-diethoxy-2-butynyl)adenine; RM6, N6-(2-butynyl)adenine; Br-iP, N6-(2-bromo-2-isopentenyl)adenine; Z (or tZ), N6-(trans-4-hydroxy-3-methyl-2-buten1-yl)adenine (i.e., zeatin); ZmCKO, cytokinin oxidase/dehydrogenase from Zea mays. 0022-2836/$ - see front matter © 2008 Elsevier Ltd. All rights reserved.

Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

Introduction Cytokinins are plant hormones regulating numerous developmental events.1 Naturally occurring cytokinins are N6-substituted adenine/adenosine derivatives carrying either an unsaturated isoprenoid chain or a benzyl moiety. Isoprenoid cytokinins are classified into isopentenyladenine (iP)-type or zeatin [N6-(trans-4-hydroxy-3-methyl-2-buten-1-yl) adenine (Z)]-type derivatives. Cytokinin signaling is triggered by the activation of a phosphorelay cascade beginning with histidine kinase–cytokinin membrane receptors.2–4 In Arabidopsis thaliana, three receptors AHK2, AHK3 and AHK4 have been described. While AHK3 has broad ligand specificity, AHK4 is activated preferentially by cytokinin free bases but not by the corresponding nucleosides. Cytokinin homeostasis in plants is regulated through their biosynthesis, interconversion, transient and/or irreversible conjugation or irreversible degradation.1 The latter step is mediated by cytokinin oxidase/dehydrogenase (CKO/CKX, EC 1.5.99.12). CKO catalyzes the oxidative breakdown of Δ2-isoprenoid cytokinins to form adenine/adenosine and the corresponding unsaturated aldehyde.5 CKO-coding gene and mRNA sequences were first reported for the maize enzyme (named ZmCKX1 or ZmCKO1, EMBL/GenBank accession numbers AF044603 and Y18377).6,7 ZmCKO1 is an extracellular, monomeric and glycosylated flavoprotein with a molecular mass of 63 kDa.7 The flavin adenine dinucleotide (FAD) cofactor is covalently attached via an 8α-N(1)-histidyl linkage. In maize, the ZmCKO1 gene belongs to a small multigene family of at least 13 putative ZmCKO genes. It is strongly expressed in the kernel, mainly in the embryo.8 It is believed that ZmCKO1 protects the early embryo from high levels of cytokinins present in the surrounding endosperm and participates in its correct development. The oxidative degradation of cytokinins mediated by CKO proceeds through a two-electron transfer to FAD cofactor with concomitant formation of an imine intermediate.9 The enzyme is able to operate as either an oxidase or a dehydrogenase. The electrons are transferred to oxygen10 or quinones11 as terminal acceptors, respectively, and the reduced FAD is reoxidized. The recently published crystal structure of ZmCKO112 revealed that the cytokinin substrate binds in a “plug-into-socket” mode and that Asp169 forms a hydrogen bond with the substrate amine group. N 6 -(Buta-2,3-dienyl)adenine (HA-8) was previously reported to inhibit CKO activity in a timeand concentration-dependent manner.7 This was confirmed by Suttle and Mornet13 for HA-8 and another similar derivative–N 6 -(penta-2,3-dienyl) adenine (HA-1). A mechanism-based mode of inactivation was suggested for both compounds. However, at that time no determination of the kinetic constants and of the target site in the enzyme was performed. Substrate analogs bearing a β-positioned halogen or unsaturated acetylenic or allenic group

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are known as mechanism-based inhibitors of many oxidases acting on amino groups. They undergo turnover-dependent conversion to electrophilic products capable of covalent binding to an active-site nucleophile, resulting in enzyme inactivation.14 Mechanism-based inhibitors are characterized by both substrate saturation kinetics and pseudo-firstorder time-dependent irreversible inactivation. The enzyme can be protected from inactivation by the addition of natural substrates or competitive inhibitors. Because of the irreversibility and specificity of the inactivation, such compounds would offer many advantages for physiological studies.15 In this article, we provide further evidence for the formation of imine intermediate during the oxidative conversion of cytokinin substrate by ZmCKO1. Taking this mechanism into consideration, we chose a group of synthetic cytokinin analogs bearing an unsaturated side chain and tested them for their substrate and inhibitory properties towards ZmCKO1. Kinetic and spectroscopic measurements showed that two of these analogs, HA-8 and HA-1, are potent mechanism-based inhibitors of the enzyme. Matrix-assisted laser desorption/ionization time-offlight (MALDI-TOF) peptide mass fingerprinting and Raman spectroscopy suggested FAD cofactor as the target site of the inhibitors. The final evidence of the inactivation mode involving FAD cofactor was provided by the crystal structures of ZmCKO1 reacted with HA-1 and HA-8, which were solved up to 1.95 Å resolution. Binding tests with the Arabidopsis cytokinin receptors AHK3 and AHK4 revealed a correlation between the ability of the tested compounds to react with ZmCKO1 and their affinity for cytokinin-specific receptors. These findings have an implication for possible physiological in vivo studies that rely on effective and specific elimination of CKO activity. The potential of such an application has already been demonstrated on a potato model.13

Results Analysis of imine intermediate Following a long-term study on CKO reaction intermediates,9 we found that the imine intermediate can form adducts in the presence of nucleophiles such as β-mercaptoethanol. Using tritiated N6-(2-isopentenyl)adenine (iP) or N6-(2-isopentenyl) adenosine (iPR) as ZmCKO1 substrates, HPLC analysis of the reaction mixture indicated the formation of several products that interconverted to a single species after 24 h (Fig. 1a). The peak eluted at 14.5 min was collected and its chemical content was analyzed. The UV spectrum of the compound gave an absorption maximum at 298 nm (ε = 38,900 M− 1 cm− 1), which clearly differed from the maximum of the unreacted substrate at 269 nm (ε = 20,000 M− 1 cm− 1) (Fig. 1b). The extinction coefficient for this compound was calculated using a concentration value deduced from the radioactivity asso-

