Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by...

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1 Short Title: Dioxygenase chemistry by a diiron enzyme 1 2 TITLE: Castor Stearoyl-ACP Desaturase Can Synthesize a Vicinal Diol by Dioxygenase Chemistry. 3 Edward J. Whittle 1 , Yuanheng Cai 1 , Jantana Keereetaweep 1 , Jin Chai 1 , Peter H. Buist 2 and John 4 Shanklin 1 *. 5 1 Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973, USA. 6 2 Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 7 5B6. 8 * To whom correspondence should be addressed: [email protected], Tel. 631 344 3414, Fax. 631 344 9 6398. 10 One-sentence summary: The Ricinus communis stearoyl-ACP desaturase is capable of dioxygenase 11 chemistry, converting oleoly-ACP to the natural product erythro-9,10-dihydroxystearoyl-ACP. 12 13 Author contributions: JS, EJW and PHB designed the research; EJW performed the research; EJW, YC, JK 14 and JC contributed analytic/computational/ tools; EJW, YC, JC, PHB and JS analyzed the data; and EJW, JS 15 and PHB wrote the paper. 16 17 Plant Physiology Preview. Published on December 5, 2019, as DOI:10.1104/pp.19.01111 Copyright 2019 by the American Society of Plant Biologists www.plantphysiol.org on October 31, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

Transcript of Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by...

Page 1: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

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Short Title: Dioxygenase chemistry by a diiron enzyme 1

2

TITLE: Castor Stearoyl-ACP Desaturase Can Synthesize a Vicinal Diol by Dioxygenase Chemistry. 3

Edward J. Whittle1, Yuanheng Cai1, Jantana Keereetaweep1, Jin Chai1, Peter H. Buist2 and John 4

Shanklin1*. 5

1Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973, USA. 6

2Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 7

5B6. 8

* To whom correspondence should be addressed: [email protected], Tel. 631 344 3414, Fax. 631 344 9

6398. 10

One-sentence summary: The Ricinus communis stearoyl-ACP desaturase is capable of dioxygenase 11

chemistry, converting oleoly-ACP to the natural product erythro-9,10-dihydroxystearoyl-ACP. 12

13

Author contributions: JS, EJW and PHB designed the research; EJW performed the research; EJW, YC, JK 14

and JC contributed analytic/computational/ tools; EJW, YC, JC, PHB and JS analyzed the data; and EJW, JS 15

and PHB wrote the paper. 16

17

Plant Physiology Preview. Published on December 5, 2019, as DOI:10.1104/pp.19.01111

Copyright 2019 by the American Society of Plant Biologists

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ABSTRACT 18

In previous work, we identified a triple mutant of the castor (Ricinus communis) stearoyl-Acyl Carrier 19

Protein desaturase (T117R/G188L/D280K) that, in addition to introducing a double bond into stearate to 20

produce oleate, performed an additional round of oxidation to convert oleate to a trans allylic alcohol 21

acid. To determine the contributions of each mutation, in the present work we generated individual 22

castor desaturase mutants carrying residue changes corresponding to those in the triple mutant and 23

investigated their catalytic activities. We observed that T117R, and to a lesser extent D280K, 24

accumulated a novel product, namely erythro-9, 10-dihydroxystearate, that we identified via its methyl 25

ester through gas chromatography/mass spectrometry and comparison with authentic standards. The 26

use of 18O2 labeling showed that the oxygens of both hydroxyl moieties originate from molecular oxygen 27

rather than water. Incubation with an equimolar mixture of 18O2 and 16O2 demonstrated that both 28

hydroxyl oxygens originate from a single molecule of O2, proving the product is the result of dioxygenase 29

catalysis. Using prolonged incubation, we discovered that wild-type castor desaturase is also capable of 30

forming erythro-9, 10-dihydroxystearate, which presents a likely explanation for its accumulation to 31

approximately 0.7% in castor oil, of which the biosynthetic origin had remained enigmatic for decades. 32

In summary, the findings presented here expand the documented constellation of diiron enzyme 33

catalysis to include a dioxygenase reactivity in which an unactivated alkene is converted to a vicinal diol. 34

35

36

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INTRODUCTION 37

Diiron clusters within the active sites of enzymes facilitate the binding of molecular oxygen and its 38

derivatives and are able to perform redox chemistry, which results in a range of chemical outcomes 39

(Edmondson and Juynh, 1996). All diiron enzymes characterized to date belong to one of two separate 40

classes, one soluble and the other membrane bound (Shanklin and Somerville, 1991). Both classes have 41

the ability to catalyze the oxidation of unactivated C-H bonds to give a range of chemical outcomes 42

(Shanklin and Cahoon, 1998; Fox et al., 2004). For instance, both soluble and membrane diiron enzyme 43

classes contain desaturase enzymes that perform the stereo- and regioselective introduction of Z- (cis) 44

double bonds into unactivated lipid acyl chains. The reactions are thought to proceed via a radical 45

mechanism initiated by abstraction of a specific hydrogen from substrate (Buist, 2004). Double bond 46

formation ensues via the abstraction of a second neighboring hydrogen. As predicted by Bloch (Bloch, 47

