Primary structure and characterization of an exopolygalacturonase from Aspergillus tubingensis

Paleocene origin of a streamlined digestive symbiosis in leaf beetles

Timing the acquisition of a beneficial microbe relative to the evolutionary history of its host can shed light on the adaptive impact of a partnership. Here, we investigated the onset and molecular evolution of an obligate symbiosis between Cassidinae leaf beetles and Candidatus Stammera capleta, a γ-proteobacterium. Residing extracellularly within foregut symbiotic organs, Stammera upgrades the digestive physiology of its host by supplementing plant cell wall-degrading enzymes. We observe that Stammera is a shared symbiont across tortoise and hispine beetles that collectively comprise the Cassidinae subfamily, despite differences in their folivorous habits. In contrast to its transcriptional profile during vertical transmission, Stammera elevates the expression of genes encoding digestive enzymes while in the foregut symbiotic organs, matching the nutritional requirements of its host. Despite the widespread distribution of Stammera across Cassidinae beetles, symbiont acquisition during the Paleocene (∼62 mya) did not coincide with the origin of the subfamily. Early diverging lineages lack the symbiont and the specialized organs that house it. Reconstructing the ancestral state of host-beneficial factors revealed that Stammera encoded three digestive enzymes at the onset of symbiosis, including polygalacturonase-a pectinase that is universally shared. Although non-symbiotic cassidines encode polygalacturonase endogenously, their repertoire of plant cell wall-degrading enzymes is more limited compared with symbiotic beetles supplemented with digestive enzymes from Stammera. Highlighting the potential impact of a symbiotic condition and an upgraded metabolic potential, Stammera-harboring beetles exploit a greater variety of plants and are more speciose compared with non-symbiotic members of the Cassidinae.

Characterization of Two Novel Rumen-Derived Exo-Polygalacturonases: Catalysis and Molecular Simulations

Pectinases are a series of enzymes that degrade pectin and have been used extensively in the food, feed, and textile industries. The ruminant animal microbiome is an excellent source for mining novel pectinases. Two polygalacturonase genes, IDSPga28-4 and IDSPga28-16, from rumen fluid cDNA, were cloned and heterologously expressed. Recombinant IDSPGA28-4 and IDSPGA28-16 were stable from pH 4.0 to 6.0, with activities of 31.2 ± 1.5 and 330.4 ± 12.4 U/mg, respectively, against polygalacturonic acid. Hydrolysis product analysis and molecular dynamics simulation revealed that IDSPGA28-4 was a typical processive exo-polygalacturonase and cleaved galacturonic acid monomers from polygalacturonic acid. IDSPGA28-16 cleaved galacturonic acid only from substrates with a degree of polymerization greater than two, suggesting a unique mode of action. IDSPGA28-4 increased the light transmittance of grape juice from 1.6 to 36.3%, and IDSPGA28-16 increased the light transmittance of apple juice from 1.9 to 60.6%, indicating potential application in the beverage industry, particularly for fruit juice clarification.

Characterization of Novel Pectinolytic Enzymes Derived from the Efficient Lignocellulose Degradation Microbiota

Diverse pectinolytic enzymes are widely applied in the food, papermaking, and other industries, and they account for more than 25% of the global industrial enzyme demands. Efficient lignocellulose degradation microbiota are reservoirs of pectinolytic enzymes and other lignocellulose-degrading genes. Metagenomics has been widely used to discover new pectinolytic enzymes. Here, we used a metagenomic strategy to characterize pectinolytic genes from one efficient lignocellulose-degrading microbiota derived from pulp and paper wastewater treatment microbiota. A total of 23 predicted full-length GH28 and PL1 family pectinolytic genes were selectively cloned and expressed in Escherichia coli, and 5 of the expressed proteins had pectinolytic activities. Among them, the characterization of one pectinolytic enzyme, PW-pGH28-3, which has a 58.4% identity with an exo-polygalacturonase gene of Aquipluma nitroreducens, was further investigated. The optimal pH and optimal temperature of PW-pGH28-3 were 8.0 and 40 °C, respectively, and its pectinolytic activity at the optimal condition was 13.5 ± 1.1 U/mg protein. Bioinformatics analyses and structural modeling suggest that PW-pGH28-3 is a novel secretory exo-polygalacturonase, which is confirmed by its hydrolysates of polygalacturonic acid. The detection of PW-pGH28-3 and other pectinolytic genes showed that efficient lignocellulose degradation microbiota could provide potential efficient pectinolytic enzymes for industrial application. In the future, improving metagenomic screening efficiency would discover efficient lignocellulose-degrading enzymes and lead to the sustainable and green utilization of lignocellulose.

