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Franco Castillo I, García Guillén E, M de la Fuente J, Silva F, Mitchell SG. Preventing fungal growth on heritage paper with antifungal and cellulase inhibiting magnesium oxide nanoparticles. J Mater Chem B 2020; 7:6412-6419. [PMID: 31642855 DOI: 10.1039/c9tb00992b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Microorganisms such as bacteria, fungi, algae and moulds are highly proficient at colonizing artistic and architectural heritage. The irreparable damage they cause to unique artefacts results in immeasurable cultural and societal losses to our shared cultural heritage, which represent an important social and economic resource for Europe. With the overall aim of preventing fungal deterioration of paper artefacts, we report the use of magnesium oxide nanoparticles (MgO NPs) of average diameter 12 nm as potent antifungal agents against fungi commonly found colonising paper heritage: A. niger, C. cladosporioides and T. reesei. Dispersions of MgO NPs on original 18th century paper samples from the Archives of the Spanish Royal Botanic Garden were effective at preventing fungal colonisation without altering the appearance of the paper artefacts. Importantly, MgO NPs also inhibit cellulase activity in the filamentous fungi T. resei and A. niger, two of the principle biodeteriogens of cellulosic materials. In addition, our report provides three simple new procedures for studying the fungal colonisation prevention properties of nanomaterials on paper samples. Overall this opens the door to the use of colourless, low-cost, and scalable nanomaterials for preventing biodeterioration in cellulose-based artefacts.
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Affiliation(s)
- Isabel Franco Castillo
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain. and CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain
| | - Esther García Guillén
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Jesús M de la Fuente
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain. and CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain
| | - Filomena Silva
- ARAID - Agencia Aragonesa para la Investigación y el Desarrollo, Av. Ranillas, 1D, 2B, 50018 Zaragoza, Spain and Universidad de Zaragoza, Facultad de Veterinaria, Calle Miguel Servet 117, 50013 Zaragoza, Spain
| | - Scott G Mitchell
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain. and CIBER-BBN, Instituto de Salud Carlos III, Madrid, Spain
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102
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Dilokpimol A, Peng M, Di Falco M, Chin A Woeng T, Hegi RMW, Granchi Z, Tsang A, Hildén KS, Mäkelä MR, de Vries RP. Penicillium subrubescens adapts its enzyme production to the composition of plant biomass. BIORESOURCE TECHNOLOGY 2020; 311:123477. [PMID: 32408196 DOI: 10.1016/j.biortech.2020.123477] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Abstract
Penicillium subrubescens is able to degrade a broad range of plant biomass and it has an expanded set of Carbohydrate Active enzyme (CAZyme)-encoding genes in comparison to other Penicillium species. Here we used exoproteome and transcriptome analysis to demonstrate the versatile plant biomass degradation mechanism by P. subrubescens during growth on wheat bran and sugar beet pulp. On wheat bran P. subrubescens degraded xylan main chain and side residues from Day 2 of cultivation, whereas it started to degrade side chains of pectin in sugar beet pulp prior to attacking the main chain on Day 3. In addition, on Day 3 the cellulolytic enzymes were highly increased. Our results confirm that P. subrubescens adapts its enzyme production to the available plant biomass and is a promising new fungal cell factory for the production of CAZymes.
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Affiliation(s)
- Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, H4B 1R6 Montreal, Quebec, Canada
| | | | - Rosa M W Hegi
- GenomeScan B.V, Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Zoraide Granchi
- GenomeScan B.V, Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, H4B 1R6 Montreal, Quebec, Canada
| | - Kristiina S Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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103
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Identification of an intracellular β-glucosidase in Aspergillus niger with transglycosylation activity. Appl Microbiol Biotechnol 2020; 104:8367-8380. [DOI: 10.1007/s00253-020-10840-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 10/23/2022]
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104
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Velasco J, Oliva B, Gonçalves AL, Lima AS, Ferreira G, França BA, Mulinari EJ, Gonçalves TA, Squina FM, Kadowaki MAS, Maiorano A, Polikarpov I, Oliveira LCD, Segato F. Functional characterization of a novel thermophilic exo-arabinanase from Thermothielavioides terrestris. Appl Microbiol Biotechnol 2020; 104:8309-8326. [PMID: 32813063 DOI: 10.1007/s00253-020-10806-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/06/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Arabinanases from glycoside hydrolase family GH93 are enzymes with exo-activity that hydrolyze the α-1,5 bonds between arabinose residues present on arabinan. Currently, several initiatives aiming to use byproducts rich in arabinan such as pectin and sugar beet pulp as raw material to produce various compounds of interest are being developed. However, it is necessary to use robust enzymes that have an optimal performance under pH and temperature conditions used in the industrial processes. In this work, the first GH93 from the thermophilic fungus Thermothielavioides terrestris (Abn93T) was heterologously expressed in Aspergillus nidulans, purified and biochemically characterized. The enzyme is a thermophilic glycoprotein (optimum activity at 70 °C) with prolonged stability in acid pHs (4.0 to 6.5). The presence of glycosylation affected slightly the hydrolytic capacity of the enzyme, which was further increased by 34% in the presence of 1 mM CoCl2. Small-angle X-ray scattering results show that Abn93T is a globular-like-shaped protein with a slight bulge at one end. The hydrolytic mechanism of the enzyme was elucidated using capillary zone electrophoresis and molecular docking calculations. Abn93T has an ability to produce (in synergism with arabinofuranosidases) arabinose and arabinobiose from sugar beet arabinan, which can be explored as fermentable sugars and prebiotics. KEY POINTS: • Thermophilic exo-arabinanase from family GH93 • Molecular basis of arabinan depolymerization.
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Affiliation(s)
- Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Aline Larissa Gonçalves
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Awana Silva Lima
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Gislene Ferreira
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bruno Alves França
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Evandro José Mulinari
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Thiago Augusto Gonçalves
- Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Fábio Márcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Marco Antonio Seiki Kadowaki
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Alfredo Maiorano
- Instituto de Pesquisas Tecnológicas do Estado de São Paulo, Diretoria de Operações e Negócios, Núcleo de Bionanomanufatura, São Paulo, SP, Brazil
| | - Igor Polikarpov
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil.
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105
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Hsu Y, Arioka M. In vitro and in vivo characterization of genes involved in mannan degradation in Neurospora crassa. Fungal Genet Biol 2020; 144:103441. [PMID: 32777385 DOI: 10.1016/j.fgb.2020.103441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 01/22/2023]
Abstract
To better understand the roles of genes involved in mannan degradation in filamentous fungi, in this study we searched, identified, and characterized one putative GH5 endo-β-mannanase (GH5-7) and two putative GH2 mannan-degrading enzymes (GH2-1 and GH2-4) in Neurospora crassa. Real-time RT-PCR analyses showed that the expression levels of these genes were significantly up-regulated when the cells were grown in mannan-containing media where the induction level of gh5-7 was the highest. All three proteins were heterologously expressed and purified. GH5-7 displayed a substrate preference toward galactomannan by showing 10-times higher catalytic efficiency than to linear β-mannan. In contrast, GH2-1 preferred short manno-oligosaccharides or β-mannan as substrates. Compared to the wild type strain, the growth of Δgh5-7 and Δgh5-7Δgh2-4 mutants, but not Δgh2-1, Δgh2-4, and Δgh2-1Δgh2-4 mutants, was poor in the cultures containing glucomannan or galactomannan as the sole carbon source, suggesting that GH5-7 plays a critical role in the utilization of heteromannans in vivo. On the other hand, all the mutants showed significantly slow growth when grown in the medium containing linear β-mannan. Collectively, these results indicate that N. crassa can utilize glucomannan and galactomannan without GH2-1 and GH2-4, but efficient degradation of β-mannan requires a concerted action of three enzymes, GH5-7, GH2-1, and GH2-4.
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Affiliation(s)
- Yunhan Hsu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Manabu Arioka
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Japan.
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106
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Satapathy S, Rout JR, Kerry RG, Thatoi H, Sahoo SL. Biochemical Prospects of Various Microbial Pectinase and Pectin: An Approachable Concept in Pharmaceutical Bioprocessing. Front Nutr 2020; 7:117. [PMID: 32850938 PMCID: PMC7424017 DOI: 10.3389/fnut.2020.00117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/22/2020] [Indexed: 12/29/2022] Open
Abstract
Both pectin and pectinase are vitally imperative biomolecules in the biotechnological sector. These molecules are a feasible non-toxic contrivance of nature with extensive applicative perception. Understanding pectic substances and their structure, unique depolymerization, and biochemical properties such as a catalytic mechanism and the strong interrelationship among these molecules could immensely enhance their applicability in industries. For instance, gaining knowledge with respect to the versatile molecular heterogeneity of the compounds could be considered as the center of concern to resolve the industrial issues from multiple aspects. In the present review, an effort has been made to orchestrate the fundamental information related to structure, depolymerization characteristics, and classification of pectin as well as the types and biochemical properties of pectinase. Furthermore, various production methods related to the optimization of the product and its significant contribution to the pharmaceutical industry (either pectinase or derived pectic substances) are described in this article.