1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 48

boomerang shape of the substrate binding channel within the desaturase drives the formation of the 49

(Z)-olefinic fatty acids. 50

There is a diverse constellation of chemical outcomes performed by variant enzymes that are 51

structurally related to the prototypical desaturase. The membrane-bound diiron-containing plant fatty 52

acid desaturase (FAD) family of FAD2 variant enzymes perform a variety of chemical transformations. 53

Using oleate as substrate, either desaturated or hydroxylated products are obtained; using linoleate as a 54

substrate, the corresponding epoxide, a conjugated double bond, or an acetylenic bond can be 55

produced. Changes in chemoselectivity are based on a relatively small number of amino acid sequence 56

differences which presumably alter the relative orientation of the substrate with respect to the active 57

site oxidant (Bhar et al., 2012). For instance, changes to only four amino acid side chains was sufficient 58

to predominantly convert a FAD2 into a hydroxylase and vice versa (Broun et al., 1998; Broadwater et 59

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al., 2002). Despite our increasing understanding of specificity determining residues within the FAD2-60

related diiron enzymes, further interpretation has been hindered by the lack of structural information 61

for these enzymes. Recently published structures of several mammalian membrane-bound desaturases 62

suggest it will be possible to solve one of the plant FAD2 class at some point and we will be able to 63

correlate changes to the enzyme structure with distinct functional outcomes (Bai et al., 2015; Wang et 64

al., 2015). 65

The soluble class of desaturase enzymes exemplified by the castor (Ricinus communis) 918:0-ACP 66

desaturase (Lindqvist, 2001) has been shown to contain members that display a variety of chain-length 67

specificities and regioselectivities (Shanklin et al., 2009). Mechanisms have been proposed for both 68

chain length specificity (Cahoon et al., 1997; Whittle and Shanklin, 2001) and for regioselectivity (Guy et 69

al., 2011). During our studies on regioselectivity, we engineered a triple mutant of the castor acyl-ACP 70

desaturase (T117R/G188L/D280K) that converts stearoyl-ACP into an allylic alcohol trans-isomer (E)-10-71

18:1-9-OH via a (Z)-9-18:1 intermediate (Whittle et al., 2008). This work described a soluble desaturase 72

acting as an olefin oxygenase similar in behavior to that displayed by another soluble diiron protein, 73

methane monooxygenase (Gherman et al., 2004). We showed that the conversion of (Z)-9-18:1 74

substrate to (E)-10-18:1-9-OH product by castor desaturase T117R/G188L/D280K proceeds via hydrogen 75

abstraction at C-11 and highly regioselective hydroxylation (>97%) at C-9 (Whittle et al., 2008). 18O-76

labeling studies show that the hydroxyl oxygen in the reaction product is exclusively derived from 77

molecular oxygen. 78

The present work was initially designed to evaluate the individual contributions of T117R, G188L, and 79

D280K in castor desaturase to allylic alcohol formation. During these experiments, we discovered a 80

novel dioxygenase reactivity of the soluble desaturase that results in the conversion of oleoyl-ACP to 81

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erythro-9, 10-dihydroxystearate. The same product was found in TMS-derivatized methyl esters from 82

castor seed where it constitutes approximately 0.7% of the total fatty acids 83

84

RESULTS 85

As part of our continuing structure-function analysis of diiron enzymes, we analyzed the contributions of 86

each of the mutations within the castor desaturase T117R/G188L/D280K triple mutant that converts 87

oleoyl-ACP into (E)-10-18:1-9-OH (Whittle et al., 2008). Each of the individual mutants was constructed 88

and tested for its activity using oleoyl-ACP as substrate. In each case, the product profiles were 89

determined by GC-MS analysis. The results are shown in Figure 1. The GC elution profile of substrate is 90

shown in Panel A (Fig. 1) and features a peak corresponding to 18:19 methyl ester (peak 1). A minor 91

shoulder peak can be attributed to 18:111 (peak 2) and is a well-known artefact of the expression 92

system. As shown in Panel B (Fig. 1), the triple mutant T117R/G188L/D280K converted most of the 93

oleoyl-ACP substrate into a mixture of the Z(cis)18:1Δ10 9OH (peak 3) and E(trans) 18:1Δ10 9OH allylic 94

alcohol (peak 4) isomers, with the E form predominating by approximately 3-fold over the Z form. 95

Reactivity of the Castor Desaturase Single Mutants T117R, G188L, and D280K. 96

Each of the single mutants was active with respect to the oleoyl-ACP substrate (Fig. 1, C, D and E). The 97

T117R mutant produced approximately 15-fold more of the E 18:1Δ10 9OH isomer than the 98

corresponding Z isomer. However, a new peak (labeled 5 in Fig. 1C) became apparent at an elution time 99

that was not characteristic of the silylated derivatives of commonly occurring fatty acid methyl esters. 100

The G188L mutant produced approximately a 1:1 mixture of E and Z isomers of 18:1Δ10 9OH (Fig. 1D), 101

but no detectable trace of the novel fatty acid species (peak 5) was produced by the T117R mutant. The 102

