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Jia J, Tan Y, Gao J, Han J, Shi P, Fang H, Zhao C. Cloning and expression of Neurospora crassa cellobiohydrolase II in Pichia pastoris. Protein Expr Purif 2024; 216:106416. [PMID: 38104790 DOI: 10.1016/j.pep.2023.106416] [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: 09/14/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
A major cellobiohydrolase of Neurospora crassa CBH2 was successfully expressed in Pichia pastoris. The maximum Avicelase activity in shake flask among seven transformants which selected on 4.0 g/L G418 plates was 0.61 U/mL. The optimal pH and temperature for Avicelase activity of the recombinant CBH2 were determined to be 4.8 and 60 °C, respectively. The new CBH2 maintained 63.5 % Avicelase activity in the range of pH 4.0-10.4, and 60.2 % Avicelase activity in the range of 30-90 °C. After incubation at 70-90 °C for 1 h, the Avicelase activity retained 60.5 % of its initial activity. The presence of Zn2+, Ca2+ or Cd2+ enhanced the Avicelase activity of the CBH2, of which Cd2+ at 10 mM causing the highest increase. The recombinant CBH2 was used to enhance the Avicel hydrolysis by improving the exo-exo-synergism between CBH2 and CBH1 in N.crassa cellulase. The enzymatic hydrolysis yield was increased by 38.1 % by adding recombinant CBH2 and CBH1, and the yield was increased by 215.4 % when the temperature is raised to 70 °C. This work provided a CBH2 with broader pH range and better heat resistance, which is a potential enzyme candidate in food, textile, pulp and paper industries, and other industrial fields.
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Affiliation(s)
- Jingsong Jia
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China; Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Yu Tan
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China; Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Jialun Gao
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China; Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Jingjing Han
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China; Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Peng Shi
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Hao Fang
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China; Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chen Zhao
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China; Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China.
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Nogueira KMV, Mendes V, Kamath KS, Cheruku A, Oshiquiri LH, de Paula RG, Carraro C, Pedersoli WR, Pereira LMS, Vieira LC, Steindorff AS, Amirkhani A, McKay MJ, Nevalainen H, Molloy MP, Silva RN. Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei. Microb Cell Fact 2024; 23:22. [PMID: 38229067 DOI: 10.1186/s12934-023-02279-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose breakdown is crucial to induce the signaling cascade that triggers cellulase production. However, the sugar transporters involved in this process in T. reesei remain poorly identified and characterized. RESULTS To address this gap, this study used temporal membrane proteomics analysis to identify five known and nine putative sugar transporters that may be involved in cellulose degradation by T. reesei. Docking analysis pointed out potential ligands for the putative sugar transporter Tr44175. Further functional validation of this transporter was carried out in Saccharomyces cerevisiae. The results showed that Tr44175 transports a variety of sugar molecules, including cellobiose, cellotriose, cellotetraose, and sophorose. CONCLUSION This study has unveiled a transporter Tr44175 capable of transporting cellobiose, cellotriose, cellotetraose, and sophorose. Our study represents the first inventory of T. reesei sugar transportome once exposed to cellulose, offering promising potential targets for strain engineering in the context of bioethanol production.
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Affiliation(s)
- Karoline Maria Vieira Nogueira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Vanessa Mendes
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Karthik Shantharam Kamath
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Anusha Cheruku
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Letícia Harumi Oshiquiri
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria, ES, 29047-105, Brazil
| | - Claudia Carraro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Wellington Ramos Pedersoli
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Lucas Matheus Soares Pereira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Luiz Carlos Vieira
- Department of Molecular and Cell Biology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Helena Nevalainen
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil.
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Zhang Y, Nada B, Baker SE, Evans JE, Tian C, Benz JP, Tamayo E. Unveiling a classical mutant in the context of the GH3 β-glucosidase family in Neurospora crassa. AMB Express 2024; 14:4. [PMID: 38180602 PMCID: PMC10770018 DOI: 10.1186/s13568-023-01658-0] [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: 11/24/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024] Open
Abstract
Classical fungal mutant strains obtained by mutagenesis have helped to elucidate fundamental metabolic pathways in the past. In the filamentous fungus Neurospora crassa, the gluc-1 strain was isolated long ago and characterized by its low level of β-glucosidase activity, which is essential for the degradation of cellulose, the most abundant biopolymer on Earth and the main polymeric component of the plant cell wall. Based on genomic resequencing, we hypothesized that the causative mutation resides in the β-glucosidase gene gh3-3 (bgl6, NCU08755). In this work, growth patterns, enzymatic activities and sugar utilization rates were analyzed in several mutant and overexpression strains related to gluc-1 and gh3-3. In addition, different mutants affected in the degradation and transport of cellobiose were analyzed. While overexpression of gh3-3 led to the recovery of β-glucosidase activity in the gluc-1 mutant, as well as normal utilization of cellobiose, the full gene deletion strain Δgh3-3 was found to behave differently than gluc-1 with lower secreted β-glucosidase activity, indicating a dominant role of the amino acid substitution in the point mutated gh3-3 gene of gluc-1. Our results furthermore confirm that GH3-3 is the major extracellular β-glucosidase in N. crassa and demonstrate that the two cellodextrin transporters CDT-1 and CDT-2 are essential for growth on cellobiose when the three main N. crassa β-glucosidases are absent. Overall, these findings provide valuable insight into the mechanisms of cellulose utilization in filamentous fungi, being an essential step in the efficient production of biorefinable sugars from agricultural and forestry plant biomass.
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Affiliation(s)
- Yuxin Zhang
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Basant Nada
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Scott E Baker
- DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - James E Evans
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - J Philipp Benz
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Elisabeth Tamayo
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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Yu NN, Ketya W, Park G. Intracellular Nitric Oxide and cAMP Are Involved in Cellulolytic Enzyme Production in Neurospora crassa. Int J Mol Sci 2023; 24:ijms24054503. [PMID: 36901932 PMCID: PMC10003064 DOI: 10.3390/ijms24054503] [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: 01/25/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Although molecular regulation of cellulolytic enzyme production in filamentous fungi has been actively explored, the underlying signaling processes in fungal cells are still not clearly understood. In this study, the molecular signaling mechanism regulating cellulase production in Neurospora crassa was investigated. We found that the transcription and extracellular cellulolytic activity of four cellulolytic enzymes (cbh1, gh6-2, gh5-1, and gh3-4) increased in Avicel (microcrystalline cellulose) medium. Intracellular nitric oxide (NO) and reactive oxygen species (ROS) detected by fluorescent dyes were observed in larger areas of fungal hyphae grown in Avicel medium compared to those grown in glucose medium. The transcription of the four cellulolytic enzyme genes in fungal hyphae grown in Avicel medium was significantly decreased and increased after NO was intracellularly removed and extracellularly added, respectively. Furthermore, we found that the cyclic AMP (cAMP) level in fungal cells was significantly decreased after intracellular NO removal, and the addition of cAMP could enhance cellulolytic enzyme activity. Taken together, our data suggest that the increase in intracellular NO in response to cellulose in media may have promoted the transcription of cellulolytic enzymes and participated in the elevation of intracellular cAMP, eventually leading to improved extracellular cellulolytic enzyme activity.
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Affiliation(s)
- Nan-Nan Yu
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Wirinthip Ketya
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Gyungsoon Park
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of Korea
- Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
- Correspondence: ; Tel.: +82-2-940-8324
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Role of the Nitrogen Metabolism Regulator TAM1 in Regulation of Cellulase Gene Expression in Trichoderma reesei. Appl Environ Microbiol 2023; 89:e0142122. [PMID: 36602369 PMCID: PMC9888229 DOI: 10.1128/aem.01421-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The filamentous fungus Trichoderma reesei is one of the most prolific cellulase producers and has been established as a model microorganism for investigating mechanisms modulating eukaryotic gene expression. Identification and functional characterization of transcriptional regulators involved in complex and stringent regulation of cellulase genes are, however, not yet complete. Here, a Zn(II)2Cys6-type transcriptional factor TAM1 that is homologous to Aspergillus nidulans TamA involved in nitrogen metabolism, was found not only to regulate ammonium utilization but also to control cellulase gene expression in T. reesei. Whereas Δtam1 cultivated with peptone as a nitrogen source did not exhibit a growth defect that was observed on ammonium, it was still significantly compromised in cellulase biosynthesis. The absence of TAM1 almost fully abrogated the rapid cellulase gene induction in a resting-cell-inducing system. Overexpression of gdh1 encoding the key ammonium assimilatory enzyme in Δtam1 rescued the growth defect on ammonium but not the defect in cellulase gene expression. Of note, mutation of the Zn(II)2Cys6 DNA-binding motif of TAM1 hardly affected cellulase gene expression, while a truncated ARE1 mutant lacking the C-terminal 12 amino acids that are required for the interaction with TAM1 interfered with cellulase biosynthesis. The defect in cellulase induction of Δtam1 was rescued by overexpression of the key transactivator for cellulase gene, XYR1. Our results thus identify a nitrogen metabolism regulator as a new modulator participating in the regulation of induced cellulase gene expression. IMPORTANCE Transcriptional regulators are able to integrate extracellular nutrient signals and exert a combinatorial control over various metabolic genes. A plethora of such factors therefore constitute a complex regulatory network ensuring rapid and accurate cellular response to acquire and utilize nutrients. Despite the in-depth mechanistic studies of functions of the Zn(II)2Cys6-type transcriptional regulator TamA and its orthologues in nitrogen utilization, their involvement in additional physiological processes remains unknown. In this study, we demonstrated that TAM1 exerts a dual regulatory role in mediating ammonium utilization and induced cellulase production in the well known cellulolytic fungus Trichoderma reesei, suggesting a potentially converged regulatory node between nitrogen utilization and cellulase biosynthesis. This study not only contributes to unveiling the intricate regulatory network underlying cellulase gene expression in cellulolytic fungus but also helps expand our knowledge of fungal strategies to achieve efficient and coordinated nutrient acquisition for rapid propagation.