Long Non-Coding RNAs profiling in pathogenesis of Verticillium dahliae: New insights in the host-pathogen interaction

Verticillium dahliae causes vascular wilt disease on cotton (Gossypium hirsutum), resulting in devastating yield loss worldwide. While little is known about the mechanism of long non-coding RNAs (lncRNAs), several lncRNAs have been implicated in numerous physiological processes and diseases. To better understand V. dahliae pathogenesis, lncRNA was conducted in a V. dahliae virulence model. Potential target genes of significantly regulated lncRNAs were predicted using cis/trans-regulatory algorithms. This study provides evidence for lncRNAs' regulatory role in pathogenesis-related genes. Interestingly, lncRNAs were identified and varying in terms of RNA length and nutrient starvation treatments. Efficient pathogen nutrition during the interaction with the host is a requisite factor during infection. Our observations directly link to mutated V. dahliae invasion, explaining infected cotton have lower pathogenicity and lethality compared to V. dahliae. Remarkably, lncRNAs XLOC_006536 and XLOC_000836 involved in the complex regulation of pathogenesis-related genes in V. dahliae were identified. For the first time the regulatory role of lncRNAs in filamentous fungi was uncovered, and it is our contention that elucidation of lncRNAs will advance our understanding in the development and pathogenesis of V. dahliae and offer alternatives in the control of the diseases caused by fungus V. dahliae attack.

Structural model and functional properties of an exo-polygalacturonase from Neosartorya glabra

A purified exo-polygalacturonase of Neosartorya glabra (EplNg) was successfully characterized. EplNg native presented 68.2 kDa, with 32% carbohydrate content. The deglycosylated form showed 46.3 kDa and isoelectric point of 5.4. The identity of EplNg was confirmed as an exo-polygalacturonase class I (EC 3.2.1.67) using mass spectrometry and Western-Blotting. Capillary electrophoresis indicated that only galacturonic acid was released by the action of EplNg on sodium polypectate, confirming an exoenzyme character. The structural model confers that EplNg has a core formed by twisted parallel β-sheets structure. Among twelve putative cysteines, ten were predicted to form disulfide bridges. The catalytic triad predicted is composed of Asp²²³, Asp²⁴⁵, and Asp²⁴⁶ aligned along with a distance in 4-5 Å, suggesting that EplNg probably does not perform the standard inverting catalytic mechanism described for the GH28 family. EplNg was active from 30 to 90 °C, with maximum activity at 65 °C, pH 5.0. The Km and Vmax determined using sodium polypectate were 6.9 mg·mL^-1 and Vmax 690 μmol·min^-1.mg^-1, respectively. EplNg was active and stable over a wide range of pH values and temperatures, confirming the interesting properties EplNg and provide a basis for the development of the enzyme in different biotechnological processes.

From secretion in Pichia pastoris to application in apple juice processing: Exo-polygalacturonase from Sporothrix schenckii 1099-18

BACKGROUND

Polygalacturonases are a group of enzymes under pectinolytic enzymes related to enzymes that hydrolyse pectic substances. Polygalacturonases have been used in various industrial applications such as fruit juice clarification, retting of plant fibers, wastewater treatment drinks fermentation, and oil extraction.

OBJECTIVES

The study was evaluated at the heterologous expression, purification, biochemical characterization, computational modeling, and performance in apple juice clarification of a new exo-polygalacturonase from Sporothrix schenckii 1099-18 (SsExo-PG) in Pichia pastoris.

METHODS

Recombinant DNA technology was used in this study. Two different pPIC9K plasmids were constructed with native signal sequence-ssexo-pg and alpha signal sequence-ssexo-pg separately. Protein expression and purification performed after plasmids transformed into the Pichia pastoris. Biochemical and structural analyses were performed by using pure SsExo-PG.

RESULTS

The purification of SsExo-PG was achieved using a Ni-NTA chromatography system. The enzyme was found to have a molecular mass of approximately 52 kDa. SsExo-PG presented as stable at a wide range of temperature and pH values, and to be more storage stable than other commercial pectinolytic enzyme mixtures. Structural analysis revealed that the catalytic residues of SsExo-PG are somewhat similar to other Exo-PGs. The KM and kcat values for the degradation of polygalacturonic acid (PGA) by the purified enzyme were found to be 0.5868 µM and 179 s-1, respectively. Cu2+ was found to enhance SsExo-PG activity while Ag2+ and Fe2+ almost completely inhibited enzyme activity. The enzyme reduced turbidity up to 80% thus enhanced the clarification of apple juice. SsExo-PG showed promising performance when compared with other commercial pectinolytic enzyme mixtures.