D280K mutant was less active than T117R and G188L, producing only a small amount of the E isomer of 103

18:1Δ10 9OH (Fig. 1E), along with a small amount of the novel fatty acid (peak 5). As expected, the wild-104

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type desaturase showed very little activity with its natural product oleoyl-ACP, but close inspection 105

revealed the production of a trace of novel species (peak 5) based on its elution time and mass spectra 106

(Fig. 1F). 107

The novel fatty acid product (peak 5) is 9,10-dihydroxystearate. 108

Mass-spectral analysis of the peak-5 product produced by the T117R mutant (Fig. 1C) revealed a 109

molecular ion of 474 AMU, consistent with an 18C fatty acid methyl ester containing two silylated 110

hydroxyl groups (Fig. 2A). Fragmentation of the product between the two silyl groups produced 111

fragments of 259 AMU for the carboxyl-containing fragment and 215 AMU for the methyl-containing 112

fragment (diagrammed in Fig. 2B), consistent with the presence of vicinal hydroxyl groups at C9 and C10. 113

The identity of the peak-5 product was confirmed by comparison of its fragmentation pattern with that 114

of a silylated authentic commercial standard of erythro-methyl 9,10-dihydroxy stearate (Fig. 2C). 115

Analysis of the peak-5 product from the D280K mutant also showed the same fragmentation pattern. 116

9,10-Dihydroxystearate produced by the T117R mutant is solely in the erythro configuration. 117

Fatty acids containing vicinal mid-chain hydroxy groups may exist as threo or erythro diastereoisomers 118

(Fig. 3). To distinguish between these possibilities, we compared the GC elution times of the novel 119

product from T117R with those of authentic threo and erythro-9, 10-dihydroxystearate standards (Fig. 4, 120

A, B, and C, respectively). The T117R product eluted as a single defined peak without any detectable 121

shoulders (Fig. 3A) and coeluted with authentic erythro standard (Fig. 4C). The authentic threo standard 122

(Fig. 4B) eluted ahead of that of the T117R product (Fig. 4A). When a small amount of the T117R product 123

was mixed with either the threo standard (Fig. 4D) or the erythro standard (Fig. 4E), two peaks were 124

seen for the sample spiked with threo standard whereas a single coeluting peak was seen for the sample 125

spiked with erythro standard. These results confirm the assignment of the T117R product as erythro-9, 126

10-dihydroxystearate. 127

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The hydroxyl oxygens at both C9 and C10 are derived from molecular oxygen. 128

The oxygen atoms in either of the two hydroxyl groups could in principle arise from water or molecular 129

oxygen (Fig. 5). To distinguish between these possibilities, T117R, oleoyl-ACP, and all assay components 130

were first degassed by multiple gas exchange cycles employing vacuum and O2-free argon with the use 131

of a Schlenk line (Arnold and Bohle, 1996) to remove residual atmospheric 16O2 from the sealed reaction 132

vials. Assay reactions were subsequently incubated in the presence of 16O2 or 18O2. We used mass-133

labeled 18:1 d2-11,11 oleoyl-ACP for these assays to ensure the product we observed was derived from 134

the enzymatic reaction rather than from endogenous oleate contaminant. Analysis of the methylated 135

silylated products from reaction under air yielded the expected 217 and 259 AMU products (the methyl 136

fragment increased by 2 AMU relative to unlabeled product results from the substitution for the two 137

hydrogens at C11 for deuterons (Fig. 6A)). The same experiment performed under 18O2 resulted in the 138

production of fragments of 219 and 261 AMU, consistent with the incorporation of one 18O at each of 139

the hydroxyl positions. 140

The formation of 9, 10-dihyroxystearate from oleate is the result of a dioxygenase reaction. 141

The incorporation of molecular oxygen at the 9 and 10 positions of oleate could in principle result from a 142

single dioxygenase reaction, or from two sequential monooxygenase reactions. To distinguish between 143

these possibilities, we degassed the samples as described above and performed a reaction under an 144

atmosphere containing an equimolar fraction of 16O2 and 18O2 (Fig. 7B) and performed mass 145

spectrometry on methylated acetonide derivatives of the product (Fig 7E). Acetonide derivatives were 146

used because they protect vicinal hydroxy groups while maximizing the detectable mass ion of the 147

product. If the reaction operates via a dioxygenase mechanism, then the oxygen atoms at both hydroxyl 148

positions should derive exclusively from either 16O2 or 18O2, resulting in either M or M+4 species. 149

Alternatively, if the mechanism employs two sequential monooxygenase reactions, a 1:2:1 pattern of 150

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M:M+2:M+4 would be expected by random incorporation of either 16O or 18O at each hydroxyl position. 151

Consistent with a dioxygenase mechanism, reactions performed under an equimolar mix of 16O2 and 18O2 152

yielded only M and M+4 peaks (355 and 359), with no detectable 357 species (Fig. 7B). Individual control 153

16O2 and 18O2 reactions only showed the expected 355 and 359 major species accompanied by minor 154

peaks at M+1 and M+2 that approximate the natural abundance of 13C (Fig. 7, A and C, respectively). 155

