1
|
Jadhav R, Mach RL, Mach-Aigner AR. Protein secretion and associated stress in industrially employed filamentous fungi. Appl Microbiol Biotechnol 2024; 108:92. [PMID: 38204136 PMCID: PMC10781871 DOI: 10.1007/s00253-023-12985-4] [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: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.
Collapse
Affiliation(s)
- Reshma Jadhav
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
| |
Collapse
|
2
|
Sun X, Gao F, Fan C, Yang S, Zhao T, Tu T, Luo H, Yao B, Huang H, Su X. Sub-genomic RNAi-assisted strain evolution of filamentous fungi for enhanced protein production. Appl Environ Microbiol 2024; 90:e0208223. [PMID: 38899886 PMCID: PMC11267940 DOI: 10.1128/aem.02082-23] [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: 11/18/2023] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Genetic engineering at the genomic scale provides a rapid means to evolve microbes for desirable traits. However, in many filamentous fungi, such trials are daunted by low transformation efficiency. Differentially expressed genes under certain conditions may contain important regulatory factors. Accordingly, although manipulating these subsets of genes only can largely reduce the time and labor, engineering at such a sub-genomic level may also be able to improve the microbial performance. Herein, first using the industrially important cellulase-producing filamentous fungus Trichoderma reesei as a model organism, we constructed suppression subtractive hybridization (SSH) libraries enriched with differentially expressed genes under cellulase induction (MM-Avicel) and cellulase repression conditions (MM-Glucose). The libraries, in combination with RNA interference, enabled sub-genomic engineering of T. reesei for enhanced cellulase production. The ability of T. reesei to produce endoglucanase was improved by 2.8~3.3-fold. In addition, novel regulatory genes (tre49304, tre120391, and tre123541) were identified to affect cellulase expression in T. reesei. Iterative manipulation using the same strategy further increased the yield of endoglucanase activity to 75.6 U/mL, which was seven times as high as that of the wild type (10.8 U/mL). Moreover, using Humicola insolens as an example, such a sub-genomic RNAi-assisted strain evolution proved to be also useful in other industrially important filamentous fungi. H. insolens is a filamentous fungus commonly used to produce catalase, albeit with similarly low transformation efficiency and scarce knowledge underlying the regulation of catalase expression. By combining SSH and RNAi, a strain of H. insolens producing 28,500 ± 288 U/mL of catalase was obtained, which was 1.9 times as high as that of the parent strain.IMPORTANCEGenetic engineering at the genomic scale provides an unparalleled advantage in microbial strain improvement, which has previously been limited only to the organisms with high transformation efficiency such as Saccharomyces cerevisiae and Escherichia coli. Herein, using the filamentous fungus Trichoderma reesei as a model organism, we demonstrated that the advantage of suppression subtractive hybridization (SSH) to enrich differentially expressed genes and the convenience of RNA interference to manipulate a multitude of genes could be combined to overcome the inadequate transformation efficiency. With this sub-genomic evolution strategy, T. reesei could be iteratively engineered for higher cellulase production. Intriguingly, Humicola insolens, a fungus with even little knowledge in gene expression regulation, was also improved for catalase production. The same strategy may also be expanded to engineering other microorganisms for enhanced production of proteins, organic acids, and secondary metabolites.
Collapse
Affiliation(s)
- Xianhua Sun
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Gao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Fan
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, China
| | - Shuyan Yang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tong Zhao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
3
|
Picazo I, Espeso EA. Interconnections between the Cation/Alkaline pH-Responsive Slt and the Ambient pH Response of PacC/Pal Pathways in Aspergillus nidulans. Cells 2024; 13:651. [PMID: 38607089 PMCID: PMC11011638 DOI: 10.3390/cells13070651] [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: 02/13/2024] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
In the filamentous ascomycete Aspergillus nidulans, at least three high hierarchy transcription factors are required for growth at extracellular alkaline pH: SltA, PacC and CrzA. Transcriptomic profiles depending on alkaline pH and SltA function showed that pacC expression might be under SltA regulation. Additional transcriptional studies of PacC and the only pH-regulated pal gene, palF, confirmed both the strong dependence on ambient pH and the function of SltA. The regulation of pacC expression is dependent on the activity of the zinc binuclear (C6) cluster transcription factor PacX. However, we found that the ablation of sltA in the pacX- mutant background specifically prevents the increase in pacC expression levels without affecting PacC protein levels, showing a novel specific function of the PacX factor. The loss of sltA function causes the anomalous proteolytic processing of PacC and a reduction in the post-translational modifications of PalF. At alkaline pH, in a null sltA background, PacC72kDa accumulates, detection of the intermediate PacC53kDa form is extremely low and the final processed form of 27 kDa shows altered electrophoretic mobility. Constitutive ubiquitination of PalF or the presence of alkalinity-mimicking mutations in pacC, such as pacCc14 and pacCc700, resembling PacC53kDa and PacC27kDa, respectively, allowed the normal processing of PacC but did not rescue the alkaline pH-sensitive phenotype caused by the null sltA allele. Overall, data show that Slt and PacC/Pal pathways are interconnected, but the transcription factor SltA is on a higher hierarchical level than PacC on regulating the tolerance to the ambient alkalinity in A. nidulans.
Collapse
Affiliation(s)
| | - Eduardo A. Espeso
- Department of Molecular and Cellular Biology, Centro de Investigaciones Biológicas (CIB) Margarita Salas, Spanish Research Council (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain;
| |
Collapse
|
4
|
Zhu Z, Zou G, Chai S, Xiao M, Wang Y, Wang P, Zhou Z. The protein methyltransferase TrSAM inhibits cellulase gene expression by interacting with the negative regulator ACE1 in Trichoderma reesei. Commun Biol 2024; 7:375. [PMID: 38548869 PMCID: PMC10978942 DOI: 10.1038/s42003-024-06072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Protein methylation is a commonly posttranslational modification of transcriptional regulators to fine-tune protein function, however, whether this regulation strategy participates in the regulation of lignocellulase synthesis and secretion in Trichoderma reesei remains unexplored. Here, a putative protein methyltransferase (TrSAM) is screened from a T. reesei mutant with the ability to express heterologous β-glucosidase efficiently even under glucose repression. The deletion of its encoding gene trsam causes a significant increase of cellulase activities in all tested T. reesei strains, including transformants of expressing heterologous genes using cbh1 promotor. Further investigation confirms that TrSAM interacts with the cellulase negative regulator ACE1 via its amino acid residue Arg383, which causes a decrease in the ACE1-DNA binding affinity. The enzyme activity of a T. reesei strain harboring ACE1R383Q increases by 85.8%, whereas that of the strains with trsam or ace1 deletion increases by more than 100%. By contrast, the strain with ACE1R383K shows no difference to the parent strain. Taken together, our results demonstrate that TrSAM plays an important role in regulating the expression of cellulase and heterologous proteins initiated by cbh1 promotor through interacting with ACE1R383. Elimination and mutation of TrSAM and its downstream ACE1 alleviate the carbon catabolite repression (CCR) in expressing cellulase and heterologous protein in varying degrees. This provides a new solution for the exquisite modification of T. reesei chassis.
Collapse
Affiliation(s)
- Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Science, 1000 Jinqi Rd, Shanghai, 201403, China
| | - Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinmei Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China.
| |
Collapse
|
5
|
Gurnani B, Natarajan R, Mohan M, Kaur K. Breaking-Down Barriers: Proposal of Using Cellulose Biosynthesis Inhibitors and Cellulase Enzyme as a Novel Treatment Modality for Vision Threatening Pythium Insidiosum Keratitis. Clin Ophthalmol 2024; 18:765-776. [PMID: 38495678 PMCID: PMC10941664 DOI: 10.2147/opth.s450665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
Pythium insidiosum, an Oomycete, causes severe keratitis that endangers vision. Its clinical, morphological, and microbiological characteristics are often indistinguishable from those of fungal keratitis, earning it the moniker "parafungus". Distinctive clinical hallmarks that set it apart from other forms of keratitis include radial keratoneuritis, tentacles, marginal infiltration, and a propensity for rapid limbal spread. The therapeutic approach to Pythium keratitis (PK) has long been a subject of debate, and topical and systemic antifungals and antibacterials have been tried with limited success. Approximately 80% of these eyes undergo therapeutic keratoplasty to salvage the eye. Hence, there is a need to innovate for alternative and better medical therapy to safeguard these eyes. The resistance of Pythium to standard antifungal treatments can be attributed to the absence of ergosterol in its cell wall. Cell walls of plants and algae have cellulose as an essential constituent. Cellulose imparts strength and structure and acts as the "skeleton" of the plant. Fungal and animal cell walls typically lack cellulose. The cellular architecture of Pythium shares a similarity with plant and algal cells through the incorporation of cellulose within its cell wall structure. Inhibitors targeting cellulose biosynthesis (CBI), such as Indaziflam, Isoxaben, and Quinoxyphen, serve as critical tools for elucidating the pathways of cellulose synthesis. Furthermore, the enzymatic action of cellulase is instrumental for the extraction of proteins and DNA. To circumvent this issue, we hypothesize that CBI's and cellulase enzymes can act on the Pythium cell wall and may effectively treat PK. The available literature supporting the hypothesis and proof of concept has also been discussed. We have also discussed these drugs' molecular mechanism of action on the Pythium cell wall. We also aim to propose how these drugs can be procured and used as a potential medical management option for this devastating entity.
