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Li J, Wiebenga A, Lipzen A, Ng V, Tejomurthula S, Zhang Y, Grigoriev IV, Peng M, de Vries RP. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi. J Fungi (Basel) 2023; 9:860. [PMID: 37623631 PMCID: PMC10455118 DOI: 10.3390/jof9080860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.
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Affiliation(s)
- Jiajia Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Sravanthi Tejomurthula
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Igor V. Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
- Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
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Le Strat Y, Mandin M, Ruiz N, Robiou du Pont T, Ragueneau E, Barnett A, Déléris P, Dumay J. Quantification of Xylanolytic and Cellulolytic Activities of Fungal Strains Isolated from Palmaria palmata to Enhance R-Phycoerythrin Extraction of Palmaria palmata: From Seaweed to Seaweed. Mar Drugs 2023; 21:393. [PMID: 37504924 PMCID: PMC10381405 DOI: 10.3390/md21070393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
R-phycoerythrin (R-PE) can be enzymatically extracted from red seaweeds such as Palmaria palmata. This pigment has numerous applications and is notably known as an antioxidant, antitumoral or anti-inflammatory agent. Enzymes secreted by P. palmata associated fungal strains were assumed to be efficient and adapted for R-PE extraction from this macroalga. The aim of the present study was to quantify both xylanolytic and cellulolytic activities of enzymatic extracts obtained from six Palmaria palmata derived fungal strains. Degradation of P. palmata biomass by fungal enzymatic extracts was also investigated, focused on soluble protein and R-PE extraction. Enzymatic extracts were obtained by solid state fermentation. Macroalgal degradation abilities were evaluated by measuring reducing sugar release using DNS assays. Soluble proteins and R-PE recovery yields were evaluated through bicinchoninic acid and spectrophotometric assays, respectively. Various enzymatic activities were obtained according to fungal isolates up to 978 U/mL for xylanase and 50 U/mL for cellulase. Enzymatic extract allowed high degrading abilities, with four of the six fungal strains assessed exhibiting at least equal results as the commercial enzymes for the reducing sugar release. Similarly, all six strains allowed the same soluble protein extraction yield and four of them led to an improvement of R-PE extraction. R-PE extraction from P. palamata using marine fungal enzymes appeared particularly promising. To the best of our knowledge, this study is the first on the use of enzymes of P. palmata associated fungi in the degradation of its own biomass for biomolecules recovery.
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Affiliation(s)
- Yoran Le Strat
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
| | - Margaux Mandin
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
| | - Nicolas Ruiz
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
| | - Thibaut Robiou du Pont
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
| | - Emilie Ragueneau
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
| | - Alexandre Barnett
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
| | - Paul Déléris
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
| | - Justine Dumay
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, F-44000 Nantes, France
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3
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Peng M, Bervoets S, Chin-A-Woeng T, Granchi Z, Hildén K, Mäkelä MR, de Vries RP. The transcriptomic response of two basidiomycete fungi to plant biomass is modulated by temperature to a different extent. Microbiol Res 2023; 270:127333. [PMID: 36804127 DOI: 10.1016/j.micres.2023.127333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Many fungi show a strong preference for specific habitats and growth conditions. Investigating the molecular mechanisms of fungal adaptation to varying environmental conditions is of great interest to biodiversity research and is important for many industrial applications. In this study, we compared the transcriptome profiles of two previously genome-sequenced white-rot wood-decay fungi, Trametes pubescens and Phlebia centrifuga, during their growth on two common plant biomass substrates (wheat straw and spruce) at two temperatures (15 °C and 25 °C). The results showed that both fungi partially tailored their molecular responses to different types of carbon sources, differentially expressing genes encoding polysaccharide degrading enzymes, transporters, proteases and monooxygenases. Notably, more lignin modification related AA2 genes and cellulose degradation related AA9 genes were differentially expressed in the tested conditions of T. pubescens than P. centrifuga. In addition, we detected more remarkable transcriptome changes to different growth temperature in P. centrifuga than in T. pubescens, which reflected their different ability to adapt to the temperature fluctuations. In P. centrifuga, differentially expressed genes (DEGs) related to temperature response mainly encode protein kinases, trehalose metabolism, carbon metabolic enzymes and glycoside hydrolases, while the main temperature-related DEGs identified in T. pubescens are only the carbon metabolic enzymes and glycoside hydrolases. Our study revealed both conserved and species-specific transcriptome changes during fungal adaptation to a changing environment, improving our understanding of the molecular mechanisms underlying fungal plant biomass conversion at varying temperatures.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Sander Bervoets
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | | | - Zoraide Granchi
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | - Kristiina 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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4
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Silva NMD, Reis GF, Costa FDF, Grisolia ME, Geraldo MR, Lustosa BPR, Lima BJFDS, Weiss VA, de Souza EM, Li R, Song Y, Nascimento MMF, Robl D, Gomes RR, de Hoog GS, Vicente VA. Genome sequencing of Cladophialophora exuberans, a novel candidate for bioremediation of hydrocarbon and heavy metal polluted habitats. Fungal Biol 2023; 127:1032-1042. [PMID: 37142362 DOI: 10.1016/j.funbio.2023.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 05/06/2023]
Abstract
Cladophialophora exuberans is a filamentous fungus related to black yeasts in the order Chaetothyriales. These melanized fungi are known for their 'dual ecology', often occurring in toxic environments and also being frequently involved in human infection. Particularly Cladophialophora exuberans, C. immunda, C. psammophila, and Exophiala mesophila have been described with a pronounced ability to degrade aromatic compounds and xenobiotic volatiles, such as benzene, toluene, ethyl-benzene, and xylene, and are candidates for bioremediation applications. The objective of the present study is the sequencing, assembly, and description of the whole genome of C. exuberans focusing on genes and pathways related to carbon and toxin management, assessing the tolerance and bioremediation of lead and copper, and verifying the presence of genes for metal homeostasis. Genomic evaluations were carried out through a comparison with sibling species including clinical and environmental strains. Tolerance of metals was evaluated via a microdilution method establishing minimum inhibitory (MIC) and fungicidal concentrations (MFC), and agar diffusion assays. Heavy metal bioremediation was evaluated via graphite furnace atomic absorption spectroscopy (GFAAS). The final assembly of C. exuberans comprised 661 contigs, with genome size of 38.10 Mb, coverage of 89.9X and a GC content of 50.8%. In addition, inhibition of growth was shown at concentrations of 1250 ppm for copper and at 625 ppm for lead, using the MIC method. In the agar tests, the strain grew at 2500 ppm of copper and lead. In GFAAS tests, uptake capacities were observed of 89.2% and 95.7% for copper and lead, respectively, after 21 experimental days. This study enabled the annotation of genes involved in heavy metal homeostasis and also contributed to a better understanding of the mechanisms used in tolerance of and adaptation to extreme conditions.
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Affiliation(s)
- Nickolas Menezes da Silva
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Guilherme Fonseca Reis
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Flávia de Fátima Costa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Maria Eduarda Grisolia
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Marlon Roger Geraldo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Bruno Paulo Rodrigues Lustosa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Bruna Jacomel Favoreto de Souza Lima
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Vinicius Almir Weiss
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Ruoyu Li
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China; Research Center for Medical Mycology, Peking University, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China
| | - Yinggai Song
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China; Research Center for Medical Mycology, Peking University, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China
| | | | - Diogo Robl
- Microbiology, Immunology and Parasitology Department, Federal University of Santa Catarina, Florianopolis, Santa Catarina, Brazil
| | - Renata Rodrigues Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - G Sybren de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Vania Aparecida Vicente
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil; Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.
