1
|
Ali SS, Alsharbaty MHM, Al-Tohamy R, Naji GA, Elsamahy T, Mahmoud YAG, Kornaros M, Sun J. A review of the fungal polysaccharides as natural biopolymers: Current applications and future perspective. Int J Biol Macromol 2024; 273:132986. [PMID: 38866286 DOI: 10.1016/j.ijbiomac.2024.132986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/14/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
As a unique natural resource, fungi are a sustainable source of lipids, polysaccharides, vitamins, proteins, and other nutrients. As a result, they have beneficial medicinal and nutritional properties. Polysaccharides are among the most significant bioactive components found in fungi. Increasing research has revealed that fungal polysaccharides (FPS) contain a variety of bioactivities, including antitumor, antioxidant, immunomodulatory, anti-inflammatory, hepatoprotective, cardioprotective, and anti-aging properties. However, the exact knowledge about FPS and their applications related to their future possibilities must be thoroughly examined to enhance a better understanding of this sustainable biopolymer source. Therefore, FPS' biological applications and their role in the food and feed industry, agriculture, and cosmetics applications were all discussed in this work. In addition, this review highlighted the mode of action of FPS on human diseases by regulating gut microbiota and discussed the mechanism of FPS as antioxidants in the living cell. The structure-activity connections of FPS were also highlighted and explored. Moreover, future perspectives were listed to pave the way for future studies of FPS applications. Hence, this study can be a scientific foundation for future FPS research and industrial applications.
Collapse
Affiliation(s)
- Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Mohammed H M Alsharbaty
- Department of Prosthodontics, College of Dentistry, University of Baghdad, Baghdad, Iraq; Branch of Prosthodontics, College of Dentistry, University of Al-Ameed, Karbala, Iraq.
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Ghassan A Naji
- Department of Prosthodontics, College of Dentistry, University of Baghdad, Baghdad, Iraq; College of Dentistry, The Iraqia University, Baghdad, Iraq.
| | - Tamer Elsamahy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yehia A-G Mahmoud
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Michael Kornaros
- Department of Chemical Engineering, University of Patras, 1 Karatheodori str, 26504 Patras, Greece.
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| |
Collapse
|
2
|
Zhang T, Li HZ, Li WT, Tian D, Ning YN, Liang X, Tan J, Zhao YH, Luo XM, Feng JX, Zhao S. Kinase POGSK-3β modulates fungal plant polysaccharide-degrading enzyme production and development. Appl Microbiol Biotechnol 2023; 107:3605-3620. [PMID: 37119203 DOI: 10.1007/s00253-023-12548-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
The filamentous fungus Penicillium oxalicum secretes integrative plant polysaccharide-degrading enzymes (PPDEs) applicable to biotechnology. Glycogen synthase kinase-3β (GSK-3β) mediates various cellular processes in eukaryotic cells, but the regulatory mechanisms of PPDE biosynthesis in filamentous fungi remain poorly understood. In this study, POGSK-3β (POX_c04478), a homolog of GSK-3β in P. oxalicum, was characterised using biochemical, microbiological and omics approaches. Knockdown of POGSK-3β in P. oxalicum using a copper-responsive promoter replacement system led to 53.5 - 63.6%, 79.0 - 92.8% and 76.8 - 94.7% decreases in the production of filter paper cellulase, soluble starch-degrading enzyme and raw starch-degrading enzyme, respectively, compared with the parental strain ΔKu70. POGSK-3β promoted mycelial growth and conidiation. Transcriptomic profiling and real-time quantitative reverse transcription PCR analyses revealed that POGSK-3β dynamically regulated the expression of genes encoding major PPDEs, as well as fungal development-associated genes. The results broadened our understanding of the regulatory functions of GKS-3β and provided a promising target for genetic engineering to improve PPDE production in filamentous fungi. KEY POINTS: • The roles of glycogen synthase kinase-3β were investigated in P. oxalicum. • POGSK-3β regulated PPDE production, mycelial growth and conidiation. • POGSK-3β controlled the expression of major PPDE genes and regulatory genes.