Collapse
Affiliation(s)
- Bharat Gurnani
- Department of Cataract, Cornea and Refractive Surgery, ASG Eye Hospital, Jodhpur, Rajasthan, 342008, India
| | - Radhika Natarajan
- Department of Cornea and Refractive Surgery, Sankara Nethralaya Medical Research Foundation, Chennai, Tamil Nadu, 600006, India
| | - Madhuvanthi Mohan
- Department of Cornea and Refractive Surgery, Sankara Nethralaya Medical Research Foundation, Chennai, Tamil Nadu, 600006, India
| | - Kirandeep Kaur
- Department of Pediatric Ophthalmology and Strabismus, ASG Eye Hospital, Jodhpur, Rajasthan, 342008, India
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Wang L, Zhao Y, Chen S, Wen X, Anjago WM, Tian T, Chen Y, Zhang J, Deng S, Jiu M, Fu P, Zhou D, Druzhinina IS, Wei L, Daly P. Growth, Enzymatic, and Transcriptomic Analysis of xyr1 Deletion Reveals a Major Regulator of Plant Biomass-Degrading Enzymes in Trichoderma harzianum. Biomolecules 2024; 14:148. [PMID: 38397385 PMCID: PMC10887015 DOI: 10.3390/biom14020148] [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: 11/14/2023] [Revised: 12/24/2023] [Accepted: 01/09/2024] [Indexed: 02/25/2024] Open
Abstract
The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed through growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had ~90% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. The expression of a subset of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes.
Collapse
Affiliation(s)
- Lunji Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; (L.W.); (Y.Z.); (X.W.); (M.J.)
| | - Yishen Zhao
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; (L.W.); (Y.Z.); (X.W.); (M.J.)
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Siqiao Chen
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing 210095, China
| | - Xian Wen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; (L.W.); (Y.Z.); (X.W.); (M.J.)
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Wilfred Mabeche Anjago
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Tianchi Tian
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Yajuan Chen
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
- Key Laboratory of Coal Processing and Efficient Utilization, China University of Mining and Technology, Xuzhou 221116, China
| | - Jinfeng Zhang
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Sheng Deng
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Min Jiu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; (L.W.); (Y.Z.); (X.W.); (M.J.)
| | - Pengxiao Fu
- Jiangsu Coastal Ecological Science and Technology Development Co., Ltd., Nanjing 210036, China;
| | - Dongmei Zhou
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Irina S. Druzhinina
- Department of Accelerated Taxonomy, The Royal Botanic Gardens Kew, London TW9 3AE, UK;
| | - Lihui Wei
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| | - Paul Daly
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.C.); (W.M.A.); (T.T.); (Y.C.); (J.Z.); (S.D.); (D.Z.)
| |
Collapse
|
8
|
Giwa AS, Ali N, Akhter MS. Cellulose Degradation Enzymes in Filamentous Fungi, A Bioprocessing Approach Towards Biorefinery. Mol Biotechnol 2023:10.1007/s12033-023-00900-1. [PMID: 37839042 DOI: 10.1007/s12033-023-00900-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023]
Abstract
The economic exploration of renewable energy resources has hot fundamentals among the countries besides dwindling energy resources and increasing public pressure. Cellulose accumulation is a major bio-natural resource from agricultural waste. Cellulases are the most potential enzymes that systematically degrade cellulosic biomass into monomers which could be further processed into several efficient value-added products via chemical and biological reactions including useful biomaterial for human benefits. This could lower the environmental risks problems followed by an energy crisis. Cellulases are mainly synthesized by special fungal genotypes. The strain Trichoderma orientalis could highly express cellulases and was regarded as an ideal strain for further research, as the genetic tools have found compatibility for cellulose breakdown by producing effective cellulose-degrading enzymes. This strain has found a cellulase production of about 35 g/L that needs further studies for advancement. The enzyme activity of strain Trichoderma orientalis needed to be further improved from a molecular level which is one of the important methods. Considering synthetic biological approaches to unveil the genetic tools will boost the knowledge about commercial cellulases bioproduction. Several genetic transformation methods were significantly cited in this study. The transformation approaches that are currently researchers are exploring is transcription regulatory factors that are deeply explained in this study, that are considered essential regulators of gene expression.
Collapse
Affiliation(s)
- Abdulmoseen Segun Giwa
- School of Environment and Civil Engineering, Nanchang Institute of Science and Technology, Nanchang, 330108, China
| | - Nasir Ali
- Institute of Biotechnology Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.
| | - Mohammed Salim Akhter
- Department of Chemistry, College of Science, University of Bahrain, Sakheer Campus Bahrain, Zallaq, Bahrain
| |
Collapse
|
9
|
Kerkaert JD, Huberman LB. Regulation of nutrient utilization in filamentous fungi. Appl Microbiol Biotechnol 2023; 107:5873-5898. [PMID: 37540250 PMCID: PMC10983054 DOI: 10.1007/s00253-023-12680-4] [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: 04/19/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
Organisms must accurately sense and respond to nutrients to survive. In filamentous fungi, accurate nutrient sensing is important in the establishment of fungal colonies and in continued, rapid growth for the exploitation of environmental resources. To ensure efficient nutrient utilization, fungi have evolved a combination of activating and repressing genetic networks to tightly regulate metabolic pathways and distinguish between preferred nutrients, which require minimal energy and resources to utilize, and nonpreferred nutrients, which have more energy-intensive catabolic requirements. Genes necessary for the utilization of nonpreferred carbon sources are activated by transcription factors that respond to the presence of the specific nutrient and repressed by transcription factors that respond to the presence of preferred carbohydrates. Utilization of nonpreferred nitrogen sources generally requires two transcription factors. Pathway-specific transcription factors respond to the presence of a specific nonpreferred nitrogen source, while another transcription factor activates genes in the absence of preferred nitrogen sources. In this review, we discuss the roles of transcription factors and upstream regulatory genes that respond to preferred and nonpreferred carbon and nitrogen sources and their roles in regulating carbon and nitrogen catabolism. KEY POINTS: • Interplay of activating and repressing transcriptional networks regulates catabolism. • Nutrient-specific activating transcriptional pathways provide metabolic specificity. • Repressing regulatory systems differentiate nutrients in mixed nutrient environments.
Collapse
Affiliation(s)
- Joshua D Kerkaert
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Lori B Huberman
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
10
|
Singh V, Raheja Y, Basotra N, Sharma G, Tsang A, Chadha BS. CRISPR/Cas9 mediated gene editing of transcription factor ACE1 for enhanced cellulase production in thermophilic fungus Rasamsonia emersonii. Fungal Biol Biotechnol 2023; 10:18. [PMID: 37658430 PMCID: PMC10472679 DOI: 10.1186/s40694-023-00165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND The filamentous fungus Rasamsonia emersonii has immense potential to produce biorefinery relevant thermostable cellulase and hemicellulase enzymes using lignocellulosic biomass. Previously in our lab, a hyper-cellulase producing strain of R. emersonii was developed through classical breeding and system biology approaches. ACE1, a pivotal transcription factor in fungi, plays a crucial role in negatively regulating the expression of cellulase genes. In order to identify the role of ACE1 in cellulase production and to further improve the lignocellulolytic enzyme production in R. emersonii, CRISPR/Cas9 mediated disruption of ACE1 gene was employed. RESULTS A gene-edited ∆ACE1 strain (GN11) was created, that showed 21.97, 20.70 and 24.63, 9.42, 18.12%, improved endoglucanase, cellobiohydrolase (CBHI), β-glucosidase, FPase, and xylanase, activities, respectively, as compared to parental strain M36. The transcriptional profiling showed that the expression of global regulator (XlnR) and different CAZymes genes including endoglucanases, cellobiohydrolase, β-xylosidase, xylanase, β-glucosidase and lytic polysaccharide mono-oxygenases (LPMOs) were significantly enhanced, suggesting critical roles of ACE1 in negatively regulating the expression of various key genes associated with cellulase production in R. emersonii. Whereas, the disruption of ACE1 significantly down-regulated the expression of CreA repressor gene as also evidenced by 2-deoxyglucose (2-DG) resistance phenotype exhibited by edited strain GN11 as well as appreciably higher constitutive production of cellulases in the presence of glucose and mixture of glucose and disaccharide (MGDs) both in batch and flask fed batch mode of culturing. Furthermore, ∆ACE1 strains were evaluated for the hydrolysis of biorefinery relevant steam/acid pretreated unwashed rice straw slurry (Praj Industries Ltd; 15% substrate loading rate) and were found to be significantly superior when compared to the benchmark enzymes produced by parent strain M36 and Cellic Ctec3. CONCLUSIONS Current work uncovers the crucial role of ACE1 in regulating the expression of the various cellulase genes and carbon catabolite repression mechanism in R. emersonii. This study represents the first successful report of utilizing CRISPR/Cas9 genome editing technology to disrupt the ACE1 gene in the thermophlic fungus R. emersonii. The improved methodologies presented in this work might be applied to other commercially important fungal strains for which genetic manipulation tools are limited.