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Fungal Assisted Valorisation of Polymeric Lignin: Mechanism, Enzymes and Perspectives. Catalysts 2023. [DOI: 10.3390/catal13010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Lignocellulose is considered one of the significant recalcitrant materials and also is difficult to break down because of its complex structure. Different microbes such as bacteria and fungi are responsible for breaking down these complex lignin structures. This article discussed briefly the lignin-degrading bacteria and their critical steps involved in lignin depolymerization. In addition, fungi are regarded as the ideal microorganism for the degradation of lignin because of their highly effective hydrolytic and oxidative enzyme systems for the breakdown of lignocellulosic materials. The white rot fungi, mainly belonging to basidiomycetes, is the main degrader of lignin among various microorganisms. This could be achieved because of the presence of lignolytic enzymes such as laccases, lignin peroxidases, and manganese peroxidases. The significance of the fungi and lignolytic enzyme’s role in lignin depolymerization, along with its mechanism and chemical pathways, are emphasized in this article.
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Identifying the gluc-1 and gluc-2 mutations in Neurospora crassa by genome resequencing. J Genet 2022. [DOI: 10.1007/s12041-022-01394-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Gila BC, Antal K, Birkó Z, Keserű JS, Pócsi I, Emri T. Strategies Shaping the Transcription of Carbohydrate-Active Enzyme Genes in Aspergillus nidulans. J Fungi (Basel) 2022; 8:jof8010079. [PMID: 35050018 PMCID: PMC8780418 DOI: 10.3390/jof8010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose, or arabinogalactan, as well as under carbon-starved conditions. We determined both carbon-stress-specific changes (weak or no carbon source vs. glucose) and carbon-source-specific changes (one type of culture vs. all other cultures). Many CAZyme genes showed carbon-stress-specific and/or carbon-source-specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan-degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan, and xylan-degrading enzyme genes was observed. Fewer upregulated genes, 81 and 107 carbon stress specific, and 6 and 16 carbon source specific, were found on lactose and in carbon-starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed carbon-source-specific upregulation on glucose, and they were enriched in β-1,4-glucanase genes. The behavioral ecological background of these characteristics was evaluated to comprehensively organize our knowledge on CAZyme production, which can lead to developing new strategies to produce enzymes for plant cell wall saccharification.
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Affiliation(s)
- Barnabás Cs. Gila
- Department of Molecular Biotechnology and Microbiology, Faculty of Sciences and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (B.C.G.); (I.P.)
- Doctoral School of Nutrition and Food Sciences, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Károly Antal
- Department of Zoology, Eszterházy Károly Catholic University, Eszterházy tér 1, 3300 Eger, Hungary;
| | - Zsuzsanna Birkó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.B.); (J.S.K.)
| | - Judit Sz. Keserű
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.B.); (J.S.K.)
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Faculty of Sciences and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (B.C.G.); (I.P.)
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Faculty of Sciences and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (B.C.G.); (I.P.)
- Correspondence:
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Duan Y, Katrolia P, Zhong A, Kopparapu NK. Production, purification and characterization of a novel antithrombotic and anticoagulant serine protease from food grade microorganism Neurospora crassa. Prep Biochem Biotechnol 2022; 52:1008-1018. [PMID: 35000560 DOI: 10.1080/10826068.2021.2023824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A novel thrombolytic enzyme was produced by food grade microorganism Neurospora crassa using agro-industrial by-products as substrates. Process parameters were optimized using Plackett-Berman and Box-Benhken design. Under the optimized fermentation conditions, high fibrinolytic activity of 403.59 U/mL was obtained. It was purified with a specific activity of 3572.4 U/mg by ammonium sulfate precipitation and SP Sepharose chromatography. The molecular weight of the enzyme was approximately 32 kDa. It exhibited maximum activity at 40 °C and pH 7.4. Its activity was enhanced by Cu2+, Na+, Zn2+, and completely inhibited by phenylmethanesulfonyl fluoride, soybean trypsin inhibitor, aprotinin, which indicates it could be a serine protease. The enzyme could degrade fibrin clot directly without the need of plasminogen activator, and effectively cleaved Aα, Bβ, γ chains of fibrinogen. It could inhibit the formation of blood clots in vitro and acts as an anticoagulant. Compared to heparin the purified enzyme showed extended anticoagulant activity. Blood clots were dissolved effectively and dissolution rate was increased with time. Based on these results, this novel enzyme has the potential to be developed as a thrombolytic agent.
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Affiliation(s)
- Yajie Duan
- College of Food Science, Southwest University, Chongqing, China
| | - Priti Katrolia
- College of Food Science, Southwest University, Chongqing, China
| | - Ailing Zhong
- College of Food Science, Southwest University, Chongqing, China
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Miao Y, Xia Y, Kong Y, Zhu H, Mei H, Li P, Feng H, Xun W, Xu Z, Zhang N, Liu D, Shen Q, Zhang R. Overcoming diverse homologous recombinations and single chimeric guide RNA competitive inhibition enhances Cas9-based cyclical multiple genes coediting in filamentous fungi. Environ Microbiol 2021; 23:2937-2954. [PMID: 33754479 DOI: 10.1111/1462-2920.15477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/18/2021] [Indexed: 12/26/2022]
Abstract
Deciphering the complex cellular behaviours and advancing the biotechnology applications of filamentous fungi increase the requirement for genetically manipulating a large number of target genes. The current strategies cannot cyclically coedit multiple genes simultaneously. In this study, we firstly revealed the existence of diverse homologous recombination (HR) types in marker-free editing of filamentous fungi, and then, demonstrated that sgRNA efficiency-mediated competitive inhibition resulted in the low integration of multiple genetic sites during coediting, which are the two major obstacles to limit the efficiency of cyclically coediting of multiple genes. To overcome these obstacles, we developed a biased cutting strategy by Cas9 to greatly enhance the desired HR type and applied a new selection marker labelling strategy for multiple donor DNAs, in which only the donor DNA with the lowest sgRNA efficiency was labelled. Combined with these strategies, we successfully developed a convenient method for cyclically coediting multiple genes in different filamentous fungi. In addition, diverse HRs resulted in a useful and convenient one-step approach for gene functional study combining both gene disruption and complementation. This research provided both a useful one-step approach for gene functional study and an efficient strategy for cyclically coediting multiple genes in filamentous fungi.
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Affiliation(s)
- Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanwei Xia
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanqiong Kong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Han Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huiling Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pan Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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11
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Chen Y, Fan X, Zhao X, Shen Y, Xu X, Wei L, Wang W, Wei D. cAMP activates calcium signalling via phospholipase C to regulate cellulase production in the filamentous fungus Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:62. [PMID: 33685506 PMCID: PMC7941909 DOI: 10.1186/s13068-021-01914-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/21/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei is one of the best producers of cellulase and has been widely studied for the production of cellulosic ethanol and bio-based products. We previously reported that Mn2+ and N,N-dimethylformamide (DMF) can stimulate cellulase overexpression via Ca2+ bursts and calcium signalling in T. reesei under cellulase-inducing conditions. To further understand the regulatory networks involved in cellulase overexpression in T. reesei, we characterised the Mn2+/DMF-induced calcium signalling pathway involved in the stimulation of cellulase overexpression. RESULTS We found that Mn2+/DMF stimulation significantly increased the intracellular levels of cAMP in an adenylate cyclase (ACY1)-dependent manner. Deletion of acy1 confirmed that cAMP is crucial for the Mn2+/DMF-stimulated cellulase overexpression in T. reesei. We further revealed that cAMP elevation induces a cytosolic Ca2+ burst, thereby initiating the Ca2+ signal transduction pathway in T. reesei, and that cAMP signalling causes the Ca2+ signalling pathway to regulate cellulase production in T. reesei. Furthermore, using a phospholipase C encoding gene plc-e deletion strain, we showed that the plc-e gene is vital for cellulase overexpression in response to stimulation by both Mn2+ and DMF, and that cAMP induces a Ca2+ burst through PLC-E. CONCLUSIONS The findings of this study reveal the presence of a signal transduction pathway in which Mn2+/DMF stimulation produces cAMP. Increase in the levels of cAMP activates the calcium signalling pathway via phospholipase C to regulate cellulase overexpression under cellulase-inducing conditions. These findings provide insights into the molecular mechanism of the cAMP-PLC-calcium signalling pathway underlying cellulase expression in T. reesei and highlight the potential applications of signal transduction in the regulation of gene expression in fungi.
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Affiliation(s)
- Yumeng Chen
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road , P.O.B. 311, Shanghai, 200237, China
| | - Xingjia Fan
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road , P.O.B. 311, Shanghai, 200237, China
| | - Xinqing 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, 200240, China
| | - Yaling Shen
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road , P.O.B. 311, Shanghai, 200237, China
| | - Xiangyang Xu
- Zaozhuang Jie Nuo Enzyme Co. Ltd., Shandong, China
| | - Liujing Wei
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road , P.O.B. 311, Shanghai, 200237, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road , P.O.B. 311, Shanghai, 200237, China.
