Structural characterization of the thermally tolerant pectin methylesterase purified from citrus sinensis fruit and its gene sequence

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.

Mechanisms of persimmon pectin methyl esterase activation by high pressure processing based on chemical experiments and molecular dynamics simulations

High pressure processing (HPP) was found to have a kinase effect on persimmon pectin methyl esterase (PME), while the mechanism remains unclear. In this study, chemical experiments and molecular dynamics (MD) simulations were used to reveal its mechanisms. Persimmon PME was first extracted and purified using ion exchange columns with 81.89% purity. After 500 MPa/5 min, PME activity increased 11.3%, the α-helix and β-folding decreased 10.8% and 6.1% compared to the 0.1 MPa group, respectively. MD results showed that HPP decreased the volume, increased the number of hydrogen bonds between PME and pectin. Under high pressure, Asp-157, Asp-136 and Gln-135 in the enzyme activity center remained stable, while the positions of Arg-225 and Gln-113 changed a lot. The conformation of the substrate binding channel also changed. The secondary structure and volume changes of the HPP-treated PME affected the active center and substrate channels, ultimately altering the activity.

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.

The use of matrix-assisted laser desorption/ionization mass spectrometry in enzyme activity assays and its position in the context of other available methods

Activity assays are indispensable for studying biochemical properties of enzymes. The purposes of measuring activity are wide ranging from a simple detection of the presence of an enzyme to kinetic experiments evaluating the substrate specificity, reaction mechanisms, and susceptibility to inhibitors. Common activity assay methods include spectroscopy, electrochemical sensors, or liquid chromatography coupled with various detection techniques. This review focuses on the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a growing and modern alternative, which offers high speed of analysis, sensitivity, versatility, possibility of automation, and cost-effectiveness. It may reveal reaction intermediates, side products or measure more enzymes at once. The addition of an internal standard or calculating the ratios of the substrate and product peak intensities and areas overcome the inherent inhomogeneous distribution of analyte and matrix in the sample spot, which otherwise results in a poor reproducibility. Examples of the application of MALDI-TOF MS for assaying hydrolases (including peptidases and β-lactamases for antibiotic resistance tests) and other enzymes are provided. Concluding remarks summarize advantages and challenges coming from the present experience, and draw future perspectives such as a screening of large libraries of chemical compounds for their substrate or inhibitory properties towards enzymes.

Purification and Characterization of a Salt-Dependent Pectin Methylesterase from Carica papaya Fruit Mesocarp-Exocarp Tissue

Pectin methylesterase (PME) is a ubiquitous cell wall enzyme, which de-esterifies and modifies pectins for food applications. Functional properties of pectin rely on molecular weight and degree of esterification, and thus de-esterification by PME influences the pectin functionality. The main aim of the study is to purify and biochemically characterize PME from the outer mesocarp-exocarp tissue of unripe Carica papaya L. fruit. The ion-exchange and gel-permeation chromatography purified enzyme exhibited a specific activity of 2363.1 ± 92.8 units/mg protein, with a fold purification of 10.6, and final recovery of 9.0%. The PME showed a low apparent mass of 27 kDa by SDS-PAGE. The optimal activity of purified PME was found at pH 7.0, and at 60 °C. The enzyme is fairly stable at 60 °C for 10 min, retaining 60% activity. The optimum activity was found with 0.25 mol/L monovalent salts indicating that this PME is salt-dependent. The K_m of PME was 0.22 mg/mL, and the V_max value was 1289.15 ± 15.9 units/mg. The increase in the calcium sensitivity of the PME-treated pectin indicated a blockwise mode of action. The PME significantly differs from other known plant PMEs in their biochemical properties. Manual inspection and MASCOT searching of generated tryptic peptides confirmed no homology to known papaya PME sequences. The preliminary results indicate that the papaya PME can be potentially utilized to modify pectin functionality at elevated temperature. However, further investigation is required to understand the usefulness of this enzyme for the modification of pectins for various food applications.

PRACTICAL APPLICATION

In this work, a small, 27 kDa papaya PME was purified by ion-exchange and gel-permeation chromatography and biochemically characterized. The papaya PME significantly differs from other known plant PMEs in their biochemical properties. The preliminary results like fair thermostability coupled with high temperature optimum indicate that the papaya PME can be potentially utilized to modify pectin functionality at high temperature. Modification of pectin functionality at elevated temperatures is advantageous since it evades the detrimental action of other pectinolytic enzymes.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014

This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.