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Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

Fig. 1. Isolation of CKO reaction intermediate. (a) HPLC of putative imine intermediate done 24 h after the reaction and isocratically eluted with 50% methanol. CKO reaction was performed in the presence of β-mercaptoethanol. Ade, adenine; iP, isopentenyladenine. (b) Shift of absorption maximum of the putative imine intermediate. Absorption spectra were measured in 50% methanol and show characteristic absorption maxima of iP (λ = 269 nm, ε ∼ 20,000 M− 1 cm− 1) and putative imine of iP (λ = 298 nm, ε ∼ 38,900 M− 1 cm− 1).

ciated with the corresponding chromatographic peak. The compound could be further reduced by sodium cyanoborohydride back to iP (or iPR) and

underwent hydrolysis to adenine (or adenosine) in 0.1 M acetic acid as analyzed by HPLC (data not shown). On the basis of these results, the compound

Table 1. N6-adenine derivatives with allenic and alkyne side chains and their reaction with ZmCKO1

Ade, adenine; +, reaction; −, no reaction; (+), extremely slow reaction. The ability of the compounds to reduce the enzyme-bound FAD (i.e., passing through the reductive CKO half-reaction) was characterized by bleaching of the cofactor absorption maximum at 445 nm. The compounds were added in an excess of 50:1. Substrate properties at 100 μM concentration were evaluated by DCPIP activity assay.16 The identity of all compounds was checked by direct-injection electrospray ionization mass spectrometry of diluted methanolic solutions on a Q-Tof micro instrument (Micromass).

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Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

was assigned to the putative imine intermediate of iP (iP-imine). The identity of putative iP-imine was confirmed in a similar trial performed in parallel with untritiated iP. The putative iP-imine, isolated after HPLC, was analyzed by electron impact mass spectrometry and provided a molecular ion (M+) with m/z 201 (C10H11N5+) and two characteristic fragment peaks with m/z 186 (loss of a methyl group, C9H8N5+) and 82 (the imine side chain, C5H8N+). Different attempts to synthesize this imine and use it as a standard were unsuccessful (René Mornet, University of Angers, personal communication). Confirmation of the production of an imine intermediate ion during the reaction catalyzed by CKO allowed a clear interpretation of subsequent experiments with synthetic reactive substrate analogs. Kinetic and spectral analyses of ZmCKO1 inhibition Ten synthetic substrate analogs (chemical formulas are given in Table 1) were studied for their substrate and inhibitory properties towards ZmCKO1.

Among these compounds, three were allenic derivatives differing in the length of their side chain [HA-1, HA-8 and N6-(4-methyl-penta-2,3-dienyl) adenine (HA-10)]. Resting oxidized ZmCKO1 provides an absorption spectrum with two distinct maxima at 360 and 445 nm in the visible region.10 The addition of HA-1 and HA-8 in a 50:1 excess resulted in complete bleaching of these absorption bands within 10 s. No bleaching was observed with HA-10 or when the compounds were mixed with free FAD (Fig. 2a), showing (particularly in the latter case) that bleaching occurs only as a result of enzymatic reaction. The original enzyme spectrum could not be restored by either prolonged aerobic incubation of the reaction mixture or dialysis. Similarly, the addition of HA-8 or HA-1 abolished fluorescence properties of the enzyme. The characteristic fluorescence emission (λmax = 525 nm; excitation at 450 nm) and excitation (λmax = 360 and 450 nm; emission at 525 nm) spectra, which were previously reported,10 could not be measured using the inactivated enzyme even after exhaustive dialysis. The reaction of ZmCKO1 with HA-8 or HA-1 also resulted in

Fig. 2. ZmCKO1 inactivation by mechanism-based inhibitors. (a) Difference absorption spectrophotometry of HA-8 interaction (500 μM) with free FAD (10 μM) and recombinant ZmCKO1 (10 μM, inset) in air-saturated 20 mM Tris–HCl, pH 8.0. The spectra were recorded at 0.1-s intervals for 10 s (indicated as 1) and then at 5-min intervals for 30 min (indicated as 2) at 30 °C. (b) Spectrophotometric titration of the FAD cofactor of ZmCKO1 with HA-8 and HA-1. Stepwise reduction of the enzyme by HA-1 ( , continuous line) and HA-8 (▴, dashed line) in 20 mM Tris–HCl, pH 8.0, was followed by decrease in absorption at 445 nm. (c and d) Time-dependent inactivation of ZmCKO1 by HA-8 and HA-1. The semilogarithmic plot was constructed for the following inhibitor concentrations: HA-8 (♦, 10; , 25; ▴, 50 μM), HA-1 (♦, 20; , 50; ▴, 100 μM). Activity was measured in 20 mM Tris–HCl, pH 8.0, at 4 °C (HA-8) and at 37 °C (HA-1) by means of the aminophenol method.17 The insets show the corresponding Kitz–Wilson replots for the determination of kinact and KI values.