That M+1 and M+2 peaks originate from natural 13C was confirmed by the fragmentation of equivalent 156

derivatives of an authentic erythro-9, 10-dihydroxystearate, which showed the same proportions of M, 157

M+1, and M+2 species (Fig. 7D). 158

The native castor desaturase can convert oleoyl-ACP to 9,10-dihydroxystearate. 159

The formation of dihydroxystearate with selected mutated desaturases prompted us to probe for the 160

formation of this compound by the wild-type enzyme. Interestingly, using a prolonged time of 161

incubation (240 min) with oleoyl-ACP as substrate, we were able to identify production of 9, 10-162

dihydroxystearate (peak 5) at low levels (Fig. 8). This compound was accompanied by lesser amounts of 163

E 18:110 9 OH (peak 4). 164

Castor oil contains erythro-9,10-dihydroxystearate. 165

The observation that the native castor desaturase can produce small amounts of 9,10-dihydroxystearate 166

correlates well with an early report by King et al (King, 1942) who isolated a small amount of 9,10-167

dihydroxystearate from castor oil. We sought to confirm this observation and analyzed a fatty acid 168

extract of castor seeds by GC-MS after methylation and silylation. Chromatograms of castor seed fatty 169

acid derivatives (Fig. 9A) showed the expected common C16 and C18 fatty acids, along with a major 170

peak of ricinoleic acid which is followed by a small discrete peak (labeled 8 in Fig. 9A inset) of 171

approximately 0.7% (of total fatty acids), which corresponds to the elution time of disilylated methyl 9, 172

10-dihydroxystearate. Mass spectral analysis of this peak revealed fragments of 215 and 259 AMU 173

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confirming its assignment as 9, 10-dihydroxystearate (compare Fig. 9B with Fig. 2A and C). Based on the 174

in vitro assays using purified enzyme reported above, we hypothesize that this 9,10 dihydroxystearate 175

arises from the dioxygenation of oleoyl-ACP product of the stearoyl-ACP desaturase. If this were the 176

case, the 9,10-dihydroxystearate would be in the erythro form as originally proposed (Morris and 177

Crouchman, 1972). We therefore conducted coelution studies with authentic threo or erythro standards 178

(Fig. 9, C-E). The 9, 10 dihydroxystearate isolated from castor eluted as a single peak (Fig. 9C) with the 179

same mobility as that of the authentic erythro standard (Fig. 9E). By contrast, two peaks were seen in 180

the spiking experiment using threo standard (Fig. 9D). 181

182

183

DISCUSSION 184

Stereoselective dihydroxylation reactions are important to the chemical industry (Borrell and Costas, 185

2017) since diols serve as valuable synthons. The osmium-based asymmetric dihydroxylation reaction 186

(Crispino and Sharpless, 1993) is a prominent example of controlled olefin oxidation and was (in part) 187

recognized by the award of the 2001 Nobel Prize in Chemistry to its inventor, K. B. Sharpless. In addition, 188

biocatalytic diol formation from aromatics by whole-cell mutant Pseudomonas cultures has furnished 189

the synthetic chemist with a variety of enantiomerically pure cyclohexadiene-cis-diols. (Hudlicky and 190

Thorpe, 1996). Much effort has also been expended to develop iron-based biomimetic catalytic 191

methodology for this reaction (Oloo and Que, 2015). Herein, we report the details of our investigation 192

into a “green chemical approach”: the castor 918:0-ACP desaturase-mediated syn-dihydroxylation of an 193

unactivated alkene in the form of oleoyl-ACP to erythro -9,10-dihydroxystearoyl-ACP. 194

Stearoyl-ACP desaturase belongs to the non-heme diiron subclass of oxidative enzymes that have been 195

shown to mediate a variety of chemical transformations including dehydrogenation and 196

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monoxygenation. Typical products include primary, secondary, and allylic alcohols in addition to the 197

conversion of double bonds to epoxides (Wallar and Lipscomb, 1996). However, a diiron center 198

performing dioxygen chemistry to convert a double bond to a vicinal diol as reported here is without 199

precedent. The closest comparable example we are aware of is arylamine oxygenase (CmlI) from the 200

chloramphenicol biosynthesis pathway, which incorporates two oxygens from O2 into the aryl‐nitro 201

product; however, this occurs in two consecutive monooxygenations (Komor et al., 2017). We envision 202

the conversion of alkene to vicinal erythro-diol in this work to be mechanistically related (Fig. 4) to that 203

described for Rieske cis-diol-forming dioxygenases (Ensley et al., 1982; Karlsson et al., 2003). More 204

specifically, we envision involvement of a bridged hydroperoxo-diiron species similar to that proposed 205

by Solomon and Srnec (Chalupsky et al., 2014) for the conversion of stearate to oleate by two 206

consecutive hydrogen atom abstractions: “ - CH2-CH2-“ to “-CH=CH-“ . When presented with an alkene 207

moiety, the vinyl hydrogens are unavailable for abstraction for steric reasons and this same species is 208

