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Scott CJR, McGregor NGS, Leadbeater DR, Oates NC, Hoßbach J, Abood A, Setchfield A, Dowle A, Overkleeft HS, Davies GJ, Bruce NC. Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates. Microbiol Spectr 2024; 12:e0394323. [PMID: 38757984 PMCID: PMC11218486 DOI: 10.1128/spectrum.03943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Parascedosporium putredinis NO1 is a plant biomass-degrading ascomycete with a propensity to target the most recalcitrant components of lignocellulose. Here we applied proteomics and activity-based protein profiling (ABPP) to investigate the ability of P. putredinis NO1 to tailor its secretome for growth on different lignocellulosic substrates. Proteomic analysis of soluble and insoluble culture fractions following the growth of P. putredinis NO1 on six lignocellulosic substrates highlights the adaptability of the response of the P. putredinis NO1 secretome to different substrates. Differences in protein abundance profiles were maintained and observed across substrates after bioinformatic filtering of the data to remove intracellular protein contamination to identify the components of the secretome more accurately. These differences across substrates extended to carbohydrate-active enzymes (CAZymes) at both class and family levels. Investigation of abundant activities in the secretomes for each substrate revealed similar variation but also a high abundance of "unknown" proteins in all conditions investigated. Fluorescence-based and chemical proteomic ABPP of secreted cellulases, xylanases, and β-glucosidases applied to secretomes from multiple growth substrates for the first time confirmed highly adaptive time- and substrate-dependent glycoside hydrolase production by this fungus. P. putredinis NO1 is a promising new candidate for the identification of enzymes suited to the degradation of recalcitrant lignocellulosic feedstocks. The investigation of proteomes from the biomass bound and culture supernatant fractions provides a more complete picture of a fungal lignocellulose-degrading response. An in-depth understanding of this varied response will enhance efforts toward the development of tailored enzyme systems for use in biorefining.IMPORTANCEThe ability of the lignocellulose-degrading fungus Parascedosporium putredinis NO1 to tailor its secreted enzymes to different sources of plant biomass was revealed here. Through a combination of proteomic, bioinformatic, and fluorescent labeling techniques, remarkable variation was demonstrated in the secreted enzyme response for this ascomycete when grown on multiple lignocellulosic substrates. The maintenance of this variation over time when exploring hydrolytic polysaccharide-active enzymes through fluorescent labeling, suggests that this variation results from an actively tailored secretome response based on substrate. Understanding the tailored secretomes of wood-degrading fungi, especially from underexplored and poorly represented families, will be important for the development of effective substrate-tailored treatments for the conversion and valorization of lignocellulose.
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Affiliation(s)
- Conor J R Scott
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Janina Hoßbach
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Alexander Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
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Valle V, Aguilar AD, Yánez P, Almeida-Naranjo CE, Cadena F, Kreiker J, Raggiotti B. On the Response to Aging of OPEFB/Acrylic Composites: A Fungal Degradation Perspective. Polymers (Basel) 2023; 15:polym15030704. [PMID: 36772005 PMCID: PMC9920969 DOI: 10.3390/polym15030704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 02/03/2023] Open
Abstract
Biological agents and their metabolic activity produce significant changes over the microstructure and properties of composites reinforced with natural fibers. In the present investigation, oil palm empty fruit bunch (OPEFB) fiber-reinforced acrylic thermoplastic composites were elaborated at three processing temperatures and subjected to water immersion, Prohesion cycle, and continuous salt-fog aging testing. After exposition, microbiological identification was accomplished in terms of fungal colonization. The characterization was complemented by weight loss, mechanical, infrared, and thermogravimetric analysis, as well as scanning electron microscopy. As a result of aging, fungal colonization was observed exclusively after continuous salt fog treatment, particularly by different species of Aspergillus spp. genus. Furthermore, salt spray promoted filamentous fungi growth producing hydrolyzing enzymes capable of degrading the cell walls of OPEFB fibers. In parallel, these fibers swelled due to humidity, which accelerated fungal growth, increased stress, and caused micro-cracks on the surface of composites. This produced the fragility of the composites, increasing Young's modulus, and decreasing both elongation at break and toughness. The infrared spectra showed changes in the intensity and appearance of bands associated with functional groups. Thermogravimetric results confirmed fungal action as the main cause of the deterioration.