Collapse
Affiliation(s)
- Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Gaurav Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
| | | |
Collapse
|
11
|
Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
Collapse
Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
| |
Collapse
|
12
|
Yan S, Xu Y, Yu XW. Role of cellulose response transporter-like protein CRT2 in cellulase induction in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:118. [PMID: 37488642 PMCID: PMC10364367 DOI: 10.1186/s13068-023-02371-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Induction of cellulase in cellulolytic fungi Trichoderma reesei is strongly activated by cellulosic carbon sources. The transport of cellulosic inducer and the perception of inducing signal is generally considered as the critical process for cellulase induction, that the inducing signal would be perceived by a sugar transporter/transceptor in T. reesei. Several sugar transporters are coexpressed during the induction stage, but which function they serve and how they work collaboratively are still difficult to elucidate. RESULTS In this study, we found that the constitutive expression of the cellulose response transporter-like protein CRT2 (previously identified as putative lactose permease TRE77517) improves cellulase induction on a cellulose, cellobiose or lactose medium. Functional studies indicate that the membrane-bound CRT2 is not a transporter of cellobiose, lactose or glucose in a yeast system, and it also does not affect cellobiose and lactose utilization in T. reesei. Further study reveals that CRT2 has a slightly similar function to the cellobiose transporter CRT1 in cellulase induction. Overexpression of CRT2 led to upregulation of CRT1 and the key transcription factor XYR1. Moreover, overexpression of CRT2 could partially compensate for the function loss of CRT1 on cellulase induction. CONCLUSIONS Our study uncovers the novel function of CRT2 in cellulase induction collaborated with CRT1 and XYR1, possibly as a signal transductor. These results deepen the understanding of the influence of sugar transporters in cellulase production.
Collapse
Affiliation(s)
- Su Yan
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiao-Wei Yu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
13
|
Dong CD, Patel AK, Madhavan A, Chen CW, Singhania RR. Significance of glycans in cellulolytic enzymes for lignocellulosic biorefinery - A review. BIORESOURCE TECHNOLOGY 2023; 379:128992. [PMID: 37011847 DOI: 10.1016/j.biortech.2023.128992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
Lignocellulosic (LC) biomass is the most abundant renewable resource for mankind gravitating society towards sustainable solution for energy that can reduce the carbon footprint. The economic feasibility of 'biomass biorefinery' depends upon the efficiency cellulolytic enzymes which is the main crux. Its high production cost and low efficiencies are the major limitations, that need to be resolved. As the complexity of the genome increases, so does the complexity of the proteome, further facilitated by protein post-translational modifications (PTMs). Glycosylation is regarded the major PTMs and hardly any recent work is focused on importance of glycosylation in cellulase. By modifying protein side chains and glycans, superior cellulases with improved stability and efficiency can be obtained. Functional proteomics relies heavily on PTMs because they regulate activity, localization, and interactions with protein, lipid, nucleic acid, and cofactor molecules. O- and N- glycosylation in cellulases influences its characteristics adding positive attributes to the enzymes.
Collapse
Affiliation(s)
- Cheng-Di Dong
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Anil Kumar Patel
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India
| | - Aravind Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam, Kerala 690 525, India
| | - Chiu-Wen Chen
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Reeta Rani Singhania
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India.
| |
Collapse
|
14
|
Arai T, Ichinose S, Shibata N, Kakeshita H, Kodama H, Igarashi K, Takimura Y. Inducer-free cellulase production system based on the constitutive expression of mutated XYR1 and ACE3 in the industrial fungus Trichoderma reesei. Sci Rep 2022; 12:19445. [PMID: 36376415 PMCID: PMC9663580 DOI: 10.1038/s41598-022-23815-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Trichoderma reesei is a widely used host for producing cellulase and hemicellulase cocktails for lignocellulosic biomass degradation. Here, we report a genetic modification strategy for industrial T. reesei that enables enzyme production using simple glucose without inducers, such as cellulose, lactose and sophorose. Previously, the mutated XYR1V821F or XYR1A824V was known to induce xylanase and cellulase using only glucose as a carbon source, but its enzyme composition was biased toward xylanases, and its performance was insufficient to degrade lignocellulose efficiently. Therefore, we examined combinations of mutated XYR1V821F and constitutively expressed CRT1, BGLR, VIB1, ACE2, or ACE3, known as cellulase regulators and essential factors for cellulase expression to the T. reesei E1AB1 strain that has been highly mutagenized for improving enzyme productivity and expressing a ß-glucosidase for high enzyme performance. The results showed that expression of ACE3 to the mutated XYR1V821F expressing strain promoted cellulase expression. Furthermore, co-expression of these two transcription factors also resulted in increased productivity, with enzyme productivity 1.5-fold higher than with the conventional single expression of mutated XYR1V821F. Additionally, that productivity was 5.5-fold higher compared to productivity with an enhanced single expression of ACE3. Moreover, although the DNA-binding domain of ACE3 had been considered essential for inducer-free cellulase production, we found that ACE3 with a partially truncated DNA-binding domain was more effective in cellulase production when co-expressed with a mutated XYR1V821F. This study demonstrates that co-expression of the two transcription factors, the mutated XYR1V821F or XYR1A824V and ACE3, resulted in optimized enzyme composition and increased productivity.
Collapse
Affiliation(s)
- Toshiharu Arai
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Sakurako Ichinose
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Nozomu Shibata
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Hiroshi Kakeshita
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan.
| | - Hiroshi Kodama
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Kazuaki Igarashi
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Yasushi Takimura
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| |
Collapse
|
15
|
Xia Y, Wang J, Guo C, Xu H, Wang W, Yang M, Shen Q, Zhang R, Miao Y. Exploring the multi-level regulation of lignocellulases in the filamentous fungus Trichoderma guizhouense NJAU4742 from an omics perspective. Microb Cell Fact 2022; 21:144. [PMID: 35842666 PMCID: PMC9288086 DOI: 10.1186/s12934-022-01869-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Filamentous fungi are highly efficient at deconstructing plant biomass by secreting a variety of enzymes, but the complex enzymatic regulation underlying this process is not conserved and remains unclear. RESULTS In this study, cellulases and xylanases could specifically respond to Avicel- and xylan-induction, respectively, in lignocellulose-degrading strain Trichoderma guizhouense NJAU4742, however, the differentially regulated cellulases and xylanases were both under the absolute control of the same TgXyr1-mediated pathway. Further analysis showed that Avicel could specifically induce cellulase expression, which supported the existence of an unknown specific regulator of cellulases in strain NJAU4742. The xylanase secretion is very complex, GH10 endoxylanases could only be induced by Avicel, while, other major xylanases were significantly induced by both Avicel and xylan. For GH10 xylanases, an unknown specific regulator was also deduced to exist. Meanwhile, the post-transcriptional inhibition was subsequently suggested to stop the Avicel-induced xylanases secretion, which explained the specifically high xylanase activities when induced by xylan in strain NJAU4742. Additionally, an economical strategy used by strain NJAU4742 was proposed to sense the environmental lignocellulose under the carbon starvation condition, that only slightly activating 4 lignocellulose-degrading genes before largely secreting all 33 TgXyr1-controlled lignocellulases if confirming the existence of lignocellulose components. CONCLUSIONS This study, aiming to explore the unknown mechanisms of plant biomass-degrading enzymes regulation through the combined omics analysis, will open directions for in-depth understanding the complex carbon utilization in filamentous fungi.
Collapse
Affiliation(s)
- 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, 210095, Nanjing, People's Republic of China
| | - Jingfan Wang
- 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, 210095, Nanjing, People's Republic of China
| | - Chuanxu Guo
- 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, 210095, Nanjing, People's Republic of China
| | - Huanhuan 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, 210095, Nanjing, People's Republic of China
| | - Wei Wang
- 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, 210095, Nanjing, People's Republic of China
| | - Mingzhu Yang
- 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, 210095, Nanjing, People's Republic of 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, 210095, Nanjing, People's Republic of 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, 210095, Nanjing, People's Republic of China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - 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, 210095, Nanjing, People's Republic of China.
| |
Collapse
|
16
|
The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom
Schizophyllum commune. mBio 2022; 13:e0062822. [PMID: 35604096 PMCID: PMC9239231 DOI: 10.1128/mbio.00628-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wood-degrading fungi in the phylum Basidiomycota play a crucial role in nutrient recycling by breaking down all components of wood. Fungi have evolved transcriptional networks that regulate expression of wood-degrading enzymes, allowing them to prioritize one nutrient source over another.
Collapse
|
17
|
Pang AP, Luo Y, Hu X, Zhang F, Wang H, Gao Y, Durrani S, Li C, Shi X, Wu FG, Li BZ, Lu Z, Lin F. Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei. Microb Cell Fact 2022; 21:90. [PMID: 35590356 PMCID: PMC9118834 DOI: 10.1186/s12934-022-01809-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown. Results We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose. Conclusions Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01809-1.
