Search Results (46)

Alkaline pectate lyases hold significant promise for various industrial applications, including the degumming processes in papermaking and textiles. In this study, a novel pectinase, PelA, derived from a strain of Paenibacillus borealis, was characterized both at the molecular level and through enzymatic analysis. This enzyme represents a distinct cluster diverging from the well-characterized Bacillus pectinases and exhibits molecular activity under alkaline conditions, with an optimal pH of 9.5. It can be classified as an endo-(1,4)-pectate lyase, capable of cleaving the α-1,4 glycosidic bonds of polygalacturonic acid via a trans-elimination mechanism. Notably, the addition of the metal ion Ca²⁺ did not enhance enzyme activity. To achieve high-level secretory expression and improve its economic viability for bioapplications, the gene copy number of pelA in the host genome was increased by constructing tandem pelA gene expression cassettes. Following optimization of cultivation conditions and monitoring of cell growth, the recombinant strain harboring the multi-copy pelA gene attained an expression level of 7520 U/mL in a bioreactor. This study successfully achieved high-level secretory expression of an alkaline pectinase, thereby enhancing its potential for industrial bioapplications and providing a reference for future research on the heterologous expression of target genes. Full article

The increasing demand for sustainable agricultural practises has sparked interest in microbes that promote plant immunity. Among these, Pseudomonas species have shown the potential to enhance induced systemic resistance (ISR) in crops. While type III secretion systems (T3SSs) in pathogenic bacteria have been widely studied for their role in local immunosuppression, their function in beneficial Pseudomonas species and on a systemic level remains largely unexplored. We show for the first time that the T3SS of a plant-beneficial Pseudomonas strain induces ISR by root colonisation. T3SS-positive Pseudomonas isolates were applied to the roots of sugar beet (Beta vulgaris L.) and systemic effects on plant immunity were assessed in leaves exposed to the pathogen P. syringae pv. aptata P21. Our results show that P. marginalis ORh26 reduced lesion size and pathogen proliferation in sugar beet leaves. ORh26 activated peroxidase and phenylalanine ammonia-lyase and upregulated NPR1 and MYC2 defence genes. Remarkably, a T3SS-deficient mutant of ORh26 failed to induce these effects. Genomic analysis identified T3SS structural genes and effector proteins, including a pectate lyase and an effector of the HopJ family, that may mediate these responses. This study reveals a previously uncharacterised role of T3SS in the induction of ISR and improves our understanding of plant–microbe interactions. Full article

Pectin is a dynamic and complex polysaccharide that forms a substantial proportion of the primary plant cell wall and middle lamella of forage ingested by grazing ruminants. Pectin methylesterases (PMEs) are enzymes that belongs to the carbohydrate esterase family 8 (CE8) and catalyze the demethylesterification of pectin, a key polysaccharide in cell walls. Here we present the crystal structure of the catalytic domain of PmeC5 that is associated with a gene from Butyrivibrio fibrisolvens D1^T that encodes a large secreted pectinesterase family protein (2089 aa) determined to a resolution of 1.33 Å. Protein in silico modelling of the secreted pectinesterase confirmed the presence of an additional pectate lyase (PL9) and adhesin-like domains. The structure of PmeC5 was the characteristic right-handed parallel β-helical topology and active site residues of Asp231, Asp253, and Arg326 typical of the enzyme class. PmeC5 is a large modular enzyme that is characteristic of rumen B. fibrisolvens megaplasmids and plays a central role in degrading plant cell wall components and releasing methanol in the rumen environment. Such secreted PMEs are significant contributors to plant fiber digestion and methane production, making them attractive targets for both methane mitigation strategies and livestock productivity enhancement. Full article

Cold-adapted pectin lyases are particularly useful in the extraction and clarification of freshly squeezed fruit juices at low temperatures, as they effectively reduce juice viscosity and improve light transmittance. With the increasing attention on low-temperature pectinase in industrial applications, the exploration of low-temperature pectinase with novel characteristics has become one of the key focuses of research and development. In this study, a 1026 bp gene, pel1Ba, encoding a 42.7 kDa pectin lyase, was cloned from sediment samples collected from the South China Sea and heterologously expressed in Escherichia coli. The purified Pel1Ba exhibited an optimal temperature of 40 °C and an optimal pH of 10, with a total enzyme activity of 5100 U/mL. Notably, Pel1Ba is a cold-adapted enzyme that retains 80% of its relative activity across the temperature range of 0–40 °C. When 20 U/mL purified Pel1Ba was added to orange juice, the juice volume increased by 43.00% and its clarity improved by 37.80%. Meanwhile, site-directed mutagenesis analysis revealed that the residual enzyme activities of the mutants A230I, F253I, and L292I were increased by 22.5%, 34.4%, and 25.1%, respectively, compared to the wild type. This study concludes that the cold-active pectate lyase Pel1Ba exhibits potential for applications in the food industry. Full article