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road , P.O.B. 311, Shanghai, 200237, China
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Quantitative Proteome Profiling Reveals Cellobiose-Dependent Protein Processing and Export Pathways for the Lignocellulolytic Response in Neurospora crassa. Appl Environ Microbiol 2020; 86:AEM.00653-20. [PMID: 32471912 DOI: 10.1128/aem.00653-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi are intensively used for producing industrial enzymes, including lignocellulases. Employing insoluble cellulose to induce the production of lignocellulases causes some drawbacks, e.g., a complex fermentation operation, which can be overcome by using soluble inducers such as cellobiose. Here, a triple β-glucosidase mutant of Neurospora crassa, which prevents rapid turnover of cellobiose and thus allows the disaccharide to induce lignocellulases, was applied to profile the proteome responses to cellobiose and cellulose (Avicel). Our results revealed a shared proteomic response to cellobiose and Avicel, whose elements included lignocellulases and cellulolytic product transporters. While the cellulolytic proteins showed a correlated increase in protein and mRNA levels, only a moderate correlation was observed on a proteomic scale between protein and mRNA levels (R 2 = 0.31). Ribosome biogenesis and rRNA processing were significantly overrepresented in the protein set with increased protein but unchanged mRNA abundances in response to Avicel. Ribosome biogenesis, as well as protein processing and protein export, was also enriched in the protein set that showed increased abundance in response to cellobiose. NCU05895, a homolog of yeast CWH43, is potentially involved in transferring a glycosylphosphatidylinositol (GPI) anchor to nascent proteins. This protein showed increased abundance but no significant change in mRNA levels. Disruption of CWH43 resulted in a significant decrease in cellulase activities and secreted protein levels in cultures grown on Avicel, suggesting a positive regulatory role for CWH43 in cellulase production. The findings should have an impact on a systems engineering approach for strain improvement for the production of lignocellulases.IMPORTANCE Lignocellulases are important industrial enzymes for sustainable production of biofuels and bio-products. Insoluble cellulose has been commonly used to induce the production of lignocellulases in filamentous fungi, which causes a difficult fermentation operation and enzyme loss due to adsorption to cellulose. The disadvantages can be overcome by using soluble inducers, such as the disaccharide cellobiose. Quantitative proteome profiling of the model filamentous fungus Neurospora crassa revealed cellobiose-dependent pathways for cellulase production, including protein processing and export. A protein (CWH43) potentially involved in protein processing was found to be a positive regulator of lignocellulase production. The cellobiose-dependent mechanisms provide new opportunities to improve the production of lignocellulases in filamentous fungi.
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13
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Feldman D, Kowbel DJ, Cohen A, Glass NL, Hadar Y, Yarden O. Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:210. [PMID: 31508149 PMCID: PMC6724289 DOI: 10.1186/s13068-019-1550-4] [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: 05/16/2019] [Accepted: 08/24/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Biofuels derived from lignocellulosic biomass are a viable alternative to fossil fuels required for transportation. Following plant biomass pretreatment, the furan derivative furfural is present at concentrations which are inhibitory to yeasts. Detoxification of furfural is thus important for efficient fermentation. Here, we searched for new genetic attributes in the fungus Neurospora crassa that may be linked to furfural tolerance. The fact that furfural is involved in the natural process of sexual spore germination of N. crassa and that this fungus is highly amenable to genetic manipulations makes it a rational candidate for this study. RESULTS Both hypothesis-based and unbiased (random promotor mutagenesis) approaches were performed to identify N. crassa genes associated with the response to furfural. Changes in the transcriptional profile following exposure to furfural revealed that the affected processes were, overall, similar to those observed in Saccharomyces cerevisiae. N. crassa was more tolerant (by ~ 30%) to furfural when carboxymethyl cellulose was the main carbon source as opposed to sucrose, indicative of a link between carbohydrate metabolism and furfural tolerance. We also observed increased tolerance in a Δcre-1 mutant (CRE-1 is a key transcription factor that regulates the ability of fungi to utilize non-preferred carbon sources). In addition, analysis of aldehyde dehydrogenase mutants showed that ahd-2 (NCU00378) was involved in tolerance to furfural as well as the predicted membrane transporter NCU05580 (flr-1), a homolog of FLR1 in S. cerevisiae. Further to the rational screening, an unbiased approach revealed additional genes whose inactivation conferred increased tolerance to furfural: (i) NCU02488, which affected the abundance of the non-anchored cell wall protein NCW-1 (NCU05137), and (ii) the zinc finger protein NCU01407. CONCLUSIONS We identified attributes in N. crassa associated with tolerance or degradation of furfural, using complementary research approaches. The manipulation of the genes involved in furan sensitivity can provide a means for improving the production of biofuel producing strains. Similar research approaches can be utilized in N. crassa and other filamentous fungi to identify additional attributes relevant to other furans or toxic chemicals.
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Affiliation(s)
- Daria Feldman
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
| | - David J. Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Adi Cohen
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
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Wang L, Yang R, Cao Y, Zheng F, Meng X, Zhong Y, Chen G, Zhang W, Liu W. CLP1, a Novel Plant Homeo Domain Protein, Participates in Regulating Cellulase Gene Expression in the Filamentous Fungus Trichoderma reesei. Front Microbiol 2019; 10:1700. [PMID: 31447796 PMCID: PMC6691364 DOI: 10.3389/fmicb.2019.01700] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023] Open
Abstract
The stringent regulatory network of cellulase gene expression in the filamentous fungus Trichoderma reesei involves multiple transcriptional regulators. However, identification and mechanistic investigation of these regulators are still insufficient. Here, we identified a novel transcriptional regulator, CLP1, a plant homeo domain (PHD) Protein that participates in regulating T. reesei cellulase gene expression. Phylogenetic analyses demonstrated that CLP1 homologs are widely distributed in filamentous fungi including Trichoderma, Penicillium, Fusarium, Neurospora, and Aspergillus species. We demonstrated that CLP1 is a nuclear protein and lack of CLP1 significantly impaired the induced expression of cellulase genes. ChIP experiments showed CLP1 binding to the cellulase gene promoters specifically under cellulose conditions and compromised XYR1 occupancy on the same promoters in the absence of CLP1 at the early induction stage. XYR1 overexpression fully rescued the defect in cellulase production but not the defect in conidia formation in the clp1 null mutant. Further analysis showed that the PHD is required for the CLP1 appropriate subcellular localization as well as the induced cellulase gene expression and conidiation. Taken together, these data demonstrated an important role of CLP1 in the regulation of cellulase and xylanase gene expression in T. reesei.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Renfei Yang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yanli Cao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Fanglin Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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15
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A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei. mSystems 2019; 4:4/4/e00161-19. [PMID: 31213522 PMCID: PMC6581689 DOI: 10.1128/msystems.00161-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression of these genes in response to two different cellulose sources. In vivo experimental validation confirmed the role of this new regulator in several other processes related to carbon source utilization and nutrient transport. Therefore, this work revealed novel forms of regulatory interaction in this model system for plant biomass deconstruction and also represented a new approach that could be easy applied to other organisms. Filamentous fungi are remarkable producers of enzymes dedicated to the degradation of sugar polymers found in the plant cell wall. Here, we integrated transcriptomic data to identify novel transcription factors (TFs) related to the control of gene expression of lignocellulosic hydrolases in Trichoderma reesei and Aspergillus nidulans. Using various sets of differentially expressed genes, we identified some putative cis-regulatory elements that were related to known binding sites for Saccharomyces cerevisiae TFs. Comparative genomics allowed the identification of six transcriptional factors in filamentous fungi that have corresponding S. cerevisiae homologs. Additionally, a knockout strain of T. reesei lacking one of these TFs (S. cerevisiaeAZF1 homolog) displayed strong reductions in the levels of expression of several cellulase-encoding genes in response to both Avicel and sugarcane bagasse, revealing a new player in the complex regulatory network operating in filamentous fungi during plant biomass degradation. Finally, RNA sequencing (RNA-seq) analysis showed the scope of the AZF1 homologue in regulating a number of processes in T. reesei, and chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) provided evidence for the direct interaction of this TF in the promoter regions of cel7a, cel45a, and swo. Therefore, we identified here a novel TF which plays a positive effect in the expression of cellulase-encoding genes in T. reesei. IMPORTANCE In this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression of these genes in response to two different cellulose sources. In vivo experimental validation confirmed the role of this new regulator in several other processes related to carbon source utilization and nutrient transport. Therefore, this work revealed novel forms of regulatory interaction in this model system for plant biomass deconstruction and also represented a new approach that could be easy applied to other organisms.
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16
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Yang J, Deng L, Zhao C, Fang H. Heterologous expression of Neurospora crassa cbh1 gene in Pichia pastoris resulted in production of a neutral cellobiohydrolase I. Biotechnol Prog 2019; 35:e2795. [PMID: 30816014 DOI: 10.1002/btpr.2795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 01/14/2019] [Accepted: 02/20/2019] [Indexed: 11/10/2022]
Abstract
The high production cost of cellulase is one of the limitations that hinder the commercialization of lignocellulose-based biorefineries. As one of the important cellulases, Neurospora crassa cellulase is not so intensively investigated as T. reesei cellulase. In this study, the cbh1gene (NCU07340) cloned from N. crassa was expressed in Pichia pastoris under the control of alcohol oxidase 1 (AOX1) promotor. Six transformants with the highest resistance to G418 were selected by two rounds of transformant screening, among which the most robust producer of the recombinant cellobiohydrolase I (CBHI) has an Avicelase activity of 0.22 U/mL. After fermentation optimization, it was improved to 0.30 U/mL. Interestingly, the optimal temperature and pH of the recombinant CBHI were 60°C and 7.2, respectively, and it was quite stable within the wide ranges of temperature and pH. This work is a good example for the future improvement and optimization of N. crassa cellulase.