Collapse
Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yongsheng Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaotong Shi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| |
Collapse
|
18
|
Mattam AJ, Chaudhari YB, Velankar HR. Factors regulating cellulolytic gene expression in filamentous fungi: an overview. Microb Cell Fact 2022; 21:44. [PMID: 35317826 PMCID: PMC8939176 DOI: 10.1186/s12934-022-01764-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/27/2022] [Indexed: 12/19/2022] Open
Abstract
The growing demand for biofuels such as bioethanol has led to the need for identifying alternative feedstock instead of conventional substrates like molasses, etc. Lignocellulosic biomass is a relatively inexpensive feedstock that is available in abundance, however, its conversion to bioethanol involves a multistep process with different unit operations such as size reduction, pretreatment, saccharification, fermentation, distillation, etc. The saccharification or enzymatic hydrolysis of cellulose to glucose involves a complex family of enzymes called cellulases that are usually fungal in origin. Cellulose hydrolysis requires the synergistic action of several classes of enzymes, and achieving the optimum secretion of these simultaneously remains a challenge. The expression of fungal cellulases is controlled by an intricate network of transcription factors and sugar transporters. Several genetic engineering efforts have been undertaken to modulate the expression of cellulolytic genes, as well as their regulators. This review, therefore, focuses on the molecular mechanism of action of these transcription factors and their effect on the expression of cellulases and hemicellulases.
Collapse
Affiliation(s)
- Anu Jose Mattam
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Yogesh Babasaheb Chaudhari
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Harshad Ravindra Velankar
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India.
| |
Collapse
|
19
|
Paul M, Mohapatra S, Kumar Das Mohapatra P, Thatoi H. Microbial cellulases - An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. BIORESOURCE TECHNOLOGY 2021; 340:125710. [PMID: 34365301 DOI: 10.1016/j.biortech.2021.125710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The inherent resistance of lignocellulosic biomass makes it impervious for industrially important enzymes such as cellulases to hydrolyze cellulose. Further, the competitive absorption behavior of lignin and hemicellulose for cellulases, due to their electron-rich surfaces augments the inappropriate utilization of these enzymes. Hence, modification of the surface charge of the cellulases to reduce its non-specific binding to lignin and enhance its affinity for cellulose is an urgent necessity. Further, maintaining the stability of cellulases by the preservation of their secondary structures using immobilization techniques will also play an integral role in its industrial production. In silico approaches for increasing the catalytic activity of cellulase enzymes is also significant along with a range of substrate specificity. In addition, enhanced productivity of cellulases by tailoring the related genes through the process of genetic engineering and higher cellulase recovery after saccharification seems to be promising areas for efficient and large-scale enzyme production concepts.
Collapse
Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India
| | - Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Bhubaneswar 751003, Odisha, India
| | - Pradeep Kumar Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India; PAKB Environment Conservation Centre, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India.
| |
Collapse
|
20
|
Filho JAF, Rosolen RR, Almeida DA, de Azevedo PHC, Motta MLL, Aono AH, dos Santos CA, Horta MAC, de Souza AP. Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. 3 Biotech 2021; 11:475. [PMID: 34777932 PMCID: PMC8548487 DOI: 10.1007/s13205-021-03032-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Fungi are key players in biotechnological applications. Although several studies focusing on fungal diversity and genetics have been performed, many details of fungal biology remain unknown, including how cellulolytic enzymes are modulated within these organisms to allow changes in main plant cell wall compounds, cellulose and hemicellulose, and subsequent biomass conversion. With the advent and consolidation of DNA/RNA sequencing technology, different types of information can be generated at the genomic, structural and functional levels, including the gene expression profiles and regulatory mechanisms of these organisms, during degradation-induced conditions. This increase in data generation made rapid computational development necessary to deal with the large amounts of data generated. In this context, the origination of bioinformatics, a hybrid science integrating biological data with various techniques for information storage, distribution and analysis, was a fundamental step toward the current state-of-the-art in the postgenomic era. The possibility of integrating biological big data has facilitated exciting discoveries, including identifying novel mechanisms and more efficient enzymes, increasing yields, reducing costs and expanding opportunities in the bioprocess field. In this review, we summarize the current status and trends of the integration of different types of biological data through bioinformatics approaches for biological data analysis and enzyme selection.
Collapse
Affiliation(s)
- Jaire A. Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Rafaela R. Rosolen
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Deborah A. Almeida
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Paulo Henrique C. de Azevedo
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Maria Lorenza L. Motta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Alexandre H. Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Clelton A. dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Maria Augusta C. Horta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Anete P. de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Institute of Biology, UNICAMP, Universidade Estadual de Campinas, Campinas, SP 13083-875 Brazil
| |
Collapse
|
21
|
Chen Y, Wang W, Liu P, Lin A, Fan X, Wu C, Li N, Wei L, Wei D. The novel repressor Rce2 competes with Ace3 to regulate cellulase gene expression in the filamentous fungus Trichoderma reesei. Mol Microbiol 2021; 116:1298-1314. [PMID: 34608686 DOI: 10.1111/mmi.14825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/22/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
The filamentous fungus Trichoderma reesei is widely used for industrial cellulase production. In T. reesei, cellulase gene expression is tightly controlled by a regulatory network involving multiple transcription factors. Here, we isolated a novel protein, Rce2, using a pull-down assay and mass spectrometry analysis, from a partial carbon catabolite de-repression mutant, T. reesei Rut-C30, cultured under glucose-repressing conditions. Deletion and overexpression of Rce2 in T. reesei wild-type QM6a and mutant Rut-C30 revealed that Rce2 acts as a repressor of cellulase gene expression. DNase I footprinting assays, electrophoretic mobility shift assays, and chromatin immunoprecipitation assays revealed that Rce2 was located in the nucleus and bound to the consensus sequences 5'-(T/A)NNNNCCG-3' and 5'-CGGNNNN(T/A)-3' in the promoters of cellulase-related genes to repress their transcription. Additionally, Rce2 antagonized Ace3 binding to the cbh1 promoter to repress its transcription. However, Rce2 was not involved in Cre1-mediated carbon catabolite repression. These results demonstrate the mechanism through which Rce2 represses the expression of cellulase genes and provide novel insights into the regulatory system of cellulases and methods that can be used for the regulation of gene expression in T. reesei.
Collapse
Affiliation(s)
- Yumeng Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Pei Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Aibo Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xingjia Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chuan Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ni Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Liujing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| |
Collapse
|
22
|
Fang H, Li C, Zhao J, Zhao C. Biotechnological Advances and Trends in Engineering Trichoderma reesei towards Cellulase Hyperproducer. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0243-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
23
|
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
Karuppiah V, Zhixiang L, Liu H, Vallikkannu M, Chen J. Co-culture of Vel1-overexpressed Trichoderma asperellum and Bacillus amyloliquefaciens: An eco-friendly strategy to hydrolyze the lignocellulose biomass in soil to enrich the soil fertility, plant growth and disease resistance. Microb Cell Fact 2021; 20:57. [PMID: 33653343 PMCID: PMC7927390 DOI: 10.1186/s12934-021-01540-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background Retention of agricultural bio-mass residues without proper treatment could affect the subsequent plant growth. In the present investigation, the co-cultivation of genetically engineered T. asperellum and B. amyloliquefaciens has been employed for multiple benefits including the enrichment of lignocellulose biodegradation, plant growth, defense potential and disease resistance. Results The Vel1 gene predominantly regulates the secondary metabolites, sexual and asexual development as well as cellulases and polysaccharide hydrolases productions. Overexpression mutant of the Trichoderma asperellum Vel1 locus (TA OE-Vel1) enhanced the activity of FPAase, CMCase, PNPCase, PNPGase, xylanase I, and xylanase II through the regulation of transcription regulating factors and the activation of cellulase and xylanase encoding genes. Further, these genes were induced upon co-cultivation with Bacillus amyloliquefaciens (BA). The co-culture of TA OE-Vel1 + BA produced the best composition of enzymes and the highest biomass hydrolysis yield of 89.56 ± 0.61%. The co-culture of TA OE-Vel1 + BA increased the corn stover degradation by the secretion of cellulolytic enzymes and maintained the C/N ratio of the corn stover amended soil. Moreover, the TA OE-Vel1 + BA increased the maize plant growth, expression of defense gene and disease resistance against Fusarium verticillioides and Cohilohorus herostrophus. Conclusion The co-cultivation of genetically engineered T. asperellum and B. amyloliquefaciens could be utilized as a profound and meaningful technique for the retention of agro residues and subsequent plant growth.