forced to transfer two oxygen atoms to substrate as shown in Fig. 4 (Pathway 1). Our oxygen-labelling 209

experiments rule out an epoxidation/hydrolysis route (Pathway 2). It is possible that our T117R mutant 210

may change the molecular architecture of the substrate binding cavity, altering the relative orientation 211

of the substrate with respect to the hydroperoxo-diiron group and facilitating deoxygenation relative to 212

the wild-type enzyme. That the diol is produced as the erythro diastereoisomer, in which both hydroxy 213

groups occur on one face (Fig. 3), is consistent with the geometry of the active site substrate-binding 214

cavity with respect to the diiron active site oxidant (Lindqvist et al., 1996), in which stearate binds in a 215

quasi-eclipsed conformation at C9 and C10, projecting the pro-(R) hydrogens towards the active site 216

oxidant (Behrouzian et al., 2002). Future availability of a crystal structure of the T117R mutant in 217

complex with bound oleoyl-ACP, or of the T117R mutant alone or with substrate bound as previously 218

modeled (Whittle et al., 2008), would be useful starting points for probing mechanistic models using 219

computational methods such as density functional theory. Indeed, homology modeling was recently 220

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shown to be a useful approach for elucidating selectivity mechanisms of desaturase enzymes such as 221

FAD2 and FAD3 (Cai et al., 2018). 222

223

The low levels of 9, 10-dihydroxystearate in castor suggests that this system is not optimized to produce 224

this particular product. Higher levels of the diol may accumulate via enzymes with active site geometries 225

that permit more efficient dioxygenation. Cardimine impatiens is an example of a plant that accumulates 226

approximately 25% of 9, 10-dihydroxystearate (and its chain-elongation products) in its seed oil 227

(Mikolajczak et al., 1964). It is tempting to speculate that it contains a desaturase that has undergone 228

mutation/selection to optimize the production of the diol from the initial alkene product. Examples of 229

desaturases with multiple sequential oxidation activity include English ivy (Hedera helix) which can 230

perform 9- followed by 4 desaturation on stearoyl-ACP (Guy et al., 2007); FM1, a fungal membrane 231

desaturases that sequentially inserts a 12 followed by a 15 double bond into oleoyl-phosphatidyl 232

ethanolamine (Cai et al., 2018); and an insect multifunctional enzyme that functions as a 11 233

desaturase, 11 acetylenase, and 13 desaturase (Serra et al., 2007). 234

Major oxygenated fatty acids such as ricinoleic- and vernolic acids are typically produced in the 235

endoplasmic reticulum by variant FAD2 membrane-bound desaturases (van de Loo et al., 1995; Lee et 236

al., 1998). On the other hand, fatty acids with unusual double bond positions such as 16:14, 16:19, 237

and 18:1 6 are synthesized within the plastid (Shanklin and Cahoon, 1998). Thus, the production of 238

oxygenated fatty acids such as the erythro-9, 10-dihydroxystearate in the plastid as reported here is very 239

unusual if not unique. It is likely that in species with high levels of accumulation such as C. impatiens, 240

there exists a variant acyl-ACP thioesterase that cleaves the vicinal diol fatty acid from its ACP adduct in 241

addition to specialized acyltransferases and other components that facilitate its transfer from the plastid 242

to triglyceride storage lipids. 243

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More than 70 years ago, 9,10-dihydroxystearate was reported as a component of castor oil (King, 1942) 244

at approximately 1% of the total fatty acids (Sreenivasan et al., 1956). The stereochemistry of the diol 245

was later determined to be the erythro configuration (Morris and Crouchman, 1972). Consistent with 246

these earlier reports, castor oil samples evaluated in the present work contained approximately 0.7% of 247

erythro -9,10-dihydroxystearate. That the wild-type castor desaturase can produce this compound was 248

an entirely unanticipated result and resolves a long-standing mystery. In addition, our results 249

underscore the remarkable plasticity of the non-heme diiron catalytic center found in the desaturase 250

family of enzymes. It appears that subtle changes in the active site architecture found in these versatile 251

oxidants can allow new reaction pathways to emerge. Further detailed mechanistic work is needed to 252

understand the relationship between reaction outcome and details of the active site architecture. 253

MATERIALS AND METHODS 254

Mutant construction 255

Synthesis of the castor (Ricinus communis) desaturase triple mutant T117R/G188L/D280K and D280K 256

single mutants were previously described (Whittle et al., 2008; Guy et al., 2011). The single mutants 257

T117R and G188L were identified by mutagenesis-selection experiments (Whittle and Shanklin, 2001). 258

The open reading frames were introduced into pET9d using XbaI and EcoRI restriction sites and the 259

resulting clones were validated by sequencing. 260

Mutant Analysis 261

Desaturases, and variants thereof, were overexpressed in E. coli BL21(DE3) with the use of pET9d. 262

Recombinant desaturase was enriched to >90% purity by 20CM cation exchange chromatography 263

(Applied Biosystems). Desaturation reactions (600 µl) (Cahoon and Shanklin, 2000) were performed by 264

incubation of the desaturase with 18:0- and 18:1-ACP substrates in the presence of recombinant spinach 265

