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The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with Forsythia × intermedia. Stereo-selective, DP-guided, monolignol-derived radical coupling in vitro was then reported to afford the optically active lignan, (+)-pinoresinol from coniferyl alcohol, provided one-electron oxidase/oxidant capacity was present. It later became evident that DPs have several distinct sub-families, presumably with different functions. Some known DPs require other essential enzymes/proteins (e.g. oxidases) for their functions. However, the lack of a fully sequenced genome for Forsythia × intermedia made it difficult to profile other components co-purified with the (+)-pinoresinol forming DP. Herein, we used an integrated bottom-up, top-down, and native mass spectrometry (MS) approach to de novo sequence the extracted proteins via adaptation of our initial report of DP solubilization and purification. Using publicly available transcriptome and genomic data from closely related species, we identified 14 proteins that were putatively associated with either DP function or the cell wall. Although their co-occurrence after extraction and chromatographic separation is suggestive for potential protein–protein interactions, none were found to form stable protein complexes with DPs in native MS under the specific experimental conditions we have explored. Interestingly, two new DP homologs were found and they formed hetero-trimers. Molecular dynamics simulations suggested that similar hetero-trimers were possible between Arabidopsis DP homologs with comparable sequence similarities. Nevertheless, our integrated mass spectrometry method development helped prepare for future investigations directed to the discovery of novel proteins and protein–protein interactions. These advantages can be highly beneficial for plant and microbial research where fully sequenced genomes may not be readily available. [ABSTRACT FROM AUTHOR]

Extended proton relay systems have been proposed for various alcohol dehydrogenases, including the Arabidopsis thaliana cinnamyl alcohol dehydrogenases (AtCADs). Following a previous structural biology investigation of AtCAD5, the potential roles of three amino acid residues in a putative proton relay system, namely Thr49, His52 and Asp57, in AtCAD5, were investigated herein. Using site-directed mutagenesis, kinetic and isothermal titration calorimetry (ITC) analyses, it was established that the Thr49 residue was essential for overall catalytic conversion, whereas His52 and Asp57 residues were not. Mutation of the Thr49 residue to Ala resulted in near abolition of catalysis, with thermodynamic data indicating a negative enthalpic change (ΔH), as well as a significant decrease in binding affinity with NADPH, in contrast to wild type AtCAD5. Mutation of His52 and Asp57 residues by Ala did not significantly change either catalytic efficiency or thermodynamic parameters. Therefore, only the Thr49 residue is demonstrably essential for catalytic function. ITC analyses also suggested that for AtCAD5 catalysis, NADPH was bound first followed by p-coumaryl aldehyde.

This comprehensive review describes the current status and knowledge of biochemical and molecular processes involved in allyl/propenyl phenol, lignan, norlignan and lignin biosynthesis. Recent advances made over the last decade are critically discussed, and placed in context with earlier studies largely dating back to the 1950s. Beginning with the recently established formation of phenylalanine in plants, each downstream biochemical conversion is described from the perspective of the mechanistic details known to this point. Particular emphasis is placed upon proteinaceous control of monolignol-derived radical-radical coupling processes, leading to lignans and lignins, as well as apparently related processes affording the various ellagitannins and phenolic terpenoids. The evidence for non-random macromolecular lignin assembly is discussed in detail, this being in contrast to earlier notions that such processes were random. The latter assumptions have largely resulted from a lack of robust analytical procedures and rigorous quantification, as well as a lack of incisive experimental design. In addition, the often-noted severe effects of modulating lignin compositions and contents on plant vascular tissue properties (i.e. in terms of compromised biophysical properties) are described herein, as well as the severe limitations as regards recent claims of compensatory 'combinatorial chemistry' lignin formation. Much of the latter confusion has also resulted from the serious deficiencies in current lignin analytical protocols and quantification, as well as in the general lack of experimental approaches/design to probe lignin primary structure(s).

Propenyl- and allyl-phenols, such as methylchavicol, p-anol and eugenol, have gained importance as flavoring agents and also as putative precursors in the biosynthesis of 9,9'-deoxygenated lignans, many of which have potential medicinal applications. In spite of several decades of investigation, however, the complete biosynthetic pathway to a propenyl/allylphenol had not yet been reported. We have subjected a Thai basil variety accumulating relatively large amounts of the simplest volatile allylphenol, methylchavicol, to in vivo administration of radiolabeled precursors and assays of protein preparations in vitro. Through these experiments, the biosynthesis of chavicol was shown to occur via the phenylpropanoid pathway to p-coumaryl alcohol. Various possibilities leading to deoxygenation of the latter were examined, including reduction of the side-chain double bond to form p-dihydrocoumaryl alcohol, followed by dehydration to afford chavicol, as well as formation of p-methoxycinnamyl alcohol, with further side-chain modification to afford methylchavicol. A third possibility studied was activation of the side-chain alcohol of p-coumaryl alcohol, e.g.via esterification, to form a more facile leaving group via reductive elimination. The latter was shown to be the case using p-coumaryl esters as potential substrates for a NAD(P)H-dependent reductase to afford chavicol, which is then O-methylated to afford methylchavicol.