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Affiliation(s)
- Sonali Satapathy
- Microbiology Research Laboratory, Post Graduate Department of Botany, Utkal University, Bhubaneswar, India
| | | | - Rout George Kerry
- Post Graduate Department of Biotechnology, Utkal University, Bhubaneswar, India
| | | | - Santi Lata Sahoo
- Microbiology Research Laboratory, Post Graduate Department of Botany, Utkal University, Bhubaneswar, India
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107
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Influence of enzymatic tempering on milling characteristics, flour quality, crystallinity and microstructure of wheat. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2020. [DOI: 10.1007/s11694-020-00445-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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108
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Takagi S, Kojima K, Ohashi S. Proteomic analysis on Aspergillus strains that are useful for industrial enzyme production. Biosci Biotechnol Biochem 2020; 84:2241-2252. [PMID: 32693695 DOI: 10.1080/09168451.2020.1794784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A simple intracellular proteomic study was conducted to investigate the biological activities of Aspergillus niger during industrial enzyme production. A strain actively secreting a heterologous enzyme was compared to a reference strain. In total, 1824 spots on 2-D gels were analyzed using MALDI-TOF MS, yielding 343 proteins. The elevated levels of UPR components, BipA, PDI, and calnexin, and proteins related to ERAD and ROS reduction, were observed in the enzyme-producer. The results suggest the occurrence of these responses in the enzyme-producers. Major glycolytic enzymes, Fba1, EnoA, and GpdA, were abundant but at a reduced level relative to the reference, indicating a potential repression of the glycolytic pathway. Interestingly, it was observed that a portion of over-expressed heterologous enzyme accumulated inside the cells and digested during fermentation, suggesting the secretion capacity of the strain was not enough for completing secretion. Newly identified conserved-proteins, likely in signal transduction, and other proteins were also investigated. Abbreviations: 2-D: two-dimensional; UPR: unfolded protein response; ER: endoplasmic reticulum; ERAD: ER-associated protein degradation; PDI: protein disulfide-isomerase; ROS: reactive oxygen species; RESS: Repression under Secretion Stress; CSAP: Conserved Small Abundant Protein; TCTP: translationally controlled tumor protein.
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Affiliation(s)
| | | | - Shinichi Ohashi
- Genome Biotechnology Laboratory, Kanazawa-Institute of Technology , Ishikawa, Japan
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109
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110
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Salgado-Bautista D, Volke-Sepúlveda T, Figueroa-Martínez F, Carrasco-Navarro U, Chagolla-López A, Favela-Torres E. Solid-state fermentation increases secretome complexity in Aspergillus brasiliensis. Fungal Biol 2020; 124:723-734. [PMID: 32690254 DOI: 10.1016/j.funbio.2020.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 04/19/2020] [Accepted: 04/25/2020] [Indexed: 02/06/2023]
Abstract
Aspergillus is used for the industrial production of enzymes and organic acids, mainly by submerged fermentation (SmF). However, solid-state fermentation (SSF) offers several advantages over SmF. Although differences related to lower catabolite repression and substrate inhibition, as well as higher extracellular enzyme production in SSF compared to SmF have been shown, the mechanisms undelaying such differences are still unknown. To explain some differences among SSF and SmF, the secretome of Aspergillus brasiliensis obtained from cultures in a homogeneous physiological state with high glucose concentrations was analyzed. Of the regulated proteins produced by SmF, 74% were downregulated by increasing the glucose concentration, whereas all those produced by SSF were upregulated. The most abundant and upregulated protein found in SSF was the transaldolase, which could perform a moonlighting function in fungal adhesion to the solid support. This study evidenced that SSF: (i) improves the kinetic parameters in relation to SmF, (ii) prevents the catabolite repression, (iii) increases the branching level of hyphae and oxidative metabolism, as well as the concentration and diversity of secreted proteins, and (iv) favors the secretion of typically intracellular proteins that could be involved in fungal adhesion. All these differences can be related to the fact that molds are more specialized to growth in solid materials because they mimic their natural habitat.
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Affiliation(s)
- Daniel Salgado-Bautista
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Tania Volke-Sepúlveda
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Francisco Figueroa-Martínez
- CONACyT Research Fellow, Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Ulises Carrasco-Navarro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
| | - Alicia Chagolla-López
- Laboratorio de Proteómica- Cinvestav Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, 36824, Guanajuato, Mexico.
| | - Ernesto Favela-Torres
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, 09340, Ciudad de México, Mexico.
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111
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Wang BT, Hu S, Yu XY, Jin L, Zhu YJ, Jin FJ. Studies of Cellulose and Starch Utilization and the Regulatory Mechanisms of Related Enzymes in Fungi. Polymers (Basel) 2020; 12:polym12030530. [PMID: 32121667 PMCID: PMC7182937 DOI: 10.3390/polym12030530] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 12/24/2022] Open
Abstract
Polysaccharides are biopolymers made up of a large number of monosaccharides joined together by glycosidic bonds. Polysaccharides are widely distributed in nature: Some, such as peptidoglycan and cellulose, are the components that make up the cell walls of bacteria and plants, and some, such as starch and glycogen, are used as carbohydrate storage in plants and animals. Fungi exist in a variety of natural environments and can exploit a wide range of carbon sources. They play a crucial role in the global carbon cycle because of their ability to break down plant biomass, which is composed primarily of cell wall polysaccharides, including cellulose, hemicellulose, and pectin. Fungi produce a variety of enzymes that in combination degrade cell wall polysaccharides into different monosaccharides. Starch, the main component of grain, is also a polysaccharide that can be broken down into monosaccharides by fungi. These monosaccharides can be used for energy or as precursors for the biosynthesis of biomolecules through a series of enzymatic reactions. Industrial fermentation by microbes has been widely used to produce traditional foods, beverages, and biofuels from starch and to a lesser extent plant biomass. This review focuses on the degradation and utilization of plant homopolysaccharides, cellulose and starch; summarizes the activities of the enzymes involved and the regulation of the induction of the enzymes in well-studied filamentous fungi.
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112
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Daly P, Peng M, Mitchell HD, Kim Y, Ansong C, Brewer H, de Gijsel P, Lipton MS, Markillie LM, Nicora CD, Orr G, Wiebenga A, Hildén KS, Kabel MA, Baker SE, Mäkelä MR, de Vries RP. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation. Environ Microbiol 2020; 22:1154-1166. [PMID: 31876091 PMCID: PMC7065180 DOI: 10.1111/1462-2920.14907] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/20/2019] [Indexed: 11/27/2022]
Abstract
Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.
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Affiliation(s)
- Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Hugh D. Mitchell
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Young‐Mo Kim
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Charles Ansong
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Heather Brewer
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Peter de Gijsel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Mary S. Lipton
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Lye Meng Markillie
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Carrie D. Nicora
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Galya Orr
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Kristiina S. Hildén
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Mirjam A. Kabel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Scott E. Baker
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Miia R. Mäkelä
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
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113
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de Vries RP, Mäkelä MR. Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches. Trends Microbiol 2020; 28:487-499. [PMID: 32396827 DOI: 10.1016/j.tim.2020.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 01/16/2020] [Indexed: 10/25/2022]
Abstract
Plant biomass degradation by fungi is a widely studied and applied field of science, due to its relevance for the global carbon cycle and many biotechnological applications. Before the genome era, many of the in-depth studies focused on a relatively small number of species, whereas now, many species can be addressed in detail, revealing the large variety in the approach used by fungi to degrade plant biomass. This variation is found at many levels and includes genomic adaptation to the preferred biomass component, but also different approaches to degrade this component by diverse sets of activities encoded in the genome. Even larger differences have been observed using transcriptome and proteome studies, even between closely related species, suggesting a high level of adaptation in individual species. A better understanding of the drivers of this diversity could be highly valuable in developing more efficient biotechnology approaches for the enzymatic conversion of plant biomass.
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Affiliation(s)
- Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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114
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Chroumpi T, Aguilar-Pontes MV, Peng M, Wang M, Lipzen A, Ng V, Grigoriev IV, Mäkelä MR, de Vries RP. Identification of a gene encoding the last step of the L-rhamnose catabolic pathway in Aspergillus niger revealed the inducer of the pathway regulator. Microbiol Res 2020; 234:126426. [PMID: 32062364 DOI: 10.1016/j.micres.2020.126426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/14/2022]
Abstract
In fungi, L-rhamnose (Rha) is converted via four enzymatic steps into pyruvate and L-lactaldehyde, which enter central carbon metabolism. In Aspergillus niger, only the genes involved in the first three steps of the Rha catabolic pathway have been identified and characterized, and the inducer of the pathway regulator RhaR remained unknown. In this study, we identified the gene (lkaA) involved in the conversion of L-2-keto-3-deoxyrhamnonate (L-KDR) into pyruvate and L-lactaldehyde, which is the last step of the Rha pathway. Deletion of lkaA resulted in impaired growth on L-rhamnose, and potentially in accumulation of L-KDR. Contrary to ΔlraA, ΔlrlA and ΔlrdA, the expression of the Rha-responsive genes that are under control of RhaR, were at the same levels in ΔlkaA and the reference strain, indicating the role of L-KDR as the inducer of the Rha pathway regulator.
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Affiliation(s)
- Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Mei Wang
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, United States
| | - Anna Lipzen
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, United States
| | - Vivian Ng
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, United States
| | - Igor V Grigoriev
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, United States
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, P.O. Box 56, Viikinkaari 9, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.
