Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control

AlphaFold-guided redesign of a plant pectin methylesterase inhibitor for broad-spectrum disease resistance

Plant cell walls are a critical site where plants and pathogens continuously struggle for physiological dominance. Here we show that dynamic remodeling of pectin methylesterification of plant cell walls is a component of the physiological and co-evolutionary struggles between hosts and pathogens. A pectin methylesterase (PsPME1) secreted by Phytophthora sojae decreases the degree of pectin methylesterification, thus synergizing with an endo-polygalacturonase (PsPG1) to weaken plant cell walls. To counter PsPME1-mediated susceptibility, a plant-derived pectin methylesterase inhibitor protein, GmPMI1, protects pectin to maintain a high methylesterification status. GmPMI1 protects plant cell walls from enzymatic degradation by inhibiting both soybean and P. sojae pectin methylesterases during infection. However, constitutive expression of GmPMI1 disrupted the trade-off between host growth and defense responses. We therefore used AlphaFold structure tools to design a modified form of GmPMI1 (GmPMI1R) that specifically targets and inhibits pectin methylesterases secreted from pathogens but not from plants. Transient expression of GmPMI1R enhanced plant resistance to oomycete and fungal pathogens. In summary, our work highlights the biochemical modification of the cell wall as an important focal point in the physiological and co-evolutionary conflict between hosts and microbes, providing an important proof of concept that AI-driven structure-based tools can accelerate the development of new strategies for plant protection.

Mutation of AtPME2, a pH-Dependent Pectin Methylesterase, Affects Cell Wall Structure and Hypocotyl Elongation

Pectin methylesterases (PMEs) modify homogalacturonan's chemistry and play a key role in regulating primary cell wall mechanical properties. Here, we report on Arabidopsis AtPME2, which we found to be highly expressed during lateral root emergence and dark-grown hypocotyl elongation. We showed that dark-grown hypocotyl elongation was reduced in knock-out mutant lines as compared to the control. The latter was related to the decreased total PME activity as well as increased stiffness of the cell wall in the apical part of the hypocotyl. To relate phenotypic analyses to the biochemical specificity of the enzyme, we produced the mature active enzyme using heterologous expression in Pichia pastoris and characterized it through the use of a generic plant PME antiserum. AtPME2 is more active at neutral compared to acidic pH, on pectins with a degree of 55-70% methylesterification. We further showed that the mode of action of AtPME2 can vary according to pH, from high processivity (at pH8) to low processivity (at pH5), and relate these observations to the differences in electrostatic potential of the protein. Our study brings insights into how the pH-dependent regulation by PME activity could affect the pectin structure and associated cell wall mechanical properties.

Genome-wide survey and evolutionary history of the pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi

Once deposited in the plant cell wall, pectin undergoes demethylesterification by endogenous pectin methylesterases (PMEs), which play various roles in growth and development, including defense against pathogen attacks. Pathogen PMEs can alter pectin's methylesterification pattern, increasing its susceptibility to degradation by other fungal pectinases and thus playing a critical role as virulence factors during early infection stages. To investigate the evolutionary history of PMEs in the Dothideomycetes class of fungi, we obtained genomic data from 15 orders (79 species) and added genomic data from 61 isolates of Corynespora cassiicola. Our analyses involved maximum likelihood phylogenies, gene genealogies, and selection analyses. Additionally, we measured PME gene expression levels of C. cassiicola using soybean as a host through RT-qPCR assays. We recovered 145 putative effector PMEs and 57 putative non-effector PMEs from across the Dothideomycetes. The PME gene family exhibits a small size (up to 5 members per genome) and comprises three major clades. The evolutionary patterns of the PME1 and PME2 clades were largely shaped by duplications and recurring gene retention events, while biased gene loss characterized the small-sized PME3 clade. The presence of five members in the PME gene family of C. cassiicola suggests that the family may play a key role in the evolutionary success of C. cassiicola as a polyphagous plant pathogen. The haplogroups Cc_PME1.1 and Cc_PME1.2 exhibited an accelerated rate of evolution, whereas Cc_PME2.1, Cc_PME2.2, and Cc_PME2.3 seem to be under strong purifying selective constraints. All five PME genes were expressed during infection of soybean leaves, with the highest levels during from six to eight days post-inoculation. The highest relative expression level was measured for CC_29_g7533, a member of the Cc_PME2.3 clade, while the remaining four genes had relatively lower levels of expression.