Hemp fibers, recognized for their breathability, specific strength, and ultraviolet resistance, are widely utilized in textile manufacturing and composite materials. Bio-degumming is a promising alternative technology to traditional chemical degumming that can be used to produce hemp fibers due to its eco-friendly nature. However, its lower efficiency has hindered its widespread adoption. The unclear and complex structure of the gums leads to a poor understanding on the enzyme types required for bio-degumming, thereby restricting improvements in its efficiency. In this study, the morphological characteristics, polysaccharide composition, and branched structure of hemp stem, roving fibers, and refined fibers were investigated using scanning electron microscopy and laser scanning confocal microscopy in combination with immunofluorescence techniques, with a view to identify the enzymes necessary for the efficient bio-degumming of hemp. The results revealed that the gums were primarily located in the middle lamella, phloem parenchyma, and certain xylem tissues. These tissues showed chunk-like, fence-like, and plate-like shapes, respectively, and tightly wrapped around the fiber bundles. In these tissues, pectin comprised low-esterified homogalacturonan, along with rhamnogalacturonan carrying galactan and arabinan branches. Xylan exhibited acetyl, arabinose, and glucuronic acid branches, while mannan displayed acetyl and galactose branches. Partial xylan and mannan were masked by pectin, and the branching structures impeded their enzymatic removal. As a consequence, the necessary enzymes and their synergistic effects for effective hemp roving degumming were elucidated. Pectin degradation was facilitated by pectate lyase and rhamnogalacturonan-degrading enzymes. Xylan and mannan were effectively removed by endo-xylanase and endo-mannanase, a process necessitating the synergistic action of branched-chain-degrading enzymes, including the esterase, α-L-arabinofuranosidase, α-galactosidase, and α-glucuronidase. This study provided practical strategies to enhance the efficiency of hemp bio-degumming. Full article

The study aimed to investigate the effects of thifluzamide (2.67 mg/L) on ‘Huangguan’ pear fruit rot caused by Rhizoctonia solani during storage, as well as the activities of polygalacturonase (PG), pectin methylesterase (PME), polygalacturonic acid trans-eliminase (PGTE), pectin methyl trans-eliminase (PMTE), xylanase, and pectate lyase (PL) secreted by R. solani. The results showed that thifluzamide treatment significantly inhibited the activities of PG, PME, PGTE, PMTE, xylanase, and PL secreted by R. solani after 3 days in vitro culture, compared to the control. Thifluzamide also increased the activities of phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and 4-coumarate CoA ligase (4CL), and the contents of flavonoids and total phenolic compounds in pear fruit. Furthermore, thifluzamide increased the expression of PcPAL, PcC4H, Pc4CL, Pcβ-1,3-GA, PcLCH, PcF3H, and PcDFR involved in phenylpropanoid metabolism in pear fruit. In conclusion, thifluzamide treatment reduced the infection ability of R. solani by inhibiting the expression of the genes encoding cell wall-degrading enzymes in R. solani. At the same time, it inhibited the activities of cell wall-degrading enzymes induced resistance against R. solani infection in ‘Huangguan’ pears by promoting phenylpropane metabolism. Full article

Flesh firmness is an important quality of pear fruits. Breeding cultivars with suitably low flesh firmness is one of the popular pear breeding goals. At present, SNP markers related to pear flesh firmness and genes affecting flesh firmness are still uncertain. In this study, a QTL analysis was performed, and the result showed that the position of 139.857 cM in lineage group 14 (LG14) had the highest average logarithm of odds (3.41) over two years. This newly discovered locus was identified as a flesh firmness-related QTL (qFirmness-LG14). The ‘C/T’ SNP was found in corresponding Marker1512129. The ‘C’ genotype is the high-firmness genotype, which is a dominant trait. The average firmness of fruits with genotype C is 21.4% higher than genotype without the C genotype. Transcriptome profiling was obtained between ‘Zaoshengxinshui’ and ‘Qiushui’ at five time points. Three candidate genes in the interval of qFirmness-LG14 might affect firmness. A gene of xyloglucan endotransglucosylase 1 (PpXTH1) was upregulated in ‘Qiushui’ at all five time points. Two transcription factors (PpHY5 and PpERF113) were upregulated in ‘Zaoshengxinshui’, which might be negative regulatory genes for high flesh firmness. The transcriptome results also isolated a large number of cell wall-related genes (e.g., Pectate lyase, Pectin acetylesterase, Pectin methylesterase, and 4-coumarate-CoA ligase) and transcription factors (e.g., ERF, WRKY). These genes are all potential upstream and downstream genes related to flesh firmness. In conclusion, this study provides valuable insights into the QTLs and molecular mechanisms associated with fruit firmness in Pyrus pyrifolia. Full article