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ACP-I (Beremand et al., 1987). Uniformly deuterated stearate was obtained from Cambridge Isotope 266

Laboratories, Andover MA, and 9,10 d2 oleate and 11, 11 d2 oleate was obtained from the collection of 267

Tulloch (Tulloch, 1983). Experiments reported herein were replicated three or more times and 268

representative results are presented. 269

Fatty acid analysis 270

Fatty acid methyl esters (FAMEs) were prepared by addition of 2 ml of 1% NaOCH3 v/v in methanol and 271

incubated for 60 min at 50°C. Fatty acid methyl esters were extracted twice into 2 ml hexane after 272

acidification with 100 µl of glacial acetic acid. Hexane was evaporated to dryness under a stream of N2, 273

and samples were resuspended in hexane for GC analysis. FAMEs were dried and resuspended in 100 µl 274

of BSTFA (N,O-bis(trimethylsilyl) trifluoroacetamide) and TMCS (trimethylchlorosilane) (Supelco) for 45 275

min at 60°C to create trimethyl silyl derivatives. Samples were analyzed with an HP5890 gas 276

chromatograph (Agilent) fitted with a 60 m x 250 µm SP-2340 capillary column (Supelco). The oven 277

temperature was raised from 100°C to 160°C at a rate of 25°C min–1 and from 160°C to 240°C at a rate of 278

10°C min–1 with a flow rate of 1.1 ml min–1. Mass spectra were analyzed using an HP5973 mass selective 279

detector (Agilent). For 18O experiments, oxygen was removed from the sample cell by repeated 280

evacuation and purging of the cell with O2-free argon using a Schlenk line. Two mixtures were prepared, 281

one containing desaturase enzyme, buffer, ferredoxin NADPH(+) reductase, and substrate, the other 282

containing ferredoxin and NADPH. The two anaerobic mixtures were transferred to sealed reaction vials 283

containing an atmosphere composed of either 16O2, 18O2 (Cambridge Isotope Laboratories, Andover MA), 284

or an equimolar mixture of 16O2 and 18O2. Reactions were terminated by the addition of toluene, and 285

fatty acids were esterified and silylated as described above for experiments designed to fragment the 286

fatty acid to reveal the position of the vicinal hydroxyl groups. Alternatively, for the labelled oxygen 287

experiments designed to determine the reaction mechanism, fatty acids were converted to methyl 288

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Page 14: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

14

esters after which vicinal hydroxy groups were converted to their acetonide derivatives (Singh et al., 289

2008). To achieve this, methyl ester samples were dried under nitrogen and resuspended in 40 µl of 4 290

mM ZrCl4 catalyst in diethyl ether, 200 µl dichloromethane (CH2Cl2), and 5 ul dimethoxypropane. The 291

mixture was incubated with shaking at 22°C for 2 hrs. The mixture was extracted with 3 ml chloroform 292

(CHCl3) and 1 ml water, separated by centrifugation (at 1,500g for 5 min.) and the lower phase was 293

collected and dried under nitrogen before resuspension in hexane for GC/MS analysis. Samples 294

were analyzed on an HP6890/5973 GC/MS equipped with a 30 m x 250 µm HP 5MS capillary 295

column (Supelco). Oven temperature was held at 100°C for 2 min, raised to 300°C at the rate of 20°C 296

min-1, and held for 2 min. 297

298

Accession Numbers 299

Sequence data from this article can be found in the GenBank/EMBL data libraries under accession 300

number M59857. 301

Acknowledgements. 302

This work was funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy 303

Sciences under contract number DE-SC0012704 to J.S. We thank Dr. John Lipscomb, Dr. Diane Cabelli 304

and Dr. Xio-Hong Yu for helpful discussion and Dr. Pat Covello for providing some of the deuterated 305

compounds prepared by Tulloch. 306

307

Figure Legends 308

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Page 15: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

15

Fig. 1 GC-MS elution profiles of TMS derivatives. Chromatograms of TMS derivatives of 18:1-ACP 309

substrate (A) and product distributions for the castor desaturase triple mutant T117R G188L D280K (B), 310

and each of the single mutants T117R (C), G188L (D), and D280K (E) reveals a novel fatty acid species 311

labeled as peak 5. Product profile of wild-type castor desaturase is included (F) as a control. Peak 312

identities: Z18:1Δ9, (1); Z18:1Δ11, (2); Z18:1Δ10 9OH, (3); E18:1Δ10 9OH, (4). 313