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Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

bleaching of the electron acceptor 2,6-dichlorophenol indophenol (DCPIP), indicating FAD reoxidation during catalysis. Chromatofocusing performed after dialysis did not show any change in the isoelectric point of the enzyme (pI = 6.25). Spectrophotometric titrations of ZmCKO1 by HA-8 and HA-1 were monitored by decreasing absorbance at 445 nm. The equivalence points were determined from linear regression of the measured absorbance curves (intersections with the zero line, Fig. 2b). The obtained molar ratio values of HA-8/ ZmCKO1 and HA-1/ZmCKO1 were 2.0 and 2.6, respectively. When the equivalence was reached, ZmCKO1 was completely inhibited in the reaction mixture. Similar values were also obtained from partition ratio plots (residual activities versus the concentration ratio [HA]/[ZmCKO1]), which allow subtraction of the number of HA molecules leading to product per inactivation event (not shown). The reaction of ZmCKO1 with HA-8 was extremely fast. To slow it down for relevant kinetic results, the reaction mixture was kept on a water–ice bath during incubation. Pseudo-first-order inhibition kinetics was observed with HA-8 concentrations ranging from 10 to 50 μM. Semilogarithmic plots of residual activity versus incubation time at 4 °C were constructed, and from the Kitz–Wilson replot (Fig. 2c), the rate of inactivation (kinact) of 0.18 min− 1 and apparent KI value (half-maximal inactivation) of 10 μM for the reaction of HA-8 with ZmCKO1 were determined. The time required for half of the enzyme to become inactivated in the presence of saturating HA-8 concentration (t1/2 at saturation) was 3.9 min. Compared to the results with HA-8, ZmCKO1 inactivation by HA-1 was much slower. The enzyme was incubated with 10–100 μM HA-1 at 37 °C and the following parameters were analyzed from the corresponding kinetic plots (Fig. 2d): kinact = 0.22 min− 1, KI = 26 μM; t1/2 at saturation was 3.6 min. Only two of the six tested substrate analogs with an alkyne side chain, namely, N6-(4-hydroxy-2butynyl)adenine (RM1) and N6-(2-butynyl)adenine (RM6), behaved as substrates, i.e., bleached the enzyme spectrum, even over a considerable time period. The addition of RM1 or RM6 in an excess of 50:1 resulted in complete bleaching of the ZmCKO1 spectrum within 10 min. However, the reaction was significantly slower compared to those with HA-1 and HA-8. The relative activity with RM1 and RM6, measured at 100 μM concentrations by the initial-rate DCPIP method, was only 0.08% (Km = 380 μM) and 0.31% (Km = 92 μM), respectively, compared to that with iP (Km = 1.1 μM). The other RM compounds did not show substrate properties in this assay. The inhibitory properties of all RM compounds were measured using 10 μM iP as a substrate. An inhibition of 10–20% was observed only at 300 μM (i.e., in a large excess towards the substrate). The 2-bromine derivative of iP [N6-(2-bromo-2isopentenyl)adenine (Br-iP)] was also found to act as a very weak inhibitor (IC50 ∼ 240 μM). Reaction of ZmCKO1 with RM1 or RM6 alone led to enzyme inhibition, and the enzyme remained inhibited even

after exhaustive dialysis. When an excess of 50:1 (500:1) towards the enzyme was used, ZmCKO1 activity was reduced to 45% (10%) with RM1 and to 95% (48%) with RM6. The measured residual activity reflected the reestablished FAD absorbance, indicating that a part of FAD was irreversibly modified. MALDI-TOF mass spectrometry of ZmCKO1 Reactive products arising from enzymatic conversion of mechanism-based inhibitors covalently bind to an important active-site component, which results in the inactivation of the enzyme. To evaluate the mode of inactivation by searching for amino acid labeling, MALDI-TOF peptide mass fingerprinting was carried out with tryptic digests of unreacted ZmCKO1 and ZmCKO1 inactivated by HA-1 or HA8. All fingerprints were almost identical and matched to the accession number T51929 in the MSDB database (data not shown). Only one significant difference was observed: peptide peaks with m/z 2778.4, 2794.4 and 2810.3, registered as well pronounced in the fingerprint of unreacted ZmCKO1, almost disappeared from the fingerprints of the inactivated enzyme. These peaks correspond to a deflavinylated cofactor tryptic peptide GHSLMGQAFAPGGVVVNMASLGDAAAPPR and its derivatives with one or two oxidized methionine residues, respectively. Interestingly, there was a signal of free FAD observed in the fingerprint spectra of ZmCKO1 and inactivated ZmCKO1 acquired using the reflectron mode for negative ions ([M − H]− = 784.1). The release of FAD probably occurred under MALDI conditions. A comparable observation has recently been reported for a fungal pyranose 2-oxidase, where FAD is covalently attached through a histidyl residue similarly as in ZmCKO1.18 In any case, no peak was observed corresponding to the cofactor peptide containing bound FAD (a theoretical m/z value of 3559, [M − H]−) or, in the case of the inactivated enzyme, an adduct of the FAD-containing peptide with an oxidation product of HA-1 or HA-8. The reason is probably the instability of the adduct during laser desorption, or the complete flavopeptide is too large for an efficient ionization. Intact mass measurements using MALDI-TOF mass spectrometry provided a relative mass value of ZmCKO1 of 69,865 ± 70, which was shifted to 70,149 ± 74 after the reaction with HA-8 (both numbers represent mean values from 10 measurements). Recombinant ZmCKO1 produced in Y. lipolytica is a highly glycosylated protein containing 22% carbohydrates. N-Glycan chains, which occupy five glycosylation sites, cause a microheterogeneity of the enzyme. Consequently, MALDI-TOF mass spectrometry of intact ZmCKO1 shows a broad quasimolecular peak10 that makes peak labeling and reading of average mass difficult. Raman spectroscopy of inactivated ZmCKO1 Peptide mass fingerprinting of the inactivated ZmCKO1 indicated possible labeling of the enzyme

Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

cofactor. Such a modification would be expected to affect characteristic FAD signals in Raman spectroscopy and could therefore provide an insight into the mechanism of inactivation. The flavin moiety of flavoproteins gives rise to 14 vibrational bands (labeled by Roman numerals I–XIV) between 1050 and 1650 cm− 1 assigned to vibrations of different parts of the flavin rings.19 These bands are strongly enhanced by the resonance Raman technique, i.e., using excitation wavelengths close to the visible absorption bands of FAD at 360–370 and 450 nm.20 To initially check the integrity of the flavin moiety, the resonance Raman spectrum (excited at 441.6 nm) of native ZmCKO1 was obtained and compared to that of a model flavoprotein, Aspergillus niger glucose oxidase. This confirmed the intactness of the flavin (data not shown). Since the studied inactivators cause bleaching of the cofactor absorption, only Raman spectra could be measured in this case without the resonance effect. Figure 3 shows Raman spectra of ZmCKO1 (either in oxidized or in reduced state) and ZmCKO1 inactivated by RM1, HA-8 and HA-1 following excitation at 532 nm. The spectrum of resting oxidized ZmCKO1 still shows the presence of characteristic FAD bands, which almost all disappear from the spectrum of the enzyme reduced by sodium borohydride. When ZmCKO1 is reacted with an excess of the weaker inhibitor RM1 it is not fully inactivated, and this is reflected in a spectrum containing some flavin cofactor bands in agreement with the spectrum of oxidized ZmCKO1. The spectra of ZmCKO1 reacted with HA-8 and HA-1 are approximately the

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same as that of the reduced enzyme. Nevertheless, some differences are clearly visible, including the appearance of several new bands (Fig. 3, labeled by arrows at 761, 1430, 1499 and 1655 cm− 1 ) and the disappearance of two bands (at 876 and 1360 cm− 1 , labeled by asterisks). Crystal structures of ZmCKO1 reacted with HA-1 and HA-8 The final evidence of FAD involvement in the mechanism of inactivation of ZmCKO1 was obtained by X-ray crystallography. The crystal structures of ZmCKO1 reacted with HA-1 and with HA-8 were solved by molecular replacement and refined up to a resolution of 1.95 Å. A summary of the refinement results together with model statistics is given in Table 2. Our ZmCKO1 structure is quasi-identical to that previously published,12 as both protein sequences differ by only two amino acids: Gly79 is replaced by Ala79 and Phe254 by Leu254. This difference is attributed to different maize cultivars initially used to obtain the cDNA or gene sequences, respectively. It was possible to fit to electron density an additional part, GRPWPASLA, at the N-terminus, leaving only 12 amino acids disordered. In addition, the sequence segments DNATAAA (amino acids 337– 343) and VAP (amino acids 462–464), all missing in the 1W1O Protein Data Bank (PDB) file, could be constructed. The amino acid sequence of ZmCKO1 contains eight possible N-glycosylation sites. Our previous results using mass spectrometry showed the presence of about 84 hexose units attributed to five N-glycosylation sites.10 The electron density map

Fig. 3. Raman spectra of ZmCKO1 excited at 532 nm. The spectra were recorded with resting oxidized ZmCKO1 (a), ZmCKO1 reduced by sodium borohydride (b) and ZmCKO1 inactivated by RM1 (c), HA-8 (d) and HA-1 (e). The spectra were normalized to the phenylalanine band at 1003 cm− 1. Asterisks and arrows indicate the bands that disappeared or appeared, respectively, upon enzyme inactivation by the studied adenine derivatives.

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Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

Table 2. Data collection and refinement statistics Data set of ZmCKO1 with Wavelength (Å) Unit cell (Å,°) a b c α=γ β Resolution (Å) Observed reflections Unique reflections Completeness (%) I/σ(I) Rsym (%)d Rcryst (%)e Rfree (%)f RMSD Bond lengths (Å) Bond angles (°) Ramachandran plot Most favorable region (%) Disallowed regions (%) No. water molecules No. sugar molecules

Cytokinin bioassays

HA-1

HA-8

0.98

0.934

250.0 51.2 51.4 90.0 94.2 30–1.95 462,226a 47,543 99.8 (99.9)c 20.0 (3.5) 6.7 (30.3) 18.73 21.59

250.7 50.2 51.2 90.0 93.8 25–1.95 182,729b 44,993 96.3 (99.2) 26.7 (12.0) 3.6 (11.2) 21.48 24.52

0.0059 1.25

0.0063 1.26

90.9 0.0 348 8

89.7 0.0 367 8

a

As indicated by Scalepack. As indicated by XDS. c Numbers in parentheses represent values in the highest resolution shell (last of 10 shells). d Rsym = ∑h∑i|I(h,i) − 〈I(h)〉|/∑h∑iI(h,i), where I(h,i) is the intensity value of the ith measurement of h and 〈I(h)〉 is the corresponding mean value of I(h) for all i measurements. e Rcryst = ∑||Fobs|−|Fcalc||/∑|Fobs|, where |Fobs| and |Fcalc| are the observed and calculated structure factor amplitudes, respectively. f Rfree is the same as Rcryst but calculated with a 10% subset of all reflections that was never used in crystallographic refinement. b