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115
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β-Mannanase Production Using Coffee Industry Waste for Application in Soluble Coffee Processing. Biomolecules 2020; 10:biom10020227. [PMID: 32033042 PMCID: PMC7072339 DOI: 10.3390/biom10020227] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/17/2022] Open
Abstract
Soluble coffee offers the combined benefits of high added value and practicality for its consumers. The hydrolysis of coffee polysaccharides by the biochemical route, using enzymes, is an eco-friendly and sustainable way to improve the quality of this product, while contributing to the implementation of industrial processes that have lower energy requirements and can reduce environmental impacts. This work describes the production of hydrolytic enzymes by solid-state fermentation (SSF), cultivating filamentous fungi on waste from the coffee industry, followed by their application in the hydrolysis of waste coffee polysaccharides from soluble coffee processing. Different substrate compositions were studied, an ideal microorganism was selected, and the fermentation conditions were optimized. Cultivations for enzymes production were carried out in flasks and in a packed-bed bioreactor. Higher enzyme yield was achieved in the bioreactor, due to better aeration of the substrate. The best β-mannanase production results were found for a substrate composed of a mixture of coffee waste and wheat bran (1:1 w/w), using Aspergillus niger F12. The enzymatic extract proved to be very stable for 24 h, at 50 °C, and was able to hydrolyze a considerable amount of the carbohydrates in the coffee. The addition of a commercial cellulase cocktail to the crude extract increased the hydrolysis yield by 56%. The production of β-mannanase by SSF and its application in the hydrolysis of coffee polysaccharides showed promise for improving soluble coffee processing, offering an attractive way to assist in closing the loops in the coffee industry and creating a circular economy.
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116
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CRISPR/Cas9 technology enables the development of the filamentous ascomycete fungus Penicillium subrubescens as a new industrial enzyme producer. Enzyme Microb Technol 2020; 133:109463. [DOI: 10.1016/j.enzmictec.2019.109463] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/08/2019] [Accepted: 11/01/2019] [Indexed: 12/21/2022]
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117
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Kun RS, Meng J, Salazar-Cerezo S, Mäkelä MR, de Vries RP, Garrigues S. CRISPR/Cas9 facilitates rapid generation of constitutive forms of transcription factors in Aspergillus niger through specific on-site genomic mutations resulting in increased saccharification of plant biomass. Enzyme Microb Technol 2020; 136:109508. [PMID: 32331715 DOI: 10.1016/j.enzmictec.2020.109508] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/16/2019] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has been successfully applied for gene editing in filamentous fungi. Previous studies reported that single stranded oligonucleotides can be used as repair templates to induce point mutations in some filamentous fungi belonging to genus Aspergillus. In Aspergillus niger, extensive research has been performed on regulation of plant biomass degradation, addressing transcription factors such as XlnR or GaaR, involved in (hemi-)cellulose and pectin utilization, respectively. Single nucleotide mutations leading to constitutively active forms of XlnR and GaaR have been previously reported. However, the mutations were performed by the introduction of versions obtained through site-directed or UV-mutagenesis into the genome. Here we report a more time- and cost-efficient approach to obtaining constitutively active versions by application of the CRISPR/Cas9 system to generate the desired mutation on-site in the A. niger genome. This was also achieved using only 60-mer single stranded oligonucleotides, shorter than the previously reported 90-mer strands. In this study, we show that CRISPR/Cas9 can also be used to efficiently change functional properties of the proteins encoded by the target gene by on-site genomic mutations in A. niger. The obtained strains with constitutively active XlnR and GaaR versions resulted in increased production of plant biomass degrading enzymes and improved release of d-xylose and l-arabinose from wheat bran, and d-galacturonic acid from sugar beet pulp.
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Affiliation(s)
- Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jiali Meng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Miia R Mäkelä
- Fungal Genetics and Biotechnology, Department of Microbiology, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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118
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Valk LC, Luttik MAH, de Ram C, Pabst M, van den Broek M, van Loosdrecht MCM, Pronk JT. A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway. Front Microbiol 2020; 10:3027. [PMID: 32010092 PMCID: PMC6978723 DOI: 10.3389/fmicb.2019.03027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
D-galacturonate, a key constituent of pectin, is a ubiquitous monomer in plant biomass. Anaerobic, fermentative conversion of D-galacturonate is therefore relevant in natural environments as well as in microbial processes for microbial conversion of pectin-containing agricultural residues. In currently known microorganisms that anaerobically ferment D-galacturonate, its catabolism occurs via the galacturonate-isomerase pathway. Redox-cofactor balancing in this pathway strongly constrains the possible range of products generated from anaerobic D-galacturonate fermentation, resulting in acetate as the predominant organic fermentation product. To explore metabolic diversity of microbial D-galacturonate fermentation, anaerobic enrichment cultures were performed at pH 4. Anaerobic batch and chemostat cultures of a dominant Lactobacillus suebicus strain isolated from these enrichment cultures produced near-equimolar amounts of lactate and acetate from D-galacturonate. A combination of whole-genome sequence analysis, quantitative proteomics, enzyme activity assays in cell extracts, and in vitro product identification demonstrated that D-galacturonate metabolism in L. suebicus occurs via a novel pathway. In this pathway, mannonate generated by the initial reactions of the canonical isomerase pathway is converted to 6-phosphogluconate by two novel biochemical reactions, catalyzed by a mannonate kinase and a 6-phosphomannonate 2-epimerase. Further catabolism of 6-phosphogluconate then proceeds via known reactions of the phosphoketolase pathway. In contrast to the classical isomerase pathway for D-galacturonate catabolism, the novel pathway enables redox-cofactor-neutral conversion of D-galacturonate to ribulose-5-phosphate. While further research is required to identify the structural genes encoding the key enzymes for the novel pathway, its redox-cofactor coupling is highly interesting for metabolic engineering of microbial cell factories for conversion of pectin-containing feedstocks into added-value fermentation products such as ethanol or lactate. This study illustrates the potential of microbial enrichment cultivation to identify novel pathways for the conversion of environmentally and industrially relevant compounds.
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Affiliation(s)
| | | | | | | | | | | | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Abstract
Capillary zone electrophoresis (CZE) has been rising in its importance in structural analysis of plant cell walls, characterization of enzymes that degrade polysaccharides, and profiling of oligosaccharides to characterize cell wall mutants. CZE with laser-induced fluorescence detection provides high separation efficiencies, high-speed analysis, with extremely small sample requirements. Here we describe the instrumentation we use and methods for attaching fluorescent labels to oligosaccharides so that they can be detected.
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120
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Patyshakuliyeva A, Falkoski DL, Wiebenga A, Timmermans K, de Vries RP. Macroalgae Derived Fungi Have High Abilities to Degrade Algal Polymers. Microorganisms 2019; 8:E52. [PMID: 31888103 PMCID: PMC7023191 DOI: 10.3390/microorganisms8010052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/13/2019] [Accepted: 12/26/2019] [Indexed: 12/21/2022] Open
Abstract
Marine fungi associated with macroalgae are an ecologically important group that have a strong potential for industrial applications. In this study, twenty-two marine fungi isolated from the brown seaweed Fucus sp. were examined for their abilities to produce algal and plant biomass degrading enzymes. Growth of these isolates on brown and green algal biomass revealed a good growth, but no preference for any specific algae. Based on the analysis of enzymatic activities, macroalgae derived fungi were able to produce algae specific and (hemi-)cellulose degrading enzymes both on algal and plant biomass. However, the production of algae specific activities was lower than the production of cellulases and xylanases. These data revealed the presence of different enzymatic approaches for the degradation of algal biomass by macroalgae derived fungi. In addition, the results of the present study indicate our poor understanding of the enzymes involved in algal biomass degradation and the mechanisms of algal carbon source utilization by marine derived fungi.
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Affiliation(s)
- Aleksandrina Patyshakuliyeva
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.P.); (D.L.F.); (A.W.)
| | - Daniel L. Falkoski
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.P.); (D.L.F.); (A.W.)
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.P.); (D.L.F.); (A.W.)
| | - Klaas Timmermans
- NIOZ Royal Netherlands Institute for Sea Research, Landsdiep 4, 1797 SZ ′t Horntje, The Netherlands;
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.P.); (D.L.F.); (A.W.)
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121
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Rezaei M, Wall H, Tarshan M, Ivarsson E. Evaluation of broiler chickens' digestibility of Neurospora intermedia biomass. Poult Sci 2019; 98:5017-5022. [PMID: 30980081 DOI: 10.3382/ps/pez174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/15/2019] [Indexed: 11/20/2022] Open
Abstract
A total of 70 broiler chickens were used to evaluate the apparent ileal digestibility coefficient (AIDC) of protein and amino acids, and apparent digestibility coefficient (ADC) of energy in the protein rich Fungal Biomass of Neurospora intermedia (FBN) obtained from bioethanol production. The chickens were housed in 10 pens with seven chickens per pen and fed one of two experimental diets between day 28 and 35 of age. The experimental diets were wheat-soybean meal-based control diet and a diet composed of 70% control diet and 30% of FBN. There were no difference (P > 0.05) between the control and FBN diet on chick feed intake and body weight at day 35. However, the AIDCs of crude protein and amino acids were significantly (P < 0.01) higher in control diet than in the FBN diet except for proline and phenylalanine. The AIDC of CP (0.74), cysteine (0.68), methionine (0.70), AME (15.6), and threonine (0.69) in FBN were comparable to the corresponding values in other protein-rich feedstuffs such as soybean meal and fish meal. The results from this study show that FBN may be an alternative protein source for poultry.
