Biochemical Characterization of a Pectate Lyase AnPL9 from Aspergillus nidulans

SbPL1CE8 from Segatella bryantii combines with SbGH28GH105 in a multi-enzyme cascade for pectic biomass utilization

Pectinases are useful biocatalysts for pectic biomass processing and are extensively used in the food/feed, textile and papermaking industries. Two pectinase genes, a pectate lyase (SbPL1CE8) and a polygalacturonase (SbGH28GH105) were isolated from Segatella bryantii and functionally characterized. Recombinant rSbPL1CE8 was most active against polygalacturonic acid (PGA) and pectin with a 60 % degree of esterification, with kcat/Km values of 721.18 ± 64.77 and 327.02 ± 22.44 mL/s/mg, respectively. Truncated rSbPL1 acted as a mesophilic alkaline pectate lyase, which was highly resistant to inactivation by methanol and ethanol. The rSbPL1CE8 exclusively digested PGA and pectin into unsaturated digalacturonate (uG2), which was further converted into galacturonic acid by rSbGH28GH105. The rSbPL1CE8 was highly effective for saccharification of waste materials from Zea mays, Oryza sativa and Arachis hypogaea processing, and for ramie fiber degumming. This novel pectate lyase has great potential for application in industrial pectic biomass processing.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022

The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

A novel pectate lyase with high specific activity from Bacillus sp. B58-2: Gene cloning, heterologous expression and use in ramie degumming

Pectinase plays a crucial role in ramie degumming. A gene encoding a putative pectate lyase from Bacillus sp. strain B58-2 was cloned and heterologously expressed in Escherichia coli. The amplified gene BvelPL1 encoded a mature protein of 400 amino acids. BvelPL1 shared the highest amino acid sequence identity (78.75%) with the enzymatically characterized pectate lyase Pel from Bacillus subtilis strain RCK (GenBank: AFH66771.1). The purified recombinant enzyme rBvelPL1-Ec exhibited a maximum specific activity of 2433.26 U/mg at pH 8.5 and 50 °C towards polygalacturonic acid. This specific activity was higher than that of most reported pectate lyases. Remarkably, the enzymatic activity of rBvelPL1-Ec increased by 23.28 times in the presence of 0.4 mM calcium ion. The effect of calcium ion on promoting the enzymatic activity of rBvelPL1-Ec was greater than that for all reported pectate lyases. After degumming with rBvelPL1-Ec, a weight loss of 21.27 ± 1.17% of circled ramie fibers was obtained, and the surfaces of the ramie fibers became smoother. Moreover, a weight loss of 30.47 ± 0.46% was obtained through enzymatic treated and subsequent NaOH treated circled ramie fibers. The excellent performance in degumming suggests that rBvelPL1-Ec may serve as a promising biocatalyst in the textile industry.

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.

Aspergillus nidulans—Natural Metabolites Powerhouse: Structures, Biosynthesis, Bioactivities, and Biotechnological Potential

Nowadays, finding out new natural scaffolds of microbial origin increases at a higher rate than in the past decades and represents an auspicious route for reinvigorating the pool of compounds entering pharmaceutical industries. Fungi serve as a depository of fascinating, structurally unique metabolites with considerable therapeutic significance. Aspergillus genus represents one of the most prolific genera of filamentous fungi. Aspergillus nidulans Winter G. is a well-known and plentiful source of bioactive metabolites with abundant structural diversity, including terpenoids, benzophenones, sterols, alkaloids, xanthones, and polyketides, many of which display various bioactivities, such as cytotoxicity, antioxidant, anti-inflammatory, antiviral, and antimicrobial activities. The current work is targeted to survey the reported literature on A. nidulans, particularly its metabolites, biosynthesis, and bioactivities, in addition to recent reports on its biotechnological potential. From 1953 till November 2022, relying on the stated data, 206 metabolites were listed, with more than 100 references.

The specificity of pectate lyase VdPelB from Verticilium dahliae is highlighted by structural, dynamical and biochemical characterizations

Pectins, complex polysaccharides and major components of the plant primary cell wall, can be degraded by pectate lyases (PLs). PLs cleave glycosidic bonds of homogalacturonans (HG), the main pectic domain, by β-elimination, releasing unsaturated oligogalacturonides (OGs). To understand the catalytic mechanism and structure/function of these enzymes, we characterized VdPelB from Verticillium dahliae. We first solved the crystal structure of VdPelB at 1.2 Å resolution showing that it is a right-handed parallel β-helix structure. Molecular dynamics (MD) simulations further highlighted the dynamics of the enzyme in complex with substrates that vary in their degree of methylesterification, identifying amino acids involved in substrate binding and cleavage of non-methylesterified pectins. We then biochemically characterized wild type and mutated forms of VdPelB. Pectate lyase VdPelB was most active on non-methylesterified pectins, at pH 8.0 in presence of Ca²⁺ ions. The VdPelB-G125R mutant was most active at pH 9.0 and showed higher relative activity compared to native enzyme. The OGs released by VdPelB differed to that of previously characterized PLs, showing its peculiar specificity in relation to its structure. OGs released from Verticillium-partially tolerant and sensitive flax cultivars differed which could facilitate the identification VdPelB-mediated elicitors of defence responses.

Development of sequence-characterized amplified region (SCAR) markers for accurate and differential identification of multienzyme-producing and non-enzymatic Aspergillus strains of industrial importance

Aspergillus strains are known to produce multiple enzymes of industrial importance. To screen Aspergillus isolates and select a strain with the ability to produce multiple enzymes and discriminate it from non-enzymatic strains, a rapid and accurate approach is required. With this background, a DNA fingerprinting-based study was conducted to develop a simple but accurate molecular detection method with the potential to discriminate multienzyme-producing Aspergillus strains from non-enzymatic strains, irrespective of species. To achieve this, Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR was employed to derive group-specific Sequence Characterized Amplified Region (SCAR) markers (i.e., markers corresponding to PCR amplicons of known DNA sequence). To this end, both group-specific (multienzyme-producing and non-enzymatic Aspergillus group) SCAR markers were sought by comparing the ERIC fingerprint profiles and used to develop primers for use in specific and differential identification of multienzyme-producing Aspergillus isolates. As an outcome, the two SCAR-PCR formats were developed. One format is for specific identification of multienzyme-producing Aspergillus strains (SCAR-PCR1), and the other for identifying non-enzymatic Aspergillus strains (SCAR-PCR2). Both SCAR-PCRs were able to discriminate between these two contrasting groups. These formats are simple but accurate and rapid compared to the time-consuming and laborious conventional methods. Therefore, they could be efficient as an alternative strategy for the high-throughput screening of industrially important Aspergillus strains.