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Affiliation(s)
- Vladimir Valle
- Departamento de Ciencias de Alimentos y Biotecnología, Escuela Politécnica Nacional, Ladrón de Guevara E11-253, Quito 170517, Ecuador
- Correspondence:
| | - Alex Darío Aguilar
- Departamento de Ciencias de Alimentos y Biotecnología, Escuela Politécnica Nacional, Ladrón de Guevara E11-253, Quito 170517, Ecuador
| | - Paola Yánez
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolquí 171103, Ecuador
| | - Cristina E. Almeida-Naranjo
- Departamento de Ciencias de Alimentos y Biotecnología, Escuela Politécnica Nacional, Ladrón de Guevara E11-253, Quito 170517, Ecuador
- Facultad de Ingeniería y Ciencias Aplicadas—Ingeniería en Biotecnología, Universidad de las Américas, Redondel del Ciclista Antigua Vía a Nayón, Quito 170124, Ecuador
| | - Francisco Cadena
- Departamento de Ciencias de Alimentos y Biotecnología, Escuela Politécnica Nacional, Ladrón de Guevara E11-253, Quito 170517, Ecuador
| | - Jerónimo Kreiker
- Centro Experimental de la Vivienda Económica (CEVE)-CONICET, AVE. Igualdad 3585, Córdoba X5003BHG, Argentina
| | - Belén Raggiotti
- Centro de Investigación, Desarrollo y Transferencia de Materiales y Calidad (CINTEMAC), UTN-FRC, Maestro M. López y Cruz Roja Argentina, Córdoba X5003BHG, Argentina
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Kubisch C, Kövilein A, Aliyu H, Ochsenreither K. RNA-Seq Based Transcriptome Analysis of Aspergillus oryzae DSM 1863 Grown on Glucose, Acetate and an Aqueous Condensate from the Fast Pyrolysis of Wheat Straw. J Fungi (Basel) 2022; 8:jof8080765. [PMID: 35893132 PMCID: PMC9394295 DOI: 10.3390/jof8080765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
Due to its acetate content, the pyrolytic aqueous condensate (PAC) formed during the fast pyrolysis of wheat straw could provide an inexpensive substrate for microbial fermentation. However, PAC also contains several inhibitors that make its detoxification inevitable. In our study, we examined the transcriptional response of Aspergillus oryzae to cultivation on 20% detoxified PAC, pure acetate and glucose using RNA-seq analysis. Functional enrichment analysis of 3463 significantly differentially expressed (log2FC >2 & FDR < 0.05) genes revealed similar metabolic tendencies for both acetate and PAC, as upregulated genes in these cultures were mainly associated with ribosomes and RNA processing, whereas transmembrane transport was downregulated. Unsurprisingly, metabolic pathway analysis revealed that glycolysis/gluconeogenesis and starch and sucrose metabolism were upregulated for glucose, whereas glyoxylate and the tricarboxylic acid (TCA) cycle were important carbon utilization pathways for acetate and PAC, respectively. Moreover, genes involved in the biosynthesis of various amino acids such as arginine, serine, cysteine and tryptophan showed higher expression in the acetate-containing cultures. Direct comparison of the transcriptome profiles of acetate and PAC revealed that pyruvate metabolism was the only significantly different metabolic pathway and was overexpressed in the PAC cultures. Upregulated genes included those for methylglyoxal degradation and alcohol dehydrogenases, which thus represent potential targets for the further improvement of fungal PAC tolerance.
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Review of advances in the development of laccases for the valorization of lignin to enable the production of lignocellulosic biofuels and bioproducts. Biotechnol Adv 2021; 54:107809. [PMID: 34333091 DOI: 10.1016/j.biotechadv.2021.107809] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/30/2022]
Abstract
Development and deployment of commercial biorefineries based on conversion of lignocellulosic biomass into biofuels and bioproducts faces many challenges that must be addressed before they are commercially viable. One of the biggest challenges faced is the efficient and scalable valorization of lignin, one of the three major components of the plant cell wall. Lignin is the most abundant aromatic biopolymer on earth, and its presence hinders the extraction of cellulose and hemicellulose that is essential to biochemical conversion of lignocellulose to fuels and chemicals. There has been a significant amount of work over the past 20 years that has sought to develop innovative processes designed to extract and recycle lignin into valuable compounds and help reduce the overall costs of the biorefinery process. Due to the complex matrix of lignin, which is essential for plant survival, the development of a reliable and efficient lignin conversion technology has been difficult to achieve. One approach that has received significant interest relies on the use of enzymes, notably laccases, a class of multi‑copper green oxidative enzymes that catalyze bond breaking in lignin to produce smaller oligomers. In this review, we first assess the different innovations of lignin valorization using laccases within the context of a biorefinery process, and then assess the latest economical advances that these innovations offered. Finally, we review laccase characterization and optimization, as well as the prospects and bottlenecks of this class of enzymes within the industrial and biorefining sectors.
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Construction of a cellulose-metabolizing Komagataella phaffii (Pichia pastoris) by co-expressing glucanases and β-glucosidase. Appl Microbiol Biotechnol 2017; 102:1297-1306. [DOI: 10.1007/s00253-017-8656-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/12/2017] [Accepted: 11/14/2017] [Indexed: 12/22/2022]
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Cold active holocellulase cocktail from Aspergillus niger SH3: process optimization for production and biomass hydrolysis. J Taiwan Inst Chem Eng 2015. [DOI: 10.1016/j.jtice.2015.04.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Improved endoxylanase production and colony morphology of Aspergillus niger DSM 26641 by γ-ray induced mutagenesis. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.10.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Isolation of Filamentous Fungi Exhibiting High Endoxylanase Activity in Lignocellulose Hydrolysate. Appl Biochem Biotechnol 2014; 175:2066-74. [DOI: 10.1007/s12010-014-1427-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 11/18/2014] [Indexed: 11/26/2022]
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