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Zhang J, Li K, Sun Y, Yao C, Liu W, Liu H, Zhong Y. An efficient CRISPR/Cas9 genome editing system based on a multiple sgRNA processing platform in Trichoderma reesei for strain improvement and enzyme production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:22. [PMID: 38342915 DOI: 10.1186/s13068-024-02468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/29/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND The CRISPR/Cas9 technology is being employed as a convenient tool for genetic engineering of the industrially important filamentous fungus Trichoderma reesei. However, multiplex gene editing is still constrained by the sgRNA processing capability, hindering strain improvement of T. reesei for the production of lignocellulose-degrading enzymes and recombinant proteins. RESULTS Here, a CRISPR/Cas9 system based on a multiple sgRNA processing platform was established for genome editing in T. reesei. The platform contains the arrayed tRNA-sgRNA architecture directed by a 5S rRNA promoter to generate multiple sgRNAs from a single transcript by the endogenous tRNA processing system. With this system, two sgRNAs targeting cre1 (encoding the carbon catabolite repressor 1) were designed and the precise deletion of cre1 was obtained, demonstrating the efficiency of sgRNAs processing in the tRNA-sgRNA architecture. Moreover, overexpression of xyr1-A824V (encoding a key activator for cellulase/xylanase expression) at the ace1 (encoding a repressor for cellulase/xylanase expression) locus was achieved by designing two sgRNAs targeting ace1 in the system, resulting in the significantly enhanced production of cellulase (up to 1- and 18-fold on the Avicel and glucose, respectively) and xylanase (up to 11- and 41-fold on the Avicel and glucose, respectively). Furthermore, heterologous expression of the glucose oxidase gene from Aspergillus niger ATCC 9029 at the cbh1 locus with the simultaneous deletion of cbh1 and cbh2 (two cellobiohydrolase coding genes) by designing four sgRNAs targeting cbh1 and cbh2 in the system was acquired, and the glucose oxidase produced by T. reesei reached 43.77 U/mL. Besides, it was found the ER-associated protein degradation (ERAD) level was decreased in the glucose oxidase-producing strain, which was likely due to the reduction of secretion pressure by deletion of the major endogenous cellulase-encoding genes. CONCLUSIONS The tRNA-gRNA array-based CRISPR-Cas9 editing system was successfully developed in T. reesei. This system would accelerate engineering of T. reesei for high-level production of enzymes including lignocellulose-degrading enzymes and other recombinant enzymes. Furthermore, it would expand the CRISPR toolbox for fungal genome editing and synthetic biology.
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Affiliation(s)
- Jiaxin Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Kehang Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yu Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Cheng Yao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Hong Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
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Yan S, Xu Y, Yu XW. Rational engineering of xylanase hyper-producing system in Trichoderma reesei for efficient biomass degradation. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:90. [PMID: 33832521 PMCID: PMC8033665 DOI: 10.1186/s13068-021-01943-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/27/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Filamentous fungus Trichoderma reesei has been widely used as a workhorse for cellulase and xylanase productions. Xylanase has been reported as the crucial accessory enzyme in the degradation of lignocellulose for higher accessibility of cellulase. In addition, the efficient hydrolysis of xylan needs the co-work of multiple xylanolytic enzymes, which rise an increasing demand for the high yield of xylanase for efficient biomass degradation. RESULTS In this study, a xylanase hyper-producing system in T. reesei was established by tailoring two transcription factors, XYR1 and ACE1, and homologous overexpression of the major endo-xylanase XYNII. The expressed xylanase cocktail contained 5256 U/mL xylanase activity and 9.25 U/mL β-xylosidase (pNPXase) activity. Meanwhile, the transcription level of the xylanolytic genes in the strain with XYR1 overexpressed was upregulated, which was well correlated with the amount of XYR1-binding sites. In addition, the higher expression of associated xylanolytic enzymes would result in more efficient xylan hydrolysis. Besides, 2310-3085 U/mL of xylanase activities were achieved using soluble carbon source, which was more efficient and economical than the traditional strategy of xylan induction. Unexpectedly, deletion of ace1 in C30OExyr1 did not give any improvement, which might be the result of the disturbed function of the complex formed between ACE1 and XYR1. The enzymatic hydrolysis of alkali pretreated corn stover using the crude xylanase cocktails as accessory enzymes resulted in a 36.64% increase in saccharification efficiency with the ratio of xylanase activity vs FPase activity at 500, compared to that using cellulase alone. CONCLUSIONS An efficient and economical xylanase hyper-producing platform was developed in T. reesei RUT-C30. The novel platform with outstanding ability for crude xylanase cocktail production would greatly fit in biomass degradation and give a new perspective of further engineering in T. reesei for industrial purposes.