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Affiliation(s)
- Mehdi Rezaei
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences (SLU), PO Box 7024, 750 07, Uppsala, Sweden
| | - Helena Wall
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences (SLU), PO Box 7024, 750 07, Uppsala, Sweden
| | - Muhammad Tarshan
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences (SLU), PO Box 7024, 750 07, Uppsala, Sweden
| | - Emma Ivarsson
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences (SLU), PO Box 7024, 750 07, Uppsala, Sweden
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122
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Kameshwar AKS, Ramos LP, Qin W. CAZymes-based ranking of fungi (CBRF): an interactive web database for identifying fungi with extrinsic plant biomass degrading abilities. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0286-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractCarbohydrate-active enzymes (CAZymes) are industrially important enzymes, which are involved in synthesis and breakdown of carbohydrates. CAZymes secreted by microorganisms especially fungi are widely used in industries. However, identifying an ideal fungal candidate is costly and time-consuming process. In this regard, we have developed a web-database “CAZymes Based Ranking of Fungi (CBRF)”, for sorting and selecting an ideal fungal candidate based on their genome-wide distribution of CAZymes. We have retrieved the complete annotated proteomic data of 443 published fungal genomes from JGI-MycoCosm web-repository, for the CBRF web-database construction. CBRF web-database was developed using open source computing programing languages such as MySQL, HTML, CSS, bootstrap, jQuery, JavaScript and Ajax frameworks. CBRF web-database sorts complete annotated list of fungi based on three selection functionalities: (a) to sort either by ascending (or) descending orders; (b) to sort the fungi based on a selected CAZy group and class; (c) to sort fungi based on their individual lignocellulolytic abilities. We have also developed a simple and basic webpage “S-CAZymes” using HTML, CSS and Java script languages. The global search functionality of S-CAZymes enables the users to understand and retrieve information about a specific carbohydrate-active enzyme and its current classification in the corresponding CAZy family. The S-CAZymes is a supporting web page which can be used in complementary with the CBRF web-database (knowing the classification of specific CAZyme in S-CAZyme and use this information further to sort fungi using CBRF web-database). The CBRF web-database and S-CAZymes webpage are hosted through Amazon® Web Services (AWS) available at http://13.58.192.177/RankEnzymes/about. We strongly believe that CBRF web-database simplifies the process of identifying a suitable fungus both in academics and industries. In future, we intend to update the CBRF web-database with the public release of new annotated fungal genomes.
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123
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Torres-Barajas LR, Alvarez-Zúñiga MT, Mendoza-Hernández G, Aguilar-Osorio G. Analysis of polysaccharide hydrolases secreted by Aspergillus flavipes FP-500 on corn cobs and wheat bran as complex carbon sources. Prep Biochem Biotechnol 2019; 50:390-400. [DOI: 10.1080/10826068.2019.1700518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lizzete Ruth Torres-Barajas
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
| | - María Teresa Alvarez-Zúñiga
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
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Division of labor in honey bee gut microbiota for plant polysaccharide digestion. Proc Natl Acad Sci U S A 2019; 116:25909-25916. [PMID: 31776248 DOI: 10.1073/pnas.1916224116] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Bees acquire carbohydrates from nectar and lipids; and amino acids from pollen, which also contains polysaccharides including cellulose, hemicellulose, and pectin. These potential energy sources could be degraded and fermented through microbial enzymatic activity, resulting in short chain fatty acids available to hosts. However, the contributions of individual microbiota members to polysaccharide digestion have remained unclear. Through analysis of bacterial isolate genomes and a metagenome of the honey bee gut microbiota, we identify that Bifidobacterium and Gilliamella are the principal degraders of hemicellulose and pectin. Both Bifidobacterium and Gilliamella show extensive strain-level diversity in gene repertoires linked to polysaccharide digestion. Strains from honey bees possess more such genes than strains from bumble bees. In Bifidobacterium, genes encoding carbohydrate-active enzymes are colocated within loci devoted to polysaccharide utilization, as in Bacteroides from the human gut. Carbohydrate-active enzyme-encoding gene expressions are up-regulated in response to particular hemicelluloses both in vitro and in vivo. Metabolomic analyses document that bees experimentally colonized by different strains generate distinctive gut metabolomic profiles, with enrichment for specific monosaccharides, corresponding to predictions from genomic data. The other 3 core gut species clusters (Snodgrassella and 2 Lactobacillus clusters) possess few or no genes for polysaccharide digestion. Together, these findings indicate that strain composition within individual hosts determines the metabolic capabilities and potentially affects host nutrition. Furthermore, the niche specialization revealed by our study may promote overall community stability in the gut microbiomes of bees.
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125
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Khosravi C, Kowalczyk JE, Chroumpi T, Battaglia E, Aguilar Pontes MV, Peng M, Wiebenga A, Ng V, Lipzen A, He G, Bauer D, Grigoriev IV, de Vries RP. Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. BMC Genomics 2019; 20:853. [PMID: 31726994 PMCID: PMC6854810 DOI: 10.1186/s12864-019-6235-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/28/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Enzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of use with respect to plant biomass degradation and for that reason have become 'model' species for this topic. A. niger is a major industrial enzyme producer that has a broad ability to degrade plant based polysaccharides. A. niger wild-type, the (hemi-)cellulolytic regulator (xlnR) and xylulokinase (xkiA1) mutant strains were grown on a monocot (corn stover, CS) and dicot (soybean hulls, SBH) substrate. The xkiA1 mutant is unable to utilize the pentoses D-xylose and L-arabinose and the polysaccharide xylan, and was previously shown to accumulate inducers for the (hemi-)cellulolytic transcriptional activator XlnR and the arabinanolytic transcriptional activator AraR in the presence of pentoses, resulting in overexpression of their target genes. The xlnR mutant has reduced growth on xylan and down-regulation of its target genes. The mutants therefore have a similar phenotype on xylan, but an opposite transcriptional effect. D-xylose and L-arabinose are the most abundant monosaccharides after D-glucose in nearly all plant-derived biomass materials. In this study we evaluated the effect of the xlnR and xkiA1 mutation during growth on two pentose-rich substrates by transcriptome analysis. RESULTS Particular attention was given to CAZymes, metabolic pathways and transcription factors related to the plant biomass degradation. Genes coding for the main enzymes involved in plant biomass degradation were down-regulated at the beginning of the growth on CS and SBH. However, at a later time point, significant differences were found in the expression profiles of both mutants on CS compared to SBH. CONCLUSION This study demonstrates the high complexity of the plant biomass degradation process by fungi, by showing that mutant strains with fairly straightforward phenotypes on pure mono- and polysaccharides, have much less clear-cut phenotypes and transcriptomes on crude plant biomass.
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Affiliation(s)
- Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Joanna E. Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Maria-Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
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126
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Matrix Discriminant Analysis Evidenced Surface-Lithium as an Important Factor to Increase the Hydrolytic Saccharification of Sugarcane Bagasse. Molecules 2019; 24:molecules24193614. [PMID: 31597244 PMCID: PMC6804010 DOI: 10.3390/molecules24193614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/10/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022] Open
Abstract
Statistical evidence pointing to the very soft change in the ionic composition on the surface of the sugar cane bagasse is crucial to improve yields of sugars by hydrolytic saccharification. Removal of Li+ by pretreatments exposing -OH sites was the most important factor related to the increase of saccharification yields using enzyme cocktails. Steam Explosion and Microwave:H2SO4 pretreatments produced unrelated structural changes, but similar ionic distribution patterns. Both increased the saccharification yield 1.74-fold. NaOH produced structural changes related to Steam Explosion, but released surface-bounded Li+ obtaining 2.04-fold more reducing sugars than the control. In turn, the higher amounts in relative concentration and periodic structures of Li+ on the surface observed in the control or after the pretreatment with Ethanol:DMSO:Ammonium Oxalate, blocked -OH and O- available for ionic sputtering. These changes correlated to 1.90-fold decrease in saccharification yields. Li+ was an activator in solution, but its presence and distribution pattern on the substrate was prejudicial to the saccharification. Apparently, it acts as a phase-dependent modulator of enzyme activity. Therefore, no correlations were found between structural changes and the efficiency of the enzymatic cocktail used. However, there were correlations between the Li+ distribution patterns and the enzymatic activities that should to be shown.
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Kim JH, Kim D, Seo SM, Kim D. Physiological effects of zero-valent iron nanoparticles in rhizosphere on edible crop, Medicago sativa (Alfalfa), grown in soil. ECOTOXICOLOGY (LONDON, ENGLAND) 2019; 28:869-877. [PMID: 31392635 DOI: 10.1007/s10646-019-02083-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
We investigated the effects of nanoscale zero-valent iron (nZVI) that has been widely used for groundwater remediation on a terrestrial crop, Medicago sativa (Alfalfa), and comprehensively addressed its development and growth in soil culture. Root lengths, chlorophyll, carbohydrate and lignin contents were compared, and no physiological phytotoxicity was observed in the plants. In the roots, using an omics-based analytical, we found evidence of OH radical-induced cell wall loosening from exposure to nZVI, resulting in increased root lengths that were approximately 1.5 times greater than those of the control. Moreover, germination index (GI) was employed to physiologically evaluate the impact of nZVI on germination and root length. In regard to chlorophyll concentration, nZVI-treated alfalfa exhibited a higher value in 20-day-old seedlings, whereas the carbohydrate and lignin contents were slightly decreased in nZVI-treated alfalfa. Additionally, evidence for translocation of nZVI into plant tissues was also found. Vibrating sample magnetometry on shoots revealed the translocation of nZVI from the root to shoot. In this study, using an edible crop as a representative model, the potential impact of reactive engineered nanomaterials that can be exposed to the ecosystem on plant is discussed.
