https://www.cell.com/trends/microbiology/pdf/S0966-842X(08)00038-3.pdf

Bacillus lipopeptides: versatile weapons for plant disease biocontrol.

Summary The functions of phenylpropanoid compounds in plant defence range from preformed or inducible physical and chemical barriers against infection to signal molecules involved in local and systemic signalling for defence gene induction. Defensive functions are not restricted to a particular class of phenylpropanoid compound, but are found in the simple hydroxycinnamic acids and monolignols through to the more complex flavonoids, isoflavonoids, and stilbenes. The enzymatic steps involved in the biosynthesis of the major classes of phenylpropanoid compounds are now well established, and many of the corresponding genes have been cloned. Less is understood about the regulatory genes that orchestrate rapid, coordinated induction of phenylpropanoid defences in response to microbial attack. Many of the biosynthetic pathway enzymes are encoded by gene families, but the specific functions of individual family members remain to be determined. The availability of the complete genome sequence of Arabidopsis thaliana, and the extensive expressed sequence tag (EST) resources in other species, such as rice, soybean, barrel medic, and tomato, allow, for the first time, a full appreciation of the comparative genetic complexity of the phenylpropanoid pathway across species. In addition, gene expression array analysis and metabolic profiling approaches make possible comparative parallel analyses of global changes at the genome and metabolome levels, facilitating an understanding of the relationships between changes in specific transcripts and subsequent alterations in metabolism in response to infection.

The phenylpropanoid pathway and plant defence—a genomics perspective

Flavonoids are secondary metabolites involved in several aspects of plant development and defence. They colour fruits and flowers, favouring seed and pollen dispersal, and contribute to plant adaptation to environmental conditions such as cold or UV stresses, and pathogen attacks. Because they affect the quality of flowers (for horticulture), fruits and vegetables, and their derivatives (colour, aroma, stringency, etc.), flavonoids have a high economic value. Furthermore, these compounds possess pharmaceutical properties extremely attractive for human health. Thanks to easily detectable mutant phenotypes, such as modification of petal pigmentation and seeds exhibiting transparent testa, the enzymes involved in the flavonoid biosynthetic pathway have been characterized in several plant species. Conserved features as well as specific differences have been described. Regulation of structural gene expression appears tightly organized in a spatial and temporal way during plant development, and is orchestrated by a ternary complex involving transcription factors from the R2R3-MYB, basic helix-loop-helix (bHLH), and WD40 classes. This MYB-bHLH-WD40 (MBW) complex regulates the genes that encode enzymes specifically involved in the late steps of the pathway leading to the biosynthesis of anthocyanins and condensed tannins. Although several genes encoding transcription factors from these three families have been identified, many gaps remain in our understanding of the regulation of this biosynthetic pathway, especially about the respective roles of bHLH and WD40 proteins. A better knowledge of the regulatory mechanisms of the flavonoid pathway is likely to favour the development of new biotechnological tools for the generation of value-added plants with optimized flavonoid content.

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Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway

Plant phenolics are secondary metabolites that encompass several classes structurally diverse of natural products biogenetically arising from the shikimate-phenylpropanoids-flavonoids pathways. Plants need phenolic compounds for pigmentation, growth, reproduction, resistance to pathogens and for many other functions. Therefore, they represent adaptive characters that have been subjected to natural Correspondence/Reprint request: Prof. Vincenzo Lattanzio, Dipartimento di Scienze Agro-Ambientali, Chimica e Difesa Vegetale, Universita degli Studi di Foggia, 71100-Foggia, Italy. E-mail: v.lattanzio@unifg.it Vincenzo Lattanzio et al. 24 selection during evolution. Plants synthesize a greater array of secondary compounds than animals because they cannot rely on physical mobility to escape their predators and have therefore evolved a chemical defence against such predators. This article, after a short review of plant phenols and polyphenols as UV sunscreens, signal compounds, pigments, internal physiological regulators or chemical messengers, examines some findings in chemical ecology concerning the role of phenolics in the resistance mechanisms of plants against fungal pathogens and phytophagous insects.