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5
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Li C, Xu Y, Wang Z, Zhu W, Du A. Mixing planting with native tree species reshapes soil fungal community diversity and structure in multi-generational eucalypt plantations in southern China. Front Microbiol 2023; 14:1132875. [PMID: 36910166 PMCID: PMC9994620 DOI: 10.3389/fmicb.2023.1132875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
The continuous planting pattern of eucalypt plantations negatively affects soil quality. A mixed planting pattern using native species implanted in pure plantations has been considered a preferable measure for this problem. However, the impact of this approachon the structure and function of fungal communities is not clear. Here, harvesting sites that had undergone two generations of eucalypt plantations were selected to investigate soil fungal community structure and the co-occurrence network characteristics in response to two silvicultural patterns involving the third generation of eucalypt plantations (E) and mixed plantations of Eucalyptus. urograndis × Cinnamomum. camphora (EC) and E. urograndis × Castanopsis. hystrix (EH). Compared with the first generation of eucalypt plantations (CK), E markedly weakened enzyme activities associated with carbon-, nitrogen-. and phosphorus-cycling. Reduced soil fungal alpha diversity, and elevated the relative abundance of Basidiomycota while decreasing the abundance of Ascomycota. In contrast, EC and EH not only enhanced fungal alpha diversity, but also reshaped fungal composition. At the class level, E caused an enrichment of oligotrophic Agaricomycetes fungi, classified into symbiotroph guild, while EC markedly decreased the abundance of those fungi and increased the abundances of Sordariomycetes, Dothideomycetes, Eurotiomycetes, and Tremellomycetes fungi, which were classified into saprotroph or pathotroph guild. Moreover, fungal network complexity and robustness topological attributes were higher or significantly higher in mixed plantations soils compared with those of pure eucalypt plantation E. Furthermore, fungal diversity, structure, and functional taxa were significantly affected by soil organic matter, pH, total nitrogen, and nitrate nitrogen.
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Affiliation(s)
- Chao Li
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Yuxing Xu
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Zhichao Wang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Wankuan Zhu
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Apeng Du
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
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Stojanović S, Stepanović J, Špirović Trifunović B, Duduk N, Dojnov B, Duduk B, Vujčić Z. Selection of Non-Mycotoxigenic Inulinase Producers in the Group of Black Aspergilli for Use in Food Processing. Food Technol Biotechnol 2022; 60:421-433. [PMID: 36816872 PMCID: PMC9901338 DOI: 10.17113/ftb.60.04.22.7521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Research background Inulinases are used for fructooligosaccharide production and they are of interest for both scientific community and industry. Black aspergilli represent a diverse group of species that has use for enzyme production, in particular some species are known as potent inulinase producers. Finding new potential producers from the environment is as important as improving the production with known strains. Safe use of enzymes produced by aspergilli in food industry is placed ahead of their benefit for inulinase production. Experimental approach Here we show a specific approach to finding/screening of newly isolated fungal inulinase producers that combines a newly developed screening method and an equally important assessment of the toxigenic potential of the fungus. In this study 39 black aspergilli collected from different substrates in Serbia were identified and assessed for inulinase production. Results and conclusions The most common species were Aspergillus tubingensis (51.2%), followed by A. niger (23.1%), A. welwitschiae (23.1%) and A. uvarum (2.6%). The isolates for inulinase production were selected using a cheap and easy, fast and non-hazardous alternative inulinase screening test developed in this work. Enzymatic activity of selected inulinase-producing strains was confirmed spectrophotometrically. Since some A. niger and A. welwitschiae strains are able to produce mycotoxins ochratoxin A (OTA) and fumonisins (FB), the toxigenic potential of selected inulinase producers was assessed analytically and genetically. Fungal enzyme producer can be considered safe for use in food industry only after comparing the results of both approaches for investigating toxic potential, the direct presence of mycotoxins in the enzyme preparation (analytically) and the presence of mycotoxin gene clusters (genetically). In some strains the absence of OTA and FB production capability was molecularly confirmed by the absence of complete or critical parts of biosynthetic gene clusters, respectively. The two best inulinase producers and mycotoxin non-producers (without mycotoxin production capability as additional safety) were selected as potential candidates for further development of enzyme production. Novelty and scientific contribution The presented innovative approach for the selection of potential fungal enzyme producer shows that only non-toxigenic fungi could be considered as useful in food industry. Although this study was done on local isolates, the approach is applicable globally.
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Affiliation(s)
- Sanja Stojanović
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Department of Chemistry, Njegoševa 12, 1100 Belgrade, Republic of Serbia
| | - Jelena Stepanović
- Institute of Pesticides and Environmental Protection, Banatska 31/b, 11080 Belgrade, Republic of Serbia
| | | | - Nataša Duduk
- University of Belgrade, Faculty of Agriculture, Nemanjina 6, 11080 Belgrade, Republic of Serbia
| | - Biljana Dojnov
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Department of Chemistry, Njegoševa 12, 1100 Belgrade, Republic of Serbia,Corresponding author: Phone: +38111328239, Fax: +381112184330, E-mail:
| | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, Banatska 31/b, 11080 Belgrade, Republic of Serbia
| | - Zoran Vujčić
- University of Belgrade, Faculty of Chemistry, Department of Biochemistry, Studentski trg 12-16, 11000 Belgrade, Republic of Serbia
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Yadav K, Dwivedi S, Gupta S, Dubey AK, Singh VK, Tanveer A, Yadav S, Yadav D. Genome mining of Fusarium reveals structural and functional diversity of pectin lyases: a bioinformatics approach. 3 Biotech 2022; 12:261. [PMID: 36082361 PMCID: PMC9445148 DOI: 10.1007/s13205-022-03333-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Pectin lyase (PNL) is an important enzyme of the pectinases group which degrades pectin polymer to 4,5-unsaturated oligogalacturonides by a unique β-elimination mechanism and is used in several industries. The existence of multigene families of pectin lyases has been investigated by mining microbial genomes. In the present study, 52 pectin lyase genes were predicted from sequenced six species of Fusarium, namely F. fujikuroi, F. graminearum, F. proliferatum, F. oxysporum, F. verticillioides and F. virguliforme. These sequences were in silico characterized for several physico-chemical, structural and functional attributes. The translated PNL proteins showed variability with 344-1142 amino acid residues, 35.44-127.41 kDa molecular weight, and pI ranging from 4.63 to 9.28. The aliphatic index ranged from 75.33 to 84.75. Multiple sequence alignment analysis showed several conserved amino acid residues and five distinct groups marked as I, II, III, IV, and V were observed in the phylogenetic tree. The Three-dimensional Structure of five of these PNLs, each representing a distinct group of phylogenetic trees was predicted using I-TASSER Server and validated. The pectin lyase proteins of Fusarium species revealed close similarity with pectin lyase of Aspergillus niger PelA(1IDJ) and PelB(1QCX). Diversity in the structural motifs was observed among Fusarium species with 2 β-sheets, 1 β-hairpin, 7-12 β bulges, 18-25 strands, 6 -11 helices, 1 helix-helix interaction, 32-49 β turns, 2-6 γ turns and 2- 3 disulfide bonds. The unique Pec_lyase domain was uniformly observed among all PNL proteins confirming its identity. The genome-wide mining of Fusarium species was attempted to provide the diversity of PNL genes, which could be explored for diverse applications after performing cloning and expression studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03333-w.