CONCLUSION

The clarification potential of SsExo-PG was revealed by comparing it with commercial pectinolytic enzymes. The following parameters of the process of apple juice clarification processes showed that SsExo-PG is highly stable and has a novel performance.

Functional roles of LaeA, polyketide synthase, and glucose oxidase in the regulation of ochratoxin A biosynthesis and virulence in Aspergillus carbonarius

Aspergillus carbonarius is the major producer of ochratoxin A (OTA) among Aspergillus species, but the contribution of this secondary metabolite to fungal virulence has not been assessed. We characterized the functions and addressed the roles of three factors in the regulation of OTA synthesis and pathogenicity in A. carbonarius: LaeA, a transcriptional factor regulating the production of secondary metabolites; polyketide synthase, required for OTA biosynthesis; and glucose oxidase (GOX), regulating gluconic acid (GLA) accumulation and acidification of the host tissue during fungal growth. Deletion of laeA in A. carbonarius resulted in significantly reduced OTA production in colonized nectarines and grapes. The ∆laeA mutant was unable to efficiently acidify the colonized tissue, as a direct result of diminished GLA production, leading to attenuated virulence in infected fruit compared to the wild type (WT). The designed Acpks-knockout mutant resulted in complete inhibition of OTA production in vitro and in colonized fruit. Interestingly, physiological analysis revealed that the colonization pattern of the ∆Acpks mutant was similar to that of the WT strain, with high production of GLA in the colonized tissue, suggesting that OTA accumulation does not contribute to A. carbonarius pathogenicity. Disruption of the Acgox gene inactivated GLA production in A. carbonarius, and this mutant showed attenuated virulence in infected fruit compared to the WT strain. These data identify the global regulator LaeA and GOX as critical factors modulating A. carbonarius pathogenicity by controlling transcription of genes important for fungal secondary metabolism and infection.

Online evaluation of the metabolic activity of Ustilago maydis on (poly)galacturonic acid

Background

Pectin is a rather complex and highly branched polysaccharide strengthening the plant cell wall. Thus, many different pectinases are required for an efficient microbial conversion of biomass waste streams with a high pectin content like citrus peel, apple pomace or sugar beet pulp. The screening and optimization of strains growing on pectic substrates requires both, quantification of the residual substrate and an accurate determination of the enzymatic activity. Galacturonic acid, the main sugar unit of pectin, is an uncommon substrate for microbial fermentations. Thus, growth and enzyme production of the applied strain has to be characterized in detail to understand the microbial system. An essential step to reach this goal is the development of online monitoring tools.

Results

In this study, a method for the online determination of residual substrate was developed for the growth of the plant pathogenic fungus Ustilago maydis on pectic substrates such as galacturonic acid. To this end, an U. maydis strain was used that expressed a heterologous exo-polygalacturonase for growth on polygalacturonic acid. The growth behavior on galacturonic acid was analyzed by online measurement of the respiration activity. A method for the online prediction of the residual galacturonic acid concentration during the cultivation, based on the overall oxygen consumption, was developed and verified by offline sampling. This sensitive method was extended towards polygalacturonic acid, which is challenging to quantify via offline measurements. Finally, the enzymatic activity in the culture supernatant was calculated and the enzyme stability during the course of the cultivation was confirmed.

Conclusion

The introduced method can reliably predict the residual (poly)galacturonic acid concentration based on the overall oxygen consumption. Based on this method, the enzymatic activity of the culture broth of an U. maydis strain expressing a heterologous exo-polygalacturonase could be calculated. It was demonstrated that the method is especially advantageous for determination of low enzymatic activities. In future, it will be applied to U. maydis strains in which the number of produced hydrolytic enzymes is increased for more efficient degradation.

Electronic supplementary material

The online version of this article (10.1186/s13036-018-0128-1) contains supplementary material, which is available to authorized users.

Production, purification and biochemical characterization of an exo-polygalacturonase from Aspergillus niger MTCC 478 suitable for clarification of orange juice

Polygalacturonases (PG) represent an important member of pectinases group of enzymes with immense industrial applications. A fungal strain Aspergillus niger MTCC478 was used for the production of polygalacturonase both under submerged and solid-state fermentation condition. Further its production was optimized under solid-state fermentation condition with media comprising of wheat bran and tea extract. Purification of an exo-PG was achieved by acetone precipitation (60-90%) and CM-cellulose column chromatography revealing 15.28-fold purification with a specific activity of 33.47 U/mg protein and 1.2% yield. A relative molecular mass of purified PG was approximately 124.0 kDa. The pH and temperature optimum was found to be 4 and 50 °C, respectively. The k cat and K m value for degradation of PGA by the purified enzyme was found to be 194 s-1 and 2.3 mg/mL, respectively. Cu2+ was found to enhance the PG activity while Ag+ completely inhibited the enzyme activity. The application of the purified PG in orange juice clarification was elucidated.