Role of phenolics in the resistance mechanisms of plants against fungal pathogens and insects.

Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense. With the availability of the full genome sequence, large collections of insertion mutants, and functional genomics tools, Arabidopsis constitutes an excellent model system to profoundly unravel the monolignol biosynthetic pathway. In a genome-wide bioinformatics survey of the Arabidopsis genome, 34 candidate genes were annotated that encode genes homologous to the 10 presently known enzymes of the monolignol biosynthesis pathway, nine of which have not been described before. By combining evolutionary analysis of these 10 gene families with in silico promoter analysis and expression data (from a reverse transcription-polymerase chain reaction analysis on an extensive tissue panel, mining of expressed sequence tags from publicly available resources, and assembling expression data from literature), 12 genes could be pinpointed as the most likely candidates for a role in vascular lignification. Furthermore, a possible novel link was detected between the presence of the AC regulatory promoter element and the biosynthesis of G lignin during vascular development. Together, these data describe the full complement of monolignol biosynthesis genes in Arabidopsis, provide a unified nomenclature, and serve as a basis for further functional studies.

http://www.plantphysiol.org/content/plantphysiol/133/3/1051.full.pdf

Genome-wide characterization of the lignification toolbox in Arabidopsis.

Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase (COMT) from alfalfa is an S-adenosyl-l-Met–dependent O-methyltransferase involved in lignin biosynthesis. COMT methylates caffeoyl- and 5-hydroxyferuloyl–containing acids, aldehydes, and alcohols in vitro while displaying a kinetic preference for the alcohols and aldehydes over the free acids. The 2.2-A crystal structure of COMT in complex with S-adenosyl-l-homocysteine (SAH) and ferulic acid (ferulate form), as well as the 2.4-A crystal structure of COMT in complex with SAH and 5-hydroxyconiferaldehyde, provide a structural understanding of the observed substrate preferences. These crystal structures identify residues lining the active site surface that contact the substrates. Structurally guided site-directed mutagenesis of active site residues was performed with the goal of altering the kinetic preferences for physiological substrates. The kinetic parameters of the COMT mutants versus wild-type enzyme are presented, and coupled with the high-resolution crystal structures, they will serve as a starting point for the in vivo manipulation of lignin monomers in transgenic plants. Ultimately, this structurally based approach to metabolic engineering will allow the further alteration of the lignin biosynthetic pathway in agronomically important plants. This approach will lead to a better understanding of the in vivo operation of the potential metabolic grid for monolignol biosynthesis.

Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase.

Chemical syntheses of caffeoyl and 5-OH coniferyl aldehydes and alcohols and determination of lignin O-methyltransferase activities in dicot and monocot species

https://digital.library.unt.edu/ark:/67531/metadc488177/m2/1/high_res_d/2004_phytochemistry_837.pdf

O-Methylation of benzaldehyde derivatives by "lignin specific" caffeic acid 3-O-methyltransferase

The present invention provides compositions comprising caffeic acid /5-hydroxyferulic acid 3/5-O-methyltransferase (COMT) in crystalline form. There are provided high resolution structures of COMT complexed with S-adenosyl-L-homocysteine (SAH) and ferulate and complexed with SAH and 5-hydroxyconiferaldehyde. The discovered structure of a COMT provides the first three-dimensional view of the structural basis for substrate selectivity by COMT between lignin precursors in the lignin biosynthetic pathway. The present invention provides further compositions derived from and methods of using the three-dimensional atomic coordinates disclosed herein.

Parvathi Kota

Papers

The phenylpropanoid pathway and plant defence—a genomics perspective

Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase.

Chemical syntheses of caffeoyl and 5-OH coniferyl aldehydes and alcohols and determination of lignin O-methyltransferase activities in dicot and monocot species

O-Methylation of benzaldehyde derivatives by "lignin specific" caffeic acid 3-O-methyltransferase

Mutant plant caffeic acid/5-hydroxyferulic acid 3/5-0-methyltransferases (comt), methods for preparation and use thereof