Crystal Structures of Bacterial Pectin Methylesterases Pme8A and PmeC2 from Rumen Butyrivibrio

Pectin is a complex polysaccharide that forms a substantial proportion of the plant's middle lamella of forage ingested by grazing ruminants. Methanol in the rumen is derived mainly from methoxy groups released from pectin by the action of pectin methylesterase (PME) and is subsequently used by rumen methylotrophic methanogens that reduce methanol to produce methane (CH4). Members of the genus Butyrivibrio are key pectin-degrading rumen bacteria that contribute to methanol formation and have important roles in fibre breakdown, protein digestion, and the biohydrogenation of fatty acids. Therefore, methanol release from pectin degradation in the rumen is a potential target for CH4 mitigation technologies. Here, we present the crystal structures of PMEs belonging to the carbohydrate esterase family 8 (CE8) from Butyrivibrio proteoclasticus and Butyrivibrio fibrisolvens, determined to a resolution of 2.30 Å. These enzymes, like other PMEs, are right-handed β-helical proteins with a well-defined catalytic site and reaction mechanisms previously defined in insect, plant, and other bacterial pectin methylesterases. Potential substrate binding domains are also defined for the enzymes.

Uncovering the interactions between PME and PMEI at the gene and protein levels: Implications for the design of specific PMEI

CONTEXT

Pectin methylesterase inhibitor (PMEI) can specifically bind and inhibit the activity of pectin methylesterase (PME), which has been widely used in fruit and vegetable juice processing. However, the limited three-dimensional structure, unclear action mechanism, low thermal stability and biological activity of PMEI severely limited its application. In this work, molecular recognition and conformational changes of PME and PMEI were analyzed by various molecular simulation methods. Then suggestions were proposed for improving thermal stability and affinity maturation of PMEI through semi-rational design.

METHODS

Phylogenetic trees of PME and PMEI were established using the Maximum likelihood (ML) method. The results show that PME and PMEI have good sequence and structure conservation in various plants, and the simulated data can be widely adopted. In this work, MD simulations were performed using AMBER20 package and ff14SB force field. Protein interaction analysis indicates that H-bonds, van der Waals forces, and the salt bridge formed of K224 with ID116 are the main driving forces for mutual molecular recognition of PME and PMEI. According to the analyses of free energy landscape (FEL), conformational cluster, and motion, the association with PMEI greatly disrupts PME's dispersed functional motion mode and biological function. By monitoring the changes of residue contact number and binding free energy, IG35M/ IG35R: IT93F and IT113W/ IT113W: ID116W mutations contribute to thermal stability and affinity maturation of the PME-PMEI complex system, respectively. This work reveals the interaction between PME and PMEI at the gene and protein levels and provides options for modifying specific PMEI.

Sequence, structure and functionality of pectin methylesterases and their use in sustainable carbohydrate bioproducts: A review

Pectin methylesterases (PMEs) are enzymes that play a critical role in modifying pectins, a class of complex polysaccharides in plant cell walls. These enzymes catalyze the removal of methyl ester groups from pectins, resulting in a change in the degree of esterification and consequently, the physicochemical properties of the polymers. PMEs are found in various plant tissues and organs, and their activity is tightly regulated in response to developmental and environmental factors. In addition to the biochemical modification of pectins, PMEs have been implicated in various biological processes, including fruit ripening, defense against pathogens, and cell wall remodelling. This review presents updated information on PMEs, including their sources, sequences and structural diversity, biochemical properties and function in plant development. The article also explores the mechanisms of PME action and the factors influencing enzyme activity. In addition, the review highlights the potential applications of PMEs in various industrial sectors related to biomass exploitation, food, and textile industries, with a focus on development of bioproducts based on eco-friendly and efficient industrial processes.