Alkaline thermostable pectinase enzyme from Aspergillus niger strain MCAS2 isolated from Manaslu Conservation Area, Gorkha, Nepal

Pectinase enzymes are one of the commercially important enzymes having great potential in various industries especially in food industry. Pectinases accounts for 25 % of global food enzymes produced and their market is increasing day by day. Therefore, the exploration of microorganism with novel characteristics has always been the focus of the research. Microorganism dwelling in unique habitat may possess unique characteristics. As such, a pectinase producing fungus Aspergillus niger strain MCAS2 was isolated from soil of Manaslu Conservation Area (MCA), Gorkha, Nepal. The optimum production of pectinase enzyme was observed at 48 h of fermentation. The pectinase enzyme was partially purified by cold acetone treatment followed by Sephadex G-75 gel filtration chromatography. The partially purified enzyme exhibited maximum activity 60 U/mg which was almost 8.5-fold higher than the crude pectinase. The approximate molecular weight of the enzyme was found to be 66 kDa as observed from SDS-PAGE. The pectinase enzyme was active at broad range of temperature (30-70 °C) and pH (6.2-9.2). Optimum temperature and pH of the pectinase enzyme were 50 °C and 8.2 respectively. The enzyme was stable up to 70 °C and about 82 % of pectinase activity was still observed at 100 °C. The thermostable and alkaline nature of this pectinase can meet the demand of various industrial processes like paper and pulp industry, in textile industry, fruit juice industry, plant tissue maceration and wastewater treatment. In addition, the effect of different metal ions on pectinase activity was also studied.

Identification and expression analysis of BoMF25, a novel polygalacturonase gene involved in pollen development of Brassica oleracea

BoMF25 acts on pollen wall. Polygalacturonase (PG) is a pectin-digesting enzyme involved in numerous plant developmental processes and is described to be of critical importance for pollen wall development. In the present study, a PG gene, BoMF25, was isolated from Brassica oleracea. BoMF25 is the homologous gene of At4g35670, a PG gene in Arabidopsis thaliana with a high expression level at the tricellular pollen stage. Collinear analysis revealed that the orthologous gene of BoMF25 in Brassica campestris (syn. B. rapa) genome was probably lost because of genome deletion and reshuffling. Sequence analysis indicated that BoMF25 contained four classical conserved domains (I, II, III, and IV) of PG protein. Homology and phylogenetic analyses showed that BoMF25 was clustered in Clade F. The putative promoter sequence, containing classical cis-acting elements and pollen-specific motifs, could drive green fluorescence protein expression in onion epidermal cells. Quantitative RT-PCR analysis suggested that BoMF25 was mainly expressed in the anther at the late stage of pollen development. In situ hybridization analysis also indicated that the strong and specific expression signal of BoMF25 existed in pollen grains at the mature pollen stage. Subcellular localization showed that the fluorescence signal was observed in the cell wall of onion epidermal cells, which suggested that BoMF25 may be a secreted protein localized in the pollen wall.

Horizontal gene transfer and functional diversification of plant cell wall degrading polygalacturonases: Key events in the evolution of herbivory in beetles

Plant cell walls are the largest reservoir of organic carbon on earth. To breach and utilize this carbohydrate-rich protective barrier, microbes secrete plant cell wall degrading enzymes (PCWDEs) targeting pectin, cellulose and hemicelluloses. There is a growing body of evidence that genomes of some herbivorous insects also encode PCWDEs, raising questions about their evolutionary origins and functions. Among herbivorous beetles, pectin-degrading polygalacturonases (PGs) are found in the diverse superfamilies Chrysomeloidea (leaf beetles, long-horn beetles) and Curculionoidea (weevils). Here our aim was to test whether these arose from a common ancestor of beetles or via horizontal gene transfer (HGT), and whether PGs kept their ancestral function in degrading pectin or evolved novel functions. Transcriptome data derived from 10 beetle species were screened for PG-encoding sequences and used for phylogenetic comparisons with their bacterial, fungal and plant counterparts. These analyses revealed a large family of PG-encoding genes of Chrysomeloidea and Curculionoidea sharing a common ancestor, most similar to PG genes of ascomycete fungi. In addition, 50 PGs from beetle digestive systems were heterologously expressed and functionally characterized, showing a set of lineage-specific consecutively pectin-degrading enzymes, as well as conserved but enzymatically inactive PG proteins. The evidence indicates that a PG gene was horizontally transferred ∼200 million years ago from an ascomycete fungus to a common ancestor of Chrysomeloidea and Curculionoidea. This has been followed by independent duplications in these two lineages, as well as independent replacement in two sublineages of Chrysomeloidea by two other subsequent HGTs. This origin, leading to subsequent functional diversification of the PG gene family within its new hosts, was a key event promoting the evolution of herbivory in these beetles.