Collapse
Affiliation(s)
- Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
- College of Food and Quality Engineering, Nanning University, Nanning, 530200, Guangxi, China
| | - Han-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Wen-Tong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Di Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yuan-Ni Ning
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xue Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Jing Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yan-Hao Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China.
| |
Collapse
|
3
|
Whole genome sequence characterization of Aspergillus terreus ATCC 20541 and genome comparison of the fungi A. terreus. Sci Rep 2023; 13:194. [PMID: 36604572 PMCID: PMC9814666 DOI: 10.1038/s41598-022-27311-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Aspergillus terreus is well-known for lovastatin and itaconic acid production with biomedical and commercial importance. The mechanisms of metabolite formation have been extensively studied to improve their yield through genetic engineering. However, the combined repertoire of carbohydrate-active enzymes (CAZymes), cytochrome P450s (CYP) enzymes, and secondary metabolites (SMs) in the different A. terreus strains has not been well studied yet, especially with respect to the presence of biosynthetic gene clusters (BGCs). Here we present a 30 Mb whole genome sequence of A. terreus ATCC 20541 in which we predicted 10,410 protein-coding genes. We compared the CAZymes, CYPs enzyme, and SMs across eleven A. terreus strains, and the results indicate that all strains have rich pectin degradation enzyme and CYP52 families. The lovastatin BGC of lovI was linked with lovF in A. terreus ATCC 20541, and the phenomenon was not found in the other strains. A. terreus ATCC 20541 lacked a non-ribosomal peptide synthetase (AnaPS) participating in acetylaszonalenin production, which was a conserved protein in the ten other strains. Our results present a comprehensive analysis of CAZymes, CYPs enzyme, and SM diversities in A. terreus strains and will facilitate further research in the function of BGCs associated with valuable SMs.
Collapse
|
4
|
Arentshorst M, Reijngoud J, van Tol DJC, Reid ID, Arendsen Y, Pel HJ, van Peij NNME, Visser J, Punt PJ, Tsang A, Ram AFJ. Utilization of ferulic acid in Aspergillus niger requires the transcription factor FarA and a newly identified Far-like protein (FarD) that lacks the canonical Zn(II) 2Cys 6 domain. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:978845. [PMID: 37746181 PMCID: PMC10512302 DOI: 10.3389/ffunb.2022.978845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/17/2022] [Indexed: 09/26/2023]
Abstract
The feruloyl esterase B gene (faeB) is specifically induced by hydroxycinnamic acids (e.g. ferulic acid, caffeic acid and coumaric acid) but the transcriptional regulation network involved in faeB induction and ferulic acid metabolism has only been partially addressed. To identify transcription factors involved in ferulic acid metabolism we constructed and screened a transcription factor knockout library of 239 Aspergillus niger strains for mutants unable to utilize ferulic acid as a carbon source. The ΔfarA transcription factor mutant, already known to be involved in fatty acid metabolism, could not utilize ferulic acid and other hydroxycinnamic acids. In addition to screening the transcription factor mutant collection, a forward genetic screen was performed to isolate mutants unable to express faeB. For this screen a PfaeB-amdS and PfaeB-lux613 dual reporter strain was engineered. The rationale of the screen is that in this reporter strain ferulic acid induces amdS (acetamidase) expression via the faeB promoter resulting in lethality on fluoro-acetamide. Conidia of this reporter strain were UV-mutagenized and plated on fluoro-acetamide medium in the presence of ferulic acid. Mutants unable to induce faeB are expected to be fluoro-acetamide resistant and can be positively selected for. Using this screen, six fluoro-acetamide resistant mutants were obtained and phenotypically characterized. Three mutants had a phenotype identical to the farA mutant and sequencing the farA gene in these mutants indeed showed mutations in FarA which resulted in inability to growth on ferulic acid as well as on short and long chain fatty acids. The growth phenotype of the other three mutants was similar to the farA mutants in terms of the inability to grow on ferulic acid, but these mutants grew normally on short and long chain fatty acids. The genomes of these three mutants were sequenced and allelic mutations in one particular gene (NRRL3_09145) were found. The protein encoded by NRRL3_09145 shows similarity to the FarA and FarB transcription factors. However, whereas FarA and FarB contain both the Zn(II)2Cys6 domain and a fungal-specific transcription factor domain, the protein encoded by NRRL3_09145 (FarD) lacks the canonical Zn(II)2Cys6 domain and possesses only the fungal specific transcription factor domain.