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Affiliation(s)
- Jie Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.,Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, Yangling, Shaanxi, China
| | - Lu Deng
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.,Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, Yangling, Shaanxi, China
| | - Chen Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.,Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, Yangling, Shaanxi, China
| | - Hao Fang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.,Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, Yangling, Shaanxi, China
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17
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Liu Q, Li J, Gao R, Li J, Ma G, Tian C. CLR-4, a novel conserved transcription factor for cellulase gene expression in ascomycete fungi. Mol Microbiol 2018; 111:373-394. [DOI: 10.1111/mmi.14160] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Ranran Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Jinyang Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Guoli Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 China
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18
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Jagadeeswaran G, Gainey L, Mort AJ. An AA9-LPMO containing a CBM1 domain in Aspergillus nidulans is active on cellulose and cleaves cello-oligosaccharides. AMB Express 2018; 8:171. [PMID: 30328527 PMCID: PMC6192940 DOI: 10.1186/s13568-018-0701-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/10/2018] [Indexed: 11/14/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper dependent enzymes that carry out oxidative cleavage of cellulose and other polysaccharides. Aspergillus nidulans, an ascomycete fungus that contains multiple AA9 LPMOs in the genome, offers an excellent model system to study their activity during the oxidative degradation of biomass. AN1602, a dual domain AA9-LPMO in A. nidulans appended with a carbohydrate-binding module, CBM1, was expressed in Pichia pastoris for analyzing oxidative cleavage on cellulosic substrates. The mass spectral and HPAEC analyses showed that the enzyme cleaves phosphoric acid swollen cellulose (PASC) in the presence of a reducing agent, yielding a range of cello-oligosaccharides. In addition to the polymeric substrate cellulose, AN1602 is also active on soluble cellohexaose, a property that is restricted to only a few characterized LPMOs. Product analysis of AN1602 cleaved cellohexaose revealed that C4 was the sole site of oxidation. The sequence and predicted structure of the catalytic domain of AN1602 matched very closely to known C4 cellohexaose active enzymes.
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19
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Alazi E, Niu J, Otto SB, Arentshorst M, Pham TTM, Tsang A, Ram AFJ. W361R mutation in GaaR, the regulator of D-galacturonic acid-responsive genes, leads to constitutive production of pectinases in Aspergillus niger. Microbiologyopen 2018; 8:e00732. [PMID: 30298571 PMCID: PMC6528562 DOI: 10.1002/mbo3.732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
Polysaccharides present in plant biomass, such as pectin, are the main carbon source for filamentous fungi. Aspergillus niger naturally secretes pectinases to degrade pectin and utilize the released monomers, mainly D‐galacturonic acid. The transcriptional activator GaaR, the repressor of D‐galacturonic acid utilization GaaX, and the physiological inducer 2‐keto‐3‐deoxy‐L‐galactonate play important roles in the transcriptional regulation of D‐galacturonic acid‐responsive genes, which include the genes encoding pectinases. In this study, we described the mutations found in gaaX and gaaR that enabled constitutive (i.e., inducer‐independent) expression of pectinases by A. niger. Using promoter‐reporter strains (PpgaX‐amdS) and polygalacturonic acid plate assays, we showed that W361R mutation in GaaR results in constitutive production of pectinases. Analysis of subcellular localization of C‐terminally eGFP‐tagged GaaR/GaaRW361R revealed important differences in nuclear accumulation of N‐ versus C‐terminally eGFP‐tagged GaaR.
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Affiliation(s)
- Ebru Alazi
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Jing Niu
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Simon B Otto
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Thi T M Pham
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Québec, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Québec, Canada
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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20
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Consolidated bioprocessing of lignocellulosic biomass to itaconic acid by metabolically engineering Neurospora crassa. Appl Microbiol Biotechnol 2018; 102:9577-9584. [DOI: 10.1007/s00253-018-9362-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/13/2018] [Accepted: 09/03/2018] [Indexed: 12/18/2022]
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21
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Lin L, Sun Z, Li J, Chen Y, Liu Q, Sun W, Tian C. Disruption of gul-1 decreased the culture viscosity and improved protein secretion in the filamentous fungus Neurospora crassa. Microb Cell Fact 2018; 17:96. [PMID: 29908565 PMCID: PMC6004096 DOI: 10.1186/s12934-018-0944-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/12/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The cellulolytic fungus Neurospora crassa is considered a potential host for enzyme and bioethanol production. However, large scale applications are hindered by its filamentous growth. Although previous investigations have shown that mycelial morphology in submerged culture can be controlled by altering physical factors, there is little knowledge available about the potential for morphology control by genetic modification. RESULTS In this study, we screened morphological mutants in the filamentous fungus N. crassa. Of the 90 morphological mutants screened, 14 mutants exhibited considerably higher viscosity compared with that of the wild type strain, and only two mutants showed low-viscosity morphologies in submerged culture. We observed that disruption of gul-1 (NCU01197), which encodes an mRNA binding protein involved in cell wall remodeling, caused pellet formation as the fermentation progressed, and resulted in the most significant decrease in viscosity of culture broth. Moreover, over-expression of gul-1 caused dramatically increased viscosity, suggesting that the gul-1 had an important function in mycelial morphology during submerged cultivation. Transcriptional profiling showed that expression of genes encoding eight GPI-anchored cell wall proteins was lowered in Δgul-1 while expression of genes associated with two non-anchored cell wall proteins was elevated. Meanwhile, the expression levels of two hydrophobin genes were also significantly altered. These results suggested that GUL-1 affected the transcription of cell wall-related genes, thereby influencing cell wall structure and mycelial morphology. Additionally, the deletion of gul-1 caused increased protein secretion, probably due to a defect in cell wall integrity, suggesting this as an alternative strategy of strain improvement for enzyme production. To confirm practical applications, deletion of gul-1 in the hyper-cellulase producing strain (∆ncw-1∆Ncap3m) significantly reduced the viscosity of culture broth. CONCLUSIONS Using the model filamentous fungus N. crassa, genes that affect mycelial morphology in submerged culture were explored through systematic screening of morphological mutants. Disrupting several candidate genes altered viscosities in submerged culture. This work provides an example for controlling fungal morphology in submerged fermentation by genetic engineering, and will be beneficial for industrial fungal strain improvement.
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Affiliation(s)
- Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Zhiyong Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yong Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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22
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Matsu-ura T, Dovzhenok AA, Coradetti ST, Subramanian KR, Meyer DR, Kwon JJ, Kim C, Salomonis N, Glass NL, Lim S, Hong CI. Synthetic Gene Network with Positive Feedback Loop Amplifies Cellulase Gene Expression in Neurospora crassa. ACS Synth Biol 2018; 7:1395-1405. [PMID: 29625007 DOI: 10.1021/acssynbio.8b00011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Second-generation or lignocellulosic biofuels are a tangible source of renewable energy, which is critical to combat climate change by reducing the carbon footprint. Filamentous fungi secrete cellulose-degrading enzymes called cellulases, which are used for production of lignocellulosic biofuels. However, inefficient production of cellulases is a major obstacle for industrial-scale production of second-generation biofuels. We used computational simulations to design and implement synthetic positive feedback loops to increase gene expression of a key transcription factor, CLR-2, that activates a large number of cellulases in a filamentous fungus, Neurospora crassa. Overexpression of CLR-2 reveals previously unappreciated roles of CLR-2 in lignocellulosic gene network, which enabled simultaneous induction of approximately 50% of 78 lignocellulosic degradation-related genes in our engineered Neurospora strains. This engineering results in dramatically increased cellulase activity due to cooperative orchestration of multiple enzymes involved in the cellulose degradation pathway. Our work provides a proof of principle in utilizing mathematical modeling and synthetic biology to improve the efficiency of cellulase synthesis for second-generation biofuel production.