now confirms that there were five glycosylated Asn residues. Ordered sugar molecules were modeled as N-acetyl-D-glucosamine residues attached to Asn63, Asn134, Asn294, Asn323 and Asn338 residues (Fig. 4a). The Asn338 site seems to be glycosylated irregularly, since the density is weaker than that of the other sites. Both solved structures revealed a strong electron density corresponding to a molecule of the inhibitor positioned in proximity of the flavin ring. The electron density of the adenine moiety of HA-1 and HA-8 has a flat shape and its edge (N3–C4–N9 linkage) is exposed to the protein surface. The density of the inhibitor prenyl side chain points upwards and it is curved perpendicularly to the density of the isoalloxazine ring of the FAD cofactor in both cases (Fig. 4b and c). Both inhibitors are hydrogen-bonded to Glu381, Asp169 and two neighboring water molecules (Fig. 4d). The densities of FAD and HA-1 (or HA-8) are clearly connected to each other. This indicates the presence of a newly established covalent bond between the C4a atom of the cofactor isoalloxazine ring and the side chain of the inhibitor. Such a binding could occur if the allenic imine intermediate attacked the reduced FAD cofactor. Interestingly, due to this new bond, the density of the isoalloxazine ring is no longer flat but bulges towards the prenyl chain (Fig. 4e).

The ability of unsaturated cytokinins to bind the cytokinin receptors AHK3 and AHK4 or to induce the accumulation of betacyanin in Amaranthus was studied (Fig. 5). In the Amaranthus bioassay, the allenic derivatives HA-1, HA-8 and HA-10 exhibited similar activities, which were significantly lower than those of iP and Z. Their binding to the Arabidopsis AHK3 and AHK4 receptors resembled the behavior of iP and Z. The following order of affinity was observed: HA-8 N HA-1 N HA-10. Thus, elongation of the allenic side chain reduced binding to AHK receptors. Among other compounds, the alkyne derivative RM1 showed the highest activity in the Amaranthus bioassay followed by N6-(4epoxy-2-butynyl)adenine (RM2) and RM6. The activity of the latter two compounds roughly corresponded to the activity of HA compounds. However, only RM1 and RM6 exhibited a good affinity to the AHK4 and AHK3 receptors. Branching of the alkyne side chain [N6 -(4,4-dimethoxy-2-butynyl)adenine (RM4) and N 6 -(4,4-diethoxy-2-butynyl)adenine (RM5)] led to a reduced binding to the receptors. N6-(2-Propynyl)adenine (RM3), which had a shorter side chain than natural cytokinins (iP, Z), was a ligand of AHK3 but not of AHK4. It exhibited no activity in the Amaranthus bioassay. Contrary to iP, Br-iP was not a ligand of AHK4. However, it showed a high activity in the Amaranthus bioassay.

Discussion Mechanism-based inhibitors (“suicide substrates”) are defined as compounds related either to a substrate or a product of an enzyme and are catalytically converted to reactive species that inactivate the enzyme.15 The inactivation is very specific and allows elimination of a desired enzymatic activity in complex mixtures. To design a functional mechanismbased inhibitor of CKO, the formation of an imine intermediate must be demonstrated. Our results confirmed that the oxidative breakdown of a cytokinin substrate by CKO involves the formation of an imine intermediate. Popelková et al.22 recently described the analysis of imine intermediates produced by the oxidation of several CKO substrates. The stability of the imines allowed their fragmentation analysis and structure assessment by tandem mass spectrometry. In our work, the imine formation by iP oxidation was demonstrated using a different methodological approach. Thus, nine possible CKO suicide substrates were analyzed, as shown in Table 1. They all contain an unsaturated (allenic or alkyne) bond between the second and third carbon atoms of the side chain. Two allenic derivatives, HA-8 and HA-1, were recently shown to cause specific time-dependent inactivation of CKO both in vitro and in vivo, which was prevented by the presence of a substrate such as iP and Z.7,13 However, the molecular mode of this inactivation has not been described. Based on its chemical structure,

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Fig. 4. Crystal structure of ZmCKO1 inactivated by allenic cytokinins. (a) Overall surface of the enzyme. β-Strands are indicated in cyan and α-helices in light blue. FAD cofactor (yellow), bound HA-1 inhibitor (green) and N-acetylglucosamines (orange) are shown in space-filling CPK representation with nitrogen atoms in blue and oxygen atoms in red. The five glycosylated Asn sites are numbered. (b and c) Binding of HA-1 (carbon atoms in green) and HA-8 (carbon atoms in black) in their 2Fo − Fc maps; contoured at 2σ. The new covalent bond between the C3 atom of the inhibitor side chain and the C4a atom of FAD is shown in brown. (d) Hydrogen-bonding interactions of the inhibitor HA-1 at the active site of ZmCKO1. (e) Detail of the covalent bond between HA-1 inhibitor and FAD cofactor. The picture was drawn using Pymol.21

HA-8 could be considered to be the closest analog of the natural ZmCKO1 substrate iP. In comparison with iP, the side chain of HA-8 lacks the branching methyl group. Unlike HA-8, the other allenic compounds HA-1 and HA-10 contain one or two additional methyl groups at the end of their allenic

side chains. Our kinetic data show that HA-8 and HA-1 fulfill all the prescribed criteria for mechanismbased inhibitors: (1) time-dependent loss of enzyme activity, (2) inactivation rate dependent on inhibitor concentration, and (3) enzyme activity that does not recover upon dialysis or gel filtration.23 The rate of

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Fig. 5. Activity of the unsaturated cytokinins in bioassays. The compounds were tested at two different concentrations (1 and 10 μM) for binding to the Arabidopsis AHK3 and AHK4 receptors (E. coli bioassay) and for cytokinin activity (Amaranthus bioassay). Incubation time was 16 or 24 h for the receptors and Amaranthus bioassay, respectively. Values shown in the AHK graphs are means of three replicates and those in the Amaranthus graph are means of five replicates.