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Affiliation(s)
- Su Yan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
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Daranagama ND, Suzuki Y, Shida Y, Ogasawara W. Involvement of Xyr1 and Are1 for Trichodermapepsin Gene Expression in Response to Cellulose and Galactose in Trichoderma reesei. Curr Microbiol 2020; 77:1506-1517. [DOI: 10.1007/s00284-020-01955-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
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Hirasawa H, Shioya K, Furukawa T, Tani S, Sumitani JI, Kawaguchi T, Morikawa Y, Shida Y, Ogasawara W. Engineering of the Trichoderma reesei xylanase3 promoter for efficient enzyme expression. Appl Microbiol Biotechnol 2018; 102:2737-2752. [DOI: 10.1007/s00253-018-8763-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
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Druzhinina IS, Kubicek CP. Genetic engineering of Trichoderma reesei cellulases and their production. Microb Biotechnol 2017; 10:1485-1499. [PMID: 28557371 PMCID: PMC5658622 DOI: 10.1111/1751-7915.12726] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/11/2017] [Accepted: 04/11/2017] [Indexed: 11/26/2022] Open
Abstract
Lignocellulosic biomass, which mainly consists of cellulose, hemicellulose and lignin, is the most abundant renewable source for production of biofuel and biorefinery products. The industrial use of plant biomass involves mechanical milling or chipping, followed by chemical or physicochemical pretreatment steps to make the material more susceptible to enzymatic hydrolysis. Thereby the cost of enzyme production still presents the major bottleneck, mostly because some of the produced enzymes have low catalytic activity under industrial conditions and/or because the rate of hydrolysis of some enzymes in the secreted enzyme mixture is limiting. Almost all of the lignocellulolytic enzyme cocktails needed for the hydrolysis step are produced by fermentation of the ascomycete Trichoderma reesei (Hypocreales). For this reason, the structure and mechanism of the enzymes involved, the regulation of their expression and the pathways of their formation and secretion have been investigated in T. reesei in considerable details. Several of the findings thereby obtained have been used to improve the formation of the T. reesei cellulases and their properties. In this article, we will review the achievements that have already been made and also show promising fields for further progress.
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Affiliation(s)
- Irina S. Druzhinina
- Microbiology GroupResearch Area Biochemical TechnologyInstitute of Chemical, Environmental and Biological EngineeringTU WienViennaAustria
| | - Christian P. Kubicek
- Microbiology GroupResearch Area Biochemical TechnologyInstitute of Chemical, Environmental and Biological EngineeringTU WienViennaAustria
- Present address:
Steinschötelgasse 7Wien1100Austria
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Shida Y, Furukawa T, Ogasawara W. Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus. Biosci Biotechnol Biochem 2016; 80:1712-29. [DOI: 10.1080/09168451.2016.1171701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.