Fig. 2. The novel fatty acid product is 9, 10-dihydroxystearate. Comparison of mass spectra of TMS 314

derivatives of the novel enzymatic product produced by the castor desaturase T117R mutant (A) and an 315

authentic erythro 9,10 dihydroxy stearate standard (C), and the fragmentation pattern giving rise to the 316

major ions at 215 and 259 AMU (B). 317

Fig. 3. The structural relationships of compounds discussed in this work. 1 Stearoyl ACP, showing two 318

hydrogens at C-9, 10 that are removed by desaturase; 2 Oleoyl ACP, the product of stearoyl 9,10 319

desaturation; 3 Erythro-9(R) ,10 (R)-dihydroxystearoyl ACP, the predicted product of 1 step direct oleate 320

dihydroxylation; 4 Threo-9(S) ,10 (R)-dihydroxystearoyl ACP, a possible product of enzymatic 2 step 321

oleate epoxidation/hydrolysis sequence. 322

Fig. 4. The 9,10-dihydroxystearate produced by the castor T117R mutant is solely in the erythro 323

configuration. Gas chromatograms of 9,10-dihydroxy- stearates are compared for the reaction product 324

of T117R (A) to those of standards: threo configuration (B), the erythro configuration (C), a mixture of 325

the T117R product and the threo standard (D), and the T117R product and the erythro standard (E). 326

Fig. 5. Two potential schemes for the conversion of oleate to erythro 9,10 dihydroxystearate by a 327

diiron-containing desaturase-dioxygenase. The initial bridged hydroperoxo species in both mechanisms 328

is inspired by large-scale multireference ab initio calculations on a related enzyme (Chalupsky et al, 329

2014). 330

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Page 16: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

16

Fig. 6. Both hydroxyl oxygens of 9,10-dihydroxystearate are derived from molecular oxygen. TMS 331

derivatives of 9, 10-dihydroxystearate product from the castor desaturase T117R mutant using 18:1 11-332

d2- substrate under air (A) or 18O2 shown in the diagram as O* (B). 333

Fig. 7. 9,10-dihydroxy stearate formation is the result of a single dioxygenase reaction. 334

Chromatograms and corresponding mass spectra of acetonide derivatives of 9,10 dihydroxy stearate 335

from reactions carried out under 16O2 (A), equimolar 16O2 and 18O2 (B), and 18O2 (C). Also depicted is an 336

authentic erythro 9,10 dihydroxy stearate standard (D) along with a diagram of its fragmentation (E). 337

Fig. 8. Upon prolonged incubation, the castor wild-type desaturase can convert 18:1 substrate to 338

erythro-9, 10-dihydroxystearate. Peak identities: Z18:1Δ9, (1); Z18:1Δ11, (2); Z18:1Δ10 9OH, (3); 339

E18:1Δ10 9OH; (4), and 9,10-dihydroxystearate (5). 340

Fig. 9. Low-level erythro-9, 10-dihydroxystearate is present in developing castor embryos. Gas 341

chromatogram of TMS derivatives of castor embryos (A) and the mass spectrum corresponding to peak 342

8, i.e., 9,10-dihydroxystearate (B). Peak identities: 16:0 (1), 18:0 (2), 18:1D9 (3), 18:1D11 (4), 18:2D9,12 343

(5), 12-OH 18:1D9 (6), 18:3D9,12,15 (7), and 9, 10 OH 18:0 (8). C-E, GC peaks for TMS derivatives of 9,10 344

dihydroxystearate from castor embryo (C), 9,10-dihydroxystearate from castor developing embryos 345

mixed with authentic threo-9,10-dihydroxystearate standard (D), and authentic erythro-9,10-346

dihydroxystearate standard (E). 347

348

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Page 20: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

4A B C

ED

Det

ecto

r R

esp

on

seD

etec

tor

Res

po

nse

Retention Time (min.)

Retention Time (min.)

1

2

1

2 3

5

1 23

4

1

2

45

12

3 4

F

1

25

9.0 9.4 9.8 10.29.0 9.4 9.8 10.29.0 9.4 9.8 10.2

9.0 9.4 9.8 10.29.0 9.4 9.8 10.29.0 9.4 9.8 10.2

Fig. 1 GC-MS elution profiles of TMS derivatives. Chromatograms of TMS derivatives of

18:1-ACP substrate (A) and product distributions for the castor desaturase triple mutant

T117R G188L D280K (B), and each of the single mutants T117R (C), G188L (D), and

D280K (E) reveals a novel fatty acid species labeled as peak 5. Product profile of wild-type

castor desaturase is included (F) as a control. Peak identities: Z18:1Δ9, (1); Z18:1Δ11, (2);

Z18:1Δ10 9OH, (3); E18:1Δ10 9OH, (4). www.plantphysiol.orgon October 31, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

Page 21: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

OSi(CH3)3

CH3-(CH2)6-CH-CH-CH-(CH2)7-CO2CH3

259

215

Fig. 2. The novel fatty acid product is 9,

10-dihydroxystearate. Comparison of

mass spectra of TMS derivatives of the

novel enzymatic product produced by the

castor desaturase T117R mutant (A) and an

authentic erythro 9,10 dihydroxy stearate

standard (C), and the fragmentation pattern

giving rise to the major ions at 215 and 259

AMU (B).