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Affiliation(s)
- Kanchan Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Shruti Dwivedi
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Supriya Gupta
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Amit K. Dubey
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Vinay K. Singh
- Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Aiman Tanveer
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Sangeeta Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
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Barrett K, Zhao H, Hao P, Bacic A, Lange L, Holck J, Meyer AS. Discovery of novel secretome CAZymes from Penicillium sclerotigenum by bioinformatics and explorative proteomics analyses during sweet potato pectin digestion. Front Bioeng Biotechnol 2022; 10:950259. [PMID: 36185449 PMCID: PMC9523869 DOI: 10.3389/fbioe.2022.950259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Novel selective enzymatic refining of sweet potato processing residues requires judicious enzyme selection and enzyme discovery. We prepared a pectinaceous cell wall polysaccharide fraction from sweet potato using an enzymatic a treatment to preserve the natural linkages and substitutions. Polysaccharide composition and linkage analysis data confirmed the pectinaceous polysaccharide fraction to be a rhamnogalacturonan I-rich fraction with a high content of arabinogalactan Type I. We hypothesized that the post-harvest tuber pathogenic fungus Penicillium sclerotigenum would harbor novel enzymes targeting selective sweet potato pectin modification. As part of the study, we also report the first genome sequence of P. sclerotigenum. We incubated the sweet potato pectinaceous fraction with P. sclerotigenum. Using proteomics accompanied by CUPP-bioinformatics analysis, we observed induced expression of 23 pectin-associated degradative enzymes. We also identified six abundantly secreted, induced proteins that do not correspond to known CAZymes, but which we suggest as novel enzymes involved in pectin degradation. For validation, the predicted CUPP grouping of putative CAZymes and the exo-proteome data obtained for P. sclerotigenum during growth on sweet potato pectin were compared with proteomics and transcriptomics data reported previously for pectin-associated CAZymes from Aspergillus niger strain NRRL3. The data infer that P. sclerotigenum has the capacity to express several novel enzymes that may provide novel opportunities for sweet potato pectin modification and valorization of sweet potato starch processing residues. In addition, the methodological approach employed represents an integrative systematic strategy for enzyme discovery.
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Affiliation(s)
- Kristian Barrett
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Pengfei Hao
- La Trobe Institute for Agriculture and Food, La Trobe University, Melbourne, VIC, Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture and Food, La Trobe University, Melbourne, VIC, Australia
| | - Lene Lange
- LLa BioEconomy, Research & Advisory, Valby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anne S. Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- *Correspondence: Anne S. Meyer,
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Liu X, Jiang Y, Liu H, Yuan H, Huang D, Wang T. Research progress and biotechnological applications of feruloyl esterases. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2116277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Xuejun Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Di Huang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
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Marinovíc M, Di Falco M, Aguilar Pontes MV, Gorzsás A, Tsang A, de Vries RP, Mäkelä MR, Hildén K. Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora. Biomolecules 2022; 12:biom12081017. [PMID: 35892327 PMCID: PMC9330253 DOI: 10.3390/biom12081017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them indispensable organisms in the global carbon cycle. In this study, we analyzed the proteomes of two closely related white rot fungi, Obba rivulosa and Gelatoporia subvermispora, during eight-week cultivation on solid spruce wood. Plant cell wall degrading carbohydrate-active enzymes (CAZymes) represented approximately 5% of the total proteins in both species. A core set of orthologous plant cell wall degrading CAZymes was shared between these species on spruce suggesting a conserved plant biomass degradation approach in this clade of basidiomycete fungi. However, differences in time-dependent production of plant cell wall degrading enzymes may be due to differences among initial growth rates of these species on solid spruce wood. The obtained results provide insight into specific enzymes and enzyme sets that are produced during the degradation of solid spruce wood in these fungi. These findings expand the knowledge on enzyme production in nature-mimicking conditions and may contribute to the exploitation of white rot fungi and their enzymes for biotechnological applications.
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Affiliation(s)
- Mila Marinovíc
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada; (M.D.F.); (A.T.)
| | - Maria Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (M.V.A.P.); (R.P.d.V.)
| | - András Gorzsás
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden;
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada; (M.D.F.); (A.T.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (M.V.A.P.); (R.P.d.V.)
| | - Miia R. Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
| | - Kristiina Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
- Correspondence:
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11
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Deletion of AA9 Lytic Polysaccharide Monooxygenases Impacts A. nidulans Secretome and Growth on Lignocellulose. Microbiol Spectr 2022; 10:e0212521. [PMID: 35658600 PMCID: PMC9241910 DOI: 10.1128/spectrum.02125-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, and bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. In Aspergillus nidulans, LPMOs from family AA9 (AnLPMO9s), along with an AA3 cellobiose dehydrogenase (AnCDH1), are cosecreted upon growth on crystalline cellulose and lignocellulosic substrates, indicating their role in the degradation of plant cell wall components. Functional analysis revealed that three target LPMO9s (AnLPMO9C, AnLPMO9F and AnLPMO9G) correspond to cellulose-active enzymes with distinct regioselectivity and activity on cellulose with different proportions of crystalline and amorphous regions. AnLPMO9s deletion and overexpression studies corroborate functional data. The abundantly secreted AnLPMO9F is a major component of the extracellular cellulolytic system, while AnLPMO9G was less abundant and constantly secreted, and acts preferentially on crystalline regions of cellulose, uniquely displaying activity on highly crystalline algae cellulose. Single or double deletion of AnLPMO9s resulted in about 25% reduction in fungal growth on sugarcane straw but not on Avicel, demonstrating the contribution of LPMO9s for the saprophytic fungal lifestyle relies on the degradation of complex lignocellulosic substrates. Although the deletion of AnCDH1 slightly reduced the cellulolytic activity, it did not affect fungal growth indicating the existence of alternative electron donors to LPMOs. Additionally, double or triple knockouts of these enzymes had no accumulative deleterious effect on the cellulolytic activity nor on fungal growth, regardless of the deleted gene. Overexpression of AnLPMO9s in a cellulose-induced secretome background confirmed the importance and applicability of AnLPMO9G to improve lignocellulose saccharification. IMPORTANCE Fungal lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that boost plant biomass degradation in combination with glycoside hydrolases. Secretion of LPMO9s arsenal by Aspergillus nidulans is influenced by the substrate and time of induction. These findings along with the biochemical characterization of novel fungal LPMO9s have implications on our understanding of their concerted action, allowing rational engineering of fungal strains for biotechnological applications such as plant biomass degradation. Additionally, the role of oxidative players in fungal growth on plant biomass was evaluated by deletion and overexpression experiments using a model fungal system.
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12
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Marone MP, Campanari MFZ, Raya FT, Pereira GAG, Carazzolle MF. Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions. PeerJ 2022; 10:e13252. [PMID: 35529479 PMCID: PMC9070324 DOI: 10.7717/peerj.13252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Abstract
Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting point to the study of the potential uses of agaves' fungi as biotechnological tools.
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Affiliation(s)
- Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Fabio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
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13
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Improved saccharification of Chlorella vulgaris biomass by fungal secreted enzymes for bioethanol production. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Buijs VA, Zuijdgeest XCL, Groenewald JZ, Crous PW, de Vries RP. Carbon utilization and growth-inhibition of citrus-colonizing Phyllosticta species. Fungal Biol 2021; 125:815-825. [PMID: 34537177 DOI: 10.1016/j.funbio.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/09/2021] [Accepted: 05/21/2021] [Indexed: 11/15/2022]
Abstract
The genus Phyllosticta includes both endophytic and phytopathogenic species that occur on a broad range of plant hosts, including Citrus. Some pathogenic species cause severe disease, such as Phyllosticta citricarpa, the causal agent of Citrus Black Spot (CBS). In contrast, other species, such as Phyllosticta capitalensis, have an endophytic lifestyle in numerous plant hosts. Carbon utilization capabilities are hypothesized to influence both host range and lifestyle, and are in part determined by the set of Carbohydrate Active Enzyme (CAZyme) encoding genes of a species. In this study, carbon utilization capabilities of five Phyllosticta species were determined, as well as the CAZyme repertoire (CAZome) encoded in their genomes. Little variation was found among species in terms of carbon utilization capabilities and CAZome. However, one of the tested carbon sources, sugar beet pulp (SBP), inhibited growth of the plant pathogens, also when combined with another carbon source, while endophytic species remained unaffected.