Collapse
Affiliation(s)
- Mark Arentshorst
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jos Reijngoud
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Daan J. C. van Tol
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Ian D. Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Yvonne Arendsen
- DSM Biosciences and Process Innovation, Center for Biotech Innovation, Delft, Netherlands
| | - Herman J. Pel
- DSM Biosciences and Process Innovation, Center for Biotech Innovation, Delft, Netherlands
| | | | - Jaap Visser
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Fungal Genetics and Technology Consultancy, Wageningen, AJ, Netherlands
| | - Peter J. Punt
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F. J. Ram
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| |
Collapse
|
5
|
Rosolen RR, Aono AH, Almeida DA, Ferreira Filho JA, Horta MAC, De Souza AP. Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1. Front Genet 2022; 13:807243. [PMID: 35281818 PMCID: PMC8912865 DOI: 10.3389/fgene.2022.807243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/04/2022] [Indexed: 12/24/2022] Open
Abstract
Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis of T. harzianum IOC-3844 and T. harzianum CBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences among Trichoderma spp. The results of the T. harzianum strains were compared with those of Trichoderma atroviride CBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed with cre1 or xyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of the cre1 and xyr1 groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts in cre1 and xyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluated T. harzianum strains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related to xyr1 and cre1 differed, suggesting that each T. harzianum strain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluated T. harzianum strains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.
Collapse
Affiliation(s)
- Rafaela Rossi Rosolen
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Déborah Aires Almeida
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Jaire Alves Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Anete Pereira De Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Anete Pereira De Souza,
| |
Collapse
|
6
|
Madhavan A, Arun KB, Sindhu R, Alphonsa Jose A, Pugazhendhi A, Binod P, Sirohi R, Reshmy R, Kumar Awasthi M. Engineering interventions in industrial filamentous fungal cell factories for biomass valorization. BIORESOURCE TECHNOLOGY 2022; 344:126209. [PMID: 34715339 DOI: 10.1016/j.biortech.2021.126209] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 05/15/2023]
Abstract
Filamentous fungi possess versatile capabilities for synthesizing a variety of valuable bio compounds, including enzymes, organic acids and small molecule secondary metabolites. The advancements of genetic and metabolic engineering techniques and the availability of sequenced genomes discovered their potential as expression hosts for recombinant protein production. Remarkably, plant-biomass degrading filamentous fungi show the unique capability to decompose lignocellulose, an extremely recalcitrant biopolymer. The basic biochemical approaches have motivated several industrial processes for lignocellulose biomass valorisation into fermentable sugars and other biochemical for biofuels, biomolecules, and biomaterials. The review gives insight into current trends in engineering filamentous fungi for enzymes, fuels, and chemicals from lignocellulose biomass. This review describes the variety of enzymes and compounds that filamentous fungi produce, engineering of filamentous fungi for biomass valorisation with a special focus on lignocellulolytic enzymes and other bulk chemicals.
Collapse
Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India.