Cloning, expression and characterization of a novel thermophilic polygalacturonase from Caldicellulosiruptor bescii DSM 6725

We cloned the gene ACM61449 from anaerobic, thermophilic Caldicellulosiruptor bescii, and expressed it in Escherichia coli origami (DE3). After purification through thermal treatment and Ni-NTA agarose column extraction, we characterized the properties of the recombinant protein (CbPelA). The optimal temperature and pH of the protein were 72 °C and 5.2, respectively. CbPelA demonstrated high thermal-stability, with a half-life of 14 h at 70 °C. CbPelA also showed very high activity for polygalacturonic acid (PGA), and released monogalacturonic acid as its sole product. The V_max and K_m of CbPelA were 384.6 U·mg⁻¹ and 0.31 mg·mL⁻¹, respectively. CbPelA was also able to hydrolyze methylated pectin (48% and 10% relative activity on 20%–34% and 85% methylated pectin, respectively). The high thermo-activity and methylated pectin hydrolization activity of CbPelA suggest that it has potential applications in the food and textile industry.

Infectious keratitis caused by Aspergillus tubingensis

PURPOSE

To report 2 cases of keratomycosis caused by Aspergillus tubingensis.

METHODS

The therapeutic courses were recorded for 2 male patients, 52 and 78 years old, with fungal keratitis caused by black Aspergillus strains. Morphological examination of the isolates was carried out on malt extract agar plates. A segment of the beta-tubulin gene was used for molecular identification. Antifungal susceptibilities were determined by the E test method for molds and the broth microdilution technique National Committee for Clinical Laboratory Standards M38-A.

RESULTS

A 52-year-old man presented with complaints of pain and redness in the right eye. The patient was successfully treated with natamycin and econazole eyedrops, itraconazole eye ointment, and oral ketoconazole. A 78-year-old man presented with total corneal necrosis in the right eye. A therapeutic keratoplasty was performed, and topical natamycin and econazole were applied. At the postoperative visit after 3 weeks, almost the full corneal graft was clear with formed anterior chamber. Black Aspergillus strains were isolated from the corneal scrapings of both cases and initially identified as Aspergillus niger based on culture characteristics. Sequence analysis of a segment of the beta-tubulin gene revealed that the isolates are representatives of A. tubingensis.

CONCLUSIONS

Aspergillus tubingensis is closely related with A. niger, the differentiation of these 2 species is difficult by classical morphological criteria. To our knowledge, the presented cases of fungal keratitis are the first reports on ocular infection caused by A. tubingensis.

A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation

The fungus Aspergillus niger is an industrial producer of pectin-degrading enzymes. The recent solving of the genomic sequence of A. niger allowed an inventory of the entire genome of the fungus for potential carbohydrate-degrading enzymes. By applying bioinformatics tools, 12 new genes, putatively encoding family 28 glycoside hydrolases, were identified. Seven of the newly discovered genes form a new gene group, which we show to encode exoacting pectinolytic glycoside hydrolases. This group includes four exo-polygalacturonan hydrolases (PGAX, PGXA, PGXB and PGXC) and three putative exo-rhamnogalacturonan hydrolases (RGXA, RGXB and RGXC). Biochemical identification using polygalacturonic acid and xylogalacturonan as substrates demonstrated that indeed PGXB and PGXC act as exo-polygalacturonases, whereas PGXA acts as an exo-xylogalacturonan hydrolase. The expression levels of all 21 genes were assessed by microarray analysis. The results from the present study demonstrate that exo-acting glycoside hydrolases play a prominent role in pectin degradation.

Characterization and mode of action of an exopolygalacturonase from the hyperthermophilic bacterium Thermotoga maritima

An intracellular pectinolytic enzyme, PelB (TM0437), from the hyperthermophilic bacterium Thermotoga maritima was functionally produced in Escherichia coli and purified to homogeneity. PelB belongs to family 28 of the glycoside hydrolases, consisting of pectin-hydrolysing enzymes. As one of the few bacterial exopolygalacturonases, it is able to remove monogalacturonate units from the nonreducing end of polygalacturonate. Detailed characterization of the enzyme showed that PelB is highly thermo-active and thermostable, with a melting temperature of 105 degrees C and a temperature optimum of 80 degrees C, the highest described to date for hydrolytic pectinases. PelB showed increasing activity on oligosaccharides with an increasing degree of polymerization. The highest activity was found on the pentamer (1000 U.mg(-1)). In addition, the affinity increased in conjunction with the length of the oligoGalpA chain. PelB displayed specificity for saturated oligoGalpA and was unable to degrade unsaturated or methyl-esterified oligoGalpA. Analogous to the exopolygalacturonase from Aspergillus tubingensis, it showed low activity with xylogalacturonan. Calculations on the subsite affinity revealed the presence of four subsites and a high affinity for GalpA at subsite +1, which is typical of exo-active enzymes. The physiological role of PelB and the previously characterized exopectate lyase PelA is discussed.