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Affiliation(s)
- Valerie A Buijs
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands; Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Xander C L Zuijdgeest
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Johannes Z Groenewald
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Pedro W Crous
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands; Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - 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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Kun RS, Garrigues S, Di Falco M, Tsang A, de Vries RP. Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components. Microb Biotechnol 2021; 14:1683-1698. [PMID: 34114741 PMCID: PMC8313289 DOI: 10.1111/1751-7915.13835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, as well as starch, proteins, lipids and lignin to a lesser extent. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger to assess the relative contribution of the regulators to the utilization of this plant biomass substrate. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on other carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization. Better understanding of the complexity and flexibility of fungal regulatory networks will facilitate the generation of more efficient fungal cell factories that use plant biomass as a substrate.
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Affiliation(s)
- Roland S. Kun
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Sandra Garrigues
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Adrian Tsang
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Ronald P. de Vries
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
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Enhanced Lignocellulolytic Enzyme Activities on Hardwood and Softwood during Interspecific Interactions of White- and Brown-Rot Fungi. J Fungi (Basel) 2021; 7:jof7040265. [PMID: 33807430 PMCID: PMC8065597 DOI: 10.3390/jof7040265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/23/2022] Open
Abstract
Wood decomposition is a sophisticated process where various biocatalysts act simultaneously and synergistically on biopolymers to efficiently break down plant cell walls. In nature, this process depends on the activities of the wood-inhabiting fungal communities that co-exist and interact during wood decay. Wood-decaying fungal species have traditionally been classified as white-rot and brown-rot fungi, which differ in their decay mechanism and enzyme repertoire. To mimic the species interaction during wood decomposition, we have cultivated the white-rot fungus, Bjerkandera adusta, and two brown-rot fungi, Gloeophyllum sepiarium and Antrodia sinuosa, in single and co-cultivations on softwood and hardwood. We compared their extracellular hydrolytic carbohydrate-active and oxidative lignin-degrading enzyme activities and production profiles. The interaction of white-rot and brown-rot species showed enhanced (hemi)cellulase activities on birch and spruce-supplemented cultivations. Based on the enzyme activity profiles, the combination of B. adusta and G. sepiarium facilitated birch wood degradation, whereas B. adusta and A. sinuosa is a promising combination for efficient degradation of spruce wood, showing synergy in β-glucosidase (BGL) and α-galactosidase (AGL) activity. Synergistic BGL and AGL activity was also detected on birch during the interaction of brown-rot species. Our findings indicate that fungal interaction on different woody substrates have an impact on both simultaneous and sequential biocatalytic activities.
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Enzymatic degradation of xyloglucans by Aspergillus species: a comparative view of this genus. Appl Microbiol Biotechnol 2021; 105:2701-2711. [PMID: 33760931 DOI: 10.1007/s00253-021-11236-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/25/2021] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Aspergillus species are closely associated with humanity through fermentation, infectious disease, and mycotoxin contamination of food. Members of this genus produce various enzymes to degrade plant polysaccharides, including starch, cellulose, xylan, and xyloglucan. This review focus on the machinery of the xyloglucan degradation using glycoside hydrolases, such as xyloglucanases, isoprimeverose-producing oligoxyloglucan hydrolases, and α-xylosidases, in Aspergillus species. Some xyloglucan degradation-related glycoside hydrolases are well conserved in this genus; however, other enzymes are not. Cooperative actions of these glycoside hydrolases are crucial for xyloglucan degradation in Aspergillus species. KEY POINTS: •Xyloglucan degradation-related enzymes of Aspergillus species are reviewed. •Each Aspergillus species possesses a different set of glycoside hydrolases. •The machinery of xyloglucan degradation of A. oryzae is overviewed.
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Draft genome of the glucose tolerant β-glucosidase producing rare Aspergillus unguis reveals complete cellulolytic machinery with multiple beta-glucosidase genes. Fungal Genet Biol 2021; 151:103551. [PMID: 33737204 DOI: 10.1016/j.fgb.2021.103551] [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] [Received: 10/29/2020] [Revised: 02/24/2021] [Accepted: 03/07/2021] [Indexed: 11/20/2022]
Abstract
Draft genome sequence of the glucose tolerant beta glucosidase (GT-BGL) producing rare fungus Aspergillus unguis NII 08,123 was generated through Next Generation Sequencing (NGS). The genome size of the fungus was estimated to be 37.1 Mb. A total of 3116 contigs were assembled using SPades, and 15,161 proteins were predicted using AUGUSTUS 3.1. Among them, 13,850 proteins were annotated using UniProt. Distribution of CAZyme genes specifically those encoding lignocellulose degrading enzymes were analyzed and compared with those from the industrial cellulase producer Trichoderma reesei in view of the huge differences in detectable enzyme activities between the fungi, despite the ability of A. unguis to grow on lignocellulose as sole carbon source. Full length gene sequence of the inducible GT-BGL could be identified through tracing back from peptide mass fingerprint. A total of 403 CAZymes were predicted from the genome, which includes 232 glycoside hydrolases (GHs), 12 carbohydrate esterases (CEs), 109 glycosyl transferases (GTs), 15 polysaccharide lyases (PLs), and 35 genes with auxiliary activities (AAs). The high level of zinc finger motif containing transcription factors could possibly hint a tight regulation of the cellulolytic machinery, which may also explain the low cellulase activities even when a complete repertoire of cellulase degrading enzyme genes are present in the fungus.
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19
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Lange L, Barrett K, Meyer AS. New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences. J Fungi (Basel) 2021; 7:jof7030207. [PMID: 33799907 PMCID: PMC8000046 DOI: 10.3390/jof7030207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 11/23/2022] Open
Abstract
Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.
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Affiliation(s)
- Lene Lange
- BioEconomy, Research & Advisory, Copenhagen, 2500 Valby, Denmark;
| | - Kristian Barrett
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
| | - Anne S. Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
- Correspondence: ; Tel.: +45-4525-2600
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20
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Chroumpi T, Peng M, Markillie LM, Mitchell HD, Nicora CD, Hutchinson CM, Paurus V, Tolic N, Clendinen CS, Orr G, Baker SE, Mäkelä MR, de Vries RP. Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates. Front Bioeng Biotechnol 2021; 9:644216. [PMID: 33763411 PMCID: PMC7982397 DOI: 10.3389/fbioe.2021.644216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after the hexose D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.