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Affiliation(s)
- Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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Fungal Biotechnology for Industrial Enzyme Production: Focus on (Hemi)cellulase Production Strategies, Advances and Challenges. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Shida Y, Yamaguchi K, Nitta M, Nakamura A, Takahashi M, Kidokoro SI, Mori K, Tashiro K, Kuhara S, Matsuzawa T, Yaoi K, Sakamoto Y, Tanaka N, Morikawa Y, Ogasawara W. The impact of a single-nucleotide mutation of bgl2 on cellulase induction in a Trichoderma reesei mutant. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:230. [PMID: 26719764 PMCID: PMC4696228 DOI: 10.1186/s13068-015-0420-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/15/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina) produces increased cellulase expression when grown on cellulose or its derivatives as a sole carbon source. It has been believed that β-glucosidases of T. reesei not only metabolize cellobiose but also contribute in the production of inducers of cellulase gene expression by their transglycosylation activity. The cellulase hyper-producing mutant PC-3-7 developed in Japan has enhanced cellulase production ability when cellobiose is used as the inducer. The comparative genomics analysis of PC-3-7 and its parent revealed a single-nucleotide mutation within the bgl2 gene encoding intracellular β-glucosidase II (BGLII/Cel1a), giving rise to an amino acid substitution in PC-3-7, which could potentially account for the enhanced cellulase expression when these strains are cultivated on cellulose and cellobiose. RESULTS To analyze the effects of the BGLII mutation in cellulase induction, we constructed both a bgl2 revertant and a disruptant. Enzymatic analysis of the transformant lysates showed that the strain expressing mutant BGLII exhibited weakened cellobiose hydrolytic activity, but produced some transglycosylation products, suggesting that the SNP in bgl2 strongly diminished cellobiase activity, but did not result in complete loss of function of BGLII. The analysis of the recombinant BGLII revealed that transglycosylation products might be oligosaccharides, composed probably of glucose linked β-1,4, β-1,3, or a mixture of both. PC-3-7 revertants of bgl2 exhibited reduced expression and inducibility of cellulase during growth on cellulose and cellobiose substrates. Furthermore, the effect of this bgl2 mutation was reproduced in the common strain QM9414 in which the transformants showed cellulase production comparable to that of PC-3-7. CONCLUSION We conclude that BGLII plays an important role in cellulase induction in T. reesei and that the bgl2 mutation in PC-3-7 brought about enhanced cellulase expression on cellobiose. The results of the investigation using PC-3-7 suggested that other mutation(s) in PC-3-7 could also contribute to cellulase induction. Further investigation is essential to unravel the mechanism responsible for cellulase induction in T. reesei.
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Affiliation(s)
- Yosuke Shida
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kaori Yamaguchi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Mikiko Nitta
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
- />Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 Japan
| | - Ayana Nakamura
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Machiko Takahashi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Shun-ichi Kidokoro
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kazuki Mori
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Kosuke Tashiro
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Satoru Kuhara
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Tomohiko Matsuzawa
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Katsuro Yaoi
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Yasumitsu Sakamoto
- />School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694 Japan
| | - Nobutada Tanaka
- />School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555 Japan
| | - Yasushi Morikawa
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Wataru Ogasawara
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
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Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics 2015; 16:326. [PMID: 25909478 PMCID: PMC4409711 DOI: 10.1186/s12864-015-1526-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/13/2015] [Indexed: 02/08/2023] Open
Abstract
Background Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a. Results In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn2Cys6 transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level. Conclusion The missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1526-0) contains supplementary material, which is available to authorized users.
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Ghassemi S, Lichius A, Bidard F, Lemoine S, Rossignol MN, Herold S, Seidl-Seiboth V, Seiboth B, Espeso EA, Margeot A, Kubicek CP. The ß-importin KAP8 (Pse1/Kap121) is required for nuclear import of the cellulase transcriptional regulator XYR1, asexual sporulation and stress resistance in Trichoderma reesei. Mol Microbiol 2015; 96:405-18. [PMID: 25626518 PMCID: PMC4390390 DOI: 10.1111/mmi.12944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 11/26/2022]
Abstract
The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes, and serves as a prime model for their genetic regulation. Most of its (hemi-)cellulolytic enzymes are obligatorily dependent on the transcriptional activator XYR1. Here, we investigated the nucleo-cytoplasmic shuttling mechanism that transports XYR1 across the nuclear pore complex. We identified 14 karyopherins in T. reesei, of which eight were predicted to be involved in nuclear import, and produced single gene-deletion mutants of all. We found KAP8, an ortholog of Aspergillus nidulans KapI, and Saccharomyces cerevisiae Kap121/Pse1, to be essential for nuclear recruitment of GFP-XYR1 and cellulase gene expression. Transformation with the native gene rescued this effect. Transcriptomic analyses of Δkap8 revealed that under cellulase-inducing conditions 42 CAZymes, including all cellulases and hemicellulases known to be under XYR1 control, were significantly down-regulated. Δkap8 strains were capable of forming fertile fruiting bodies but exhibited strongly reduced conidiation both in light and darkness, and showed enhanced sensitivity towards abiotic stress, including high osmotic pressure, low pH and high temperature. Together, these data underscore the significance of nuclear import of XYR1 in cellulase and hemicellulase gene regulation in T. reesei, and identify KAP8 as the major karyopherin required for this process.