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Affiliation(s)
- Toru Matsu-ura
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio 45267-0529, United States
| | - Andrey A. Dovzhenok
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio 45221-0025, United States
| | - Samuel T. Coradetti
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Krithika R. Subramanian
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio 45267-0529, United States
- Department of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039, United States
| | - Daniel R. Meyer
- Department of Biomedical, Chemical, and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio 45221-0012, United States
| | - Jaesang J. Kwon
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio 45267-0529, United States
| | - Caleb Kim
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio 45267-0529, United States
| | - Nathan Salomonis
- Department of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039, United States
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039, United States
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Sookkyung Lim
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio 45221-0025, United States
| | - Christian I. Hong
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio 45267-0529, United States
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039, United States
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Schmoll M. Regulation of plant cell wall degradation by light in Trichoderma. Fungal Biol Biotechnol 2018; 5:10. [PMID: 29713489 PMCID: PMC5913809 DOI: 10.1186/s40694-018-0052-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022] Open
Abstract
Trichoderma reesei (syn. Hypocrea jecorina) is the model organism for industrial production of plant cell wall degradating enzymes. The integration of light and nutrient signals for adaptation of enzyme production in T. reesei emerged as an important regulatory mechanism to be tackled for strain improvement. Gene regulation specific for cellulase inducing conditions is different in light and darkness with substantial regulation by photoreceptors. Genes regulated by light are clustered in the genome, with several of the clusters overlapping with CAZyme clusters. Major cellulase transcription factor genes and at least 75% of glycoside hydrolase encoding genes show the potential of light dependent regulation. Accordingly, light dependent protein complex formation occurs within the promoters of cellulases and their regulators. Additionally growth on diverse carbon sources is different between light and darkness and dependent on the presence of photoreceptors in several cases. Thereby, also light intensity plays a regulatory role, with cellulase levels dropping at higher light intensities dependent in the strain background. The heterotrimeric G-protein pathway is the most important nutrient signaling pathway in the connection with light response and triggers posttranscriptional regulation of cellulase expression. All G-protein alpha subunits impact cellulase regulation in a light dependent manner. The downstream cAMP pathway is involved in light dependent regulation as well. Connections between the regulatory pathways are mainly established via the photoreceptor ENV1. The effect of photoreceptors on plant cell wall degradation also occurs in the model filamentous fungus Neurospora crassa. In the currently proposed model, T. reesei senses the presence of plant biomass in its environment by detection of building blocks of cellulose and hemicellulose. Interpretation of the respective signals is subsequently adjusted to the requirements in light and darkness (or on the surface versus within the substrate) by an interconnection of nutrient signaling with light response. This review provides an overview on the importance of light, photoreceptors and related signaling pathways for formation of plant cell wall degrading enzymes in T. reesei. Additionally, the relevance of light dependent gene regulation for industrial fermentations with Trichoderma as well as strategies for exploitation of the observed effects are discussed.
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Affiliation(s)
- Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
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24
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Liu B, Kognole AA, Wu M, Westereng B, Crowley MF, Kim S, Dimarogona M, Payne CM, Sandgren M. Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from
Heterobasidion irregulare
reveal amino acids important for substrate recognition. FEBS J 2018; 285:2225-2242. [DOI: 10.1111/febs.14472] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/28/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Bing Liu
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - Abhishek A. Kognole
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - Miao Wu
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - Bjørge Westereng
- Department of Chemistry, Biotechnology, and Food Science Norwegian University of Life Sciences Ås Norway
| | | | - Seonah Kim
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Maria Dimarogona
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
- Department of Chemical Engineering University of Patras Greece
| | - Christina M. Payne
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
- Directorate of Engineering Division of Chemical, Bioengineering, Environmental, and Transport Systems National Science Foundation Alexandria VA USA
| | - Mats Sandgren
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
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Quantitative multiplexed profiling of Penicillium funiculosum secretome grown on polymeric cellulase inducers and glucose. J Proteomics 2018; 179:150-160. [PMID: 29597011 DOI: 10.1016/j.jprot.2018.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/16/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
Filamentous fungi respond to the need to secure utilisable carbon from their growth milieu by secreting unique extracellular proteins depending upon the types of polymeric substrates. We have here profiled the variations in the secretome pattern of a non-model hypercellulolytic fungus - Penicillium funiculosum, grown in minimal media containing four different polymeric cellulase inducers, i.e., Avicel, wheat bran, ammonium-pretreated wheat straw and Avicel & wheat bran, and glucose over its early and late log phases of growth. Of the 137 secreted proteins validated at 1% FDR, we identified the quantified proteins in three clusters as early, persistently or lately expressed. The type of carbon substrate present in the culture media significantly affected the levels of cellulolytic enzymes expression by the fungus. The top abundant proteins quantified in the secretome for Avicel and wheat bran were cellobiohydrolaseI [GH7-CBM1], cellobiohydrolaseII [GH6-CBM1], β-glucosidase [GH3], arabinofuranosidase [GH51] and β-xylosidase [GH3], with bicupin being highest in case of wheat straw. Our results further suggested that the fungus secreted the extracellular proteins in waves, such that the initial responders act to hydrolyse the composite substrates in the culture environment before the second wave of proteins which tend to be more tailored to the specific substrate in the cultivating media. BIOLOGICAL SIGNIFICANCE In this article, we have comprehensively examined the dynamics of the secretome of a non-model hypercellulolytic fungus produced in response to model and composite cellulase inducers. Our study has provided additional insights into how the fungus enzyme machinery responds to the presence of different polymeric cellulase inducers over the two different growth phases (early growth and late growth phase). The comprehensive typing and quantification of the different proteins present in the secretomes of the cellulolytic fungal strains in response to diverse nutrient sources hold many prospects in understanding the fungus unique enzyme machinery and dynamics for the downstream biotechnological applications.
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Nogueira KMV, de Paula RG, Antoniêto ACC, dos Reis TF, Carraro CB, Silva AC, Almeida F, Rechia CGV, Goldman GH, Silva RN. Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:84. [PMID: 29619080 PMCID: PMC5879799 DOI: 10.1186/s13068-018-1084-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/17/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Trichoderma reesei is a saprophytic fungus implicated in the degradation of polysaccharides present in the cell wall of plants. T. reesei has been recognized as the most important industrial fungus that secretes and produces cellulase enzymes that are employed in the production of second generation bioethanol. A few of the molecular mechanisms involved in the process of biomass deconstruction by T. reesei; in particular, the effect of sugar transporters and induction of xylanases and cellulases expression are yet to be known. RESULTS In our study, we characterized a novel sugar transporter, which was previously identified by our group through in silico analysis of RNA-seq data. The novel T. reesei 69957-sugar transport system (Tr69957) is capable of transporting xylose, mannose, and cellobiose using a T. reesei 69957-sugar transport system in Saccharomyces cerevisiae. The deletion of Tr69957 in T. reesei affected the fungal growth and biomass accumulation, and the sugar uptake in the presence of mannose, cellobiose, and xylose. Molecular docking studies revealed that Tr69957 shows reduced protein-ligand binding energy for interactions towards disaccharides in comparison with monosaccharides. Furthermore, the deletion of Tr69957 affected the gene expression of cellobiohydrolases (cel7a and cel6a), β-glucosidases (cel3a and cel1a), and xylanases (xyn1 and xyn2) in the cultures of parental and mutant strains in the presence of cellobiose and sugarcane bagasse (SCB). CONCLUSION The transporter Tr69957 of T. reesei can transport cellobiose, xylose, and mannose, and can affect the expression of a few genes encoding enzymes, such as cellulases and xylanases, in the presence of SCB. We showed for the first time that a filamentous fungus (T. reesei) contains a potential mannose transporter that may be involved in the degradation of cellulose.
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Affiliation(s)
- Karoline M. V. Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP Brazil
| | | | - Thaila F. dos Reis
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Cláudia Batista Carraro
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Alinne Costa Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Carem Gledes Vargas Rechia
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Gustavo H. Goldman
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Roberto N. Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP Brazil
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de Eugenio LI, Méndez-Líter JA, Nieto-Domínguez M, Alonso L, Gil-Muñoz J, Barriuso J, Prieto A, Martínez MJ. Differential β-glucosidase expression as a function of carbon source availability in Talaromyces amestolkiae: a genomic and proteomic approach. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:161. [PMID: 28649280 PMCID: PMC5481877 DOI: 10.1186/s13068-017-0844-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 06/08/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Genomic and proteomic analysis are potent tools for metabolic characterization of microorganisms. Although cellulose usually triggers cellulase production in cellulolytic fungi, the secretion of the different enzymes involved in polymer conversion is subjected to different factors, depending on growth conditions. These enzymes are key factors in biomass exploitation for second generation bioethanol production. Although highly effective commercial cocktails are available, they are usually deficient for β-glucosidase activity, and genera like Penicillium and Talaromyces are being explored for its production. RESULTS This article presents the description of Talaromyces amestolkiae as a cellulase-producer fungus that secretes high levels of β-glucosidase. β-1,4-endoglucanase, exoglucanase, and β-glucosidase activities were quantified in the presence of different carbon sources. Although the two first activities were only induced with cellulosic substrates, β-glucosidase levels were similar in all carbon sources tested. Sequencing and analysis of the genome of this fungus revealed multiple genes encoding β-glucosidases. Extracellular proteome analysis showed different induction patterns. In all conditions assayed, glycosyl hydrolases were the most abundant proteins in the supernatants, albeit the ratio of the diverse enzymes from this family depended on the carbon source. At least two different β-glucosidases have been identified in this work: one is induced by cellulose and the other one is carbon source-independent. The crudes induced by Avicel and glucose were independently used as supplements for saccharification of slurry from acid-catalyzed steam-exploded wheat straw, obtaining the highest yields of fermentable glucose using crudes induced by cellulose. CONCLUSIONS The genome of T. amestolkiae contains several genes encoding β-glucosidases and the fungus secretes high levels of this activity, regardless of the carbon source availability, although its production is repressed by glucose. Two main different β-glucosidases have been identified from proteomic shotgun analysis. One of them is produced under different carbon sources, while the other is induced in cellulosic substrates and is a good supplement to Celluclast in saccharification of pretreated wheat straw.