Biochemical Characterization and Molecular Insights into Substrate Recognition of Pectin Methylesterase from Phytophthora Infestans

Pectin methylesterases (PMEs) are a class of carbohydrate-active enzymes that act on the O6-methyl ester groups of the homogalacturonan component of pectins, resulting in de-esterification of the substrate polymers and formation of pectate and methanol. PMEs occur in higher plants and microorganisms, including fungi, oomycetes, bacteria, and archaea. Microbial PMEs play a crucial role in pathogens’ invasion of plant tissues. Here, we have determined the structural and functional properties of Pi-PME, a PME from the oomycete plant pathogen Phytophthora infestans. This enzyme exhibits maximum activity at alkaline pH (8.5) and is active over a wide temperature range (25–50 °C). In silico determination of the structure of Pi-PME reveals that the protein consists essentially of three parallel β-sheets interconnected by loops that adopt an overall β-helix organization. The loop regions in the vicinity of the active site are extended compared to plant and fungal PMEs, but they are shorter than the corresponding bacterial and insect regions. Molecular dynamic simulations revealed that Pi-PME interacts most strongly with partially de-methylated homogalacturonans, suggesting that it preferentially uses this type of substrates. The results are compared and discussed with other known PMEs from different organisms, highlighting the specific features of Pi-PME.

Arabidopsis root responses to salinity depend on pectin modification and cell wall sensing

Owing to its detrimental effect on plant growth, salinity is an increasing worldwide problem for agriculture. To understand the molecular mechanisms activated in response to salt in Arabidopsis thaliana, we investigated the Catharanthus roseus receptor-like kinase 1-like family, which contains sensors that were previously shown to be involved in sensing the structural integrity of the cell walls. We found that herk1 the1-4 double mutants, lacking the function of HERKULES1 (HERK1) and combined with a gain-of-function allele of THESEUS1 (THE1), strongly respond to salt application, resulting in an intense activation of stress responses, similarly to plants lacking FERONIA (FER) function. We report that salt triggers pectin methyl esterase (PME) activation and show its requirement for the activation of several salt-dependent responses. Because chemical inhibition of PMEs alleviates these salt-induced responses, we hypothesize a model in which salt directly leads to cell wall modifications through the activation of PMEs. Responses to salt partly require the functionality of FER alone or HERK1/THE1 to attenuate salt effects, highlighting the complexity of the salt-sensing mechanisms that rely on cell wall integrity.

Summary: Salt-triggered activation of pectin methyl esterase changes pectin in Arabidopsis, inducing at least two pathways: a CrRLK1L-dependent pathway downregulating salt stress responses and a CrRLK1L-independent pathway that activates downstream signaling.

Characterization of an Aspergillus niger for Efficient Fatty Acid Ethyl Ester Synthesis in Aqueous Phase and the Molecular Mechanism

Fatty acid ethyl esters are important flavor chemicals in strong-flavor baijiu. Microorganisms are the main contributors to ester synthesis during baijiu manufacture. However, the ester synthesis was unstable between batches. This was owing to a limited knowledge of the mechanisms for ester synthesis by microorganisms. In this work, a fatty acid ethyl ester synthesizing Aspergillus niger strain CGMCC (China General Microbiological Culture Collection) 3.4309 was identified. The conversion ratios of ethyl valerate, ethyl caproate, ethyl caprylate, and ethyl caprate were 7.87, 29.20, 94.80, and 85.20%, respectively, under the optimized conditions. A comparison of transcriptomes under the initial and optimized ester synthetic conditions indicated that 23 genes were upregulated in transcription level and encoded enzymes with potential abilities for ester synthesis. Eleven of the enzymes were expressed, and three of them, numbered An605, An1097, and An3131, showed the ability to catalyze fatty acid ethyl ester synthesis under aqueous phase, with capric acid as the preferred substrate. The possible enzymatic catalytic mechanism was proposed based on homology modeling and molecular docking. This study reported for the first time that A. niger showed the ability to efficiently catalyze the synthesis of short- and medium-chain fatty acid ethyl esters in aqueous phase, identified the key enzymes, and analyzed the basic enzymatic properties. This is helpful to promote the application of related microorganisms and enzyme resources in the baijiu industry.