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Affiliation(s)
- Sara Ghassemi
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Alexander Lichius
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Fréderique Bidard
- IFP Energies nouvelles1-4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Sophie Lemoine
- Ecole Normale Supérieure, Institut de Biologie de l'ENSIBENS, Plateforme Génomique, Paris, F-75005, France
| | - Marie-Noëlle Rossignol
- Ecole Normale Supérieure, Institut de Biologie de l'ENSIBENS, Plateforme Génomique, Paris, F-75005, France
| | - Silvia Herold
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
- ACIB GmbH, c/o Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Antoine Margeot
- IFP Energies nouvelles1-4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Christian P Kubicek
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
- *For correspondence. E-mail ; Tel. (+ 1) 43 1 58801 166085; Fax (+ 1) 43 1 58801 17299
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Silva-Rocha R, Castro LDS, Antoniêto ACC, Guazzaroni ME, Persinoti GF, Silva RN. Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei. PLoS One 2014; 9:e99366. [PMID: 24941042 PMCID: PMC4062390 DOI: 10.1371/journal.pone.0099366] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/13/2014] [Indexed: 12/22/2022] Open
Abstract
In this work, we report the in silico identification of the cis-regulatory elements for XYR1 and CRE1 proteins in the filamentous fungus Trichoderma reesei, two regulators that play a central role in the expression of cellulase genes. Using four datasets of condition-dependent genes from RNA-seq and RT-qPCR experiments, we performed unsupervised motif discovery and found two short motifs resembling the proposed binding consensus for XYR1 and CRE1. Using these motifs, we analysed the presence and arrangement of putative cis-regulatory elements recognized by both regulators and found that shortly spaced sites were more associated with XYR1- and CRE1-dependent promoters than single, high-score sites. Furthermore, the approach used here allowed the identification of the previously reported XYR1-binding sites from cel7a and xyn1 promoters, and we also mapped the potential target sequence for this regulator at the cel6a promoter that has been suggested but not identified previously. Additionally, seven other promoters (for cel7b, cel61a, cel61b, cel3c, cel3d, xyn3 and swo genes) presented a putative XYR1-binding site, and strong sites for CRE1 were found at the xyr1 and cel7b promoters. Using the cis-regulatory architectures nearly defined for XYR1 and CRE1, we performed genome-wide identification of potential targets for direct regulation by both proteins and important differences on their functional regulons were elucidated. Finally, we performed binding site mapping on the promoters of differentially expressed genes found in T. reesei mutant strains lacking xyr1 or cre1 and found that indirect regulation plays a key role on their signalling pathways. Taken together, the data provided here sheds new light on the mechanisms for signal integration mediated by XYR1 and CRE1 at cellulase promoters.
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Affiliation(s)
- Rafael Silva-Rocha
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Lilian dos Santos Castro
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | | | | | - Gabriela Felix Persinoti
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
- * E-mail:
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Wang J, Zeng D, Mai G, Liu G, Yu S. Homologous constitutive expression of Xyn III in Trichoderma reesei QM9414 and its characterization. Folia Microbiol (Praha) 2013; 59:229-33. [PMID: 24178623 DOI: 10.1007/s12223-013-0288-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 10/15/2013] [Indexed: 11/25/2022]
Abstract
Xylanase III (Xyn III), a specific endoxylanase that belongs to family 10 of the glycoside hydrolases, was overexpressed in Trichoderma reesei QM9414 using a constitutive strong promoter of the gene encoding pyruvate decarboxylase (pdc). The maximum recombinant xylanase activity achieved was 817.2 ± 65.2 U/mL in the transformant fermentation liquid. The productivities of Xyn III accounted for approximately 53% of the total protein secreted by the recombinant. The enzyme was optimally active at 60 °C and pH 6. The recombinant Xyn III was stable at pH 5-8. This is the first report on the homologous expression of xyn3 in T. reesei QM9414. The properties of Xyn III make it promising in a variety of industrial use.