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Anju Alphonsa Jose
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | | | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy & Environmental Sustainability, Lucknow 226001. Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, PR China
| |
Collapse
|
7
|
Aliyu H, Gorte O, Neumann A, Ochsenreither K. Global Transcriptome Profile of the Oleaginous Yeast Saitozyma podzolica DSM 27192 Cultivated in Glucose and Xylose. J Fungi (Basel) 2021; 7:758. [PMID: 34575796 PMCID: PMC8466774 DOI: 10.3390/jof7090758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/08/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022] Open
Abstract
Unlike conventional yeasts, several oleaginous yeasts, including Saitozyma podzolica DSM 27192, possess the innate ability to grow and produce biochemicals from plant-derived lignocellulosic components such as hexose and pentose sugars. To elucidate the genetic basis of S. podzolica growth and lipid production on glucose and xylose, we performed comparative temporal transcriptome analysis using RNA-seq method. Approximately 3.4 and 22.2% of the 10,670 expressed genes were differentially (FDR < 0.05, and log2FC > 1.5) expressed under batch and fed batch modes, respectively. Our analysis revealed that a higher number of sugar transporter genes were significantly overrepresented in xylose relative to glucose-grown cultures. Given the low homology between proteins encoded by most of these genes and those of the well-characterised transporters, it is plausible to conclude that S. podzolica possesses a cache of putatively novel sugar transporters. The analysis also suggests that S. podzolica potentially channels carbon flux from xylose via both the non-oxidative pentose phosphate and potentially via the first steps of the Weimberg pathways to yield xylonic acid. However, only the ATP citrate lyase (ACL) gene showed significant upregulation among the essential oleaginous pathway genes under nitrogen limitation in xylose compared to glucose cultivation. Combined, these findings pave the way toward the design of strategies or the engineering of efficient biomass hydrolysate utilization in S. podzolica for the production of various biochemicals.
Collapse
Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (O.G.); (A.N.)
| | | | | | - Katrin Ochsenreither
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (O.G.); (A.N.)
| |
Collapse
|
8
|
|
9
|
Tanaka M, Gomi K. Induction and Repression of Hydrolase Genes in Aspergillus oryzae. Front Microbiol 2021; 12:677603. [PMID: 34108952 PMCID: PMC8180590 DOI: 10.3389/fmicb.2021.677603] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
The filamentous fungus Aspergillus oryzae, also known as yellow koji mold, produces high levels of hydrolases such as amylolytic and proteolytic enzymes. This property of producing large amounts of hydrolases is one of the reasons why A. oryzae has been used in the production of traditional Japanese fermented foods and beverages. A wide variety of hydrolases produced by A. oryzae have been used in the food industry. The expression of hydrolase genes is induced by the presence of certain substrates, and various transcription factors that regulate such expression have been identified. In contrast, in the presence of glucose, the expression of the glycosyl hydrolase gene is generally repressed by carbon catabolite repression (CCR), which is mediated by the transcription factor CreA and ubiquitination/deubiquitination factors. In this review, we present the current knowledge on the regulation of hydrolase gene expression, including CCR, in A. oryzae.
Collapse
Affiliation(s)
- Mizuki Tanaka
- Biomolecular Engineering Laboratory, School of Food and Nutritional Science, University of Shizuoka, Shizuoka, Japan
| | - Katsuya Gomi
- Laboratory of Fermentation Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| |
Collapse
|
10
|
Najjarzadeh N, Matsakas L, Rova U, Christakopoulos P. How Carbon Source and Degree of Oligosaccharide Polymerization Affect Production of Cellulase-Degrading Enzymes by Fusarium oxysporum f. sp. lycopersici. Front Microbiol 2021; 12:652655. [PMID: 33841380 PMCID: PMC8032549 DOI: 10.3389/fmicb.2021.652655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Cellulases are a group of enzymes responsible for the degradation of cellulose, which is one of the most abundant polymers on Earth. The three main groups of cellulases are endoglucosidases, exoglucosidases, and β-glucosidases; however, the mechanism of induction of these enzymes remains poorly characterized. Cellooligosaccharides are among the main inducers of these enzymes in filamentous fungi, yet it is not clear how their degree of polymerization may affect the strength of induction. In the present study, we investigated the effect of different carbohydrate-based inducers, such as lactose, sophorose, cellooligosaccharides, and xylooligosacharides, characterized by different concentrations and degree of polymerization, on cellulases production by the fungus Fusarium oxysporum f. sp. lycopersici, which is one of the most studied lignocellulose degrading fungi with the ability to consume both cellulose and hemicellulose. Moreover, the effect of carbon source on cellulase induction was assessed by growing the biomass on sucrose or glycerol. Results showed a correlation between induction efficiency and the cellooligosaccharides' concentration and size, as well as the carbon source available. Specifically, cellotetraose was a better inducer when sucrose was the carbon source, while cellobiose yielded a better result on glycerol. These findings can help optimize industrial cellulase production.