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Affiliation(s)
- Jae-Hwan Kim
- Advanced Geo-materials R&D Department, Pohang Branch, Korea Institute of Geoscience and Mineral Resources, Pohang, 37559, Republic of Korea.
| | - Daniel Kim
- Advanced Geo-materials R&D Department, Pohang Branch, Korea Institute of Geoscience and Mineral Resources, Pohang, 37559, Republic of Korea
| | - Sung Man Seo
- Advanced Geo-materials R&D Department, Pohang Branch, Korea Institute of Geoscience and Mineral Resources, Pohang, 37559, Republic of Korea
| | - Daeyoung Kim
- Department of Nanomaterials Science and Engineering, University of Science and Technology, Daejeon, Republic of Korea
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128
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Mlaik N, Sayadi S, Hamza M, Khoufi S. Production and characterization of β-glucosidase from Aspergillus niger fermentation: Application for organic fraction of municipal solid waste hydrolysis and methane enhancement. Biotechnol Prog 2019; 36:e2902. [PMID: 31469516 DOI: 10.1002/btpr.2902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 08/06/2019] [Accepted: 08/27/2019] [Indexed: 11/11/2022]
Abstract
The anaerobic digestion of the organic fraction of municipal solid waste (OFMSW) is currently an attractive treatment process with energy production in the form of biogas. Hydrolysis is the rate-limiting step for the anaerobic digestion of solid wastes. Thus, in the present study fungal enzymatic pretreatment of OFMSW was applied to enhance biogas production. Two enzyme cocktails rich on β-glucosidase were produced from submerged fermentation of Aspergillus niger on basal medium using OFMSW as carbon source and urea (Urea cocktail) and Ulva rigida as nitrogen source (Ulva cocktail). Ulva cocktail displayed an important effect on OFMSW solubilization. Therefore, an increase of reducing sugar concentration about 60% was obtained which was in correlation with chemical oxygen demand (COD) increase. The performance of enzymatic pretreatment on anaerobic digestion of OFMSW was studied by conducting biochemical methane potential tests. Results showed that the enzymatic pretreatment improved methane yield of OFMSW even at high solid concentration. High methane yield about 500 ml/g total volatile solid was obtained, which corresponds up to 68% enhancement over the control.
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Affiliation(s)
- Najoua Mlaik
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Manel Hamza
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Sonia Khoufi
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sfax, Tunisia
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129
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Ito T, Sato A, Takahashi I, Ito T, Takano K, Noge K, Okuda M, Hashizume K. Identification of enzymes from genus Trichoderma that can accelerate formation of ferulic acid and ethyl ferulate in collaboration with rice koji enzyme in sake mash. J Biosci Bioeng 2019; 128:177-182. [DOI: 10.1016/j.jbiosc.2019.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/22/2018] [Accepted: 01/18/2019] [Indexed: 11/28/2022]
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Antunes FAF, Chandel AK, Terán-Hilares R, Ingle AP, Rai M, Dos Santos Milessi TS, da Silva SS, Dos Santos JC. Overcoming challenges in lignocellulosic biomass pretreatment for second-generation (2G) sugar production: emerging role of nano, biotechnological and promising approaches. 3 Biotech 2019; 9:230. [PMID: 31139545 DOI: 10.1007/s13205-019-1761-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/13/2019] [Indexed: 01/12/2023] Open
Abstract
Production of green chemicals and biofuels in biorefineries is the potential alternative for petrochemicals and gasoline in transitioning of petro-economy into bioeconomy. However, an efficient biomass pretreatment process must be considered for the successful deployment of biorefineries, mainly for use of lignocellulosic raw materials. However, biomass recalcitrance plays a key role in its saccharification to obtain considerable sugar which can be converted into ethanol or other biochemicals. In the last few decades, several pretreatment methods have been developed, but their feasibility at large-scale operations remains as a persistent bottleneck in biorefineries. Pretreatment methods such as hydrodynamic cavitation, ionic liquids, and supercritical fluids have shown promising results in terms of either lignin or hemicellulose removal, thus making remaining carbohydrate fraction amenable to the enzymatic hydrolysis for clean and high amount of fermentable sugar production. However, their techno-economic feasibility at industrial scale has not been yet studied in detail. Besides, nanotechnological-based technologies could play an important role in the economically viable 2G sugar production in future. Considering these facts, in the present review, we have discussed the existing promising pretreatment methods for lignocellulosic biomass and their challenges, besides this strategic role of nano and biotechnological approaches towards the viability and sustainability of biorefineries is also discussed.
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Affiliation(s)
- Felipe Antonio Fernandes Antunes
- 1Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Estrada Municipal do Campinho, s/n-Campinho, Lorena, 12602-810 Brazil
| | - Anuj Kumar Chandel
- 1Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Estrada Municipal do Campinho, s/n-Campinho, Lorena, 12602-810 Brazil
| | - Ruly Terán-Hilares
- 1Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Estrada Municipal do Campinho, s/n-Campinho, Lorena, 12602-810 Brazil
| | - Avinash P Ingle
- 3Nanotechnology Laboratory, Department of Biotechnology, SGB Amravati University, Amravati, 444 602 India
| | - Mahendra Rai
- 3Nanotechnology Laboratory, Department of Biotechnology, SGB Amravati University, Amravati, 444 602 India
| | | | - Silvio Silvério da Silva
- 1Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Estrada Municipal do Campinho, s/n-Campinho, Lorena, 12602-810 Brazil
| | - Júlio César Dos Santos
- 1Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Estrada Municipal do Campinho, s/n-Campinho, Lorena, 12602-810 Brazil
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131
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Malik AD, Furtado IJ. Haloferax sulfurifontis GUMFAZ2 producing xylanase-free cellulase retrieved from Haliclona sp. inhabiting rocky shore of Anjuna, Goa-India. J Basic Microbiol 2019; 59:692-700. [PMID: 30980726 DOI: 10.1002/jobm.201800672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/28/2019] [Accepted: 03/28/2019] [Indexed: 11/07/2022]
Abstract
Salt stable cellulases are implicated in detritic food webs of marine invertebrates for their role in the degradation of cellulosic material. A haloarchaeon, Haloferax sulfurifontis GUMFAZ2 producing cellulase was successfully isolated from marine Haliclona sp., a sponge inhabiting the rocky intertidal region of Anjuna, Goa. The culture produced extracellular xylanase-free cellulase with a maximum activity of 11.7 U/ml, using carboxymethylcellulose-Na (CMC-Na), as a sole source of carbon in 3.5 M NaCl containing medium, pH 7 at 40°C and produced cellobiose and glucose, detectable by thin-layer chromatography. Nondenaturing polyacrylamide gel electrophoresis of the crude enzyme, revealed a single protein band of 19.6 kDa which on zymographic analysis exhibited cellulase activity while corresponding sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed a molecular weight of 46 kDa. Unlike conventional cellulases, this enzyme is active in presence of 5 M NaCl and does not have accompanying xylanase activity, hence can be considered as xylanase-free cellulase. Such enzymes from haloarchaea offer great potential for biotechnological application because of their stability at high salinity and is therefore worth pursuing.
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Affiliation(s)
- Alisha D Malik
- Department of Microbiology, Goa University, Taleigao Plateau, Goa, India
| | - Irene J Furtado
- Department of Microbiology, Goa University, Taleigao Plateau, Goa, India
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132
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Fang W, Latgé JP. Microbe Profile: Aspergillus fumigatus: a saprotrophic and opportunistic fungal pathogen. MICROBIOLOGY-SGM 2019; 164:1009-1011. [PMID: 30066670 PMCID: PMC6152418 DOI: 10.1099/mic.0.000651] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aspergillus fumigatus is a saprotrophic fungus that continuously disseminates spores (conidia) into the environment. It is also the most common and opportunistic aerial fungal pathogen, causing allergic and chronic lung pathologies including the fatal invasive aspergillosis in immunocompromised patients. The pathobiology of aspergillosis is complex and depends on the competence of the host immune system. Moreover, A. fumigatus has become a model to study unique features of fungi. This includes the fungal cell wall, which not only acts as a rigid skeleton for protection against hostile environments but also plays significant roles during infection by manipulating the host immune response.
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Affiliation(s)
- Wenxia Fang
- 1National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Nanning, PR China
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133
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Mutations in AraR leading to constitutive expression of arabinolytic genes in Aspergillus niger under derepressing conditions [corrected]. Appl Microbiol Biotechnol 2019; 103:4125-4136. [PMID: 30963207 PMCID: PMC6486530 DOI: 10.1007/s00253-019-09777-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022]
Abstract
The AraR transcription factor of Aspergillus niger encodes a Zn(II)2Cys6 transcription factor required for the induction of genes encoding arabinolytic enzymes. One of the target genes of AraR is abfA, encoding an arabinofuranosidase. The expression of abfA as well as other L-arabinose-induced genes in A. niger requires the presence of L-arabinose or its derivative L-arabitol as an inducer to activate AraR-dependant gene expression. In this study, mutants were isolated that express L-arabinose-induced genes independently of the presence of an inducer under derepressing conditions. To obtain these mutants, a reporter strain was constructed in a ΔcreA background containing the L-arabinose-responsive promoter (PabfA) fused to the acetamidase (amdS) gene. Spores of the ΔcreA PabfA-amdS reporter strain were UV-mutagenized and mutants were obtained by their ability to grow on acetamide without the presence of inducer. From a total of 164 mutants, 15 mutants were identified to contain transacting mutations resulting in high arabinofuranosidase activity in the medium after growth under non-inducing conditions. Sequencing of the araR gene of the 15 constitutive mutants revealed that 14 mutants carried a mutation in AraR. Some mutations were found more than once and in total nine different point mutations were identified in AraR. The AraRN806I point mutation was reintroduced into a parental strain and confirmed that this point mutation leads to inducer-independent expression of AraR target genes. The inducer independent of L-arabinose-induced genes in the AraRN806I mutant was found to be sensitive to carbon catabolite repression, indicating that the CreA-mediated carbon catabolite repression is dominant over the AraRN806I mutant allele. These mutations in AraR provide new opportunities to improve arabinase production in industrial fungal strains.