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Affiliation(s)
- Juan Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China,
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The influence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in D-xylose, L-arabinose and steam-exploded sugarcane bagasse. Fungal Genet Biol 2013; 60:29-45. [PMID: 23892063 DOI: 10.1016/j.fgb.2013.07.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 07/03/2013] [Accepted: 07/17/2013] [Indexed: 12/29/2022]
Abstract
The interest in the conversion of plant biomass to renewable fuels such as bioethanol has led to an increased investigation into the processes regulating biomass saccharification. The filamentous fungus Aspergillus niger is an important microorganism capable of producing a wide variety of plant biomass degrading enzymes. In A. niger the transcriptional activator XlnR and its close homolog, AraR, controls the main (hemi-)cellulolytic system responsible for plant polysaccharide degradation. Sugarcane is used worldwide as a feedstock for sugar and ethanol production, while the lignocellulosic residual bagasse can be used in different industrial applications, including ethanol production. The use of pentose sugars from hemicelluloses represents an opportunity to further increase production efficiencies. In the present study, we describe a global gene expression analysis of A. niger XlnR- and AraR-deficient mutant strains, grown on a D-xylose/L-arabinose monosaccharide mixture and steam-exploded sugarcane bagasse. Different gene sets of CAZy enzymes and sugar transporters were shown to be individually or dually regulated by XlnR and AraR, with XlnR appearing to be the major regulator on complex polysaccharides. Our study contributes to understanding of the complex regulatory mechanisms responsible for plant polysaccharide-degrading gene expression, and opens new possibilities for the engineering of fungi able to produce more efficient enzymatic cocktails to be used in biofuel production.
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Wang S, Liu G, Wang J, Yu J, Huang B, Xing M. Enhancing cellulase production in Trichoderma reesei RUT C30 through combined manipulation of activating and repressing genes. ACTA ACUST UNITED AC 2013; 40:633-41. [DOI: 10.1007/s10295-013-1253-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
Abstract
Abstract
To investigate whether enzyme production can be enhanced in the Trichoderma reesei industrial hyperproducer strain RUT C30 by manipulation of cellulase regulation, the positive regulator Xyr1 was constitutively expressed under the control of the strong T. reesei pdc promoter, resulting in significantly enhanced cellulase activity in the transformant during growth on cellulose. In addition, constitutive expression of xyr1 combined with downregulation of the negative regulator encoding gene ace1 further increased cellulase and xylanase activities. Compared with RUT C30, the resulting transformant exhibited 103, 114, and 134 % greater total secreted protein levels, filter paper activity, and CMCase activity, respectively. Surprisingly, strong increases in xyr1 basal expression levels resulted in very high levels of CMCase activity during growth on glucose. These findings demonstrate the feasibility of improving cellulase production by modifying regulator expression, and suggest an attractive new single-step approach for increasing total cellulase productivity in T. reesei.
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Affiliation(s)
- Shaowen Wang
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
- grid.27446.33 0000000417899163 School of Life Sciences Northeast Normal University 130024 Changchun China
| | - Gang Liu
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
| | - Juan Wang
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
| | - Jianteng Yu
- Department of Marine Biology Shenzhen Key Laboratory of Marine Biotechnology and Ecology 518060 Shenzhen China
| | - Baiqu Huang
- grid.27446.33 0000000417899163 School of Life Sciences Northeast Normal University 130024 Changchun China
| | - Miao Xing
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
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Nitta M, Furukawa T, Shida Y, Mori K, Kuhara S, Morikawa Y, Ogasawara W. A new Zn(II)2Cys6-type transcription factor BglR regulates β-glucosidase expression in Trichoderma reesei. Fungal Genet Biol 2012; 49:388-97. [DOI: 10.1016/j.fgb.2012.02.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/07/2012] [Accepted: 02/25/2012] [Indexed: 11/25/2022]
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de Souza WR, de Gouvea PF, Savoldi M, Malavazi I, de Souza Bernardes LA, Goldman MHS, de Vries RP, de Castro Oliveira JV, Goldman GH. Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:40. [PMID: 22008461 PMCID: PMC3219568 DOI: 10.1186/1754-6834-4-40] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/18/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Considering that the costs of cellulases and hemicellulases contribute substantially to the price of bioethanol, new studies aimed at understanding and improving cellulase efficiency and productivity are of paramount importance. Aspergillus niger has been shown to produce a wide spectrum of polysaccharide hydrolytic enzymes. To understand how to improve enzymatic cocktails that can hydrolyze pretreated sugarcane bagasse, we used a genomics approach to investigate which genes and pathways are transcriptionally modulated during growth of A. niger on steam-exploded sugarcane bagasse (SEB). RESULTS Herein we report the main cellulase- and hemicellulase-encoding genes with increased expression during growth on SEB. We also sought to determine whether the mRNA accumulation of several SEB-induced genes encoding putative transporters is induced by xylose and dependent on glucose. We identified 18 (58% of A. niger predicted cellulases) and 21 (58% of A. niger predicted hemicellulases) cellulase- and hemicellulase-encoding genes, respectively, that were highly expressed during growth on SEB. CONCLUSIONS Degradation of sugarcane bagasse requires production of many different enzymes which are regulated by the type and complexity of the available substrate. Our presently reported work opens new possibilities for understanding sugarcane biomass saccharification by A. niger hydrolases and for the construction of more efficient enzymatic cocktails for second-generation bioethanol.