inactivation (kinact) of 0.18 min− 1 determined using incubation at 4 °C indicates that HA-8 is an exceptionally strong inactivator. Similar values have been described, e.g., for the fast inactivation of plant diamine oxidases by 1,5-diamino-2-pentyne, but they were obtained at 30 °C.14 HA-1 had kinetic parameters of inactivation similar to those of HA-8. These two compounds have a similar affinity for the active site. However, the rate constant of inactivation for HA-1 was measured at substantially higher temperature (37 °C) than that for HA-8 (4 °C). Taking the Arrhenius equation into consideration, the rate of ZmCKO1 inactivation by HA-8 is roughly eight times faster (i.e., multiplied by 23 assuming a temperature difference of 3 × 10 °C). The isoelectric point of ZmCKO1 did not change after inactivation by HA-1 or HA-8. For that reason, a modification of a nucleophilic amino acid side chain seemed unlikely. MALDI-TOF peptide mass fingerprinting suggested that the inactivating reaction might influence the enzyme cofactor, but this could not be further confirmed by tandem mass spectrometric analysis of the labeled cofactor pep-

tide. In any case, the observed differences between Raman spectra of the inactivated enzyme and native ZmCKO1 (showing the FAD vibrational bands) can be interpreted in favor of a FAD modification as well. Some vibrational modes involving the cofactor were affected; moreover, the inactivation was accompanied by alterations in such signals, probably indicating the localization of the labeling to the C4a atom of FAD (for numbering of atoms, see Fig. 6). Based on previously published observations,19,20,24 the affected signals at 876 and 1499 cm− 1 could refer to the C4a–C10a and C4a–C10/ C4a–N5 stretching vibrations, respectively; those at 758 and 1430 cm− 1 seem to involve vibrations of ring I constituents (stretching C7–C8 vibrations and bending vibrations of the methyl groups at C7 and C8, respectively).19,25 The latter vibrations were influenced indirectly because of the distortion of the whole cofactor izoalloxazine plane. The other altered signals at 1360 and 1645 cm− 1, which might reflect C10a–N10 and C2fO plus C10afN1 vibrations (rings II and III),20,25 respectively, were probably affected for the same reason.

Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

895

Fig. 6. Mechanism of ZmCKO1 inactivation by allenic substrate analogs. In the first step (reductive half-reaction), the enzyme reacts with HA-1 or HA-8 and, as a result, the FAD cofactor is reduced and the corresponding allenic imine intermediate released. Then the allenic intermediate imine undergoes hydrolysis to form the corresponding allenic aldehyde and adenine followed by cofactor reoxidation (route A) or the strongly electrophilic C3 atom of the allenic imine intermediate attacks the C4a atom of the reduced cofactor and a covalent modification of the cofactor occurs (HA–FAD adduct, route B).

The crystal structure of ZmCKO1 with the imine product of iP oxidation bound at the active site has already been described.12 With regard to the reaction mechanism, the substrate amine group points away from the flavin ring and this stereochemically disqualifies the possibility of a nucleophilic attack by the substrate N10 atom on the C4a position of the oxidized cofactor. Therefore, a mechanism involving a direct hydride transfer to the flavin seems to be favored.12 The involvement of the C4a atom of the FAD cofactor in the process of mechanism-based inactivation was confirmed by X-ray crystallography, which clearly demonstrated covalent binding of HA-1 and HA-8 to FAD. Based on the above results, we propose the following mechanism of CKO inactivation (Fig. 6). In the first step, i.e., the reductive half-reaction, the oxidized form of the enzyme (E-FAD) is reduced by the allenic substrate (E-FADH−) via hydride transfer as previously suggested.12 When HA-8 or HA-1 is converted to the

corresponding imine, the side-chain allene is activated, making the C3 atom strongly electrophilic. The activated allenic imine may immediately and irreversibly attack the reduced cofactor at the C4a position and form a covalent bond. For a successful inhibitor attack, the flavin cofactor must be reduced because it is only in the reduced state that the C4a atom is nucleophilic. As can be observed from the crystal structure with HA-1 and HA-8, this covalent linkage breaks the original planarity of the cofactor isoalloxazine ring. The newly arranged bond angles at the C4a atom correspond to sp3 hybridization (109°), which contrasts with the previous planar sp2 hybridization (120°). So far, three positions of the isoalloxazine ring in FAD and flavin mononucleotide (FMN) have been observed to be modified by inactivators: the C4a atom,26 the N5 atom27–29 and the C6 atom.30 In accordance with the discussed structural similarity to the iP substrate, HA-8 was found to be the most potent mechanism-based

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Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