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Affiliation(s)
- Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Lye Meng Markillie
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hugh D Mitchell
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Chelsea M Hutchinson
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Vanessa Paurus
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nikola Tolic
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Chaevien S Clendinen
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Galya Orr
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott E Baker
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
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21
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Peng M, Khosravi C, Lubbers RJM, Kun RS, Aguilar Pontes MV, Battaglia E, Chen C, Dalhuijsen S, Daly P, Lipzen A, Ng V, Yan J, Wang M, Visser J, Grigoriev IV, Mäkelä MR, de Vries RP. CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner. ACTA ACUST UNITED AC 2021; 7:100050. [PMID: 33778219 PMCID: PMC7985698 DOI: 10.1016/j.tcsw.2021.100050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 12/15/2022]
Abstract
Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Roland S Kun
- 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
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Cindy Chen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Sacha Dalhuijsen
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Juying Yan
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Mei Wang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Igor V Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, United States.,Department of Plant and Microbial Biology, University of California Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - 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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23
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Alvarez-Zúñiga MT, Castañeda García D, Aguilar Osorio G. Effect of different carbon sources on the growth and enzyme production of a toxigenic and a non-toxigenic strain of Aspergillus flavus. Prep Biochem Biotechnol 2020; 51:769-779. [DOI: 10.1080/10826068.2020.1858426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- María Teresa Alvarez-Zúñiga
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
| | - Diana Castañeda García
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
| | - Guillermo Aguilar Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
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24
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Barrett K, Hunt CJ, Lange L, Meyer AS. Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes. Nucleic Acids Res 2020; 48:W110-W115. [PMID: 32406917 PMCID: PMC7319580 DOI: 10.1093/nar/gkaa375] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 11/13/2022] Open
Abstract
The CUPP platform includes a web server for functional annotation and sub-grouping of carbohydrate active enzymes (CAZymes) based on a novel peptide-based similarity assessment algorithm, i.e. protein grouping according to Conserved Unique Peptide Patterns (CUPP). This online platform is open to all users and there is no login requirement. The web server allows the user to perform genome-based annotation of carbohydrate active enzymes to CAZy families, CAZy subfamilies, CUPP groups and EC numbers (function) via assessment of peptide-motifs by CUPP. The web server is intended for functional annotation assessment of the CAZy inventory of prokaryotic and eukaryotic organisms from genomic DNA (up to 30MB compressed) or directly from amino acid sequences (up to 10MB compressed). The custom query sequences are assessed using the CUPP annotation algorithm, and the outcome is displayed in interactive summary result pages of CAZymes. The results displayed allow for inspection of members of the individual CUPP groups and include information about experimentally characterized members. The web server and the other resources on the CUPP platform can be accessed from https://cupp.info.
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Affiliation(s)
- Kristian Barrett
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Cameron J Hunt
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lene Lange
- LLa-BioEconomy, Research & Advisory, 2500 Valby, Denmark
| | - Anne S Meyer
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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25
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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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26
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de Boer C, McGregor NGS, Peterse E, Schröder SP, Florea BI, Jiang J, Reijngoud J, Ram AFJ, van Wezel GP, van der Marel GA, Codée JDC, Overkleeft HS, Davies GJ. Glycosylated cyclophellitol-derived activity-based probes and inhibitors for cellulases. RSC Chem Biol 2020; 1:148-155. [PMID: 34458755 PMCID: PMC8341922 DOI: 10.1039/d0cb00045k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/15/2020] [Indexed: 11/24/2022] Open
Abstract
Cellulases and related β-1,4-glucanases are essential components of lignocellulose-degrading enzyme mixtures. The detection of β-1,4-glucanase activity typically relies on monitoring the breakdown of purified lignocellulose-derived substrates or synthetic chromogenic substrates, limiting the activities which can be detected and complicating the tracing of activity back to specific components within complex enzyme mixtures. As a tool for the rapid detection and identification of β-1,4-glucanases, a series of glycosylated cyclophellitol inhibitors mimicking β-1,4-glucan oligosaccharides have been synthesised. These compounds are highly efficient inhibitors of HiCel7B, a well-known GH7 endo-β-1,4-glucanase. An elaborated activity-based probe facilitated the direct detection and identification of β-1,4-glucanases within a complex fungal secretome without any detectable cross-reactivity with β-d-glucosidases. These probes and inhibitors add valuable new capacity to the growing toolbox of cyclophellitol-derived probes for the activity-based profiling of biomass-degrading enzymes.
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Affiliation(s)
- Casper de Boer
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York Heslington York YO10 5DD UK
| | - Evert Peterse
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Sybrin P Schröder
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Bogdan I Florea
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Jianbing Jiang
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Jos Reijngoud
- Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Arthur F J Ram
- Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Gilles P van Wezel
- Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | | | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York Heslington York YO10 5DD UK
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27
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Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
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Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
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28
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Zeuner B, Thomsen TB, Stringer MA, Krogh KBRM, Meyer AS, Holck J. Comparative Characterization of Aspergillus Pectin Lyases by Discriminative Substrate Degradation Profiling. Front Bioeng Biotechnol 2020; 8:873. [PMID: 32850731 PMCID: PMC7406575 DOI: 10.3389/fbioe.2020.00873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/07/2020] [Indexed: 11/13/2022] Open
Abstract
Fungal genomes often contain several copies of genes that encode carbohydrate active enzymes having similar activity. The copies usually have slight sequence variability, and it has been suggested that the multigenecity represents distinct reaction optima versions of the enzyme. Whether the copies represent differences in substrate attack proficiencies of the enzyme have rarely been considered. The genomes of Aspergillus species encode several pectin lyases (EC 4.2.2.10), which all belong to polysaccharide lyase subfamily PL1_4 in the CAZy database. The enzymes differ in terms of sequence identity and phylogeny, and exhibit structural differences near the active site in their homology models. These enzymes catalyze pectin degradation via eliminative cleavage of the α-(1,4) glycosidic linkages in homogalacturonan with a preference for linkages between methyl-esterified galacturonate residues. This study examines four different pectin lyases (PelB, PelC, PelD, and PelF) encoded by the same Aspergillus sp. (namely A. luchuensis), and further compares two PelA pectin lyases from two related Aspergillus spp. (A. aculeatus and A. tubingensis). We report the phylogeny, enzyme kinetics, and enzymatic degradation profiles of the enzymes' action on apple pectin, citrus pectin, and sugar beet pectin. All the pectin lyases exerted highest reaction rate on apple pectin [degree of methoxylation (DM) 69%, degree of acetylation (DAc) 2%] and lowest reaction rate on sugar beet pectin (DM 56%, DAc 19%). Activity comparison at pH 5-5.5 produced the following ranking: PelB > PelA > PelD > PelF > PelC. The evolution of homogalacturonan-oligomer product profiles during reaction was analyzed by liquid chromatography with mass spectrometry (LC-MS) detection. This analyses revealed subtle differences in the product profiles indicating distinct substrate degradation preferences amongst the enzymes, notably with regard to acetyl substitutions. The LC-MS product profiling analysis thus disclosed that the multigenecity appears to provide the fungus with additional substrate degradation versatility. This product profiling furthermore represents a novel approach to functionally compare pectin-degrading enzymes, which can help explain structure-function relations and reaction properties of disparate copies of carbohydrate active enzymes. A better understanding of the product profiles generated by pectin modifying enzymes has significant implications for targeted pectin modification in food and biorefinery processes.
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Affiliation(s)
- Birgitte Zeuner
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thore Bach Thomsen
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Anne S Meyer
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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29
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Barrett K, Jensen K, Meyer AS, Frisvad JC, Lange L. Fungal secretome profile categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium. Sci Rep 2020; 10:5158. [PMID: 32198418 PMCID: PMC7083838 DOI: 10.1038/s41598-020-61907-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/28/2020] [Indexed: 01/02/2023] Open
Abstract
Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitat-related substrate utilization. Despite its importance for fitness, enzyme secretome composition is not used in fungal classification, since an overarching relationship between CAZyme profiles and fungal phylogeny/taxonomy has not been established. For 465 Ascomycota and Basidiomycota genomes, we predicted CAZyme-secretomes, using a new peptide-based annotation method, Conserved-Unique-Peptide-Patterns, enabling functional prediction directly from sequence. We categorized each enzyme according to CAZy-family and predicted molecular function, hereby obtaining a list of "EC-Function;CAZy-Family" observations. These "Function;Family"-based secretome profiles were compared, using a Yule-dissimilarity scoring algorithm, giving equal consideration to the presence and absence of individual observations. Assessment of "Function;Family" enzyme profile relatedness (EPR) across 465 genomes partitioned Ascomycota from Basidiomycota placing Aspergillus and Penicillium among the Ascomycota. Analogously, we calculated CAZyme "Function;Family" profile-similarities among 95 Aspergillus and Penicillium species to form an alignment-free, EPR-based dendrogram. This revealed a stunning congruence between EPR categorization and phylogenetic/taxonomic grouping of the Aspergilli and Penicillia. Our analysis suggests EPR grouping of fungi to be defined both by "shared presence" and "shared absence" of CAZyme "Function;Family" observations. This finding indicates that CAZymes-secretome evolution is an integral part of fungal speciation, supporting integration of cladogenesis and anagenesis.