Collapse
Affiliation(s)
- Valliappan Karuppiah
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Lu Zhixiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Murugappan Vallikkannu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China. .,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China.
| |
Collapse
|
26
|
Effects of the Transcription Factor Ace2 from Trichoderma reesei on Cellulase and Hemicellulase Expression in Trichoderma orientalis EU7-22. Appl Biochem Biotechnol 2021; 193:2098-2109. [PMID: 33608806 DOI: 10.1007/s12010-021-03529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Trichoderma orientalis (T. orientalis) EU7-22 has a complete cellulase system and shows a remarkable enzyme activity with high potential in the industry. Ace2 is an important transcriptional factor for cellulase and hemicellulase expression in Trichoderma reesei (T. reesei). However, the ace2 gene cannot be found in the genome of T. orientalis. Researches show that the mechanism of cellulase transcriptional regulation in T. orientalis keeps high similarity with T. reesei up till now. So, in this study, the ace2 of Trichoderma reesei QM9414 was heterologous expressed in T. orientalis EU7-22. As a result, xylanase activity and β-glucosidase activity of ace2 heterogeneous expression strains are improved and total cellulase activity is decreased. The result of qPCR is in accordance with enzyme activities. This study provides a reference for an in-depth study on transcriptional regulation mechanisms of T. orientalis.
Collapse
|
27
|
Shibata N, Kakeshita H, Igarashi K, Takimura Y, Shida Y, Ogasawara W, Koda T, Hasunuma T, Kondo A. Disruption of alpha-tubulin releases carbon catabolite repression and enhances enzyme production in Trichoderma reesei even in the presence of glucose. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:39. [PMID: 33557925 PMCID: PMC7869464 DOI: 10.1186/s13068-021-01887-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/19/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Trichoderma reesei is a filamentous fungus that is important as an industrial producer of cellulases and hemicellulases due to its high secretion of these enzymes and outstanding performance in industrial fermenters. However, the reduction of enzyme production caused by carbon catabolite repression (CCR) has long been a problem. Disruption of a typical transcriptional regulator, Cre1, does not sufficiently suppress this reduction in the presence of glucose. RESULTS We found that deletion of an α-tubulin (tubB) in T. reesei enhanced both the amount and rate of secretory protein production. Also, the tubulin-disrupted (ΔtubB) strain had high enzyme production and the same enzyme profile even if the strain was cultured in a glucose-containing medium. From transcriptome analysis, the ΔtubB strain exhibited upregulation of both cellulase and hemicellulase genes including some that were not originally induced by cellulose. Moreover, cellobiose transporter genes and the other sugar transporter genes were highly upregulated, and simultaneous uptake of glucose and cellobiose was also observed in the ΔtubB strain. These results suggested that the ΔtubB strain was released from CCR. CONCLUSION Trichoderma reesei α-tubulin is involved in the transcription of cellulase and hemicellulase genes, as well as in CCR. This is the first report of overcoming CCR by disrupting α-tubulin gene in T. reesei. The disruption of α-tubulin is a promising approach for creating next-generation enzyme-producing strains of T. reesei.
Collapse
Affiliation(s)
- Nozomu Shibata
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Hiroshi Kakeshita
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
| | - Kazuaki Igarashi
- Biological Science Research, Kao Corporation, 2606 Akabane, Ichikai, Haga, Tochigi, 321-3497, Japan
| | - Yasushi Takimura
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
| | - Yosuke Shida
- 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
| | - Tohru Koda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| |
Collapse
|
28
|
Pirayre A, Duval L, Blugeon C, Firmo C, Perrin S, Jourdier E, Margeot A, Bidard F. Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30. BMC Genomics 2020; 21:885. [PMID: 33302864 PMCID: PMC7731781 DOI: 10.1186/s12864-020-07281-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungus Trichoderma reesei. Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network of T. reesei Rut-C30. RESULTS Experimental results on the Rut-C30 hyperproducing strain confirmed the impact of sugar mixtures on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network built using BRANE Cut software reveals three sub-networks related to i) a positive correlation between lactose concentration and cellulase production, ii) a particular dependence of the lactose onto the β-glucosidase regulation and iii) a negative regulation of the development process and growth. CONCLUSIONS This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration of xyr1, clr2 and ace3 for cellulase and hemicellulase induction and production, a fine regulation of the β-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains in industry-like conditions.
Collapse
Affiliation(s)
- Aurélie Pirayre
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France.
| | - Laurent Duval
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
- Laboratoire d'Informatique Gaspard-Monge (LIGM), ESIEE Paris, Université-Gustave Eiffel, Marne-la-Vallée, F-77454, France
| | - Corinne Blugeon
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Cyril Firmo
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Sandrine Perrin
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Etienne Jourdier
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Frédérique Bidard
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| |
Collapse
|
29
|
Zheng F, Yang R, Cao Y, Zhang W, Lv X, Meng X, Zhong Y, Chen G, Zhou Q, Liu W. Engineering Trichoderma reesei for Hyperproduction of Cellulases on Glucose to Efficiently Saccharify Pretreated Corncobs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12671-12682. [PMID: 33140639 DOI: 10.1021/acs.jafc.0c04663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The filamentous fungus Trichoderma reesei (teleomorph Hypocrea jecorina) is widely used as a cellulase producer in the industry. Herein, we describe the rational engineering of the publicly available T. reesei QM9414 strain to achieve a remarkable high-level production of cellulase on glucose. Overexpression of the key cellulase regulator XYR1 by the copper-repressible promoter Ptcu1 was first implemented to achieve a full cellulase production in the context of catabolite repression (CCR) while eliminating the requirement of inducing sugars for enzyme production. The T. reesei bgl1 gene was further overexpressed to compensate for its low β-glucosidase activity on glucose. This overexpression resulted in a 102% increase in FPase activity compared with the CCR-released RUT-C30 strain cultured on Avicel. Moreover, the saccharification efficiency toward pretreated corncob residues by crude enzymes from the engineered strain on glucose increased by 85% compared with that treated by enzymes from RUT-C30 cultivated on Avicel. The engineered T. reesei strain thus shows great potential as a viable alternative to deliver commercial cellulases after further optimization for efficient saccharification of agricultural waste.
Collapse
Affiliation(s)
- Fanglin Zheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Renfei Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Yanli Cao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Xinxing Lv
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| | - Qingxin Zhou
- Shandong Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Institute of Agro-Food Science and Technology, No.202 Gongye North Road, Jinan 250100, P. R. China
- College of Life Science, Shandong Normal University, No.88 Wenhua East Road, Jinan 250014, P. R. China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, Shandong 266237, P. R. China
| |
Collapse
|
30
|
Molecular engineering to improve lignocellulosic biomass based applications using filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:73-109. [PMID: 33934853 DOI: 10.1016/bs.aambs.2020.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lignocellulosic biomass is an abundant and renewable resource, and its utilization has become the focus of research and biotechnology applications as a very promising raw material for the production of value-added compounds. Filamentous fungi play an important role in the production of various lignocellulolytic enzymes, while some of them have also been used for the production of important metabolites. However, wild type strains have limited efficiency in enzyme production or metabolic conversion, and therefore many efforts have been made to engineer improved strains. Examples of this are the manipulation of transcriptional regulators and/or promoters of enzyme-encoding genes to increase gene expression, and protein engineering to improve the biochemical characteristics of specific enzymes. This review provides and overview of the applications of filamentous fungi in lignocellulosic biomass based processes and the development and current status of various molecular engineering strategies to improve these processes.
Collapse
|
31
|
Derntl C, Mach R, Mach-Aigner A. Application of the human estrogen receptor within a synthetic transcription factor in Trichoderma reesei. Fungal Biol Biotechnol 2020; 7:12. [PMID: 32765896 PMCID: PMC7396459 DOI: 10.1186/s40694-020-00102-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/17/2020] [Indexed: 12/28/2022] Open
Abstract
Background Synthetic gene expression systems offer a possibility for controllable and targeted induction of the expression of genes of interest, which is a fundamental technique necessary for basic research and industrial applications. The human estrogen receptor α contains a ligand binding domain that enforces dimerization and nuclear import upon binding of the inducer 17β-estradiol. In this study, we tested the potential of this ligand binding domain to be used in filamentous fungi as an auto-regulatory domain in a synthetic transcription factor. Results We constructed the synthetic transcription factor SynX by fusing the DNA-binding domain of Xyr1 (Xylanase Regulator 1), the transactivation domain of Ypr1 (Yellow Pigment Regulator 1), and the ligand binding domain of the human estrogen receptor α. SynX is able to strongly induce the gene expression of xylanases and an aldose reductase by addition of 17β-estradiol, but SynX does not induce gene expression of cellulases. Importantly, the induction of xylanase activities is mostly carbon source independent and can be fine-tuned by controlling the concentration of 17β-estradiol. Conclusion The ability of SynX to induce gene expression of xylanase encoding genes by addition of 17β-estradiol demonstrates that the ligand binding domain of the human estrogen receptor α works in filamentous fungi, and that it can be combined with a transactivation domain other than the commonly used transactivation domain of herpes simplex virion protein VP16.