inhibitor of ZmCKO1, followed by HA-1. Conversely, HA-10 did not react with the enzyme at all. Besides allenic cytokinins, alkyne compounds (RM1–6) were also studied. RM6 is the closest analog of iP, while RM1 is structurally similar to zeatin due to the presence of a hydroxyl group. RM3 contains only a short side chain (three carbon atoms), and RM2, RM4 and RM5 are branched methoxy or ethoxy derivatives of RM1. Both RM6 and RM1 were found to be weak substrates of ZmCKO1 with Km values being much higher than those for iP or Z.10 Although RM6 is a better substrate than RM1, the inactivation was stronger with RM1. Because these two compounds caused time-dependent inactivation of ZmCKO1, they can also be considered to be mechanism-based inhibitors, which, although much weaker than HA-8 and HA-1, follow the same inhibition mechanism. Some of the alkyne compounds under study and all three allenic compounds showed measurable biological activity in the bioassays performed. The structural similarity of HA-1, HA-8 and HA-10 to iP was reflected in cytokinin binding and Amaranthus assays, which confirmed a significant cytokinin activity of the compounds. Among alkyne derivatives, only RM1 and RM6 were found to be good ligands of the Arabidopsis cytokinin receptors AHK4 and AHK3. Our results show that the active site of ZmCKO1 and the binding sites of the AHK3 and AHK4 cytokinin receptors share similar structural– functional features with respect to the side chain of iP-type cytokinins. For HA as well as RM compounds, the elongation or branching of the side chain leads to both loss of substrate properties towards ZmCKO1 and reduced binding to AHK3 and AHK4 receptors. Likewise, the introduction of bromine to the isoprenoid side chain of iP leads to a decreased ability to bind cytokinin receptors and loss of substrate properties towards ZmCKO1. The possible application of the allenic compounds was recently shown by Suttle and Mornet,13 who demonstrated that their use for plant leaf treatment led to the accumulation of a glycosylated cytokinin (iP7G) and cytokinin nucleotide (iPMP). It would imply that a compensatory homeostatic mechanism occurs after the elimination of CKO activity, which is reflected in a shift of cytokinin conversion to O- and N-glycosides and nucleotides involving O- and N-glucosyltransferases31 and adenine phosphoribosyltransferase or adenosine kinase,1 respectively. Using mechanism-based inhibitors of CKO to treat whole plants or particular plant organs and tissues followed by metabolomic or proteomic analyses might provide useful data to elucidate the role of CKO in modulation of cytokinin levels in plants.

analogs. The inactivating reaction is further evidence of imine formation during the catalytic cycle of the enzyme. Only if the imine double bond is formed by substrate oxidation is the allenic group in the substrate side chain activated for nucleophilic attack. If the imine is not formed, the allenic group is not activated, as demonstrated by the reaction with FAD alone. With regard to the biological significance of the characterized mechanism-based inhibitors, these offer the possibility of fast and irreversible blocking of cytokinin degradation by eliminating the redox function of CKO cofactor. Preparation of a suicide substrate of CKO lacking any ligand properties on cytokinin receptors, i.e., one that would not trigger the cytokinin signaling pathway, would be highly desirable, and attempts are currently in progress to synthesize such a substrate.

Conclusion

Cytokinin degradation by ZmCKO1 and the concomitant imine intermediate production were monitored by measuring radioactive products derived from [3H]purinelabelled iP or iPR (Institute of Experimental Botany, Czech Academy of Sciences, Prague). The reactions were carried out using 2 μM tritiated substrate, 3 mM β-mercaptoetha-

In this work, we identified the target site and mechanism of cytokinin oxidase/dehydrogenase inhibition by unsaturated allenic and alkyne cytokinin

Materials and Methods Enzyme and chemicals Recombinant ZmCKO1 was expressed and purified as previously described.10 4-Aminophenol, DCPIP, iP, transzeatin and bicinchoninic acid–protein assay kit, were purchased from Sigma-Aldrich Chemie (Steinheim, Germany). Matrices for MALDI-TOF mass spectrometry were purchased from Bruker Daltonik (Bremen, Germany). Allenic and alkyne adenine derivatives32 were kindly provided by Prof. René Mornet, University of Angers, France. The compounds were dissolved in dimethyl sulfoxide or 70% ethanol and kept as 20 mM stock solutions at −20 °C. The corresponding chemical formulas are presented in Table 1. All other chemicals were of analyticalpurity grade. Activity and protein assays CKO activity in the dehydrogenase mode was assayed either by the DCPIP method16 or by the aminophenol method17 at 37 °C. Enzyme kinetics and rapid scanning experiments were performed on a DU-7500 photodiode array spectrophotometer (Beckman, Fullerton, CA). Kinetic parameters of ZmCKO1 inactivation were evaluated following previously published enzymological approaches.33 Since the ZmCKO1 reaction with HA-8 was extremely fast at 37 °C, the enzyme had to be incubated with the inhibitor on a water–ice bath. Protein content was estimated using a colorimetric assay with bicinchoninic acid; bovine serum albumin was used as a standard.34 Chromatofocusing was performed on a Mono P HR 5/20 column (Amersham Biosciences, Uppsala, Sweden) as previously described.10 HPLC and mass spectrometry of reaction intermediate

Mechanism-Based Inhibitors of Cytokinin Oxidase/Dehydrogenase

nol and ZmCKO1 in 20 mM Tris–HCl buffer, pH 7.4 at 30 °C for 1 h. Samples were further treated as previously described.35 HPLC analysis was performed on a C8 LiChrospher 60 RP-select B column (125 × 4 mm, 5 μm particles; Merck, Darmstadt, Germany) eluted isocratically with 50% methanol at a flow rate of 1 ml min− 1. The HPLC system was a Waters 600E gradient instrument equipped with a programmable multiwavelength detector 490E. Radioactivity was measured with an online Flo-oneβ instrument from Radiomatic (La Queue lez Yvelines, France). Electron impact mass spectrometry was performed with a Finnigan MAT 95 mass spectrometer (Thermo Electron, Bremen, Germany). Full-scan spectra were obtained by scanning the mass range m/z 50–400. Cofactor assays Fluorescence spectra were acquired on an Aminco Bowman Series 2 spectrofluorimeter (Thermo Electron Corporation, Madison, USA) according to Kopečný et al.10 Spectrophotometric titrations of FAD cofactor in ZmCKO1 were performed on a Lambda 11 spectrophotometer (Perkin-Elmer, Überlingen, Germany) equipped with an electromagnetic stirring adapter and thermostated at 30 °C. A sample of 20 μM ZmCKO1 in 20 mM Tris–HCl buffer, pH 8.0, was titrated by stepwise addition of 2-μl aliquots of 2 mM HA-1 or HA-8 in the same buffer. After each addition, the mixture was stirred for 10 min and absorbance at 450 nm was recorded. MALDI-TOF mass spectrometry ZmCKO1 was reacted with HA-1 or HA-8 using a molar excess of 50:1 for the inhibitor. The inactivated enzyme was separated by SDS-PAGE (10% resolving gel) and stained using the Bio-Safe Coomassie Stain (Bio-Rad, Hercules, CA). The bands were excised from the gel slab and in-gel digested by a modified trypsin. MALDI-TOF protein intact mass measurements and peptide mass fingerprinting were performed as described,36 except that the instrument used was a Microflex MALDI-TOF LRF20 (Bruker Daltonik). Intact mass measurements were performed using “super” dihydroxybenzoic acid as a matrix.36