Collapse
Affiliation(s)
| | | | | | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| |
Collapse
|
11
|
Reijngoud J, Arentshorst M, Ruijmbeek C, Reid I, Alazi ED, Punt PJ, Tsang A, Ram AFJ. Loss of function of the carbon catabolite repressor CreA leads to low but inducer-independent expression from the feruloyl esterase B promoter in Aspergillus niger. Biotechnol Lett 2021; 43:1323-1336. [PMID: 33738610 PMCID: PMC8197723 DOI: 10.1007/s10529-021-03104-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
Objective
With the aim to decipher the mechanisms involved in the transcriptional regulation of feruloyl esterase encoded by faeB, a genetic screen was performed to isolate A. niger mutants displaying inducer-independent expression from the faeB promoter.
Result PfaeB-amdS and PfaeB-lux dual reporter strains were constructed and used to isolate trans-acting mutants in which the expression of both reporters was increased, based on the ability to grow on acetamide plates and higher luciferase activity, respectively. The genetic screen on the non-inducing carbon source D-fructose yielded in total 111 trans-acting mutants. The genome of one of the mutants was sequenced and revealed several SNPs, including a point mutation in the creA gene encoding a transcription factor known to be involved in carbon catabolite repression. Subsequently, all mutants were analyzed for defects in carbon catabolite repression by determining sensitivity towards allyl alcohol. All except four of the 111 mutants were sensitive to allyl alcohol, indicating that the vast majority of the mutants are defective in carbon catabolite repression. The creA gene of 32 allyl alcohol sensitive mutants was sequenced and 27 of them indeed contained a mutation in the creA gene. Targeted deletion of creA in the reporter strain confirmed that the loss of CreA results in constitutive expression from the faeB promoter. Conclusion
Loss of function of CreA leads to low but inducer-independent expression from the faeB promoter in A. niger. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-021-03104-2.
Collapse
Affiliation(s)
- Jos Reijngoud
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Bioscienz, Goeseelsstraat 10, 4817 MV, Breda, The Netherlands
| | - Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Claudine Ruijmbeek
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Ian Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Ebru Demirci Alazi
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Peter J Punt
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| |
Collapse
|
12
|
Gao L, He X, Guo Y, Wu Z, Zhao J, Liu G, Qu Y. Combinatorial Engineering of Transcriptional Activators in Penicillium oxalicum for Improved Production of Corn-Fiber-Degrading Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2539-2548. [PMID: 33619954 DOI: 10.1021/acs.jafc.0c07659] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Enzymatic conversion of corn fiber to fermentable sugars is beneficial to improving the economic efficiency of corn processing. In this work, the filamentous fungus Penicillium oxalicum was found to secrete enzymes for efficient saccharification of un-pretreated corn fiber. Separate engineering of transcriptional activators ClrB, XlnR, and AraR led to enhanced production of different sets of lignocellulolytic enzymes. Particularly, the enzymes produced by XlnR- and AraR-engineered strains showed a synergistic effect in corn fiber saccharification. Combinatorial engineering of all three activators generated a strain MCAX with 3.1- to 51.0-fold increases in lignocellulolytic enzyme production compared with the parent strain. In addition, the enzymes of strain MCAX released significantly more fermentable sugars from corn fiber than those of the parent strain at the same protein dosage. The results suggest that this strain has potential for on-site production of enzymes for corn fiber saccharification.