The contribution of ionic interactions to the conformational stability and function of polygalacturonase from A. niger

Aspergillus niger produces multiple forms of polygalacturonases with molecular masses ranging from 30 to 60 kDa. The high molecular weight polygalacturonase (61+/-2 kDa) from A. niger possesses a pH optimum of 4.3 and a pI of 3.9. The enzyme exhibited high sensitivity, both in terms of activity and structure, in the pH range of 4.3-7.0. The enzyme was irreversibly inactivated at pH 7.0. The enzyme is predominantly rich in parallel beta structure. There is unfolding of the enzyme molecule between 4.3 and 7.0 resulting in irreversible loss of secondary and tertiary structure with the exposure of hydrophobic surfaces. ANS binding measurements, intrinsic fluorescence and acrylamide quenching measurements have confirmed the unfolding and exposure of hydrophobic surfaces. The midpoint of pH transition for both activity and secondary structure is 6.2+/-0.1. The pH-induced changes of polygalacturonase confirm the role of histidine residues in structure and activity of the enzyme. The irreversible nature of inactivation is due to the unfolding induced exposure of hydrophobic surfaces leading to association/aggregation of the molecule. Size exclusion chromatography measurements have established the association of enzyme at higher pH. Urea induced unfolding measurements at pH 4.3 and 7.0 have confirmed the loss in stability as we approach neutral pH.

Resolution of the structural isomers of partially methylesterified oligogalacturonides by polysaccharide analysis using carbohydrate gel electrophoresis

Pectins differing in their degree and pattern of methylesterification are important in diverse aspects of plant physiology and also in many industrial applications. Determination of methylesterification fine structure and knowledge of enzyme specificities in modification and fragmentation of pectin are key to understanding the relationship between structure and function. The development of methodologies for the detection, separation and sequencing of different partially methylesterified oligogalacturonides (Me-OGAs) is consequently very important. Polysaccharide analysis using carbohydrate gel electrophoresis (PACE) has been shown to be powerful for the quantitative resolution of species different in degree of polymerization (DP) and/or degree of methylesterification (DM). Mass spectrometry (MS) has, to date, been the only tool with which to obtain isomeric information. However, it is not quantitative, and the presence of isobaric species makes the interpretation of the fragmentation patterns complicated. Here, we present evidence that Me-OGAs with the same DP and DM but different patterns of methylesterification (structural isomers) can easily be separated and quantified using PACE.

On the separation, detection and quantification of pectin derived oligosaccharides by capillary electrophoresis

Having previously reported that capillary electrophoresis can be used as a tool for the analysis of partially methyl-esterified oligogalacturonides we now describe a method that improves the resolution of individual oligomers, and detail a more rigorous quantification scheme that uses an internal standard and takes into account the relative molecular absorbance of different partially methyl-esterified species. The internal consistency of the method is subsequently demonstrated by performing the quantification of an endo-polygalacturonase pectin digest before and after de-methylation of the resultant oligomers.

Purified tomato polygalacturonase activity during thermal and high-pressure treatment

Extracted tomato polygalacturonase was purified by cation-exchange chromatography (and gel filtration) and characterized for molar mass, isoelectric point, as well as optimal pH for polygalacturonase activity. The enzymatic reaction of purified tomato polygalacturonase on polygalacturonic acid as substrate was investigated during a combined high-pressure/temperature treatment in a temperature range of 25 degrees to 80 degrees C and in a pressure range of 0.1 to 500 MPa at pH 4.4 (the pH of tomato-based products). The optimal temperature for initial tomato polygalacturonase activity in the presence of polygalacturonic acid at atmospheric pressure is about 55 degrees to 60 degrees C. The optimal temperature for initial tomato polygalacturonase activity during processing shifted to lower values at elevated pressure as compared with atmospheric pressure, and the catalytic activity of pure tomato polygalacturonase decreased with increasing pressure, which was mostly pronounced at higher temperatures. The elution profiles of the degradation products on high-performance anion-exchange chromatography indicated that for both thermal and high-pressure treatment all oligomers were present in very small amounts in the initial stage of polygalacturonase activity. The amounts of monomer and small oligomers increased with increasing incubation times, whereas the amount of larger oligomers decreased due to further degradation.