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Affiliation(s)
- Kristian Barrett
- Department for Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Kristian Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Anne S Meyer
- Department for Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Jens C Frisvad
- Department for Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800, Lyngby, Denmark.
| | - Lene Lange
- LLa Bioeconomy, Research & Advisory, Karensgade 5, DK-2500, Valby, Denmark
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30
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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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31
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A comparative genomics study of 23 Aspergillus species from section Flavi. Nat Commun 2020; 11:1106. [PMID: 32107379 PMCID: PMC7046712 DOI: 10.1038/s41467-019-14051-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi. Aspergillus fungi classified within the section Flavi include harmful and beneficial species. Here, Kjærbølling et al. analyse the genomes of 23 Flavi species, showing high genetic diversity and potential for synthesis of over 13,700 CAZymes and 1600 secondary metabolites.
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32
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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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Li J, Liu Y, Hai X, Shangguan Z, Deng L. Dynamics of soil microbial C:N:P stoichiometry and its driving mechanisms following natural vegetation restoration after farmland abandonment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133613. [PMID: 31377350 DOI: 10.1016/j.scitotenv.2019.133613] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 05/22/2023]
Abstract
Vegetation restoration after farmland abandonment has increased greatly and is commonly used to improve soil fertility and ecosystem service. Knowledge of soil community-level elemental homeostasis following natural vegetation restoration is specially limited for the abandoned farmlands. This study examined the changes in soil microbial biomass stoichiometry and homeostasis with a chronosequence of 3, 8, 13, 18, 23 and 30 years following natural vegetation restoration since farmland abandonment on the Loess Plateau, China. Vegetation communities, soil properties, microbial communities, and enzyme activities were analyzed to study the drivers on soil microbial C:N:P stoichiometry. The results showed that soil microbial biomass C: N ratios had little change following natural vegetation restoration since farmland abandonment, natural vegetation >23 years had significantly enhanced the microbial biomass C:P and N:P ratios by 26.1%-133.9% and 31.7%-67.4%, respectively. However, microbial biomass C:N, C:P and N:P ratios were constrained following natural vegetation restoration. Vegetation restoration for 30 years enhanced urease and alkaline phosphatase activities by 125.4% and 42.9%, respectively, which showed synchronous changes with N and P contents in microbial biomass. Soil fungi, urease and alkaline phosphatase were the drivers to the changes in microbial C:N:P stoichiometry. The results suggest that long-term vegetation restoration (>23 years) will aggravate microbial P limitation, however, soil microorganism maintained the homeostatic regulation of stoichiometric ratios to mitigate P limitation. Fungi played a strong role in shaping microbial community-level elemental homeostasis and nutrient cycling through releasing N-converting and P-converting enzymes into soil following natural vegetation restoration.
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Affiliation(s)
- Jiwei Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuying Hai
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhouping Shangguan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Deng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Rubio MV, Terrasan CRF, Contesini FJ, Zubieta MP, Gerhardt JA, Oliveira LC, de Souza Schmidt Gonçalves AE, Almeida F, Smith BJ, de Souza GHMF, Dias AHS, Skaf M, Damasio A. Redesigning N-glycosylation sites in a GH3 β-xylosidase improves the enzymatic efficiency. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:269. [PMID: 31754374 PMCID: PMC6854716 DOI: 10.1186/s13068-019-1609-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/04/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND β-Xylosidases are glycoside hydrolases (GHs) that cleave xylooligosaccharides and/or xylobiose into shorter oligosaccharides and xylose. Aspergillus nidulans is an established genetic model and good source of carbohydrate-active enzymes (CAZymes). Most fungal enzymes are N-glycosylated, which influences their secretion, stability, activity, signalization, and protease protection. A greater understanding of the N-glycosylation process would contribute to better address the current bottlenecks in obtaining high secretion yields of fungal proteins for industrial applications. RESULTS In this study, BxlB-a highly secreted GH3 β-xylosidase from A. nidulans, presenting high activity and several N-glycosylation sites-was selected for N-glycosylation engineering. Several glycomutants were designed to investigate the influence of N-glycans on BxlB secretion and function. The non-glycosylated mutant (BxlBnon-glyc) showed similar levels of enzyme secretion and activity compared to the wild-type (BxlBwt), while a partially glycosylated mutant (BxlBN1;5;7) exhibited increased activity. Additionally, there was no enzyme secretion in the mutant in which the N-glycosylation context was changed by the introduction of four new N-glycosylation sites (BxlBCC), despite the high transcript levels. BxlBwt, BxlBnon-glyc, and BxlBN1;5;7 formed similar secondary structures, though the mutants had lower melting temperatures compared to the wild type. Six additional glycomutants were designed based on BxlBN1;5;7, to better understand its increased activity. Among them, the two glycomutants which maintained only two N-glycosylation sites each (BxlBN1;5 and BxlBN5;7) showed improved catalytic efficiency, whereas the other four mutants' catalytic efficiencies were reduced. The N-glycosylation site N5 is important for improved BxlB catalytic efficiency, but needs to be complemented by N1 and/or N7. Molecular dynamics simulations of BxlBnon-glyc and BxlBN1;5 reveals that the mobility pattern of structural elements in the vicinity of the catalytic pocket changes upon N1 and N5 N-glycosylation sites, enhancing substrate binding properties which may underlie the observed differences in catalytic efficiency between BxlBnon-glyc and BxlBN1;5. CONCLUSIONS This study demonstrates the influence of N-glycosylation on A. nidulans BxlB production and function, reinforcing that protein glycoengineering is a promising tool for enhancing thermal stability, secretion, and enzymatic activity. Our report may also support biotechnological applications for N-glycosylation modification of other CAZymes.
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Affiliation(s)
- Marcelo Ventura Rubio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - César Rafael Fanchini Terrasan
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Fabiano Jares Contesini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Mariane Paludetti Zubieta
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Jaqueline Aline Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Leandro Cristante Oliveira
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000 Brazil
| | | | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP 14049-900 Brazil
| | - Bradley Joseph Smith
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Gustavo Henrique Martins Ferreira de Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Artur Hermano Sampaio Dias
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas, SP 13084-862 Brazil
| | - Munir Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas, SP 13084-862 Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
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dos Santos Gomes AC, Falkoski D, Battaglia E, Peng M, Nicolau de Almeida M, Coconi Linares N, Meijnen JP, Visser J, de Vries RP. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:220. [PMID: 31534479 PMCID: PMC6745793 DOI: 10.1186/s13068-019-1556-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Myceliophthora thermophila is a thermophilic ascomycete fungus that is used as a producer of enzyme cocktails used in plant biomass saccharification. Further development of this species as an industrial enzyme factory requires a detailed understanding of its regulatory systems driving the production of plant biomass-degrading enzymes. In this study, we analyzed the function of MtXlr1, an ortholog of the (hemi-)cellulolytic regulator XlnR first identified in another industrially relevant fungus, Aspergillus niger. RESULTS The Mtxlr1 gene was deleted and the resulting strain was compared to the wild type using growth profiling and transcriptomics. The deletion strain was unable to grow on xylan and d-xylose, but showed only a small growth reduction on l-arabinose, and grew similar to the wild type on Avicel and cellulose. These results were supported by the transcriptome analyses which revealed reduction of genes encoding xylan-degrading enzymes, enzymes of the pentose catabolic pathway and putative pentose transporters. In contrast, no or minimal effects were observed for the expression of cellulolytic genes. CONCLUSIONS Myceliophthora thermophila MtXlr1 controls the expression of xylanolytic genes and genes involved in pentose transport and catabolism, but has no significant effects on the production of cellulases. It therefore resembles more the role of its ortholog in Neurospora crassa, rather than the broader role described for this regulator in A. niger and Trichoderma reesei. By revealing the range of genes controlled by MtXlr1, our results provide the basic knowledge for targeted strain improvement by overproducing or constitutively activating this regulator, to further improve the biotechnological value of M. thermophila.