The cinnamyl alcohol dehydrogenase (CAD) multigene family in planta encodes proteins catalyzing the reductions of various phenylpropenyl aldehyde derivatives in a substrate versatile manner, and whose metabolic products are the precursors of structural lignins, health-related lignans, and various other metabolites. In Arabidopsis thaliana, the two isoforms, AtCAD5 and AtCAD4, are the catalytically most active being viewed as mainly involved in the formation of guaiacyl/syringyl lignins. In this study, we determined the crystal structures of AtCAD5 in the apo-form and as a binary complex with NADP+, respectively, and modeled that of AtCAD4. Both AtCAD5 and AtCAD4 are dimers with two zinc ions per subunit and belong to the Zn-dependent medium chain dehydrogenase/reductase (MDR) superfamily, on the basis of their overall 2-domain structures and distribution of secondary structural elements. The catalytic Zn2+ ions in both enzymes are tetrahedrally coordinated, but differ from those in horse liver alcohol dehydrogenase since the carboxyl side-chain of Glu70 is ligated to Zn2+ instead of water. Using AtCAD5, site-directed mutagenesis of Glu70 to alanine resulted in loss of catalytic activity, thereby indicating that perturbation of the Zn2+ coordination was sufficient to abolish catalytic activity. The substrate-binding pockets of both AtCAD5 and AtCAD4 were also examined, and found to be significantly different and smaller compared to that of a putative aspen sinapyl alcohol dehydrogenase (SAD) and a putative yeast CAD. While the physiological roles of the aspen SAD and the yeast CAD are uncertain, they nevertheless have a high similarity in the overall 3D structures to AtCAD5 and 4. With the bona fide CAD's from various species, nine out of the twelve residues which constitute the proposed substrate-binding pocket were, however, conserved. This is provisionally considered as indicative of a characteristic fingerprint for the CAD family.

Secoisolariciresinol dehydrogenase (SDH) catalyzes the NAD+ dependent enantiospecific conversion of secoisolariciresinol into matairesinol. In Podophyllum species, (-)-matairesinol is metabolized into the antiviral compound, podophyllotoxin, which can be semi-synthetically converted into the anticancer agents, etoposide, teniposide and Etopophos. Matairesinol is also a precursor of the cancer-preventative "mammalian" lignan, enterolactone, formed in the gut following ingestion of, for example, various high fiber dietary foods, as well as being an intermediate to numerous defense compounds in vascular plants. This study investigated the mode of enantiospecific Podophyllum SDH catalysis, the order of binding, and the stereospecificity of hydride abstraction/transfer from secoisolariciresinol to NAD+. SDH contains a highly conserved catalytic triad (Ser153, Tyr167 and Lys171), whose activity was abolished with site-directed mutagenesis of Tyr167Ala and Lys171Ala, whereas mutagenesis of Ser153Ala only resulted in a much reduced catalytic activity. Isothermal titration calorimetry measurements indicated that NAD+ binds first followed by the substrate, (-)-secoisolariciresinol. Additionally, for hydride transfer, the incoming hydride abstracted from the substrate takes up the pro-S position in the NADH formed. Taken together, a catalytic mechanism for the overall enantiospecific conversion of (-)-secoisolariciresinol into (-)-matairesinol is proposed.

The creosote bush (Larrea tridentata) lignans are linked via 8-8' bonds, with the simplest apparently being E-p-anol derived. Of the latter, four of the six theoretically possible diastereoisomers were isolated, namely (-)-larreatricin, (-)-8'-epi-larreatricin, meso-3,3'-didemethoxynectandrin B and the new compounds, (+)- and (-)-3,3'-didemethoxyverrucosins. Following synthesis of each in either racemic or meso form, and chiral HPLC separation of the antipodes of the racemates, it was established that naturally occurring (-)-larreatricin and (-)-8'-epi-larreatricin were present in 92 and 98% enantiomeric excess, respectively, whereas 3,3'-didemethoxyverrucosin was essentially racemic and 3,3'-didemethoxynectandrin B was in the meso-form. The evidence suggests that formation of these lignans occurs under regiospecific, rather than stereoselective, coupling control. This contrasts with laccase-catalyzed "random" coupling of E-p-anol in vitro which generates the corresponding racemic 8-8', 8-3' and 8-O-4' linked dimeric moieties.