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Despite an ever-increasing interest for the use of pectin-derived oligogalacturonides (OGs) as biological control agents in agriculture, very little information exists-mainly for technical reasons-on the nature and activity of the OGs that accumulate during pathogen infection. Here we developed a sensitive OG profiling method, which revealed unsuspected features of the OGs generated during infection of Arabidopsis thaliana with the fungus Botrytis cinerea. Indeed, in contrast to previous reports, most OGs were acetyl-and methylesterified, and 80% of them were produced by fungal pectin lyases, not by polygalacturonases. Polygalacturonase products did not accumulate as larger size OGs but were converted into oxidized GalA dimers. Finally, the comparison of the OGs and transcriptomes of leaves infected with B. cinerea mutants with reduced pectinolytic activity but with decreased or increased virulence, respectively, identified candidate OG elicitors. In conclusion, OG analysis provides insights into the enzymatic arms race between plant and pathogen and facilitates the identification of defense elicitors. oligogalacturonides | plant-pathogen interaction | Arabidopsis thaliana | Botrytis cinerea | pectin lyase T he cell wall forms the first line of defense in the interaction of plants with their microbial environment. Cell walls consist of complex polysaccharide networks, which combine multiple functional properties such as strength (to resist turgor pressure), ex-tensibility (to allow growth), as well as protection against microbial attack. Such protection involves so called \"basal immunity,\" which is triggered upon recognition of pathogen-associated molecular patterns but also of plant-derived molecules associated with infection, referred to as damage-associated molecular patterns (DAMPs). The latter include cell wall-derived oligosaccharides with elicitor activity (also called oligosaccharins) (1) that are produced during infection with microbes and, in particular, necrotrophic bacteria and fungi, which feed on cell walls and have large arsenals of cell wall-degrading enzymes (2). A major source of cell wall-derived DAMPs are pectins. The pectic polymer, homogalacturonan (HG) for example, represents in Arabidopsis 20% of the wall of growing cells. HG is a linear polymer of α-1-4-linked galacturonic acid (GalA) residues secreted in a methylesterified (on C6) and often acetylesterified (on C2 and/or C3) form (3), which can be enzymatically deacetylesterified by pectin acetylesterases and demethylesterified by pectin methyl-esterases (PMEs) in muro (4). Demethylesterification exposes the polymer to degradation by polygalacturonases (PGs) and pectate lyases (PLs, that cleave unmethylesterified HG by β-elimination, thus generating an unsaturated bond at the nonreducing end), which can be of plant or fungal origin. HG demethylesterification plays a key role in the control of cell wall rheology underlying plant growth (5). In addition, HG turnover generates oligogalacturonides (OGs)

The Arabidopsis thaliana PECTIN METHYLESTERASE INHIBITOR 3 (PMEI3) gene is frequently used as a tool to manipulate pectin methylesterase activity in vivo, in studies assessing its role in the control of cell expansion. One limitation of these studies is that the exact biochemical activity of this protein has not yet been determined. In this manuscript we produced the protein in Pichia pastoris and characterized its activity in vitro. Like other PMEIs, PMEI3 inhibits PME activity in acidic pH conditions for a variety of cell wall extracts and for purified PME preparations, but does not affect PME activity at neutral pH. This suggests that the previously observed in vivo effects reflect the inhibition of PME activity at low pH. The protein is remarkable heat stable and shows higher activity against PME3 than against PME2, illustrating how different members of the large PMEI family can differ in their specificities towards PME targets. Finally, application of purified PMEI3 on Arabidopsis thaliana seedlings showed a dose-dependent inhibition of homogalacturonan de-methylesterification and root growth. Purified recombinant PMEI3 is therefore a powerful tool to study the connection between pectin methylesterification and cell expansion. Competing Interest Statement The authors have declared no competing interest.

The fine-tuning of pectins by polygalacturonases (PGs) plays a key role in modulating plant cell wall chemistry and mechanics, impacting plant development. In plants, the high number of PGs encoded in the genome questions the regulation of pectin depolymerization and the roles of distinct isozymes in the control of development. Here we report the first crystal structures of two PGs from Arabidopsis, PGLR and ADPG2 whose expression overlap in roots. Albeit having overall conserved folds and active sites, PGLR and ADPG2 differed in the structure of their binding grooves and in the amino-acids of the subsites. We determined the structural features that explain the absence of inhibition of the plant PGs by endogenous PG-Inhibiting Proteins (PGIPs). By combining molecular dynamic simulations, analysis of enzymes kinetics and hydrolysis products, we showed that subtle differences in PGLR and ADPG2 structures translated into distinct enzyme-substrate dynamics and enzymes processivities. Using the plant root as a developmental model, exogenous application of purified enzymes showed that these distinct PGLR/ADPG2 processivities ultimately translated into different impacts on development. The highly processive ADPG2 had major effects on both root cell elongation and cell adhesion. Our study suggests that, in plants, gene redundancy is unlikely to reflect redundant biochemical specificities. Isozymes of distinct specificities and processivities are likely to be of major importance for the fine spatial and temporal regulation of pectin structure. Competing Interest Statement The authors have declared no competing interest. Footnotes * Novel elements in the discussion.