GhPEL48_Dt, a Pectate lyase (PEL, EC4.2.2.2), is a crucial enzyme involved in cell-wall modification and pectin degradation. Studies have shown that the GhPEL48_Dt also plays a significant role in cotton-fiber development; however, the specific function and regulatory mechanism of GhPEL48_Dt in cotton-fiber development are still not fully understood. Here, we found that the histone deacetylase inhibitor-Trichostatin A significantly reduces the transcript levels of GhPEL48_Dt and its enzyme activity. Further, silencing of GhPEL48_Dt significantly inhibits the initiation and elongation of cotton fibers by promoting pectin degradation, and the heterologous expression of GhPEL48_Dt promotes the development of trichomes and root hairs in Arabidopsis, which suggests that GhPEL48_Dt plays a positive and conserved role in single cell i.e., fiber, root hair, and leaf trichome development. Collectively, this paper provides a comprehensive analysis of the fundamental characteristics and functions of GhPEL48_Dt in fiber development, including the regulatory role of histone acetylation on GhPEL48_Dt, which contributes to the understanding of pectin degradation pathways and establishes a theoretical foundation for elucidating its regulatory mechanism. Full article

Pectin is a structural polysaccharide and a major component of plant cell walls. Pectate lyases are a class of enzymes that degrade demethylated pectin by cleaving the α-1,4-glycosidic bond, and they play an important role in plant growth and development. Currently, little is known about the PL gene family members and their involvement in salt stress in potato. In this study, we utilized bioinformatics to identify members of the potato pectate lyase gene family and analyzed their gene and amino acid sequence characteristics. The results showed that a total of 27 members of the pectate lyase gene family were identified in potato. Phylogenetic tree analysis revealed that these genes were divided into eight groups. Analysis of their promoters indicated that several members’ promoter regions contained a significant number of hormone and stress response elements. Further, we found that several members responded positively to salt treatment under single salt and mixed salt stress. Since StPL18 exhibited a consistent expression pattern under both single and mixed salt stress conditions, its subcellular localization was determined. The results indicated that StPL18 is localized in the endoplasmic reticulum membrane. The results will establish a foundation for analyzing the functions of potato pectate lyase family members and their expression under salt stress. Full article

Akebia trifoliata fruit is prone to crack after ripening, but little is known about the mechanism underlying the cracking process. This study integrated transcriptomic and metabolomic data, revealing significant changes in 398 metabolites and 8414 genes during ripening and cracking, mainly impacting cell-wall metabolism. Multi-omics joint analysis indicated that genes related to polygalacturonase, pectate lyase, α-amylase, and glycogen phosphorylase were up-regulated after cracking, degrading cell wall and starch. Concurrently, diminished photosynthetic metabolism and heightened phenylpropanoid metabolism suggested alterations in cuticle structure, potentially impacting cell-wall robustness. Numerous auxin and abscisic acid signaling-related genes were expressed, and we assume that they contributed to the promoting peel growth. These alterations collectively might compromise peel strength and elevate expanding pressure, potentially leading to A. trifoliata cracking. Transcription factors, predominantly ethylene response factors and helix-loop-helix family members, appeared to regulate these metabolic shifts. These findings provide valuable insights into A. trifoliata cracking mechanisms; however, direct experimental validation of these assumptions is necessary to strengthen these conclusions and expedite their commercial utilization. Full article

The rapid ripening of soursop (Annona muricata L.) fruits is owing to its high respiration rate. Several enzymes affect the fruit cell wall in this process, resulting in the depolymerization of pectin primarily in the homogalacturonan. The main group of enzymes affecting the pectin content of soursop fruits include polygalacturonase (PG), pectate lyase (PL), pectin methylesterase (PME), and PME inhibitors (PMEis). In this study, pectin-degrading enzymes were analyzed using bioinformatic tools to uncover the gaps in our knowledge of this fruit. In this context, 67 genes encoding PG, 33 PL, 58 PME, and 39 PMEi isoenzymes were found. These genes were categorized into several families based on the results of phylogenetic analysis. Regarding the analysis of gene expression, a total of 25 were identified as differentially expressed genes (DEGs) in PG, while 3, 21, and 15 were found for PL, PME, and PMEis, respectively. Likewise, functional enrichment analysis demonstrated that the DEGs are involved in the modification of the cell wall, specifically in the degradation of pectin. On the other hand, gene co-expression networks revealed that the genes PG32 and PG35 affect the expression of PGs, as well as PL19 of the PL family, PME20, PME32, and PME35 of the PME family, and PMEi04 of the PMEi family. This suggests that they have a significant impact on the softening of soursop fruits. Full article