Effects of ultrasound on the enzymatic degradation of pectin

Ultrasound-assisted enzymatic maceration (UAEM) has gained considerable interest in the fruit juice industry, owing to its potential to increase juice yield and content of polyphenols while simultaneously saving time and energy. In this study, the effects of UAEM (ultrasonic probe, 20 kHz, 21 W*cm^-2 and 33 W*cm^-2) on pectin degradation in a continuous circulation system were investigated over 60 and 90 min. Main pectinolytic enzymes activities of (polygalacturonase, pectin lyase and pectin methylesterase) of a commercial enzyme preparation were examined for individual synergistic effects with US. Pectin hydrolysis by UAEM differed significantly compared to treatment with ultrasound or enzymes alone regarding the profile of degradation products compared to treatment with ultrasound or enzymes alone. Ultrasound fragmented pectin to less branched oligomers of medium molecular weight (Mp approx. 150 kDa), which were further degraded by pectinolytic activities. The low molecular weight fraction (<30 kDa), which is known to be beneficial for juice-quality by adding nutritional value and stabilizing polyphenols, was enriched in small oligomers of homogalacturonan-derived, rhamnogalacturonan I-derived, and rhamnogalacturonan II-derived residues. Synergistic effects of ultrasound application enhanced the effective activities of polygalacturonase and pectin lyase and even prolonged their performance over 90 min, whereas the effective activity of pectin methylesterase was not affected. Final marker concentrations determined by each enzyme assay revealed a considerable higher total process output after UAEM treatment at reduced temperature (30 °C) comparable to the output after conventional batch maceration at 50 °C. The obtained results demonstrate the high potential of UAEM to produce high-quality juice by controlling pectin degradation while reducing process temperature and equally highlight the matrix and enzyme specific effects of a simultaneous US treatment.

New insights into the specificity and processivity of two novel pectinases from Verticillium dahliae

Pectin, the major non-cellulosic component of primary cell wall can be degraded by polygalacturonases (PGs) and pectin methylesterases (PMEs) during pathogen attack on plants. We characterized two novel enzymes, VdPG2 and VdPME1, from the fungal plant pathogen Verticillium dahliae. VdPME1 was most active on citrus methylesterified pectin (55-70%) at pH 6 and a temperature of 40 °C, while VdPG2 was most active on polygalacturonic acid at pH 5 and a temperature of 50 °C. Using LC-MS/MS oligoprofiling, and various pectins, the mode of action of VdPME1 and VdPG2 were determined. VdPME1 was shown to be processive, in accordance with the electrostatic potential of the enzyme. VdPG2 was identified as endo-PG releasing both methylesterified and non-methylesterified oligogalacturonides (OGs). Additionally, when flax roots were used as substrate, acetylated OGs were detected. The comparisons of OGs released from Verticillium-susceptible and partially resistant flax cultivars identified new possible elicitor of plant defence responses.

Characterization of an acidic pectin methylesterase from Paenibacillus xylanexedens and its application in fruit processing

A pectinase-producing bacterial isolate, identified as Paenibacillus xylanexedens SZ 29, was screened by using the soil dilution plate with citrus pectin and congo red. A pectin methylesterase gene (Pxpme) was cloned and expressed in Escherichia coli. The gene coded for a protein with 334 amino acids and a calculated molecular mass of 36.76 kDa. PxPME showed the highest identity of 32.4% with the characterized carbohydrate esterase family 8 pectin methylesterase from Daucus carota. The recombined PxPME showed a specific activity with 39.38 U/mg against citrus pectin with >65% methylesterification. The optimal pH and temperature for PxPME activity were 5.0 and 45 °C. Its K_m and V_max value were determined to be 1.43 mg/mL and 71.5 μmol/mg·min, respectively. Moreover, PxPME could increase the firmness of pineapple cubes by 114% when combined with CaCl₂. The acidic and mesophilic properties make PxPME a potential candidate for application in the fruit processing.

Development of an Innovative Process for High-Temperature Fruit Juice Extraction Using a Novel Thermophilic Endo-Polygalacturonase From Penicillium oxalicum

Efficient and cost-effective production of thermophilic endo-polygalacturonase is desirable for industrial fruit juice production, because its application could shorten the processing time and lower the production cost, by eliminating the separate step of pectin degradation. However, no endo-polygalacturonase that both functions well at sufficiently high temperature and can be manufactured economically, has been reported previously. In this study, the cDNA encoding a thermophilic endo-polygalacturonase from Penicillium oxalicum CZ1028, was cloned and over-expressed in Pichia pastoris GS115 and Escherichia coli BL21(DE3). The recombinant proteins PoxaEnPG28B-Pp (from P. pastoris) and PoxaEnPG28B-Ec (from E. coli) were isolated and purified. PoxaEnPG28B-Pp was sufficiently thermostable for potential industrial use, but PoxaEnPG28B-Ec was not. The optimal pH and temperature of PoxaEnPG28B-Pp were pH 5.0 and 65°C, respectively. The enzyme had a low K_m of 1.82 g/L and a high V_max of 77882.2 U/mg, with polygalacturonic acid (PGA) as substrate. The performance of PoxaEnPG28B-Pp in depectinization of papaya, plantain and banana juices at 65°C for 15 min was superior to that of a reported mesophilic endo-polygalacturonase. PoxaEnPG28B-Pp is the first endo-polygalacturonase reported to show excellent performance at high temperature. An innovative process, including a step of simultaneous heat-treatment and depectinization of fruit pulps with PoxaEnPG28B-Pp, is reported for the first time.