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Affiliation(s)
- Laura I. de Eugenio
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Juan A. Méndez-Líter
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Manuel Nieto-Domínguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lola Alonso
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Jesús Gil-Muñoz
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge Barriuso
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Alicia Prieto
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Jesús Martínez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Analysis of Light- and Carbon-Specific Transcriptomes Implicates a Class of G-Protein-Coupled Receptors in Cellulose Sensing. mSphere 2017; 2:mSphere00089-17. [PMID: 28497120 PMCID: PMC5425790 DOI: 10.1128/msphere.00089-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/14/2017] [Indexed: 01/16/2023] Open
Abstract
In fungi, most metabolic processes are subject to regulation by light. For Trichoderma reesei, light-dependent regulation of cellulase gene expression is specifically shown. Therefore, we intended to unravel the relationship between regulation of enzymes by the carbon source and regulation of enzymes by light. Our two-dimensional analysis included inducing and repressing carbon sources which we used to compare light-specific regulation to dark-specific regulation and to rule out effects specific for a single carbon source. We found close connections with respect to gene regulation as well as significant differences in dealing with carbon in the environment in light and darkness. Moreover, our analyses showed an intricate regulation mechanism for substrate degradation potentially involving surface sensing and provide a basis for knowledge-based screening for strain improvement. In fungi, most metabolic processes are subject to regulation by light. Trichoderma reesei is adapted to degradation of plant cell walls and regulates production of the required enzymes in a manner dependent on the nutrient source and the light status. Here we investigated the interrelated relevance of two regulation levels of the transcriptome of T. reesei: light regulation and carbon source-dependent control. We show that the carbon source (cellulose, lactose, sophorose, glucose, or glycerol) is the major source of variation, with light having a modulating effect on transcript regulation. A total of 907 genes were regulated under cellulase-inducing conditions in light, and 947 genes were regulated in darkness, with 530 genes overlapping (1,324 in total). Only 218 of the 1,324 induction-specific genes were independent of light and not regulated by the BLR1, BLR2, and ENV1 photoreceptors. Analysis of the genomic distribution of genes regulated by light upon growth on cellulose revealed considerable overlap of light-regulated clusters with induction-specific clusters and carbohydrate-active enzyme (CAZyme) clusters. Further, we found evidence for the operation of a sensing mechanism for solid cellulosic substrates, with regulation of genes such as swo1, cip1, and cip2 or of genes encoding hydrophobins which is related to the cyclic AMP (cAMP)-dependent regulatory output of ENV1. We identified class XIII G-protein-coupled receptors (GPCRs) CSG1 and CSG2 in T. reesei as putative cellulose/glucose-sensing GPCRs. Our data indicate that the cellulase regulation pathway is bipartite, comprising a section corresponding to transcriptional regulation and one corresponding to posttranscriptional regulation, with the two connected by the function of CSG1. IMPORTANCE In fungi, most metabolic processes are subject to regulation by light. For Trichoderma reesei, light-dependent regulation of cellulase gene expression is specifically shown. Therefore, we intended to unravel the relationship between regulation of enzymes by the carbon source and regulation of enzymes by light. Our two-dimensional analysis included inducing and repressing carbon sources which we used to compare light-specific regulation to dark-specific regulation and to rule out effects specific for a single carbon source. We found close connections with respect to gene regulation as well as significant differences in dealing with carbon in the environment in light and darkness. Moreover, our analyses showed an intricate regulation mechanism for substrate degradation potentially involving surface sensing and provide a basis for knowledge-based screening for strain improvement.
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Waters JC, Nixon A, Dwyer M, Biffinger JC, Lee K. Developing elite Neurospora crassa strains for cellulosic ethanol production using fungal breeding. J Ind Microbiol Biotechnol 2017; 44:1137-1144. [PMID: 28429154 PMCID: PMC5511601 DOI: 10.1007/s10295-017-1941-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/27/2017] [Indexed: 01/14/2023]
Abstract
The demand for renewable and sustainable energy has generated considerable interest in the conversion of cellulosic biomass into liquid fuels such as ethanol using a filamentous fungus. While attempts have been made to study cellulose metabolism through the use of knock-out mutants, there have been no systematic effort to characterize natural variation for cellulose metabolism in ecotypes adapted to different habitats. Here, we characterized natural variation in saccharification of cellulose and fermentation in 73 ecotypes and 89 laboratory strains of the model fungus Neurospora crassa. We observed significant variation in both traits among natural and laboratory generated populations, with some elite strains performing better than the reference strain. In the F1 population N345, 15% of the population outperformed both parents with the top performing strain having 10% improvement in ethanol production. These results suggest that natural alleles can be exploited through fungal breeding for developing elite industrial strains for bioethanol production.
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Affiliation(s)
- Joshua C Waters
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, 08103, USA
| | - Andrew Nixon
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, 08103, USA
| | - Morgan Dwyer
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, 08103, USA
| | - Justin C Biffinger
- Chemistry Department, US Naval Research Laboratory, Washington D.C., 20375, USA
| | - Kwangwon Lee
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, 08103, USA.
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, 08103, USA.
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Deciphering the Regulatory Network between the SREBP Pathway and Protein Secretion in Neurospora crassa. mBio 2017; 8:mBio.00233-17. [PMID: 28420736 PMCID: PMC5395666 DOI: 10.1128/mbio.00233-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Sterol regulatory element binding proteins (SREBPs) are conserved from yeast to mammalian cells and function in the regulation of sterol homeostasis. In fungi, the SREBP pathway has been implicated in the adaptation to hypoxia and in virulence. In Neurospora crassa and Trichoderma reesei, the SREBP pathway also negatively regulates protein secretion under lignocellulolytic conditions. Here we utilized global transcriptional profiling combined with genetic and physiological analyses to address the regulatory link between the SREBP pathway and protein secretion in N. crassa. Our results demonstrated that the function of the SREBP pathway in ergosterol biosynthesis and adaptation to hypoxia was conserved in N. crassa. Under lignocellulolytic conditions, the SREBP pathway was highly activated, resulting in the reduced expression of lytic polysaccharide monooxygenases, which require molecular oxygen for catalytic activity. Additionally, activation of the SREBP pathway under lignocellulolytic conditions repressed a set of genes predicted to be involved in the endoplasmic reticulum stress response. Here we show that the inability of a hac-1 mutant, which bears a deletion of the major regulator of the unfolded protein response (UPR), to efficiently produce cellulases and utilize cellulose was suppressed by mutations in the SREBP pathway. The analyses presented here demonstrated new SREBP pathway functions, including linkages to the UPR, and provide new clues for genetic engineering of filamentous fungi to improve their production of extracellular proteins. The role of SREBP transcription factors in the regulation of sterol biosynthesis is conserved from humans to yeast. In filamentous fungi, this pathway regulates the secretion of lignocellulolytic enzymes during plant biomass deconstruction. Here we show that the SREBP pathway in Neurospora crassa regulates the production of specific cellulases, lytic polysaccharide monooxygenases that utilize molecular oxygen. Via global transcriptional profile and genetic analyses, a relationship between the SREBP pathway and the unfolded protein response (UPR) pathway was revealed, suggesting a regulatory interplay of these two pathways in the trafficking of plant biomass-degrading enzymes. These findings have implications for our understanding of the cross talk of the SREBP and UPR pathways in other organisms and will guide the rational engineering of fungal strains to improve cellulolytic enzyme production.
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Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F. Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:209. [PMID: 28912831 PMCID: PMC5588705 DOI: 10.1186/s13068-017-0897-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/29/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype. RESULTS Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions. CONCLUSION We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.
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Affiliation(s)
- Christa Ivanova
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- Present Address: Genetics of Biofilms Unit, Department of Microbiology, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jonas Ramoni
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Thiziri Aouam
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Alexa Frischmann
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Stéphane Le Crom
- Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, 75005 Paris, France
| | - Sophie Lemoine
- École normale supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l’École normale supérieure (IBENS), Plateforme Génomique, 75005 Paris, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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Cations Optimization for Protein Enrichment in Rice Straw by Mixed Cultures of Neurospora crassa 14-8 and Candida utilis Using Response Surface Methodology. Appl Biochem Biotechnol 2016; 182:804-817. [DOI: 10.1007/s12010-016-2363-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/06/2016] [Indexed: 12/26/2022]
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Amores GR, Guazzaroni ME, Arruda LM, Silva-Rocha R. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories. Curr Genomics 2016; 17:85-98. [PMID: 27226765 PMCID: PMC4864837 DOI: 10.2174/1389202917666151116212255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/23/2015] [Accepted: 06/01/2015] [Indexed: 01/03/2023] Open
Abstract
Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant
biomass and this feature has a tremendous potential for biofuel production from renewable sources.
The past decades have been marked by a remarkable progress in the genetic engineering of fungi to
generate industry-compatible strains needed for some biotech applications. In this sense, progress in
this field has been marked by the utilization of high-throughput techniques to gain deep understanding
of the molecular machinery controlling the physiology of these organisms, starting thus the Systems
Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized
promoters in order to construct new expression systems with enhanced performance under the conditions of
interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of
fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms
relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction
of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered
promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact
in the final performance of the process of interest. We expect to provide here some new directions to drive future research
directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.
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Druzhinina IS, Kubicek CP. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:69-147. [PMID: 27261782 DOI: 10.1016/bs.aambs.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.