Collapse
Affiliation(s)
- Liwei Gao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 11 Keyuanjingsi Road, 266101 Qingdao, China
| | - Xin He
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Yingjie Guo
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Zehua Wu
- Research and Development Department, Shandong Shouguang Juneng Golden Corn Co., Ltd., Anshun Street, Shouguang, 262700 Weifang, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| |
Collapse
|
13
|
|
14
|
Molecular engineering to improve lignocellulosic biomass based applications using filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:73-109. [PMID: 33934853 DOI: 10.1016/bs.aambs.2020.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lignocellulosic biomass is an abundant and renewable resource, and its utilization has become the focus of research and biotechnology applications as a very promising raw material for the production of value-added compounds. Filamentous fungi play an important role in the production of various lignocellulolytic enzymes, while some of them have also been used for the production of important metabolites. However, wild type strains have limited efficiency in enzyme production or metabolic conversion, and therefore many efforts have been made to engineer improved strains. Examples of this are the manipulation of transcriptional regulators and/or promoters of enzyme-encoding genes to increase gene expression, and protein engineering to improve the biochemical characteristics of specific enzymes. This review provides and overview of the applications of filamentous fungi in lignocellulosic biomass based processes and the development and current status of various molecular engineering strategies to improve these processes.
Collapse
|
15
|
Frawley D, Bayram Ö. The pheromone response module, a mitogen-activated protein kinase pathway implicated in the regulation of fungal development, secondary metabolism and pathogenicity. Fungal Genet Biol 2020; 144:103469. [PMID: 32950720 DOI: 10.1016/j.fgb.2020.103469] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
Mitogen-activated protein kinase (MAPK) pathways are highly conserved from yeast to human and are required for the regulation of a multitude of biological processes in eukaryotes. A pentameric MAPK pathway known as the Fus3 pheromone module was initially characterised in Saccharomyces cerevisiae and was shown to regulate cell fusion and sexual development. Individual orthologous pheromone module genes have since been found to be highly conserved in fungal genomes and have been shown to regulate a diverse array of cellular responses, such as cell growth, asexual and sexual development, secondary metabolite production and pathogenicity. However, information regarding the assembly and structure of orthologous pheromone modules, as well as the mechanisms of signalling and their biological significance is limited, specifically in filamentous fungal species. Recent studies have provided insight on the utilization of the pheromone module as a central signalling hub for the co-ordinated regulation of fungal development and secondary metabolite production. Various proteins of this pathway are also known to regulate reproduction and virulence in a range of plant pathogenic fungi. In this review, we discuss recent findings that help elucidate the structure of the pheromone module pathway in a myriad of fungal species and its implications in the control of fungal growth, development, secondary metabolism and pathogenicity.
Collapse
Affiliation(s)
- Dean Frawley
- Biology Department, Callan Building, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Özgür Bayram
- Biology Department, Callan Building, Maynooth University, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
16
|
Li JX, Zhang F, Jiang DD, Li J, Wang FL, Zhang Z, Wang W, Zhao XQ. Diversity of Cellulase-Producing Filamentous Fungi From Tibet and Transcriptomic Analysis of a Superior Cellulase Producer Trichoderma harzianum LZ117. Front Microbiol 2020; 11:1617. [PMID: 32760377 PMCID: PMC7372938 DOI: 10.3389/fmicb.2020.01617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
Filamentous fungi are widely used for producing cellulolytic enzymes to degrade lignocellulosic biomass. Microbial resources from Tibet have received great attention due to the unique geographic and climatic conditions in the Qinghai-Tibet Plateau. However, studies on cellulase producing fungal strains originated from Tibet remain very limited, and so far no studies have been focused on regulation of cellulase production of the specific strains thereof. Here, filamentous fungal strains were isolated from soil, plant, and other environments in Tibet, and cellulase-producing strains were further investigated. A total of 88 filamentous fungal strains were identified, and screening of cellulase-producing fungi revealed that 16 strains affiliated with the genera Penicillium, Trichoderma, Aspergillus, and Talaromyces exhibited varying cellulolytic activities. Among these strains, T. harzianum isolate LZ117 is the most potent producer. Comparative transcriptome analysis using T. harzianum LZ117 and the control strain T. harzianum K223452 cultured on cellulose indicated an intensive modulation of gene transcription related to protein synthesis and quality control. Furthermore, transcription of xyr1 which encodes the global transcriptional activator for cellulase expression was significantly up-regulated. Transcription of cre1 and other predicted repressors controlling cellulase gene expression was decreased in T. harzianum LZ117, which may contribute to enhancing formation of primary cellulases. To our knowledge, this is the first report that the transcription landscape at the early enzyme production stage of T. harzianum was comprehensively described, and detailed analysis on modulation of transporters, regulatory proteins as well as protein synthesis and processing was presented. Our study contributes to increasing the catalog of publicly available transcriptome data from T. harzianum, and provides useful clues for unraveling the biotechnological potential of this species for lignocellulosic biorefinery.