Pectins, complex polysaccharides and major components of the plant primary cell wall, can be degraded by pectate lyases (PLs). PLs cleave glycosidic bonds of homogalacturonans (HG), the main pectic domain, by beta-elimination, releasing unsaturated oligogalacturonides (OGs). To understand the catalytic mechanism and structure/function of these enzymes, we characterized VdPelB from Verticillium dahliae, a plant pathogen. We first solved the crystal structure of VdPelB at 1.2A resolution showing that it is a right-handed parallel beta-helix structure. Molecular dynamics (MD) simulations further highlighted the dynamics of the enzyme in complex with substrates that vary in their degree of methylesterification, identifying amino acids involved in substrate binding and cleavage of non-methylesterified pectins. We then biochemically characterized wild type and mutated forms of VdPelB. VdPelB was most active on non-methylesterified pectins, at pH 8 in presence of Ca2+ ions. VdPelB-G125R mutant was most active at pH 9 and showed higher relative activity compared to native enzyme. The OGs released by VdPelB differed to that of previously characterized PLs, showing its peculiar specificity in relation to its structure. OGs released from Verticillium-partially tolerant and sensitive flax cultivars differed which could facilitate the identification VdPelB-mediated elicitors of defence responses.Competing Interest StatementThe authors have declared no competing interest.

Pectin methylesterases (PMEs) modify homogalacturonan’s (HG) chemistry and play a key role in regulating primary cell wall mechanical properties. How PME activity can fine-tune pectin structure in the growing plant has remained elusive. Here we report on the Arabidopsis AtPME2, which we found to be highly expressed during lateral root emergence and dark-grown hypocotyl elongation. We produced the mature active enzyme using heterologous expression in Pichia pastoris and characterized it through the use of a generic plant PME antiserum suitable for detecting recombinant and native enzyme independent of species source. At neutral pH AtPME2 is preferentially active on pectins with a degree of 55-70% methylesterification and can be inhibited by PME inhibitor protein (PMEI). We show that the mode of action for AtPME2 can switch from full processivity (at pH 8), creating large blocks of unmethylated galacturonic acid, to low processivity (at pH 5) and relate these observations to the differences in electrostatic potential of the protein at acidic and alkaline pH. To assess the role of AtPME2 in development, we characterized two knock-out lines. We show that in the context of acidified apoplast, low-processive demethylesterification by AtPME2 can loosen the cell wall, with consequent increase in cell elongation and etiolated hypocotyl length. Our study brings insights into how the pH-dependent regulation by PME activity could affect pectin structure and associated cell wall mechanical properties in expansion. The processivity of AtPME2, a pectin methylesterase that fine-tunes cell wall pectins is modulated by pH in vitro and impacts the mechanical properties of the wall, affecting development in planta.

Abstract Pectin methylesterases (PMEs) modify homogalacturonan’s chemistry and thereby play a key role in regulating primary cell wall mechanical properties. How PME activity can fine-tune pectin structure in the growing plant has remained elusive, in part due to the lack of available biochemically-characterized enzymes to empirically test functional properties. Here we report on AtPME2, which we found to be highly expressed during lateral root emergence as well as root and hypocotyl elongation. Production of mature active enzyme in Pichia pastoris allowed its biochemical characterization. We show that AtPME2 can switch from full processivity (at pH 8), creating large blocks of unmethylated galacturonic acid, to low processivity (at pH 5) and relate these observations to the differences in electrostatic potential of the protein. We also produced a generic plant PME antiserum suitable for detecting recombinant and native enzyme independent of species source. In the context of acidified apoplast, we showed using reverse genetics that low-processive demethylesterification by AtPME2 can loosen the cell wall, with consequent increase in cell elongation and etiolated hypocotyl length. Our study brings insights into how the pH-dependent regulation by PME activity could affect pectin structure and associated cell wall mechanical properties in expansion. Footnotes * ↵* contributed equally to the work as senior authors.