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134
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Omori WP, Pinheiro DG, Kishi LT, Fernandes CC, Fernandes GC, Gomes-Pepe ES, Pavani CD, Lemos EGDM, Souza JAMD. Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction. Genet Mol Biol 2019; 42:145-150. [PMID: 30856245 PMCID: PMC6428131 DOI: 10.1590/1678-4685-gmb-2017-0376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/10/2018] [Indexed: 02/06/2023] Open
Abstract
The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome of Thermomonospora sp. CIT 1, such as α-amylase, catalase-peroxidases, β-mannanase, and arabinanase, demonstrating the potential of this bacterium to deconstruct the components of starch, lignin, and hemicellulose. In addition, the draft genome of Thermomonospora sp. CIT 1 contains 18 genes that do not share identity with five other species of Thermomonospora, suggesting that this bacterium has different genetic characteristics than those present in genomes reported so far for this genus. These findings add a new dimension to the current understanding of the functional profile of this microorganism that inhabits agro-industrial waste, which may boost new gene discoveries and be of importance for application in the production of bioethanol.
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Affiliation(s)
- Wellington P Omori
- Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Daniel G Pinheiro
- Departamento de Tecnologia, Laboratório de Bioinformática, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Luciano T Kishi
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Camila C Fernandes
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Gabriela C Fernandes
- Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Elisângela S Gomes-Pepe
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Claudio D Pavani
- Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Eliana G de M Lemos
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Jackson A M de Souza
- Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
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135
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Al-Huqail AA, Behiry SI, Salem MZM, Ali HM, Siddiqui MH, Salem AZM. Antifungal, Antibacterial, and Antioxidant Activities of Acacia Saligna (Labill.) H. L. Wendl. Flower Extract: HPLC Analysis of Phenolic and Flavonoid Compounds. Molecules 2019; 24:molecules24040700. [PMID: 30781352 PMCID: PMC6412425 DOI: 10.3390/molecules24040700] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 11/16/2022] Open
Abstract
In this study, for the environmental development, the antifungal, antibacterial, and antioxidant activities of a water extract of flowers from Acacia saligna (Labill.) H. L. Wendl. were evaluated. The extract concentrations were prepared by dissolving them in 10% DMSO. Wood samples of Melia azedarach were treated with water extract, and the antifungal activity was examined at concentrations of 0%, 1%, 2%, and 3% against three mold fungi; Fusarium culmorum MH352452, Rhizoctonia solani MH352450, and Penicillium chrysogenum MH352451 that cause root rot, cankers, and green fruit rot, respectively, isolated from infected Citrus sinensis L. Antibacterial evaluation of the extract was assayed against four phytopathogenic bacteria, including Agrobacterium tumefaciens, Enterobacter cloacae, Erwinia amylovora, and Pectobacterium carotovorum subsp. carotovorum, using the micro-dilution method to determine the minimum inhibitory concentrations (MICs). Further, the antioxidant capacity of the water extract was measured via 2,2'-diphenylpicrylhydrazyl (DPPH). Phenolic and flavonoid compounds in the water extract were analyzed using HPLC: benzoic acid, caffeine, and o-coumaric acid were the most abundant phenolic compounds; while the flavonoid compounds naringenin, quercetin, and kaempferol were identified compared with the standard flavonoid compounds. The antioxidant activity of the water extract in terms of IC50 was considered weak (463.71 μg/mL) compared to the standard used, butylated hydroxytoluene (BHT) (6.26 μg/mL). The MIC values were 200, 300, 300, and 100 µg/mL against the growth of A. tumefaciens, E. cloacae, E. amylovora, and P. carotovorum subsp. carotovorum, respectively, which were lower than the positive control used (Tobramycin 10 μg/disc). By increasing the extract concentration, the percentage inhibition of fungal mycelial was significantly increased compared to the control treatment, especially against P. chrysogenum, suggesting that the use of A. saligna flower extract as an environmentally friendly wood bio-preservative inhibited the growth of molds that cause discoloration of wood and wood products.
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Affiliation(s)
- Asma A Al-Huqail
- Chair of Climate Change, Environmental Development and Vegetation Cover, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Said I Behiry
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt.
| | - Mohamed Z M Salem
- Forestry and Wood Technology Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria 21545, Egypt.
| | - Hayssam M Ali
- Chair of Climate Change, Environmental Development and Vegetation Cover, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
- Timber Trees Research Department, Sabahia Horticulture Research Station, Horticulture Research Institute, Agriculture Research Center, Alexandria 21526, Egypt.
| | - Manzer H Siddiqui
- Chair of Climate Change, Environmental Development and Vegetation Cover, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Abdelfattah Z M Salem
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, 50000 Estado de México, Mexico.
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136
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In vitro biodegradation potential of airborne Aspergilli and Penicillia. Naturwissenschaften 2019; 106:8. [DOI: 10.1007/s00114-019-1603-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/29/2018] [Accepted: 01/29/2019] [Indexed: 01/11/2023]
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137
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Isik Z, Arikan EB, Bouras HD, Dizge N. Bioactive ultrafiltration membrane manufactured from Aspergillus carbonarius M333 filamentous fungi for treatment of real textile wastewater. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.01.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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138
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Kuivanen J, Biz A, Richard P. Microbial hexuronate catabolism in biotechnology. AMB Express 2019; 9:16. [PMID: 30701402 PMCID: PMC6353982 DOI: 10.1186/s13568-019-0737-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
The most abundant hexuronate in plant biomass is D-galacturonate. D-Galacturonate is the main constituent of pectin. Pectin-rich biomass is abundantly available as sugar beet pulp or citrus processing waste and is currently mainly used as cattle feed. Other naturally occurring hexuronates are D-glucuronate, L-guluronate, D-mannuronate and L-iduronate. D-Glucuronate is a constituent of the plant cell wall polysaccharide glucuronoxylan and of the algal polysaccharide ulvan. Ulvan also contains L-iduronate. L-Guluronate and D-mannuronate are the monomers of alginate. These raw materials have the potential to be used as raw material in biotechnology-based production of fuels or chemicals. In this communication, we will review the microbial pathways related to these hexuronates and their potential use in biotechnology.
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139
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Llanos A, Déjean S, Neugnot-Roux V, François JM, Parrou JL. Carbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule. Microb Cell Fact 2019; 18:14. [PMID: 30691469 PMCID: PMC6348686 DOI: 10.1186/s12934-019-1062-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/13/2019] [Indexed: 11/19/2022] Open
Abstract
Background Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities but also the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator. The purpose of this study was to evaluate the specificities of the industrial fungus Talaromyces versatilis, getting clues into the role of XlnR and the importance of glucose repression at the transcriptional level, to provide further levers for cocktail production. Results By studying a set of 62 redundant genes representative of several categories of enzymes, our results underlined the huge plasticity of transcriptional responses when changing nutritional status. As a general trend, the more heterogeneous the substrate, the more efficient to trigger activation. Genetic modifications of xlnR led to significant reorganisation of transcriptional patterns. Just a minimal set of genes actually fitted in a simplistic model of regulation by a transcriptional activator, and this under specific substrates. On the contrary, the diversity of xlnR+ versus ΔxlnR responses illustrated the existence of complex and unpredicted patterns of co-regulated genes that were highly dependent on the culture condition, even between genes that encode members of a functional category of enzymes. They notably revealed a dual, substrate-dependant repressor-activator role of XlnR, with counter-intuitive transcripts regulations that targeted specific genes. About glucose, it appeared as a formal repressive sugar as we observed a massive repression of most genes upon glucose addition to the mycelium grown on wheat straw. However, we also noticed a positive role of this sugar on the basal expression of a few genes, (notably those encoding cellulases), showing again the strong dependence of these regulatory mechanisms upon promoter and nutritional contexts. Conclusions The diversity of transcriptional patterns appeared to be the rule, while common and stable behaviour, both within gene families and with fungal literature, the exception. The setup of a new biotechnological process to reach optimized, if not customized expression patterns of enzymes, hence appeared tricky just relying on published data that can lead, in the best scenario, to approximate trends. We instead encourage preliminary experimental assays, carried out in the context of interest to reassess gene responses, as a mandatory step before thinking in (genetic) strategies for the improvement of enzyme production in fungi.![]() Electronic supplementary material The online version of this article (10.1186/s12934-019-1062-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agustina Llanos
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.,Adisseo France S.A.S, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219-Université de Toulouse; CNRS-UPS, 31062, Toulouse Cedex 9, France
| | | | - Jean M François
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France
| | - Jean-Luc Parrou
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.