Collapse
Affiliation(s)
- Jia-Xiang Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Jun Li
- R&D Center, JALA Group Co., Shanghai, China
| | | | | | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
17
|
Zhang T, Liu H, Lv B, Li C. Regulating Strategies for Producing Carbohydrate Active Enzymes by Filamentous Fungal Cell Factories. Front Bioeng Biotechnol 2020; 8:691. [PMID: 32733865 PMCID: PMC7360787 DOI: 10.3389/fbioe.2020.00691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
Abstract
Filamentous fungi are important eukaryotic organisms crucial in substrate degradation and carbon cycle on the earth and have been harnessed as cell factories for the production of proteins and other high value-added products in recent decades. As cell factories, filamentous fungi play a crucial role in industrial protein production as both native hosts and heterologous hosts. In this review, the regulation strategies of carbohydrate active enzyme expression at both transcription level and protein level are introduced, and the transcription regulations are highlighted with induction mechanism, signaling pathway, and promoter and transcription factor regulation. Afterward, the regulation strategies in protein level including suitable posttranslational modification, protein secretion enhancement, and protease reduction are also presented. Finally, the challenges and perspectives in this field are discussed. In this way, a comprehensive knowledge regarding carbohydrate active enzyme production regulation at both transcriptional and protein levels is provided with the particular goal of aiding in the practical application of filamentous fungi for industrial protein production.
Collapse
Affiliation(s)
- Teng Zhang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Hu Liu
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| |
Collapse
|
18
|
Díaz GV, Coniglio RO, Alvarenga AE, Zapata PD, Villalba LL, Fonseca MI. Secretomic analysis of cheap enzymatic cocktails of Aspergillus niger LBM 134 grown on cassava bagasse and sugarcane bagasse. Mycologia 2020; 112:663-676. [PMID: 32574526 DOI: 10.1080/00275514.2020.1763707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Currently, agroindustrial wastes are little used for generating value-added products; hence, their use of these waste to produce enzymatic cocktails for the conversion of lignocellulosic biomass to fermentable sugars is a very interesting alternative in the second-generation bioethanol process. The Ascomycota fungus Aspergillus niger LBM 134 produces hydrolytic enzymes in large proportions. In this work, A. niger LBM 134 was grown on sugarcane and cassava bagasses under optimized conditions. To identify the extracellular enzymes involved in the degradation of these agroindustrial wastes, the secretomes of the culture supernatants of the fungus were analyzed and validated by biochemical assays of the enzymatic activities. A. niger LBM 134 secreted higher quantities of xylanases and accessory hemicellulases when it grew on sugarcane bagasse, whereas more cellulases, amylases, and pectinases were secreted when it grew on cassava bagasse. These findings suggest two promising enzyme cocktails for the hydrolysis of lignocellulose carbohydrate polymers to fermentable sugars. These bioinformatic analysis were functional validates through enzymatic biochemical assays that confirm the biotechnological potential of A. niger LBM 134 for the bioconversion of hemicellulosic substrates such as sugarcane and cassava bagasses.