Collapse
Affiliation(s)
- Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Robert Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Astrid Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| |
Collapse
|
32
|
Luo Y, Valkonen M, Jackson RE, Palmer JM, Bhalla A, Nikolaev I, Saloheimo M, Ward M. Modification of transcriptional factor ACE3 enhances protein production in Trichoderma reesei in the absence of cellulase gene inducer. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:137. [PMID: 32782473 PMCID: PMC7412840 DOI: 10.1186/s13068-020-01778-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/29/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Trichoderma reesei is one of the best-known cellulolytic organisms, producing large quantities of a complete set of extracellular cellulases and hemicellulases for the degradation of lignocellulosic substances. Hence, T. reesei is a biotechnically important host and it is used commercially in enzyme production, of both native and foreign origin. Many strategies for producing enzymes in T. reesei rely on the cbh1 and other cellulase gene promoters for high-level expression and these promoters require induction by sophorose, lactose or other inducers for high productivity during manufacturing. RESULTS We described an approach for producing high levels of secreted proteins by overexpression of a transcription factor ACE3 in T. reesei. We refined the ace3 gene structure and identified specific ACE3 variants that enable production of secreted cellulases and hemicellulases on glucose as a sole carbon source (i.e., in the absence of an inducer). These specific ACE3 variants contain a full-length Zn2Cys6 binuclear cluster domain at the N-terminus and a defined length of truncations at the C-terminus. When expressed at a moderate level in the fungal cells, the ACE3 variants can induce high-level expression of cellulases and hemicellulases on glucose (i.e., in the absence of an inducer), and further improve expression on lactose or glucose/sophorose (i.e., in the presence of an inducer). Finally, we demonstrated that this method is applicable to industrial strains and fermentation conditions, improving protein production both in the absence and in the presence of an inducer. CONCLUSIONS This study demonstrates that overexpression of ACE3 variants enables a high level of protein production in the absence of an inducer, and boosts protein production in the presence of an inducer. It is an efficient approach to increase protein productivity and to reduce manufacturing costs.
Collapse
Affiliation(s)
- Yun Luo
- DuPont Industrial Biosciences, Genencor Research Center, 925 Page Mill Road, Palo Alto, CA 94304 USA
| | - Mari Valkonen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Raymond E. Jackson
- DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE 19803 USA
| | - Jonathan M. Palmer
- DuPont Industrial Biosciences, Genencor Research Center, 925 Page Mill Road, Palo Alto, CA 94304 USA
| | - Aditya Bhalla
- DuPont Industrial Biosciences, Genencor Research Center, 925 Page Mill Road, Palo Alto, CA 94304 USA
| | - Igor Nikolaev
- DuPont Industrial Biosciences, Genencor B.V., Willem Einthovenstraat 4, 2342 BH Oegstgeest, The Netherlands
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Michael Ward
- DuPont Industrial Biosciences, Genencor Research Center, 925 Page Mill Road, Palo Alto, CA 94304 USA
| |
Collapse
|
33
|
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]
|
34
|
Meng QS, Zhang F, Wang W, Liu CG, Zhao XQ, Bai FW. Engineering the Effector Domain of the Artificial Transcription Factor to Improve Cellulase Production by Trichoderma reesei. Front Bioeng Biotechnol 2020; 8:675. [PMID: 32671045 PMCID: PMC7330100 DOI: 10.3389/fbioe.2020.00675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/01/2020] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungal strains of Trichoderma reesei have been widely used for cellulase production, and great effort has been devoted to enhancing their cellulase titers for the economic biorefinery of lignocellulosic biomass. In our previous studies, artificial zinc finger proteins (AZFPs) with the Gal4 effector domain were used to enhance cellulase biosynthesis in T. reesei, and it is of great interest to modify the AZFPs to further improve cellulase production. In this study, the endogenous activation domain from the transcription activator Xyr1 was used to replace the activation domain of Gal4 of the AZFP to explore impact on cellulase production. The cellulase producer T. reesei TU-6 was used as a host strain, and the engineered strains containing the Xyr1 and the Gal4 activation domains were named as T. reesei QS2 and T. reesei QS1, respectively. Compared to T. reesei QS1, activities of filter paper and endoglucanases in crude cellulase produced by T. reesei QS2 increased 24.6 and 50.4%, respectively. Real-time qPCR analysis also revealed significant up-regulation of major genes encoding cellulase in T. reesei QS2. Furthermore, the biomass hydrolytic performance of the cellulase was evaluated, and 83.8 and 97.9% more glucose was released during the hydrolysis of pretreated corn stover using crude enzyme produced by T. reesei QS2, when compared to the hydrolysis with cellulase produced by T. reesei QS1 and the parent strain T. reesei TU-6. As a result, we proved that the effector domain in the AZFPs can be optimized to construct more effective artificial transcription factors for engineering T. reesei to improve its cellulase production.
Collapse
Affiliation(s)
- Qing-Shan Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
35
|
Zhang T, Liu H, Lv B, Li C. Regulating Strategies for Producing Carbohydrate Active Enzymes by Filamentous Fungal Cell Factories. Front Bioeng Biotechnol 2020; 8:691. [PMID: 32733865 PMCID: PMC7360787 DOI: 10.3389/fbioe.2020.00691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
Abstract
Filamentous fungi are important eukaryotic organisms crucial in substrate degradation and carbon cycle on the earth and have been harnessed as cell factories for the production of proteins and other high value-added products in recent decades. As cell factories, filamentous fungi play a crucial role in industrial protein production as both native hosts and heterologous hosts. In this review, the regulation strategies of carbohydrate active enzyme expression at both transcription level and protein level are introduced, and the transcription regulations are highlighted with induction mechanism, signaling pathway, and promoter and transcription factor regulation. Afterward, the regulation strategies in protein level including suitable posttranslational modification, protein secretion enhancement, and protease reduction are also presented. Finally, the challenges and perspectives in this field are discussed. In this way, a comprehensive knowledge regarding carbohydrate active enzyme production regulation at both transcriptional and protein levels is provided with the particular goal of aiding in the practical application of filamentous fungi for industrial protein production.
Collapse
Affiliation(s)
- Teng Zhang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Hu Liu
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| |
Collapse
|
36
|
Martins-Santana L, Paula RGD, Silva AG, Lopes DCB, Silva RDN, Silva-Rocha R. CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a. Genet Mol Biol 2020; 43:e20190244. [PMID: 32384133 PMCID: PMC7212764 DOI: 10.1590/1678-4685-gmb-2019-0244] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023] Open
Abstract
Trichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Here we investigated the role of CRZ1 and Ca2+signaling in the fungus T. reesei QM6a concerning holocellulases production. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reeseiAcrz1 strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei, highlighting the role of the major regulator Ca2+ on the signaling for holocellulases transcriptional control in the most part of cellulases genes here investigated. This work presents new evidence on the regulatory role of CRZ1 and Ca2+ sensing in the regulation of cellulolytic enzymes in T. reesei, evidencing significant and previously unknown function of this Ca2+sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca2+ transport.
Collapse
Affiliation(s)
- Leonardo Martins-Santana
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Laboratório de Biologia Sistêmica e Sintética, Ribeirão Preto, SP, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil
| | - Renato Graciano de Paula
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil.,Universidade Federal do Espírito Santo, Centro de Ciências da Saúde, Departamento de Ciências Fisiológicas, Vitória, ES, Brazil
| | - Adriano Gomes Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Laboratório de Biologia Sistêmica e Sintética, Ribeirão Preto, SP, Brazil
| | - Douglas Christian Borges Lopes
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil
| | - Roberto do Nascimento Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Laboratório de Biologia Sistêmica e Sintética, Ribeirão Preto, SP, Brazil
| |
Collapse
|
37
|
Cai L, Xu S, Lu T, Lin D, Yao S. Salt-tolerant mechanism of marine Aspergillus niger cellulase cocktail and improvement of its activity. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2019.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
38
|
Meng QS, Zhang F, Liu CG, Zhao XQ, Bai FW. Identification of a novel repressor encoded by the putative gene ctf1 for cellulase biosynthesis in Trichoderma reesei through artificial zinc finger engineering. Biotechnol Bioeng 2020; 117:1747-1760. [PMID: 32124970 DOI: 10.1002/bit.27321] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 11/09/2022]
Abstract
Strains from Trichoderma reesei have been used for cellulase production with a long history. It has been well known that cellulase biosynthesis by the fungal species is controlled through regulators, and elucidation of their regulation network is of great importance for engineering T. reesei with robust cellulase production. However, progress in this regard is still very limited. In this study, T. reesei RUT-C30 was transformed with an artificial zinc finger protein (AZFP) library, and the mutant T. reesei M2 with improved cellulase production was screened. Compared to its parent strain, the filter paper activity and endo-β-glucanase activity in cellulases produced by T. reesei M2 increased 67.2% and 35.3%, respectively. Analysis by quantitative reverse transcription polymerase chain reaction indicated significant downregulation of the putative gene ctf1 in T. reesei M2, and its deletion mutants were thus developed for further studies. An increase of 36.9% in cellulase production was observed in the deletion mutants, but when ctf1 was constitutively overexpressed in T. reesei RUT-C30 under the control of the strong pdc1 promoter, cellulase production was substantially compromised. Comparative transcriptomic analysis revealed that the deletion of ctf1 upregulated transcription of gene encoding the regulator VIB1, but downregulated transcription of gene encoding another regulator RCE1, which consequently upregulated genes encoding the transcription factors XYR1 and ACE3 for the activation of genes encoding cellulolytic enzymes. As a result, ctf1 was characterized as a gene encoding a repressor for cellulase production in T. reesei RUT-C30, which is significant for further elucidating molecular mechanism underlying cellulase biosynthesis by the fungal species for rational design to develop robust strains for cellulase production. And in the meantime, AZFP transformation was validated to be an effective strategy for identifying functions of putative genes in the genome of T. reesei.