897

al.37 Data analyses, including background and buffer subtraction, were performed with the LabSpec (JobinYvon-Spex) and GRAMS (Thermo Galactic) software packages. Enzyme crystallization, data collection and processing Crystals of the enzyme with a typical size of 0.2 mm × 0.06 mm × 0.06 mm were grown by the hanging-drop vapor-diffusion method for several weeks at 20 °C using 100 mM Tris–HCl buffer (pH 7.0) with 26–30% (w/v) PEG (polyethylene glycol) 1500 as a reservoir solution. The hanging drop (4 μl) contained 7 mg ml− 1 ZmCKO1, 0.5% (w/v) n-octyl β-D-glucoside, and 7–14% PEG 1500. In the case of HA-1, the enzyme crystals in the hanging drop were infiltrated with the inhibitor (0.5 mM final concentration) for 1 h. In the case of HA-8, ZmCKO1 was cocrystallized in the presence of 1.5 mM of inhibitor. All crystals were soaked in a cryoprotectant solution (the reservoir solution supplemented with 20% glycerol) and subsequently frozen at 100 K. Diffraction data were collected at the European Synchrotron Radiation Facility (Grenoble, France) on the BM-30A (HA-1 complex) and ID14-1 (HA-8 complex) beamlines using a CCD detector. Crystals were monoclinic, space group C2, with one molecule per asymmetric unit. Data processing and scaling were performed using the DENZO and SCALEPACK programs38 for the HA-1 complex and the XDS program39 for the HA-8 complex. Structure solution, model building and refinement The crystal structures of ZmCKO1 reacted with HA-1 and HA-8 were solved by molecular replacement at 3.5 Å resolution using the program MOLREP40 and the PDB coordinate file 1W1O as a template.12 CNS 1.1 was used for refinement.41 Water molecules were placed in residual density above 2.5 σ. The final models contain one polypeptide chain, one FAD molecule, one inhibitor molecule, eight N-acetyl-D-glucosamine molecules, glycerol and water molecules. Their analyses were carried out using the program PROCHECK.42 Bacterial receptor binding assay and Amaranthus bioassay

Raman spectroscopy The enzyme was measured in oxidized (native), reduced and inactivated states in 20 mM Tris–HCl buffer, pH 8.0. Reduction was achieved by the addition of sodium borohydride in 50-fold excess. Inactivation was performed by the addition of HA-1, HA-8 or RM1 (all in a 10-fold excess). Before measurements, the enzyme was diafiltered using a 10-kDa cutoff filter (Millipore, Bedford, USA) against the same buffer to remove traces of reactants. Raman spectra were acquired at 20 °C on a Spex 270M spectrograph (Jobin-Yvon-Spex, Longjumeau, France). The 441.6-nm line of a He–Cd laser (Liconix, Sunnyvale, CA) was used for the excitation of resonance Raman spectrum of ZmCKO1 with 12 mW of radiant power at the sample. Non-resonance Raman spectra were excited by the 532-nm line of a Verdi V2 laser (Coherent, Santa Clara, CA). The radiant power at the sample was 200 mW. Samples of 12-μl total volume were placed into a microcuvette and a total of 30 spectra, each measured for 60 s, was accumulated in 90° geometry. The calibration procedure was done according to the method of Dostál et

Escherichia coli strains KMI001 harboring the plasmid pIN-III-AHK4 or pSTV28-AHK3 for heterologous expression of A. thaliana cytokinin receptors (histidine kinases CRE1/AHK4 and AHK3, respectively) were used for the binding assay. Such a test system for cytokinins relying on activation of the β-galactosidase reporter gene has already been described.3,4 Induced and non-induced (control) strains were cultured as described by Spíchal et al.43 in M9 medium containing 0.1% casamino acids at 25 °C for 16 h. Cytokinin activity was also determined by a standard bioassay based on the induction of betacyanin biosynthesis in the cotyledons of Amaranthus seedlings grown in the dark.44 The experiments were conducted over a wide concentration range (from 10− 8 to 10− 4 M). Protein Data Bank accession numbers The atomic coordinates and structure factors have been deposited in the PDB with the following accession codes: 3BW7 for HA-1 complex and 3C0P for HA-8 complex.

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Acknowledgements We thank C. Pethe for her initial contribution to the project. This work was supported by grant GAČR 522/08/P113 from Czech Science Foundation and MSM 6198959215 from the Ministry of Education, Youth and Sports of the Czech Republic. M.S., L.S., V.M. and P.A. were supported by another grant MSM 6198959216 from the same provider.

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