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β-Fructofuranosidase and β -D-Fructosyltransferase from New Aspergillus carbonarius PC-4 Strain Isolated from Canned Peach Syrup: Effect of Carbon and Nitrogen Sources on Enzyme Production. ScientificWorldJournal 2019; 2019:6956202. [PMID: 30728756 PMCID: PMC6341271 DOI: 10.1155/2019/6956202] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 11/16/2018] [Accepted: 12/02/2018] [Indexed: 11/17/2022] Open
Abstract
β-fructofuranosidase (invertase) and β-D-fructosyltransferase (FTase) are enzymes used in industrial processes to hydrolyze sucrose aiming to produce inverted sugar syrup or fructooligosaccharides. In this work, a black Aspergillus sp. PC-4 was selected among six filamentous fungi isolated from canned peach syrup which were initially screened for invertase production. Cultivations with pure carbon sources showed that invertase and FTase were produced from glucose and sucrose, but high levels were also obtained from raffinose and inulin. Pineapple crown was the best complex carbon source for invertase (6.71 U/mL after 3 days of cultivation) and FTase production (14.60 U/mL after 5 days of cultivation). Yeast extract and ammonium chloride nitrogen sources provided higher production of invertase (6.80 U/mL and 6.30 U/mL, respectively), whereas ammonium nitrate and soybean protein were the best nitrogen sources for FTase production (24.00 U/mL and 24.90 U/mL, respectively). Fermentation parameters for invertase using yeast extract were YP/S = 536.85 U/g and PP = 1.49 U/g/h. FTase production showed values of YP/S = 2,627.93 U/g and PP = 4.4 U/h using soybean protein. The screening for best culture conditions showed an increase of invertase production values by 5.10-fold after 96 h cultivation compared to initial experiments (fungi bioprospection), while FTase production increased by 14.60-fold (44.40 U/mL) after 168 h cultivation. A. carbonarius PC-4 is a new promising strain for invertase and FTase production from low cost carbon sources, whose synthesized enzymes are suitable for the production of inverted sugar, fructose syrups, and fructooligosaccharides.
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141
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Tiwari S, Verma T. Cellulose as a Potential Feedstock for Cellulose Enzyme Production. Fungal Biol 2019. [DOI: 10.1007/978-3-030-14726-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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142
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International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans. Appl Microbiol Biotechnol 2018; 103:1363-1377. [PMID: 30539259 DOI: 10.1007/s00253-018-9525-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/30/2022]
Abstract
The first global genomic, proteomic, and secondary metabolomic characterization of the filamentous fungus Aspergillus nidulans following growth onboard the International Space Station (ISS) is reported. The investigation included the A. nidulans wild-type and three mutant strains, two of which were genetically engineered to enhance secondary metabolite production. Whole genome sequencing revealed that ISS conditions altered the A. nidulans genome in specific regions. In strain CW12001, which features overexpression of the secondary metabolite global regulator laeA, ISS conditions induced the loss of the laeA stop codon. Differential expression of proteins involved in stress response, carbohydrate metabolic processes, and secondary metabolite biosynthesis was also observed. ISS conditions significantly decreased prenyl xanthone production in the wild-type strain and increased asperthecin production in LO1362 and CW12001, which are deficient in a major DNA repair mechanism. These data provide valuable insights into the adaptation mechanism of A. nidulans to spacecraft environments.
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143
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Ebert B, Birdseye D, Liwanag AJM, Laursen T, Rennie EA, Guo X, Catena M, Rautengarten C, Stonebloom SH, Gluza P, Pidatala VR, Andersen MCF, Cheetamun R, Mortimer JC, Heazlewood JL, Bacic A, Clausen MH, Willats WGT, Scheller HV. The Three Members of the Arabidopsis Glycosyltransferase Family 92 are Functional β-1,4-Galactan Synthases. PLANT & CELL PHYSIOLOGY 2018; 59:2624-2636. [PMID: 30184190 DOI: 10.1093/pcp/pcy180] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/31/2018] [Indexed: 05/18/2023]
Abstract
Pectin is a major component of primary cell walls and performs a plethora of functions crucial for plant growth, development and plant-defense responses. Despite the importance of pectic polysaccharides their biosynthesis is poorly understood. Several genes have been implicated in pectin biosynthesis by mutant analysis, but biochemical activity has been shown for very few. We used reverse genetics and biochemical analysis to study members of Glycosyltransferase Family 92 (GT92) in Arabidopsis thaliana. Biochemical analysis gave detailed insight into the properties of GALS1 (Galactan synthase 1) and showed galactan synthase activity of GALS2 and GALS3. All proteins are responsible for adding galactose onto existing galactose residues attached to the rhamnogalacturonan-I (RG-I) backbone. Significant GALS activity was observed with galactopentaose as acceptor but longer acceptors are favored. Overexpression of the GALS proteins in Arabidopsis resulted in accumulation of unbranched β-1, 4-galactan. Plants in which all three genes were inactivated had no detectable β-1, 4-galactan, and surprisingly these plants exhibited no obvious developmental phenotypes under standard growth conditions. RG-I in the triple mutants retained branching indicating that the initial Gal substitutions on the RG-I backbone are added by enzymes different from GALS.
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Affiliation(s)
- Berit Ebert
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Devon Birdseye
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - April J M Liwanag
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tomas Laursen
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emilie A Rennie
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xiaoyuan Guo
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Michela Catena
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carsten Rautengarten
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Solomon H Stonebloom
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pawel Gluza
- School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Venkataramana R Pidatala
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mathias C F Andersen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Roshan Cheetamun
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Jenny C Mortimer
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Mads H Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - William G T Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik V Scheller
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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144
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Ochoa-Jiménez VA, Berumen-Varela G, Burgara-Estrella A, Orozco-Avitia JA, Ojeda-Contreras ÁJ, Trillo-Hernández EA, Rivera-Domínguez M, Troncoso-Rojas R, Báez-Sañudo R, Datsenka T, Handa AK, Tiznado-Hernández ME. Functional analysis of tomato rhamnogalacturonan lyase gene Solyc11g011300 during fruit development and ripening. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:31-40. [PMID: 30212659 DOI: 10.1016/j.jplph.2018.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Rhamnogalacturonan I (RG-I) is a domain of plant cell wall pectin. The rhamnogalacturonan lyase (RGL) enzyme (EC 4.2.2.23) degrades RG-I by cleaving the α-1,4 glycosidic bonds located between the l-rhamnose and d-galacturonic residues of the main chain. While RGL's biochemical mode of action is well known, its effects on plant physiology remain unclear. To investigate the role of the RGL enzyme in plants, we have expressed the Solyc11g011300 gene under a constitutive promoter (CaMV35S) in tomato cv. 'Ohio 8245' and evaluated the expression of this and other RGL genes, enzymatic activity and alterations in vegetative tissue, and tomato physiology in transformed lines compared to the positive control (plants harboring the pCAMBIA2301 vector) and the isogenic line. The highest expression levels of the Solyc11g011300, Solyc04g076630, and Solyc04g076660 genes were observed in leaves and roots and at 10 and 20 days after anthesis (DAA). Transgenic lines exhibited lower RGL activity in leaves and roots and during fruit ripening, whereas higher activity was observed at 10, 20, and 30 DAA than in the isogenic line and positive control. Both transgenic lines showed a lower number of seeds and fruits, higher root length, and less pollen germination percentage and viability. In red ripe tomatoes, transgenic fruits showed greater firmness, longer shelf life, and reduced shriveling than did the isogenic line. Additionally, a delay of one week in fruit ripening in transgenic fruits was also recorded. Altogether, our data demonstrate that the Solyc11g011300 gene participates in pollen tube germination, fruit firmness, and the fruit senescence phenomena that impact postharvest shelf life.
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Affiliation(s)
- Verónica-Alhelí Ochoa-Jiménez
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico; Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Guillermo Berumen-Varela
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico; Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Alexel Burgara-Estrella
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo, Sonora, 83000, Mexico
| | - Jesús-Antonio Orozco-Avitia
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico
| | - Ángel-Javier Ojeda-Contreras
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico
| | - Eduardo-Antonio Trillo-Hernández
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico
| | - Marisela Rivera-Domínguez
- Coordinación de Ciencia de los Alimentos, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico
| | - Rosalba Troncoso-Rojas
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico
| | - Reginaldo Báez-Sañudo
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico
| | - Tatsiana Datsenka
- Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Avtar K Handa
- Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Martín-Ernesto Tiznado-Hernández
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km. 0.6, Apdo Postal 1735, Hermosillo, Sonora, 83304, Mexico.
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145
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Pavlov IY, Eneyskaya EV, Bobrov KS, Polev DE, Ivanen DR, Kopylov AT, Naryzhny SN, Kulminskaya AA. Comprehensive Analysis of Carbohydrate-Active Enzymes from the Filamentous Fungus Scytalidium candidum 3C. BIOCHEMISTRY (MOSCOW) 2018; 83:1399-1410. [PMID: 30482151 DOI: 10.1134/s000629791811010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Complete enzymatic degradation of plant polysaccharides is a result of combined action of various carbohydrate-active enzymes (CAZymes). In this paper, we demonstrate the potential of the filamentous fungus Scytalidium candidum 3C for processing of plant biomass. Structural annotation of the improved assembly of S. candidum 3C genome and functional annotation of CAZymes revealed putative gene sequences encoding such proteins. A total of 190 CAZyme-encoding genes were identified, including 104 glycoside hydrolases, 52 glycosyltransferases, 28 oxidative enzymes, and 6 carbohydrate esterases. In addition, 14 carbohydrate-binding modules were found. Glycoside hydrolases secreted during the growth of S. candidum 3C in three media were analyzed with a variety of substrates. Mass spectrometry analysis of the fungal culture liquid revealed the presence of peptides identical to 36 glycoside hydrolases, three proteins without known enzymatic function belonging to the same group of families, and 11 oxidative enzymes. The activity of endo-hemicellulases was determined using specially synthesized substrates in which the glycosidic bond between monosaccharide residues was replaced by a thio-linkage. During analysis of the CAZyme profile of S. candidum 3C, four β-xylanases from the GH10 family and two β-glucanases from the GH7 and GH55 families were detected, partially purified, and identified.