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Affiliation(s)
- I S Druzhinina
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - C P Kubicek
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fuller K, Dunlap J, Loros J. Fungal Light Sensing at the Bench and Beyond. ADVANCES IN GENETICS 2016; 96:1-51. [DOI: 10.1016/bs.adgen.2016.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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A Neurospora crassa ÿ-glucosidase with potential for lignocellulose hydrolysis shows strong glucose tolerance and stimulation by glucose and xylose. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Ogunmolu FE, Kaur I, Gupta M, Bashir Z, Pasari N, Yazdani SS. Proteomics Insights into the Biomass Hydrolysis Potentials of a Hypercellulolytic Fungus Penicillium funiculosum. J Proteome Res 2015; 14:4342-58. [PMID: 26288988 DOI: 10.1021/acs.jproteome.5b00542] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The quest for cheaper and better enzymes needed for the efficient hydrolysis of lignocellulosic biomass has placed filamentous fungi in the limelight for bioprospecting research. In our search for efficient biomass degraders, we identified a strain of Penicillium funiculosum whose secretome demonstrates high saccharification capabilities. Our probe into the secretome of the fungus through qualitative and label-free quantitative mass spectrometry based proteomics studies revealed a high abundance of inducible CAZymes and several nonhydrolytic accessory proteins. The preferential association of these proteins and the attending differential biomass hydrolysis gives an insight into their interactions and clues about possible roles of novel hydrolytic and nonhydrolytic proteins in the synergistic deconstruction of lignocellulosic biomass. Our study thus provides the first comprehensive insight into the repertoire of proteins present in a high-performing secretome of a hypercellulolytic Penicillium funiculosum, their relative abundance in the secretome, and the interaction dynamics of the various protein groups in the secretome. The gleanings from the stoichiometry of these interactions hold a prospect as templates in the design of cost-effective synthetic cocktails for the optimal hydrolysis of biomass.
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Affiliation(s)
- Funso Emmanuel Ogunmolu
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Inderjeet Kaur
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Mayank Gupta
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Zeenat Bashir
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Nandita Pasari
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Syed Shams Yazdani
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
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Pei X, Fan F, Lin L, Chen Y, Sun W, Zhang S, Tian C. Involvement of the adaptor protein 3 complex in lignocellulase secretion in Neurospora crassa revealed by comparative genomic screening. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:124. [PMID: 26300971 PMCID: PMC4545925 DOI: 10.1186/s13068-015-0302-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/30/2015] [Indexed: 06/02/2023]
Abstract
BACKGROUND Lignocellulase hypersecretion has been achieved in industrial fungal workhorses such as Trichoderma reesei, but the underlying mechanism associated with this process is not well understood. Although previous comparative genomic studies have revealed that the mutagenic T. reesei strain RUT-C30 harbors hundreds of mutations compared with its parental strain QM6a, how these mutations actually contribute to the hypersecretion phenotype remains to be elucidated. RESULTS In this study, we systematically screened gene knockout (KO) mutants in the cellulolytic fungus Neurospora crassa, which contains orthologs of potentially defective T. reesei RUT-C30 mutated genes. Of the 86 deletion mutants screened in N. crassa, 12 exhibited lignocellulase production more than 25% higher than in the wild-type (WT) strain and 4 showed nearly 25% lower secretion. We observed that the deletion of Ncap3m (NCU03998), which encodes the μ subunit of the adaptor protein 3 (AP-3) complex in N. crassa, led to the most significant increase in lignocellulase secretion under both Avicel and xylan culture conditions. Moreover, strains lacking the β subunit of the AP-3 complex, encoded by Ncap3b (NCU06569), had a similar phenotype to ΔNcap3m, suggesting that the AP-3 complex is involved in lignocellulase secretion in N. crassa. We also found that the transcriptional abundance of major lignocellulase genes in ΔNcap3m was maintained at a relatively higher level during the late stage of fermentation compared with the WT, which might add to the hypersecretion phenotype. Finally, we found that importation of the T. reesei ap3m ortholog Trap3m into ΔNcap3m can genetically restore secretion of lignocellulases to normal levels, which suggests that the effect of the AP-3 complex on lignocellulase secretion is conserved in cellulolytic ascomycetes. CONCLUSIONS Using the model cellulolytic fungus N. crassa, we explored potential hypersecretion-related mutations in T. reesei strain RUT-C30. Through systematic genetic screening of 86 corresponding orthologous KO mutants in N. crassa, we identified several genes, particularly those encoding the AP-3 complex that contribute to lignocellulase secretion. These findings will be useful for strain improvement in future lignocellulase and biomass-based chemical production.
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Affiliation(s)
- Xue Pei
- />College of Plant Sciences, Jilin University, Changchun, 130062 China
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Feiyu Fan
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Liangcai Lin
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yong Chen
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Shihong Zhang
- />College of Plant Sciences, Jilin University, Changchun, 130062 China
| | - Chaoguang Tian
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Abstract
Neurospora crassa is an important model organism for filamentous fungi as well as for circadian biology and photobiology. Although the community-accumulated tool set for the molecular analysis of Neurospora is extensive, two components are missing: (1) dependable reference genes whose level of expression are relatively constant across light/dark cycles and as a function of time of day and (2) a catalog of primers specifically designed for real-time PCR (RT-PCR). To address the first of these we have identified genes that are optimal for use as reference genes in RT-PCR across a wide range of expression levels; the mRNA/transcripts from these genes have potential for use as reference noncycling transcripts outside of Neurospora. In addition, we have generated a genome-wide set of RT-PCR primers, thereby streamlining the analysis of gene expression. In validation studies these primers successfully identified target mRNAs arising from 70% (34 of 49) of all tested genes and from all (28) of the moderately to highly expressed tested genes.
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Montenegro-Montero A, Goity A, Larrondo LF. The bZIP Transcription Factor HAC-1 Is Involved in the Unfolded Protein Response and Is Necessary for Growth on Cellulose in Neurospora crassa. PLoS One 2015; 10:e0131415. [PMID: 26132395 PMCID: PMC4488935 DOI: 10.1371/journal.pone.0131415] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/02/2015] [Indexed: 12/15/2022] Open
Abstract
High protein secretion capacity in filamentous fungi requires an extremely efficient system for protein synthesis, folding and transport. When the folding capacity of the endoplasmic reticulum (ER) is exceeded, a pathway known as the unfolded protein response (UPR) is triggered, allowing cells to mitigate and cope with this stress. In yeast, this pathway relies on the transcription factor Hac1, which mediates the up-regulation of several genes required under these stressful conditions. In this work, we identified and characterized the ortholog of the yeast HAC1 gene in the filamentous fungus Neurospora crassa. We show that its mRNA undergoes an ER stress-dependent splicing reaction, which in N. crassa removes a 23 nt intron and leads to a change in the open reading frame. By disrupting the N. crassa hac-1 gene, we determined it to be crucial for activating UPR and for proper growth in the presence of ER stress-inducing chemical agents. Neurospora is naturally found growing on dead plant material, composed primarily by lignocellulose, and is a model organism for the study of plant cell wall deconstruction. Notably, we found that growth on cellulose, a substrate that requires secretion of numerous enzymes, imposes major demands on ER function and is dramatically impaired in the absence of hac-1, thus broadening the range of physiological functions of the UPR in filamentous fungi. Growth on hemicellulose however, another carbon source that necessitates the secretion of various enzymes for its deconstruction, is not impaired in the mutant nor is the amount of proteins secreted on this substrate, suggesting that secretion, as a whole, is unaltered in the absence of hac-1. The characterization of this signaling pathway in N. crassa will help in the study of plant cell wall deconstruction by fungi and its manipulation may result in important industrial biotechnological applications.
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Affiliation(s)
- Alejandro Montenegro-Montero
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandra Goity
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F. Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail:
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Xiong D, Wang Y, Tian C. Transcriptomic profiles of the smoke tree wilt fungus Verticillium dahliae under nutrient starvation stresses. Mol Genet Genomics 2015; 290:1963-77. [DOI: 10.1007/s00438-015-1052-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/22/2015] [Indexed: 11/27/2022]
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Three-phasic fermentation systems for enzyme production with sugarcane bagasse in stirred tank bioreactors: Effects of operational variables and cultivation method. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Guerriero G, Hausman JF, Strauss J, Ertan H, Siddiqui KS. Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:180-93. [PMID: 25804821 PMCID: PMC4937988 DOI: 10.1016/j.plantsci.2015.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 05/05/2023]
Abstract
The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocallimastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg.
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna (BOKU), University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria; Health and Environment Department, Austrian Institute of Technology GmbH - AIT, University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Khawar Sohail Siddiqui
- Biology Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia.
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Fan F, Ma G, Li J, Liu Q, Benz JP, Tian C, Ma Y. Genome-wide analysis of the endoplasmic reticulum stress response during lignocellulase production in Neurospora crassa. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:66. [PMID: 25883682 PMCID: PMC4399147 DOI: 10.1186/s13068-015-0248-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/27/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lignocellulolytic fungal cells suffer endoplasmic reticulum (ER) stress during lignocellulase synthesis; however, an understanding of this integrated process on a genome-wide scale remains poor. Here, we undertook a systematic investigation of this process in Neurospora crassa (N. crassa) using transcriptomic analysis coupled with genetic screens. RESULTS A set of 766 genes was identified as the ER stress response targets (ESRTs) in N. crassa under cellulose utilization conditions. Among these, the expression of 223 and 186 genes showed dependence on IRE-1 and HAC-1, respectively. A total of 527 available mutants for ESRT genes were screened, 249 of which exhibited ER stress susceptibility, including 100 genes with unknown function. Disruption of ire-1 or hac-1 in N. crassa did not affect transcriptional induction of lignocellulase genes by cellulose but severely affected secretion of the corresponding enzymes. A global investigation of transcription factors (TFs) discovered three novel regulators (RES-1, RES-2, RRG-2) involved in lignocellulase secretion. Production of lignocellulases in Δres-1 increased by more than 30% in comparison to wild type (WT), while secretion decreased by nearly 30% in strains Δres-2 and Δrrg-2. Transcriptional profiling of the three TF mutants suggests they are deeply involved in lignocellulase secretion and ER stress response. CONCLUSIONS Here, we determined the transcriptional scope of the ER stress response during lignocellulase synthesis in the model cellulolytic fungus N. crassa. Through genome-wide mutant screening and analysis, dozens of novel genes were discovered to be involved in the process. The findings of this work will be useful for strain improvement to facilitate lignocellulase and biomass-based chemical production.