Collapse
Affiliation(s)
- Qing-Shan Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
39
|
Wang BT, Hu S, Yu XY, Jin L, Zhu YJ, Jin FJ. Studies of Cellulose and Starch Utilization and the Regulatory Mechanisms of Related Enzymes in Fungi. Polymers (Basel) 2020; 12:polym12030530. [PMID: 32121667 PMCID: PMC7182937 DOI: 10.3390/polym12030530] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 12/24/2022] Open
Abstract
Polysaccharides are biopolymers made up of a large number of monosaccharides joined together by glycosidic bonds. Polysaccharides are widely distributed in nature: Some, such as peptidoglycan and cellulose, are the components that make up the cell walls of bacteria and plants, and some, such as starch and glycogen, are used as carbohydrate storage in plants and animals. Fungi exist in a variety of natural environments and can exploit a wide range of carbon sources. They play a crucial role in the global carbon cycle because of their ability to break down plant biomass, which is composed primarily of cell wall polysaccharides, including cellulose, hemicellulose, and pectin. Fungi produce a variety of enzymes that in combination degrade cell wall polysaccharides into different monosaccharides. Starch, the main component of grain, is also a polysaccharide that can be broken down into monosaccharides by fungi. These monosaccharides can be used for energy or as precursors for the biosynthesis of biomolecules through a series of enzymatic reactions. Industrial fermentation by microbes has been widely used to produce traditional foods, beverages, and biofuels from starch and to a lesser extent plant biomass. This review focuses on the degradation and utilization of plant homopolysaccharides, cellulose and starch; summarizes the activities of the enzymes involved and the regulation of the induction of the enzymes in well-studied filamentous fungi.
Collapse
|
40
|
Effect of VIB Gene on Cellulase Production of Trichoderma orientalis EU7-22. Appl Biochem Biotechnol 2020; 191:1444-1455. [DOI: 10.1007/s12010-020-03260-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
|
41
|
Mattila HK, Mäkinen M, Lundell T. Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:26. [PMID: 32123543 PMCID: PMC7038570 DOI: 10.1186/s13068-020-01677-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/05/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fungal decomposition of wood is considered as a strictly aerobic process. However, recent findings on wood-decaying fungi to produce ethanol from various lignocelluloses under oxygen-depleted conditions lead us to question this. We designed gene expression study of the white rot fungus Phlebia radiata (isolate FBCC0043) by adopting comparative transcriptomics and functional genomics on solid lignocellulose substrates under varying cultivation atmospheric conditions. RESULTS Switch to fermentative conditions was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides. Changes in the expression profiles of CAZy (carbohydrate-active enzyme) encoding genes upon oxygen depletion, lead into an alternative wood decomposition strategy. Surprisingly, we noticed higher cellulolytic activity under fermentative conditions in comparison to aerobic cultivation. In addition, our results manifest how oxygen depletion affects over 200 genes of fungal primary metabolism including several transcription factors. We present new functions for acetate generating phosphoketolase pathway and its potential regulator, Adr1 transcription factor, in carbon catabolism under oxygen depletion. CONCLUSIONS Physiologically resilient wood-decomposing Basidiomycota species P. radiata is capable of thriving under respirative and fermentative conditions utilizing only untreated lignocellulose as carbon source. Hypoxia-response mechanism in the fungus is, however, divergent from the regulation described for Ascomycota fermenting yeasts or animal-pathogenic species of Basidiomycota.
Collapse
Affiliation(s)
- Hans Kristian Mattila
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
| | - Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
- Present Address: VTT Technical Research Centre of Finland Ltd, 02044 VTT Espoo, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
42
|
Fonseca LM, Parreiras LS, Murakami MT. Rational engineering of the Trichoderma reesei RUT-C30 strain into an industrially relevant platform for cellulase production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:93. [PMID: 32461765 PMCID: PMC7243233 DOI: 10.1186/s13068-020-01732-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/14/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND The path for the development of hypersecreting strains of Trichoderma reesei capable of producing industrially relevant enzyme titers remains elusive despite over 70 years of research and industrial utilization. Herein, we describe the rational engineering of the publicly available T. reesei RUT-C30 strain and a customized process for cellulase production based on agroindustrial by-products. RESULTS A CRISPR/Cas9 system was used to introduce six genetic modifications in RUT-C30. Implemented changes included the constitutive expression of a mutated allele of the cellulase master regulator XYR1, the expression of two heterologous enzymes, the β-glucosidase CEL3A from Talaromyces emersonii and the invertase SUC1 from Aspergillus niger, and the deletion of genes encoding the cellulase repressor ACE1 and the extracellular proteases SLP1 and PEP1. These alterations resulted in a remarkable increase of protein secretion rates by RUT-C30 and amended its well described β-glucosidase deficiency while enabling the utilization of sucrose and eliminating the requirement of inducing sugars for enzyme production. With a developed sugarcane molasses-based bioprocess, the engineered strain reached an extracellular protein titer of 80.6 g L-1 (0.24 g L-1 h-1), which is the highest experimentally supported titer so far reported for T. reesei. The produced enzyme cocktail displayed increased levels of cellulase and hemicellulase activities, with particularly large increments being observed for the specific activities of β-glucosidase (72-fold) and xylanase (42-fold). Notably, it also exhibited a saccharification efficiency similar to that of a commercially available cellulase preparation in the deconstruction of industrially pretreated sugarcane straw. CONCLUSION This work demonstrates the rational steps for the development of a cellulase hyperproducing strain from a well-characterized genetic background available in the public domain, the RUT-C30, associated with an industrially relevant bioprocess, paving new perspectives for Trichoderma research on cellulase production.
Collapse
Affiliation(s)
- Lucas Miranda Fonseca
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo 13083-100 Brazil
| | - Lucas Salera Parreiras
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo 13083-100 Brazil
| | - Mario Tyago Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo 13083-100 Brazil
| |
Collapse
|
43
|
Xue Y, Han J, Li Y, Liu J, Gan L, Long M. Promoting cellulase and hemicellulase production from Trichoderma orientalis EU7-22 by overexpression of transcription factors Xyr1 and Ace3. BIORESOURCE TECHNOLOGY 2020; 296:122355. [PMID: 31711906 DOI: 10.1016/j.biortech.2019.122355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 05/07/2023]
Abstract
The construction of hyper-production strains of cellulase is the prerequisite for the production of biofuels or biochemicals. Trichoderma orientalis EU7-22 with complete cellulase system shows the potential for cellulase production in industrial scale. To improve the cellulase production, two crucial transcription activators Xyr1 and Ace3 were constitutively overexpressed in EU7-22 strain. Cellulase, xylanase and protein secretion were significantly improved in the recombinant strain dxyA-8 under inducing culture, which were 2.34, 0.68 and 1.06 folds higher than those of EU7-22, respectively. Moreover, the FPase and CMCase activities were up to 2.55 IU/mL and 90.38 IU/mL with glucose as carbon source, which were 2.12 and 1.95 folds higher than those of EU7-22 under inducing condition, respectively. Reducing sugar released from pretreated spartina that hydrolyzed by crude enzyme from dxyA-8 had achieved 24% improvement. Therefore, overexpression of these transcription factors effectively promotes the production of cellulase and hemicellulase of Trichoderma orientalis EU7-22.