Collapse
Affiliation(s)
- Gabriela Verónica Díaz
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Romina Olga Coniglio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Adriana Elizabet Alvarenga
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - María Isabel Fonseca
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| |
Collapse
|
19
|
Díaz RD, Larrondo LF. A circadian clock in Neurospora crassa functions during plant cell wall deconstruction. Fungal Biol 2020; 124:501-508. [PMID: 32389313 DOI: 10.1016/j.funbio.2020.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 01/24/2023]
Abstract
Circadian clocks are autonomous timers that are believed to confer organisms a selective advantage by enabling processes to occur at appropriate times of the day. In the model fungus Neurospora crassa, 20-40 % of its genes are reported to be under circadian regulation, as assayed in simple sugar media. Although it has been well-described that Neurospora efficiently deconstructs plant cell wall components, little is known regarding the status of the clock when Neurospora grows on cellulosic material, or whether such a clock has an impact on any of the genes involved in this process. Through luciferase-based reporters and fluorescent detection assays, we show that a clock is functioning when Neurospora grows on cellulose-containing wheat straw as the only carbon and nitrogen source. Additionally, we found that the major cellobiohydrolase encoding gene involved in plant cell wall deconstruction, cbh-1, is rhythmically regulated by the Neurospora clock, in a manner that depends on cellulose concentration and on the transcription factor CRE-1, known as a key player in carbon-catabolite repression in this fungus. Our findings are a step towards a more comprehensive understanding on how clock regulation modulates cellulose degradation, and thus Neurospora's physiology.
Collapse
Affiliation(s)
- Rodrigo D Díaz
- Millennium Institute for Integrative Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Luis F Larrondo
- Millennium Institute for Integrative Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile.
| |
Collapse
|
20
|
van Munster JM, Daly P, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Arvas M, Raulo R, Pullan ST, Delmas S, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:69. [PMID: 32313551 PMCID: PMC7155255 DOI: 10.1186/s13068-020-01702-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production. RESULTS We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds. CONCLUSION In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.
Collapse
Affiliation(s)
- Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Manchester Institute of Biotechnology (MIB) & School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present Address: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | | | | | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT Espoo, Finland
| | - Roxane Raulo
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Public Health England, National Infection Service, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, 75005 Paris, France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| |
Collapse
|
21
|
Mäkelä MR, Hildén K, Kowalczyk JE, Hatakka A. Progress and Research Needs of Plant Biomass Degradation by Basidiomycete Fungi. GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
22
|
Gao L, Li S, Xu Y, Xia C, Xu J, Liu J, Qin Y, Song X, Liu G, Qu Y. Mutation of a Conserved Alanine Residue in Transcription Factor AraR Leads to Hyperproduction of α‐l‐Arabinofuranosidases inPenicillium oxalicum. Biotechnol J 2019; 14:e1800643. [DOI: 10.1002/biot.201800643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Liwei Gao
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghai China
| | - Shiying Li
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
| | - Yanning Xu
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
| | - Chengqiang Xia
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
| | - Jiadi Xu
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
- National Glycoengineering Research CenterShandong UniversityQingdao China
| | - Jun Liu
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
| | - Yuqi Qin
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
- National Glycoengineering Research CenterShandong UniversityQingdao China
| | - Xin Song
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
| | - Guodong Liu
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghai China
| | - Yinbo Qu
- State Key Laboratory of Microbial TechnologyShandong University27 Binhai Road 266237 Qingdao China
- National Glycoengineering Research CenterShandong UniversityQingdao China
| |
Collapse
|
23
|
On-site produced and commercially available alkali-active xylanases compared for xylan extraction from sugarcane bagasse. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Xia C, Li Z, Xu Y, Yang P, Gao L, Yan Q, Li S, Wang Y, Qu Y, Song X. Introduction of heterologous transcription factors and their target genes into Penicillium oxalicum leads to increased lignocellulolytic enzyme production. Appl Microbiol Biotechnol 2019; 103:2675-2687. [DOI: 10.1007/s00253-018-09612-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/18/2018] [Accepted: 12/28/2018] [Indexed: 12/16/2022]
|