Green Fluorescent Detection of Fungal Colonization and Endopolygalacturonase Gene Expression in the Interaction of Alternaria citri with Citrus

ABSTRACT Alternaria citri, a postharvest pathogen, produces endopolygalacturonase (endoPG) and causes black rot on citrus fruit. We previously described that an endoPG-disrupted mutant of Alternaria citri was significantly reduced in its ability to macerate plant tissue and cause black rot symptoms on citrus. In order to investigate colonization of citrus fruit tissues by Alternaria citri, pTEFEGFP carrying a green fluorescent protein (GFP) gene was introduced into wild-type Alternaria citri and its endoPG-disrupted mutant (M60). Green fluorescence was observed in spores, germ tubes, appressoria, and infection hyphae of transformants G1 (derived from wild type) and GM4 (derived from M60). Hyphae of G1 but not GM4 vertically penetrated the peel, but the hyphae of both G1 and GM4 spread equally in the juice sac area of citrus fruit. Green fluorescence of Alternaria citri transformant EPG7 carrying a GFP gene under control of the endoPG gene promoter of Alternaria citri was induced by pectin in the peel during the infection stage, but repressed completely in the juice sac area, likely by carbon catabolite repression by sugars in the juice.

Cloning expression and characterization of a thermostable exopolygalacturonase from Thermotoga maritima

A gene encoding for a thermostable exopolygalacturonase (exo-PG) from hyperthermophilic Thermotoga maritima has been cloned into a T7 expression vector and expressed in Escherichia coli. The gene encoded a polypeptide of 454 residues with a molecular mass of 51,304 Da. The recombinant enzyme was purified to homogeneity by heat treatment and nickel affinity chromatography. The thermostable enzyme had maximum of hydrolytic activity for polygalacturonate at 95 degrees C, pH 6.0 and retains 90% of activity after heating at 90 degrees C for 5 h. Study of the catalytic activity of the exopolygalacturonase, investigated by means of 1H NMR spectroscopy revealed an inversion of configuration during hydrolysis of alpha-(1-->4)-galacturonic linkage.

Characterization of a Ralstonia solanacearum operon required for polygalacturonate degradation and uptake of galacturonic acid

The bacterial wilt pathogen Ralstonia solanacearum produces three extracellular polygalacturonases (PGs): PehA, PehB, and PehC. All three PGs hydrolyze pectin's polygalacturonic acid backbone, but each releases different reaction products. PehA and PehB contribute significantly to pathogen virulence, probably by facilitating root invasion and colonization. To determine the collective contribution of PGs to virulence and saprophytic survival, we cloned, characterized, and mutated the R. solanacearum pehC gene, which encodes a distinctive monogalacturonate-releasing exo-PG. The virulence of a pehC mutant on tomato was indistinguishable from that of its wild-type parent; thus, this exo-PG alone does not contribute significantly to wilt pathogenesis. Unexpectedly, a completely PG-deficient triple pehA/B/C mutant was slightly more virulent than a pehA/B mutant. PehC may degrade galacturonide elicitors of host defense, thereby protecting the pathogen from plant antimicrobial responses. A galacturonate transporter gene, exuT, is immediately downstream of pehC and the two genes are co-transcribed. It has been hypothesized that galacturonic acid released by PGs from plant cell walls nourishes bacteria during pathogenesis. To separate the pectolytic and nutrient-generating roles of the PGs, we made an exuT mutant, which still produces all three isozymes of PG but cannot uptake PG degradation products. This exuT mutant had wild-type virulence on tomato, demonstrating that metabolism of galacturonic acid does not contribute significantly to bacterial success inside the plant.

Expression profiling of pectinolytic genes from Aspergillus niger

The expression of 26 pectinolytic genes from Aspergillus niger was studied in a wild type strain and a CreA derepressed strain, under 16 different growth conditions, to obtain an expression profile for each gene. These expression profiles were then submitted to cluster analysis to identify subsets of genes with similar expression profiles. With the exception of the feruloyl esterase encoding genes, all genes were expressed in the presence of D-galacturonic acid, polygalacturonate, and/or sugar beet pectin. Despite this general observation five distinct groups of genes were identified. The major group consisted of 12 genes of which the corresponding enzymes act on the pectin backbone and for which the expression, in general, is higher after 8 and 24 h of incubation, than after 2 or 4 h. Two other groups of genes encoding pectin main chain acting enzymes were detected. Two additional groups contained genes encoding L-arabinose and D-galactose releasing enzymes, and ferulic acid releasing enzymes, respectively. The genes encoding beta-galactosidase and the L-arabinose releasing enzymes were not only expressed in the presence of D-galacturonic acid, but also in the presence of L-arabinose, suggesting that they are under the control of two regulatory systems. Similarly, the rhamnogalacturonan acetylesterase encoding gene was not only expressed in the presence of D-galacturonic acid, polygalacturonate and sugar beet pectin, but also in the presence of L-rhamnose. The data presented provides indications for a general pectinolytic regulatory system responding to D-galacturonic acid or a metabolite derived from it. In addition, subsets of pectinolytic genes are expressed in response to the presence of L-arabinose, L-rhamnose or ferulic acid.