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Affiliation(s)
- Ana Carolina dos Santos Gomes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Daniel Falkoski
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present Address: Novozymes Latin America, Professor Francisco Ribeiro Street 683, Araucária, PR 83707-660 Brazil
| | - Evy Battaglia
- 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
| | - Maira Nicolau de Almeida
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- DuPont Industrial Biosciences, Archimedesweg 30, 2333 CN Leiden, The Netherlands
- Present Address: Federal University of São João del Rei, Praça Dom Helvécio, 74, São João del Rei, Minas Gerais Brazil
| | - Nancy Coconi Linares
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jean-Paul Meijnen
- DuPont Industrial Biosciences, Archimedesweg 30, 2333 CN Leiden, The Netherlands
- Present Address: Dutch DNA Biotech BV, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - 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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da Costa RR, Vreeburg SM, Shik JZ, Aanen DK, Poulsen M. Can interaction specificity in the fungus-farming termite symbiosis be explained by nutritional requirements of the fungal crop? FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Podolsky IA, Seppälä S, Lankiewicz TS, Brown JL, Swift CL, O'Malley MA. Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing. Annu Rev Chem Biomol Eng 2019; 10:105-128. [PMID: 30883214 DOI: 10.1146/annurev-chembioeng-060718-030340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Industrial biotechnology has the potential to decrease our reliance on petroleum for fuel and bio-based chemical production and also enable valorization of waste streams. Anaerobic microorganisms thrive in resource-limited environments and offer an array of novel bioactivities in this regard that could revolutionize biomanufacturing. However, they have not been adopted for widespread industrial use owing to their strict growth requirements, limited number of available strains, difficulty in scale-up, and genetic intractability. This review provides an overview of current and future uses for anaerobes in biotechnology and bioprocessing in the postgenomic era. We focus on the recently characterized anaerobic fungi (Neocallimastigomycota) native to the digestive tract of large herbivores, which possess a trove of enzymes, pathways, transporters, and other biomolecules that can be harnessed for numerous biotechnological applications. Resolving current genetic intractability, scale-up, and cultivation challenges will unlock the potential of these lignocellulolytic fungi and other nonmodel micro-organisms to accelerate bio-based production.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Thomas S Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Candice L Swift
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
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Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation. Biotechnol Adv 2019; 37:107361. [PMID: 30825514 DOI: 10.1016/j.biotechadv.2019.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 12/26/2022]
Abstract
Fungal strain engineering is commonly used in many areas of biotechnology, including the production of plant biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of plant biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.
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The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum. N Biotechnol 2019; 51:57-66. [PMID: 30797054 DOI: 10.1016/j.nbt.2019.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/07/2018] [Accepted: 02/20/2019] [Indexed: 11/22/2022]
Abstract
Guar gum consists mainly of galactomannan and constitutes the endosperm of guar seeds that acts as a reserve polysaccharide for germination. Due to its molecular structure and physical properties, this biopolymer has been considered as one of the most important and widely used gums in industry. However, for many of these applications this (hemi-)cellulosic structure needs to be modified or (partially) depolymerized in order to customize and improve its physicochemical properties. In this study, transcriptome, exoproteome and enzyme activity analyses were employed to decipher the complete enzymatic arsenal for guar gum depolymerization by Aspergillus niger. This multi-omic analysis revealed a set of 46 genes encoding carbohydrate-active enzymes (CAZymes) responding to the presence of guar gum, including CAZymes not only with preferred activity towards galactomannan, but also towards (arabino-)xylan, cellulose, starch and pectin, likely due to trace components in guar gum. This demonstrates that the purity of substrates has a strong effect on the resulting enzyme mixture produced by A. niger and probably by other fungi as well, which has significant implications for the commercial production of fungal enzyme cocktails.
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Abstract
Proteomics is the large-scale analysis of proteins rendered possible by modern mass spectrometry analysis methods capable of identifying thousands of peptides/proteins in a fast high-throughput manner. Here I describe protocols for the preparation of fungal culture protein samples for mass spectrometry-based proteomics analysis including protein sample cleanup, proteolytic digestion, LC-MS/MS separation, and database search protein identification.
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Affiliation(s)
- Marcos Rafael Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
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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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Amoikon TLS, Aké MDF, Djéni NT, Grondin C, Casaregola S, Djè KM. Diversity and enzymatic profiles of indigenous yeasts isolated from three types of palm wines produced in Côte d'Ivoire. J Appl Microbiol 2018; 126:567-579. [PMID: 30418694 DOI: 10.1111/jam.14154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/27/2018] [Accepted: 10/31/2018] [Indexed: 11/28/2022]
Abstract
AIMS To investigate the genotypic diversity and enzymatic activity of yeast flora isolated from spontaneous fermenting saps of various palm trees (Borassus aethiopum, Raphia hookeri, Elaeis guineensis) tapped for palm wines. METHODS AND RESULTS PCR-restriction fragment length polymorphism of ITS-5.8S rDNA combined to 26S rRNA gene and/or the partial ACT1 gene sequencing were applied for yeast characterization, and their enzymatic profiles assessed by using API ZYM kits. Thirteen genera and 23 species were identified, with the highest diversity (14 species) in raffia wine. Saccharomyces cerevisiae was dominant and common to all palm wines. Some potentially pathogenic yeasts were also isolated. The majority of tested strains displayed high amylo-peptidase, phosphatase, β-glucosidase and α-glucosidase activities and esterase activity. CONCLUSIONS Diverse yeast species colonized palm wines, among which some were related to a specific type of wine and the majority of them have the ability to digest starch, sugar, protein or lipid. SIGNIFICANCE AND IMPACT OF THE STUDY This study is a first step in understanding the significance of indigenous yeast flora of palm wines from Côte d'Ivoire. This knowledge is important as a tool for establishing new indigenous yeast collection; which could be used for the product quality improvement and as enzyme sources for biotechnological purposes.