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Affiliation(s)
- Feiyu Fan
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
- />University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China
| | - Guoli Ma
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
- />University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China
| | - Jingen Li
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
- />University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China
| | - Qian Liu
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
| | - Johan Philipp Benz
- />Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - Chaoguang Tian
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
| | - Yanhe Ma
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China
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Wang B, Cai P, Sun W, Li J, Tian C, Ma Y. A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:21. [PMID: 25691917 PMCID: PMC4330645 DOI: 10.1186/s13068-015-0208-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/20/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Crop residue is an abundant, low-cost plant biomass material available worldwide for use in the microbial production of enzymes, biofuels, and valuable chemicals. However, the diverse chemical composition and complex structure of crop residues are more challenging for efficient degradation by microbes than are homogeneous polysaccharides. In this study, the transcriptional responses of Neurospora crassa to various plant straws were analyzed using RNA-Seq, and novel beneficial factors for biomass-induced enzyme production were evaluated. RESULTS Comparative transcriptional profiling of N. crassa grown on five major crop straws of China (barley, corn, rice, soybean, and wheat straws) revealed a highly overlapping group of 430 genes, the biomass commonly induced core set (BICS). A large proportion of induced carbohydrate-active enzyme (CAZy) genes (82 out of 113) were also conserved across the five plant straws. Excluding 178 genes within the BICS that were also upregulated under no-carbon conditions, the remaining 252 genes were defined as the biomass regulon (BR). Interestingly, 88 genes were only induced by plant biomass and not by three individual polysaccharides (Avicel, xylan, and pectin); these were denoted as the biomass unique set (BUS). Deletion of one BUS gene, the transcriptional regulator rca-1, significantly improved lignocellulase production using plant biomass as the sole carbon source, possibly functioning via de-repression of the regulator clr-2. Thus, this result suggests that rca-1 is a potential engineering target for biorefineries, especially for plant biomass direct microbial conversion processes. CONCLUSIONS Transcriptional profiling revealed a large core response to different sources of plant biomass in N. crassa. The sporulation regulator rca-1 was identified as beneficial for biomass-based enzyme production.
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Affiliation(s)
- Bang Wang
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Pengli Cai
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenliang Sun
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chaoguang Tian
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yanhe Ma
- />Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Reilly MC, Qin L, Craig JP, Starr TL, Glass NL. Deletion of homologs of the SREBP pathway results in hyper-production of cellulases in Neurospora crassa and Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:121. [PMID: 26288653 PMCID: PMC4539670 DOI: 10.1186/s13068-015-0297-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/24/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND The filamentous fungus Neurospora crassa efficiently utilizes plant biomass and is a model organism for genetic, molecular and cellular biology studies. Here, a set of 567 single-gene deletion strains was assessed for cellulolytic activity as compared to the wild-type parental strain. Mutant strains included were those carrying a deletion in: (1) genes encoding proteins homologous to those implicated in the Saccharomyces cerevisiae secretion apparatus; (2) genes that are homologous to those known to differ between the Trichoderma reesei hyper-secreting strain RUT-C30 and its ancestral wild-type strain; (3) genes encoding proteins identified in the secretome of N. crassa when cultured on plant biomass and (4) genes encoding proteins predicted to traverse the secretory pathway. RESULTS The 567 single-gene deletion collection was cultured on crystalline cellulose and a comparison of levels of secreted protein and cellulase activity relative to the wild-type strain resulted in the identification of seven hyper-production and 18 hypo-production strains. Some of these deleted genes encoded proteins that are likely to act in transcription, protein synthesis and intracellular trafficking, but many encoded fungal-specific proteins of undetermined function. Characterization of several mutants peripherally linked to protein processing or secretion showed that the hyper- or hypo-production phenotypes were primarily a response to cellulose. The altered secretome of these strains was not limited to the production of cellulolytic enzymes, yet was part of the cellulosic response driven by the cellulase transcription factor CLR-2. Mutants implicated the loss of the SREBP pathway, which has been found to regulate ergosterol biosynthesis genes in response to hypoxic conditions, resulted in a hyper-production phenotype. Deletion of two SREBP pathway components in T. reesei also conferred a hyper-production phenotype under cellulolytic conditions. CONCLUSIONS These studies demonstrate the utility of screening the publicly available N. crassa single-gene deletion strain collection for a particular phenotype. Mutants in a predicted E3 ligase and its target SREBP transcription factor played an unanticipated role in protein production under cellulolytic conditions. Furthermore, phenotypes similar to those observed in N. crassa were seen following the targeted deletion of orthologous SREBP pathway loci in T. reesei, a fungal species commonly used in industrial enzyme production.
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Affiliation(s)
- Morgann C Reilly
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Lina Qin
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - James P Craig
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Trevor L Starr
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - N Louise Glass
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
- />The Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
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Wang H, Pan J, Wang J, Wang N, Zhang J, Li Q, Wang D, Zhou X. Succinic acid production from xylose mother liquor by recombinant Escherichia coli strain. BIOTECHNOL BIOTEC EQ 2014; 28:1042-1049. [PMID: 26019590 PMCID: PMC4433926 DOI: 10.1080/13102818.2014.952501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/30/2014] [Indexed: 01/25/2023] Open
Abstract
Succinic acid (1,4-butanedioic acid) is identified as one of important building-block chemicals. Xylose mother liquor is an abundant industrial residue in xylitol biorefining industry. In this study, xylose mother liquor was utilized to produce succinic acid by recombinant Escherichia coli strain SD121, and the response surface methodology was used to optimize the fermentation media. The optimal conditions of succinic acid fermentation were as follows: 82.62 g L−1 total initial sugars, 42.27 g L−1 MgCO3 and 17.84 g L−1 yeast extract. The maximum production of succinic acid was 52.09 ± 0.21 g L−1 after 84 h with a yield of 0.63 ± 0.03 g g−1 total sugar, approaching the predicted value (53.18 g L−1). It was 1.78-fold of the production of that obtained with the basic medium. This was the first report on succinic acid production from xylose mother liquor by recombinant E. coli strains with media optimization using response surface methodology. This work suggested that the xylose mother liquor could be an alternative substrate for the economical production of succinic acid by recombinant E. coli strains.
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Affiliation(s)
- Honghui Wang
- College of Chemistry and Chemical Engineering, Chongqing University , Chongqing 400044 , China
| | - Jiachuan Pan
- Department of Biomedical and Chemical Engineering, Syracuse University , Syracuse, NY 13244 , USA
| | - Jing Wang
- College of Chemistry and Chemical Engineering, Chongqing University , Chongqing 400044 , China
| | - Nan Wang
- College of Chemistry and Chemical Engineering, Chongqing University , Chongqing 400044 , China
| | - Jie Zhang
- College of Chemistry and Chemical Engineering, Chongqing University , Chongqing 400044 , China
| | - Qiang Li
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering , Chinese Academy of Sciences , Beijing 100190 , China
| | - Dan Wang
- College of Chemistry and Chemical Engineering, Chongqing University , Chongqing 400044 , China
| | - Xiaohua Zhou
- College of Chemistry and Chemical Engineering, Chongqing University , Chongqing 400044 , China
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49
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van Munster JM, Daly P, Delmas S, Pullan ST, Blythe MJ, Malla S, Kokolski M, Noltorp ECM, Wennberg K, Fetherston R, Beniston R, Yu X, Dupree P, Archer DB. The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. Fungal Genet Biol 2014; 72:34-47. [PMID: 24792495 PMCID: PMC4217149 DOI: 10.1016/j.fgb.2014.04.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/21/2014] [Accepted: 04/18/2014] [Indexed: 11/06/2022]
Abstract
Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that the transcriptional response after 6h of exposure to wheat straw was very different from the response at 24h of exposure to the same substrate. For example, less than half of the genes encoding carbohydrate active enzymes that were induced after 24h of exposure to wheat straw, were also induced after 6h exposure. Importantly, over a third of the genes induced after 6h of exposure to wheat straw were also induced during 6h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. We show, using proteomics, that carbon-starved cultures indeed release CAZymes with predicted activity on plant polysaccharides. Analysis of the enzymatic activity and the reaction products, indicates that these proteins are enzymes that can degrade various plant polysaccharides to generate both known, as well as potentially new, inducers of CAZymes.
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Affiliation(s)
- Jolanda M van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Stéphane Delmas
- 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.
| | - Martin J Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Sunir Malla
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Emelie C M Noltorp
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Kristin Wennberg
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Richard Fetherston
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Richard Beniston
- Biological Mass Spectrometry Facility biOMICS, University of Sheffield, Brook Hill Road, Sheffield S3 7HF, UK.
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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50
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Physical methods for genetic transformation of fungi and yeast. Phys Life Rev 2014; 11:184-203. [DOI: 10.1016/j.plrev.2014.01.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 01/27/2023]
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