A novel enzyme activity involving the demethylation of specific partially methylated oligogalacturonides

Studies of the enzymic digestion of pectic substrates using different polygalacturonase (PG) preparations have revealed evidence for a previously unreported enzyme activity carried out by a contaminating enzyme in one of the preparations. This observed activity involves the demethylation of specific oligogalacturonides, namely 2-methyltrigalacturonic acid and 2,3-dimethyltetragalacturonic acid. However, no large-scale demethylation of highly methylated polymeric substrates is found, demonstrating that the enzyme responsible is not a conventional pectin methylesterase (PME). Furthermore, it has been shown that a commercial sample of fungal PME from Aspergillus niger demethylates all of the oligogalacturonides present as primary products of endo-PG digestion, in contrast with the activity observed here. On the basis of the known methyl ester distribution of the endo-PG-generated fragments and knowledge of which of these oligogalacturonides are demethylated, it is concluded that the observed activity can be explained by the existence of an exo-acting methylesterase that attacks the non-reducing end of the oligogalacturonide molecules.

Purification and partial characterization of exopolygalacturonase I from Penicillium frequentans

A polygalacturonase with a molecular mass of 74 kDa, an isoelectric point around pH 4.2 and pH--and temperature optima of 3.9 and 50 degrees C, respectively, was purified from a culture fluid of Penicillium frequentans. The enzyme was characterized as an exo-alpha-1,4-polygalacturonase (exo-PG I). Km and Vmax for sodium polypectate hydrolysis were 0.68 g/l and 596.8 U x mg(-1), respectively. The enzyme, a glycoprotein with a carbohydrate content of 81%, is probably the main pectinase of Penicillium frequentans responsible for cleaving monomer units from the non-reducing end of pectin.

Purification and characterisation of two exo-polygalacturonases from Aspergillus niger able to degrade xylogalacturonan and acetylated homogalacturonan

Two exo-polygalacturonases (EC 3.2.1.67) were purified from a commercial Aspergillus niger enzyme preparation by ammonium sulfate precipitation, preparative electrofocusing, anion-exchange and size-exclusion chromatographies. The enzymes had molar masses of 82 kDa (exo-PG1) and 56 kDa (exo-PG2). Exo-PG1 was stable over wider pH and temperature ranges than exo-PG2. Addition of 0.01 mM HgCl(2) increased the exo-PG2 activity 3.4 times but did not affect exo-PG1. Analysis of the reaction products of (reduced) pentagalacturonate by high-performance anion-exchange chromatography revealed that both enzymes split the substrate from the non-reducing end in a multi-chain attack mode. Exo-PG1 had a broad specificity towards oligogalacturonates with different degrees of polymerisation, while digalacturonate was the most favorable substrate for exo-PG2. Both enzymes degraded xylogalacturonan from pea hull in an exo manner to produce galacturonic acid and Xyl-GalA disaccharide, as identified by electrospray ionization-ion trap mass spectrometry (ESI-ITMS). Moreover, exo-PGs split acetylated homogalacturonan in an exo manner, producing galacturonic acid and acetylated galacturonic acid, as shown by ESI-ITMS.

Endopolygalacturonase is encoded by a multigene family in the basidiomycete Chondrostereum purpureum

The basidiomycete Chondrostereum purpureum produces several plant cell wall-degrading enzymes, including endopolygalacturonase (endoPG). Degenerate oligonucleotide primers were designed according to conserved regions of endoPG genes from various fungi, plants, and bacteria and used to amplify members of this gene family from C. purpureum. Four different amplification products showed significant similarity to known endoPGs and were used as hybridization probes to screen a library of genomic DNA sequences and to retrieve five full-length endoPG genes (epgA, epgB1, epgB2, epgC, and epgD). The identities between the deduced polypeptides for epgA, epgB1, epgC, and epgD ranged from 61.8 to 80.0%, while the deduced polypeptides for epgB1 and epgB2 shared 97.1% identity. Phylogenetic analysis suggested that the duplication of existing endoPG genes occurred after the divergence of the ascomycetes and basidiomycetes. C. purpureum is the first basidiomycete fungus for which the endoPG gene family has been described.