Fruit softening is a crucial factor that controls shelf life and commercial value. Pectate lyase (PL) has a major role in strawberry fruit softening. However, the PL gene family in strawberry has not been comprehensively analyzed. In this study, 65 FaPL genes were identified in the octoploid strawberry genome. Subcellular localization prediction indicated that FaPLs are mostly localized to the extracellular and cytoplasmic spaces. Duplication event analysis suggested that FaPL gene family expansion is mainly driven by whole genome or segmental duplication. The FaPL family members were classified into six groups according to the phylogenetic analysis. Among them, FaPL1, 3, 5, 20, 25, 42, and 57 had gradually increased expressions during strawberry fruit development and ripening and higher expression levels in the fruits with less firmness than that in firmer fruit. This result suggested that these members are involved in strawberry softening. Furthermore, overexpression of FaPL1 significantly reduced the fruit firmness, ascorbic acid (AsA), and malondialdehyde (MDA) content but obviously increased the anthocyanins, soluble proteins, and titratable acidity (TA), while it had no apparent effects on flavonoids, phenolics, and soluble sugar content. These findings provide basic information on the FaPL gene family for further functional research and indicate that FaPL1 plays a vital role in strawberry fruit softening. Full article

The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding. Full article

Rice (Oryza sativa L.) is one of the most widely grown crops in the world, and is a staple food for more than half of the global total population. Root-knot nematodes (RKNs), Meloidogyne spp., and especially M. graminicola, seem to be significant rice pests, which makes them the most economically important plant-parasitic nematode in this crop. RKNs develop a feeding site in galls by causing host cells to differentiate into hypertrophied, multinucleate, metabolically active cells known as giant cells. This grazing framework gives the nematode a constant food source, permitting it to develop into a fecund female and complete its life cycle inside the host root. M. graminicola effector proteins involved in nematode parasitism, including pioneer genes, were functionally characterized in earlier studies. Molecular modelling and docking studies were performed on Meloidogyne graminicola protein targets, such as β-1,4-endoglucanase, pectate lyase, phospholipase B-like protein, and G protein-coupled receptor kinase, to understand the binding affinity of Beta-D-Galacturonic Acid, 2,6,10,15,19,23-hexamethyltetracosane, (2S)-2-amino-3-phenylpropanoic acid, and 4-O-Beta-D-Galactopyranosyl-Alpha-D-Glucopyranose against ligand molecules of rice. This study discovered important molecular aspects of plant–nematode interaction and candidate effector proteins that were regulated by M. graminicola-infected rice plants. To the best of our knowledge, this is the first study to describe M. graminicola’s molecular adaptation to host parasitism. Full article

Pectobacterium versatile (formally P. carotovorum) causes disease on diverse plant species by synthesizing and secreting copious amount of plant-cell-wall-degrading exoenzymes including pectate lyases, polygalacturonases, cellulases, and proteases. Exoenzyme production and virulence are controlled by many factors of bacterial, host, and environmental origin. The ion channel forming the magnesium, nickel, and cobalt transporter CorA is required for exoenzyme production and full virulence in strain Ecc71. We investigated CorA’s role as a virulence factor and its expression in P. versatile. Inhibiting the transport function of CorA by growing a CorA⁺ strain in the presence of specific CorA inhibitor, cobalt (III) hexaammine (Co (III)Hex), has no effect on exoenzyme production. Transcription of pel-1, encoding a pectate lyase isozyme, is decreased in the absence of CorA, suggesting that CorA influences exoenzyme production at the transcriptional level, although apparently not through its transport function. CorA⁻ and CorA⁺ strains grown in the presence of Co (III)Hex transcriptionally express corA at higher levels than CorA⁺ strains in the absence of an inhibitor, suggesting the transport role of corA contributes to autorepression. The expression of corA is about four-fold lower in HrpL⁻ strains lacking the hrp-specific extracytoplasmic sigma factor. The corA promoter region contains a sequence with a high similarity to the consensus Hrp box, suggesting that corA is part of Hrp regulon. Our data suggest a complex role, possibly requiring the physical presence of the CorA protein in the virulence of the Pectobacterium versatile strain Ecc71. Full article