Rel

ativ

e A

bu

nd

ance

474

M

73

+

mass/charge

259215

(CH3)3SiO

Rel

ativ

e A

bu

nd

ance

474

M

73

+

259

mass/charge

215

A

B

C

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Page 22: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

Fig. 3. The structural relationships of compounds discussed in this work. 1

Stearoyl ACP, showing two hydrogens at C-9, 10 that are removed by desaturase; 2

Oleoyl ACP, the product of stearoyl 9,10 desaturation; 3 Erythro-9(R) ,10 (R)-

dihydroxystearoyl ACP, the predicted product of 1 step direct oleate dihydroxylation;

4 Threo-9(S) ,10 (R)-dihydroxystearoyl ACP, a possible product of enzymatic 2 step

oleate epoxidation/hydrolysis sequence. www.plantphysiol.orgon October 31, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

Page 23: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

Fig. 4. The 9,10-dihydroxystearate produced by the

castor T117R mutant is solely in the erythro

configuration. Gas chromatograms of 9,10-dihydroxy-

stearates are compared for the reaction product of T117R

(A) to those of standards: threo configuration (B), the

erythro configuration (C), a mixture of the T117R

product and the threo standard (D), and the T117R

product and the erythro standard (E).

Det

ecto

r R

esp

on

se

Retention Time

A

B

C

E

D

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Page 24: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

Fig. 5. Two potential schemes for the conversion of oleate to erythro 9,10

dihydroxystearate by a diiron-containing desaturase-dioxygenase. The initial bridged

hydroperoxo species in both mechanisms is inspired by large-scale multireference ab initio

calculations on a related enzyme (Chalupsky et al, 2014). www.plantphysiol.orgon October 31, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

Page 25: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

CH3-(CH2)6-CD2-CH-CH-(CH2)7-CO2CH3

CH3-(CH2)6-CD2-CH-CH-(CH2)7-CO2CH3

Fig. 6. Both hydroxyl oxygens of 9,10-dihydroxystearate are derived from molecular oxygen.

TMS derivatives of 9, 10-dihydroxystearate product from the castor desaturase T117R mutant

using 18:1 11-d2- substrate under air (A) or 18O2 shown in the diagram as O* (B).

Det

ecto

r R

esp

on

se

Retention Time

Det

ecto

r R

esp

on

se

Retention Time

Rel

ativ

e A

bu

nd

ance

480

M+

mass/charge

A

Rel

ativ

e A

bu

nd

ance

476

M+

mass/charge

217 259

261219

73

73

OSi(CH3)3

259

217

(CH3)3SiO

*OSi(CH3)3

261

219

(CH3)3SiO*

B

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Page 26: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

355

357

355 359

359

355 357

A

B

C

356

356 360

360

Det

ecto

r R

esp

on

se

Retention Time Mass/Charge

Retention Time Mass/Charge

D

Det

ecto

r R

esp

on

se

355

357

356

Fig. 7. 9,10-dihydroxy stearate formation is the result of a

single dioxygenase reaction. Chromatograms and

corresponding mass spectra of acetonide derivatives of 9,10

dihydroxy stearate from reactions carried out under 16O2

(A), equimolar 16O2 and 18O2 (B), and 18O2 (C). Also

depicted is an authentic erythro 9,10 dihydroxy stearate

standard (D) along with a diagram of its fragmentation (E).

E

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Page 27: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

1

Fig. 8. Upon prolonged incubation, the castor wild-type desaturase can convert 18:1 substrate to

erythro-9, 10-dihydroxystearate. Peak identities: Z18:1Δ9, (1); Z18:1Δ11, (2); Z18:1Δ10 9OH, (3);

E18:1Δ10 9OH; (4), and 9,10-dihydroxystearate (5).

Det

ecto

r R

esp

on

se

2

4

5

Retention Time (min.)

9.0 9.4 9.8 10.2

www.plantphysiol.orgon October 31, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

Page 28: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

Fig. 9. Low-level erythro-9, 10-dihydroxystearate is present in developing castor embryos. Gas

chromatogram of TMS derivatives of castor embryos (A) and the mass spectrum corresponding to peak

8 , i.e., 9,10-dihydroxystearate (B). Peak identities: 16:0 (1), 18:0 (2), 18:1D9 (3), 18:1D11 (4),

18:2D9,12 (5), 12-OH 18:1D9 (6), 18:3D9,12,15 (7), and 9, 10 OH 18:0 (8). C-E, GC peaks for TMS

derivatives of 9,10 dihydroxystearate from castor embryo (C), 9,10-dihydroxystearate from castor

developing embryos mixed with authentic threo-9,10-dihydroxystearate standard (D), and authentic

erythro-9,10-dihydroxystearate standard (E).

Rel

ativ

e A

bu

nd

ance

474

M

73

+

259

mass/charge

215

A

Det

ecto

r R

esp

on

se

1 2

3

4

5

6

7

B

Retention Time

8

Det

ecto

r R

esp

on

se

Retention Time

C

D

E

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Page 29: Dioxygenase chemistry by a diiron enzymeDec 05, 2019  · 48 1969) and subsequently confirmed by X-ray crystallography (Lindqvist et al., 1996; Bai et al., 2015), the 49 boomerang

Parsed CitationsArnold EV, Bohle DS (1996) Isolation and oxygenation reactions of nitrosylmyoglobins. Nitric Oxide, Pt B 269: 41-55

Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

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