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Affiliation(s)
- I Yu Pavlov
- National Research Center "Kurchatov Institute", B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad Region, 188300, Russia
| | - E V Eneyskaya
- National Research Center "Kurchatov Institute", B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad Region, 188300, Russia
| | - K S Bobrov
- National Research Center "Kurchatov Institute", B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad Region, 188300, Russia
| | - D E Polev
- Resource Center for Molecular and Cell Technologies and "Centre Biobank", St. Petersburg State University, Stary Peterhof, St. Petersburg, 198504, Russia.
| | - D R Ivanen
- National Research Center "Kurchatov Institute", B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad Region, 188300, Russia
| | - A T Kopylov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121, Russia
| | - S N Naryzhny
- National Research Center "Kurchatov Institute", B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad Region, 188300, Russia. .,Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121, Russia
| | - A A Kulminskaya
- National Research Center "Kurchatov Institute", B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad Region, 188300, Russia. .,Peter the Great St. Petersburg Polytechnic University, Department of Medical Physics, St. Petersburg, 194021, Russia
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146
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Dong Y, Sun Q, Zhang Y, Wang X, Liu P, Xiao Y, Fang Z. Complete genome of Gongronella sp. w5 provides insight into its relationship with plant. J Biotechnol 2018; 286:1-4. [DOI: 10.1016/j.jbiotec.2018.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
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147
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Berumen-Varela G, Ochoa-Jiménez VA, Burgara-Estrella A, Trillo-Hernández EA, Ojeda-Contreras ÁJ, Orozco-Avitia A, Rivera-Domínguez M, Troncoso-Rojas R, Báez-Sañudo R, Datsenka T, Handa AK, Tiznado-Hernández ME. Functional analysis of a tomato (Solanum lycopersicum L.) rhamnogalacturonan lyase promoter. JOURNAL OF PLANT PHYSIOLOGY 2018; 229:175-184. [PMID: 30121402 DOI: 10.1016/j.jplph.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 06/08/2023]
Abstract
The enzyme rhamnogalacturonan lyase (RGL) cleaves α-1,4 glycosidic bonds located between rhamnose and galacturonic acid residues in the main chain of rhamnogalacturonan-I (RG-I), a component of the plant cell wall polymer pectin. Although the mode of action of RGL is well known, its physiological functions associated with fruit biology are less understood. Here, we generated transgenic tomato plants expressing the β-glucuronidase (GUS) reporter gene under the control of a -504 bp or a -776 bp fragment of the promoter of a tomato RGL gene, Solyc11g011300. GUS enzymatic activity and the expression levels of GUS and Solyc11g011300 were measured in a range of organs and fruit developmental stages. GUS staining was undetectable in leaves and roots, but high GUS enzymatic activity was detected in flowers and red ripe (RR) fruits. Maximal expression levels of Solyc11g011300 were detected at the RR developmental stage. GUS activity was 5-fold higher in flowers expressing GUS driven by the -504 bp RGL promoter fragment (RGFL3::GUS) than in the isogenic line, and 1.7-fold higher when GUS gene was driven by the -776 bp RGL promoter fragment (RGLF2::GUS) or the constitutive CaMV35S promoter. Quantitative real-time polymerase chain reaction analysis showed that the highest expression of GUS was in fruits at 40 days after anthesis, for both promoter fragments. The promoter of Solyc11g011300 is predicted to contain cis-acting elements, and to be active in pollen grains, pollen tubes, flowers and during tomato fruit ripening, suggesting that the Solyc11g011300 promoter is transcriptionally active and organ-specific.
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Affiliation(s)
- Guillermo Berumen-Varela
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México; Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Verónica-Alhelí Ochoa-Jiménez
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México; Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Alexel Burgara-Estrella
- Departamento de Investigación en Física, Universidad de Sonora, Hermosillo, Sonora 83000, Mexico
| | - Eduardo-Antonio Trillo-Hernández
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México
| | - Ángel-Javier Ojeda-Contreras
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México
| | - Antonio Orozco-Avitia
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México
| | - Marisela Rivera-Domínguez
- Coordinación de Ciencia de los Alimentos, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México
| | - Rosalba Troncoso-Rojas
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México
| | - Reginaldo Báez-Sañudo
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México
| | - Tatsiana Datsenka
- Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Avtar K Handa
- Department of Horticulture and Landscape Architecture, Purdue University, 1165 Horticulture Building, West Lafayette, IN, 47907-1165, USA
| | - Martín-Ernesto Tiznado-Hernández
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a la Victoria Km 0.6, Hermosillo, Sonora 83304, México.
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148
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Emri T, Antal K, Riley R, Karányi Z, Miskei M, Orosz E, Baker S, Wiebenga A, de Vries R, Pócsi I. Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance. Stud Mycol 2018; 91:23-36. [PMID: 30425415 PMCID: PMC6231086 DOI: 10.1016/j.simyco.2018.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The contribution of stress protein duplication and deletion events to the evolution of the Aspergilli was studied. We performed a large-scale homology analysis of stress proteins and generated and analysed three stress defence system models based on Saccharomyces cerevisiae, Schizosaccharomyces pombe and Aspergillus nidulans. Although both yeast-based and A. nidulans-based models were suitable to trace evolutionary changes, the A. nidulans-based model performed better in mapping stress protein radiations. The strong Mantel correlation found between the positions of species in the phylogenetic tree on the one hand and either in the A. nidulans-based or S. cerevisiae-based models on the other hand demonstrated that stress protein expansions and reductions contributed significantly to the evolution of the Aspergilli. Interestingly, stress tolerance attributes correlated well with the number of orthologs only for a few stress proteins. Notable examples are Ftr1 iron permease and Fet3 ferro-O2-oxidoreductase, elements of the reductive iron assimilation pathway, in the S. cerevisiae-based model, as well as MpkC, a HogA-like mitogen activated protein kinase in the A. nidulans-based model. In the case of the iron assimilation proteins, the number of orthologs showed a positive correlation with H2O2-induced stress tolerance while the number of MpkC orthologs correlated positively with Congo Red induced cell wall stress, sorbitol induced osmotic stress and H2O2 induced oxidative stress tolerances. For most stress proteins, changes in the number of orthologs did not correlate well with any stress tolerance attributes. As a consequence, stress tolerance patterns of the studied Aspergilli did not correlate with either the sets of stress response proteins in general or with the phylogeny of the species studied. These observations suggest that stress protein duplication and deletion events significantly contributed to the evolution of stress tolerance attributes of Aspergilli. In contrast, there are other processes, which may counterbalance the effects of stress gene duplications or deletions including (i) alterations in the structures of stress proteins leading to changes in their biological activities, (ii) varying biosynthesis of stress proteins, (iii) rewiring stress response regulatory networks or even (iv) acquiring new stress response genes by horizontal gene transfer. All these multilevel changes are indispensable for the successful adaptation of filamentous fungi to altering environmental conditions, especially when these organisms are entering new ecological niches.
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Affiliation(s)
- T. Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
| | - K. Antal
- Department of Zoology, Faculty of Sciences, Eszterházy Károly University, Eszterházy tér 1., H-3300, Eger, Hungary
| | - R. Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Z. Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - M. Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - E. Orosz
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
| | - S.E. Baker
- Environmental Molecular Sciences Division, Earth and Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - A. Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - I. Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
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149
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Bartemes KR, Kita H. Innate and adaptive immune responses to fungi in the airway. J Allergy Clin Immunol 2018; 142:353-363. [PMID: 30080527 PMCID: PMC6083885 DOI: 10.1016/j.jaci.2018.06.015] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Fungi are ubiquitous outdoors and indoors. Exposure, sensitization, or both to fungi are strongly associated with development of asthma and allergic airway diseases. Furthermore, global climate change will likely increase the prevalence of fungi and enhance their antigenicity. Major progress has been made during the past several years regarding our understanding of antifungal immunity. Fungi contain cell-wall molecules, such as β-glucan and chitin, and secrete biologically active proteases and glycosidases. Airway epithelial cells and innate immune cells, such as dendritic cells, are equipped with cell-surface molecules that react to these fungal products, resulting in production of cytokines and proinflammatory mediators. As a result, the adaptive arm of antifungal immunity, including TH1-, TH2-, and TH17-type CD4+ T cells, is established, reinforcing protection against fungal infection and causing detrimental immunopathology in certain subjects. We are only in the beginning stages of understanding the complex biology of fungi and detailed mechanisms of how they activate the immune response that can protect against or drive diseases in human subjects. Here we describe our current understanding with an emphasis on airway allergic immune responses. The gaps in our knowledge and desirable future directions are also discussed.
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Affiliation(s)
- Kathleen R Bartemes
- Division of Allergic Diseases, Department of Internal Medicine, and the Department of Immunology, Mayo Clinic, Rochester, Minn
| | - Hirohito Kita
- Division of Allergic Diseases, Department of Internal Medicine, and the Department of Immunology, Mayo Clinic, Rochester, Minn.
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150
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Saroj P, P M, Narasimhulu K. Characterization of thermophilic fungi producing extracellular lignocellulolytic enzymes for lignocellulosic hydrolysis under solid-state fermentation. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0216-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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