Structural determination of Enzyme-Graphene Nanocomposite Sensor Material

State-of-the-art ultra-sensitive blood glucose-monitoring biosensors, based on glucose oxidase (GOx) covalently linked to a single layer graphene (SLG), will be a valuable next generation diagnostic tool for personal glycemic level management. We report here our observations of sensor matrix structure obtained using a multi-physics approach towards analysis of small-angle neutron scattering (SANS) on graphene-based biosensor functionalized with GOx under different pH conditions for various hierarchical GOx assemblies within SLG. We developed a methodology to separately extract the average shape of GOx molecules within the hierarchical assemblies. The modeling is able to resolve differences in the average GOx dimer structure and shows that treatment under different pH conditions lead to differences within the GOx at the dimer contact region with SLG. The coupling of different analysis methods and modeling approaches we developed in this study provides a universal approach to obtain detailed structural quantifications, for establishing robust structure-property relationships. This is an essential step to obtain an insight into the structure and function of the GOx-SLG interface for optimizing sensor performance.

Resolving solution conformations of the model semi-flexible polyelectrolyte homogalacturonan using molecular dynamics simulations and small-angle x-ray scattering

The conformation of polyelectrolytes in the solution state has long been of interest in polymer science. Herein we utilize all atom molecular dynamics simulations (MD) and small-angle x-ray scattering experiments (SAXS) to elucidate the molecular structure of the model polyelectrolyte homogalacturonan. Several degrees of polymerization were studied and in addition partial methylesterification of the otherwise charge-carrying carboxyl groups was used in order to generate samples with varying intra-chain charge distributions. It is shown that at length scales above around 1nm the conformation of isolated chains has surprisingly little dependence on the charge distribution or the concentration of attendant monovalent salts, reflective of the intrinsic stiffness of the saccharide rings and the dynamical constraints of the glycosidic linkage. Indeed the conformation of isolated chains over all accessible length scales is well described by the atomic coordinates available from fibre diffraction studies. Furthermore, in more concentrated systems it is shown that, after careful analysis of the SAXS data, the form of the inter-particle effects heralded by the emergence of a so-called polyelectrolyte peak, can be extracted, and that this phenomena can be reproduced by multiple chain MD simulations.

On the electrophoretic mobilities of partially charged oligosaccharides as a function of charge patterning and degree of polymerization

Fully or partially charged oligosaccharide molecules play a key role in many areas of biology, where their fine structures are crucial in determining their functionality. However, the separation of specific charged oligosaccharides from similar moieties that typically coexist in extracted samples, even for those that are unbranched, and in cases where each saccharide moiety can only carry a single charge or not, is far from trivial. Typically such molecules are characterized by a degree of polymerization n and a number m (and distribution) of charged residues, and must be separated from a plethora of similar species possessing different combinations of n and m. Furthermore, the separation of the possible n!/m!(n-m)! isomers of each species of fixed n and m is a formidable challenge to analytical chemists. Herein, we report the results of molecular dynamics simulations that have been performed in order to calculate the free solution electrophoretic mobilities of galacturonides and charged oligosaccharides derived from digests of the important plant cell-wall polysaccharide pectin. The simulations are compared with an experiment and are found to correctly predict the loss of resolution of fully charged species above a critical degree of polymerization n and the ionic strength dependence of the electrophoretic mobilities of different partially charged oligosaccharides. It is expected that having a predictive tool for the calculation of the electrophoretic mobilities of differently charged oligosaccharide species in hand will allow experimental conditions that optimize the resolution of particular species to be ascertained and understood.

Carbohydrate Esterases: An Overview

Carbohydrate esterases are a group of enzymes which release acyl or alkyl groups attached by ester linkage to carbohydrates. The CAZy database, which classifies enzymes that assemble, modify, and break down carbohydrates and glycoconjugates, classifies all carbohydrate esterases into 16 families. This chapter is an overview of the research for nearly 50 years around the main groups of carbohydrate esterases dealing with the degradation of polysaccharides, their main biochemical and molecular traits, as well as its application for the synthesis of high added value esters.