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Affiliation(s)
- T L S Amoikon
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, Abidjan, Côte d'Ivoire.,Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, France
| | - M D F Aké
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, Abidjan, Côte d'Ivoire
| | - N T Djéni
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, Abidjan, Côte d'Ivoire
| | - C Grondin
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, France
| | - S Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, France
| | - K M Djè
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, Abidjan, Côte d'Ivoire
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Zheng F, Liu J, Basit A, Miao T, Jiang W. Insight to Improve α-L-Arabinofuranosidase Productivity in Pichia pastoris and Its Application on Corn Stover Degradation. Front Microbiol 2018; 9:3016. [PMID: 30631307 PMCID: PMC6315152 DOI: 10.3389/fmicb.2018.03016] [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] [Received: 06/08/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022] Open
Abstract
α-L-arabinofuranosidase (ARA) with enhanced specific activity and in large amounts, is needed for a variety of industrial applications. To improve ARA production with engineered methylotrophic yeast Pichia pastoris, a genetically modified ara gene from Aspergillus niger ND-1 was investigated. Through codon optimization and rational replacement of α-factor signal peptide with the native propeptide (MFSRRNLVALGLAATVSA), ARA production was improved from 2.61 ± 0.13 U/mL to 14.37 ± 0.22 U/mL in shaking flask culture (a 5.5-fold increase). Results of N-terminal sequencing showed that secreted active ARA of recombinant strain p-oARA had theoretical initial five amino acids (GPCDI) comparable to the mature sequences of α-oARA (EAEAG) and αp-oARA (NLVAL). The kinetic values have been determined for ARA of recombinant strain p-oARA (Vmax = 747.55 μmol/min/mg, Km = 5.36 mmol/L), optimal activity temperature 60°C and optimal pH 4.0. Scaling up of ARA production by p-oARA in a 7.5-L fermentor resulted in remarkably high extracellular ARA specific activity (479.50 ± 12.83 U/mg) at 168 h, and maximal production rate 164.47 ± 4.40 U/mL. In studies of corn stover degradation activity, degree of synergism for ARA and xylanase was 32.4% and enzymatic hydrolysis yield for ARA + xylanase addition was 15.9% higher than that of commercial cellulase, indicating significant potential of ARA for catalytic conversion of corn stover to fermentable sugars for biofuel production.
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Affiliation(s)
- Fengzhen Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Junquan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Abdul Basit
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wei Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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45
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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46
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Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR. Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nat Genet 2018; 50:1688-1695. [PMID: 30349117 DOI: 10.1038/s41588-018-0246-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/23/2018] [Indexed: 01/27/2023]
Abstract
Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.
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Affiliation(s)
- Tammi C Vesth
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jane L Nybo
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sebastian Theobald
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens C Frisvad
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kristian F Nielsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jakob B Hoof
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julian Brandl
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Amyris, Inc., Emeryville, CA, USA
| | - John M Gladden
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Sandia National Laboratory, Livermore, CA, USA
| | - Pallavi Phatale
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Morten T Nielsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ellen K Lyhne
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin E Kogle
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kimchi Strasser
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Erin McDonnell
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Cindy Chen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Matt Nolan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Jon K Magnuson
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Blake A Simmons
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - 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
| | - Uffe H Mortensen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Scott E Baker
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA. .,Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Mikael R Andersen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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47
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Midorikawa GEO, Correa CL, Noronha EF, Filho EXF, Togawa RC, Costa MMDC, Silva-Junior OB, Grynberg P, Miller RNG. Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse. Front Bioeng Biotechnol 2018; 6:123. [PMID: 30280097 PMCID: PMC6153317 DOI: 10.3389/fbioe.2018.00123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq transcriptome profiling was conducted on a strain of Aspergillus tamarii, efficient in biomass polysaccharide degradation, in order to identify genes encoding proteins involved in plant biomass saccharification. Enzyme production and gene expression was compared following growth in liquid and semi-solid culture with steam-exploded sugarcane bagasse (SB) (1% w/v) and glucose (1% w/v) employed as contrasting sole carbon sources. Enzyme production following growth in liquid minimum medium supplemented with SB resulted in 0.626 and 0.711 UI.mL-1 xylanases after 24 and 48 h incubation, respectively. Transcriptome profiling revealed expression of over 7120 genes, with groups of genes modulated according to solid or semi-solid culture, as well as according to carbon source. Gene ontology analysis of genes expressed following SB hydrolysis revealed enrichment in xyloglucan metabolic process and xylan, pectin and glucan catabolic process, indicating up-regulation of genes involved in xylanase secretion. According to carbohydrate-active enzyme (CAZy) classification, 209 CAZyme-encoding genes were identified with significant differential expression on liquid or semi-solid SB, in comparison to equivalent growth on glucose as carbon source. Up-regulated CAZyme-encoding genes related to cellulases (CelA, CelB, CelC, CelD) and hemicellulases (XynG1, XynG2, XynF1, XylA, AxeA, arabinofuranosidase) showed up to a 10-fold log2FoldChange in expression levels. Five genes from the AA9 (GH61) family, related to lytic polysaccharide monooxygenase (LPMO), were also identified with significant expression up-regulation. The transcription factor gene XlnR, involved in induction of hemicellulases, showed up-regulation on liquid and semi-solid SB culture. Similarly, the gene ClrA, responsible for regulation of cellulases, showed increased expression on liquid SB culture. Over 150 potential transporter genes were also identified with increased expression on liquid and semi-solid SB culture. This first comprehensive analysis of the transcriptome of A. tamarii contributes to our understanding of genes and regulatory systems involved in cellulose and hemicellulose degradation in this fungus, offering potential for application in improved enzymatic cocktail development for plant biomass degradation in biorefinery applications.
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Affiliation(s)
| | - Camila Louly Correa
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | | | | | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
| | | | | | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
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48
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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: 11] [Impact Index Per Article: 1.8] [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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49
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Mäkelä M, DiFalco M, McDonnell E, Nguyen T, Wiebenga A, Hildén K, Peng M, Grigoriev I, Tsang A, de Vries R. Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. Stud Mycol 2018; 91:79-99. [PMID: 30487660 PMCID: PMC6249967 DOI: 10.1016/j.simyco.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.
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Affiliation(s)
- M.R. Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - M. DiFalco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - E. McDonnell
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - T.T.M. Nguyen
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - 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
| | - K. Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - M. Peng
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - I.V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - A. Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - 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
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50
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Regulation of Aspergillus nidulans CreA-Mediated Catabolite Repression by the F-Box Proteins Fbx23 and Fbx47. mBio 2018; 9:mBio.00840-18. [PMID: 29921666 PMCID: PMC6016232 DOI: 10.1128/mbio.00840-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The attachment of one or more ubiquitin molecules by SCF (Skp-Cullin-F-box) complexes to protein substrates targets them for subsequent degradation by the 26S proteasome, allowing the control of numerous cellular processes. Glucose-mediated signaling and subsequent carbon catabolite repression (CCR) are processes relying on the functional regulation of target proteins, ultimately controlling the utilization of this carbon source. In the filamentous fungus Aspergillus nidulans, CCR is mediated by the transcription factor CreA, which modulates the expression of genes encoding biotechnologically relevant enzymes. Although CreA-mediated repression of target genes has been extensively studied, less is known about the regulatory pathways governing CCR and this work aimed at further unravelling these events. The Fbx23 F-box protein was identified as being involved in CCR and the Δfbx23 mutant presented impaired xylanase production under repressing (glucose) and derepressing (xylan) conditions. Mass spectrometry showed that Fbx23 is part of an SCF ubiquitin ligase complex that is bridged via the GskA protein kinase to the CreA-SsnF-RcoA repressor complex, resulting in the degradation of the latter under derepressing conditions. Upon the addition of glucose, CreA dissociates from the ubiquitin ligase complex and is transported into the nucleus. Furthermore, casein kinase is important for CreA function during glucose signaling, although the exact role of phosphorylation in CCR remains to be determined. In summary, this study unraveled novel mechanistic details underlying CreA-mediated CCR and provided a solid basis for studying additional factors involved in carbon source utilization which could prove useful for biotechnological applications.IMPORTANCE The production of biofuels from plant biomass has gained interest in recent years as an environmentally friendly alternative to production from petroleum-based energy sources. Filamentous fungi, which naturally thrive on decaying plant matter, are of particular interest for this process due to their ability to secrete enzymes required for the deconstruction of lignocellulosic material. A major drawback in fungal hydrolytic enzyme production is the repression of the corresponding genes in the presence of glucose, a process known as carbon catabolite repression (CCR). This report provides previously unknown mechanistic insights into CCR through elucidating part of the protein-protein interaction regulatory system that governs the CreA transcriptional regulator in the reference organism Aspergillus nidulans in the presence of glucose and the biotechnologically relevant plant polysaccharide xylan.
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