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Affiliation(s)
- Wagner R de Souza
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Paula F de Gouvea
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Marcela Savoldi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos, Brazil
| | - Luciano A de Souza Bernardes
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, CEP 45662-000, Ilhéus, Bahia, Brazil
| | - Maria Helena S Goldman
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, CEP 14040-901, Ribeirão Preto, São Paulo, Brazil
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Juliana V de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
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Xylose triggers reversible phosphorylation of XlnR, the fungal transcriptional activator of xylanolytic and cellulolytic genes in Aspergillus oryzae. Biosci Biotechnol Biochem 2011; 75:953-9. [PMID: 21597200 DOI: 10.1271/bbb.100923] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
XlnR is a transcription factor that mediates D-xylose-triggered induction of xylanolytic and cellulolytic genes in Aspergillus. In order to clarify the molecular mechanisms underlying XlnR-mediated induction, Aspergillus oryzae XlnR was fused with the c-myc tag and examined by Western blotting. Phosphate-affinity SDS-PAGE revealed that XlnR was present as a mixture of variously phosphorylated forms in the absence of D-xylose, and that D-xylose triggered additional phosphorylation of the protein. D-Xylose-triggered phosphorylation was a rapid process occurring within 5 min prior to the accumulation of xynG2 mRNA, and removal of D-xylose caused slow dephosphorylation, leading to less-phosphorylated forms. At 30 min after removal, the phosphorylation status was almost identical to that in the absence of D-xylose, and the level of xynG2 mRNA started to decrease. These results indicate that XlnR is highly phosphorylated when it is active in transactivation, implying that D-xylose-triggered reversible phosphorylation controls XlnR activity.
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Genes regulated by AoXlnR, the xylanolytic and cellulolytic transcriptional regulator, in Aspergillus oryzae. Appl Microbiol Biotechnol 2009; 85:141-54. [DOI: 10.1007/s00253-009-2236-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 08/24/2009] [Accepted: 08/31/2009] [Indexed: 10/20/2022]
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Furukawa T, Shida Y, Kitagami N, Mori K, Kato M, Kobayashi T, Okada H, Ogasawara W, Morikawa Y. Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Fungal Genet Biol 2009; 46:564-74. [PMID: 19393758 DOI: 10.1016/j.fgb.2009.04.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Revised: 04/15/2009] [Accepted: 04/15/2009] [Indexed: 11/20/2022]
Abstract
The transcriptional activator XYR1 is the central regulator that governs cellulolytic and xylanolytic gene expression in Trichoderma reesei. However, despite its biological importance, relatively little is known about its functional binding sequences. In the present study, we investigated the binding characteristics and specific target for XYR1 by using DNase I footprinting analysis and electrophoretic mobility shift assays. We demonstrate that XYR1 can interact not only with the 5'-GGCTAA-3' motif but also with several 5'-GGC(A/T)(3)-3' motifs. In silico analysis revealed that the 5'-GGC(A/T)(3)-3' motifs are widespread as single site in 5'-upstream region of all the XYR1-regulated genes. Furthermore, we defined the important nucleotides within the binding site that contribute to specific interaction with XYR1. Our results suggest that, together with the inverted repeat motifs, the single 5'-GGC(A/T)(4)-3' motifs play important roles as functional XYR1-binding sites in the regulation of cellulase and xylanase gene expression in T. reesei.
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Affiliation(s)
- Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Rahman Z, Shida Y, Furukawa T, Suzuki Y, Okada H, Ogasawara W, Morikawa Y. Evaluation and characterization of Trichoderma reesei cellulase and xylanase promoters. Appl Microbiol Biotechnol 2009; 82:899-908. [DOI: 10.1007/s00253-008-1841-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 11/30/2022]
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