Collapse
Affiliation(s)
- Yong Xue
- College of Energy, Xiamen University, Xiamen 361005, PR China
| | - Jiang Han
- College of Energy, Xiamen University, Xiamen 361005, PR China
| | - Yuyu Li
- College of Energy, Xiamen University, Xiamen 361005, PR China
| | - Jian Liu
- College of Energy, Xiamen University, Xiamen 361005, PR China; Xiamen Key Laboratory of High-valued Conversion Technology of Agricultural Biomass, Xiamen University, Xiamen, PR China.
| | - Lihui Gan
- College of Energy, Xiamen University, Xiamen 361005, PR China; Xiamen Key Laboratory of High-valued Conversion Technology of Agricultural Biomass, Xiamen University, Xiamen, PR China.
| | - Minnan Long
- College of Energy, Xiamen University, Xiamen 361005, PR China; Fujian Vocational College of Bioengineering, Fuzhou, PR China.
| |
Collapse
|
44
|
Beier S, Hinterdobler W, Bazafkan H, Schillinger L, Schmoll M. CLR1 and CLR2 are light dependent regulators of xylanase and pectinase genes in Trichoderma reesei. Fungal Genet Biol 2019; 136:103315. [PMID: 31816399 DOI: 10.1016/j.fgb.2019.103315] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/22/2019] [Accepted: 12/01/2019] [Indexed: 11/28/2022]
Abstract
Regulation of plant cell wall degradation is of utmost importance for understanding the carbon cycle in nature, but also to improve industrial processes aimed at enzyme production for next generation biofuels. Thereby, the transcription factor networks in different fungi show conservation as well as striking differences, particularly between Trichoderma reesei and Neurospora crassa. Here, we aimed to gain insight into the function of the transcription factors CLR1 and CLR2 in T. reesei, which are crucial for cellulase gene expression in N. crassa. We studied impacts on gene regulation with cellulose, xylan, pectin and chitin, growth on 95 different carbon sources as well as an involvement in regulation of secondary metabolism or development. We found that CLR1 is present in the genome of T. reesei and other Trichoderma spp., albeit with considerably lower homology compared to other ascomycetes. CLR1 and CLR2 regulate pectinase transcript levels upon growth on pectin, no major function was detected on chitin. CLR1 and CLR2 form a positive feedback cycle on xylan and were found to be responsible for balancing co-regulation of xylanase genes in light and darkness with distinct and in part opposite regulatory effects of up to 8fold difference. Our data suggest that CLR1 and CLR2 have evolved differently in T. reesei compared to other fungi. We propose a model in which their main function is in adjustment of regulation of xylanase gene expression to different light conditions and to balance transcript levels of genes involved in plant cell wall degradation according to their individual relevance for this process.
Collapse
Affiliation(s)
- Sabrina Beier
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria.
| | - Wolfgang Hinterdobler
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria.
| | - Hoda Bazafkan
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria.
| | - Lukas Schillinger
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria.
| | - Monika Schmoll
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria.
| |
Collapse
|
45
|
The Putative Transcription Factor Gene thaB Regulates Cellulase and Xylanase Production at the Enzymatic and Transcriptional Level in the Fungus Talaromyces cellulolyticus. Appl Biochem Biotechnol 2019; 190:1360-1370. [PMID: 31773396 DOI: 10.1007/s12010-019-03190-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022]
Abstract
Talaromyces cellulolyticus is a promising strain for industrial cellulase production. In this study, the thaB gene, which is a homologue of the hap2/B gene in other filamentous fungi, was isolated and characterized. When grown in the presence of cellulose, culture supernatants of a thaB-disrupted strain (YDTha) exhibited decreased cellulase and xylanase enzymatic activities compared to the control strain. Furthermore, YDTha exhibited lower expression of the genes encoding cellulases and xylanases compared to the control strain. When cellobiose and lactose (soluble carbon sources) were used as carbon sources, the expression of the genes encoding cellulases and xylanases was decreased in both the YDTha and the control strains, though the expression levels in YDTha remained lower than those in the control strain. These results suggested that thaB has a positive role in cellulase and xylanase production in T. cellulolyticus.
Collapse
|
46
|
Wang F, Zhang R, Han L, Guo W, Du Z, Niu K, Liu Y, Jia C, Fang X. Use of fusion transcription factors to reprogram cellulase transcription and enable efficient cellulase production in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:244. [PMID: 31636703 PMCID: PMC6792246 DOI: 10.1186/s13068-019-1589-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/09/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Trichoderma reesei is widely used for cellulase production and accepted as an example for cellulase research. Cre1-mediated carbon catabolite repression (CCR) can significantly inhibit the transcription of cellulase genes during cellulase fermentation in T. reesei. Early efforts have been undertaken to modify Cre1 for the release of CCR; however, this approach leads to arrested hyphal growth and decreased biomass accumulation, which negatively affects cellulase production. RESULTS In this study, novel fusion transcription factors (fTFs) were designed to release or attenuate CCR inhibition in cellulase transcription, while Cre1 was left intact to maintain normal hyphal growth. Four designed fTFs were introduced into the T. reesei genome, which generated several transformants, named Kuace3, Kuclr2, Kuace2, and Kuxyr1. No obvious differences in growth were observed between the parent and transformant strains. However, the transcription levels of cel7a, a major cellulase gene, were significantly elevated in all the transformants, particularly in Kuace2 and Kuxyr1, when grown on lactose as a carbon source. This suggested that CCR inhibition was released or attenuated in the transformant strains. The growth of Kuace2 and Kuxyr1 was approximately equivalent to that of the parent strain in fed-batch fermentation process. However, we observed a 3.2- and 2.1-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of the parent strain. Moreover, we observed a 6.1- and 3.9-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of Δcre1 strain. CONCLUSIONS A new strategy based on fTFs was successfully established in T. reesei to improve cellulase titers without impairing fungal growth. This study will be valuable for lignocellulosic biorefining and for guiding the development of engineering strategies for producing other important biochemical compounds in fungal species.
Collapse
Affiliation(s)
- Fangzhong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong China
| | - Ruiqin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Lijuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Wei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Zhiqiang Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Yucui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Chunjiang Jia
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| |
Collapse
|
47
|
Novy V, Nielsen F, Seiboth B, Nidetzky B. The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:238. [PMID: 31624500 PMCID: PMC6781402 DOI: 10.1186/s13068-019-1571-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/21/2023]
Abstract
Biorefineries, designed for the production of lignocellulose-based chemicals and fuels, are receiving increasing attention from the public, governments, and industries. A major obstacle for biorefineries to advance to commercial scale is the high cost of the enzymes required to derive the fermentable sugars from the feedstock used. As summarized in this review, techno-economic studies suggest co-localization and integration of enzyme manufacturing with the cellulosic biorefinery as the most promising alternative to alleviate this problem. Thus, cultivation of Trichoderma reesei, the principal producer of lignocellulolytic enzymes, on the lignocellulosic biomass processed on-site can reduce the cost of enzyme manufacturing. Further, due to a complex gene regulation machinery, the fungus can adjust the gene expression of the lignocellulolytic enzymes towards the characteristics of the feedstock, increasing the hydrolytic efficiency of the produced enzyme cocktail. Despite extensive research over decades, the underlying regulatory mechanisms are not fully elucidated. One aspect that has received relatively little attention in literature is the influence the characteristics of a lignocellulosic substrate, i.e., its chemical and physical composition, has on the produced enzyme mixture. Considering that the fungus is dependent on efficient enzymatic degradation of the lignocellulose for continuous supply of carbon and energy, a relationship between feedstock characteristics and secretome composition can be expected. The aim of this review was to systematically collect, appraise, and aggregate data and integrate results from studies analyzing enzyme production by T. reesei on insoluble cellulosic model substrates and lignocellulosic biomass. The results show that there is a direct effect of the substrate's complexity (rated by structure, composition of the lignin-carbohydrate complex, and recalcitrance in enzymatic saccharification) on enzyme titers and the composition of specific activities in the secretome. It further shows that process-related factors, such as substrate loading and cultivation set-up, are direct targets for increasing enzyme yields. The literature on transcriptome and secretome composition further supports the proposed influence of substrate-related factors on the expression of lignocellulolytic enzymes. This review provides insights into the interrelation between the characteristics of the substrate and the enzyme production by T. reesei, which may help to advance integrated enzyme manufacturing of substrate-specific enzymes cocktails at scale.
Collapse
Affiliation(s)
- Vera Novy
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Fredrik Nielsen
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Bernhard Seiboth
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
| |
Collapse
|
48
|
Derntl C, Mach RL, Mach-Aigner AR. Fusion transcription factors for strong, constitutive expression of cellulases and xylanases in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:231. [PMID: 31583017 PMCID: PMC6767844 DOI: 10.1186/s13068-019-1575-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/22/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The filamentous ascomycete T. reesei is industrially used to produce cellulases and xylanases. Cost-effective production of cellulases is a bottleneck for biofuel production. Previously, different strain and process optimizations were deployed to enhance enzyme production rates. One approach is the overexpression of the main activator Xyr1 and a second is the construction of synthetic transcription factors. Notably, these genetic manipulations were introduced into strains bearing the wild-type xyr1 gene and locus. RESULTS Here, we constructed a Xyr1-deficient strain expressing a non-functional truncated version of Xyr1. This strain was successfully used as platform strain for overexpression of Xyr1, which enhanced the cellulase and xylanase production rates under inducing conditions, with the exception of lactose-there the cellulase production was severely reduced. Further, we introduced fusion transcription factors consisting of the DNA-binding domain of Xyr1 and the transactivation domain of either Ypr1 or Ypr2 (regulators of the sorbicillinoid biosynthesis gene cluster). The fusion of Xyr1 and Ypr2 yielded a moderately transactivating transcription factor, whereas the fusion of Xyr1 and Ypr1 yielded a highly transactivating transcription factor that induced xylanases and cellulases nearly carbon source independently. Especially, high production levels of xylanases were achieved on glycerol. CONCLUSION During this study, we constructed a Xyr1-deficient strain that can be fully reconstituted, which makes it an ideal platform strain for Xyr1-related studies. The mere overexpression of Xyr1 turned out not to be a successful strategy for overall enhancement of the enzyme production rates. We gained new insights into the regulatory properties of transcription factors by constructing respective fusion proteins. The Xyr1-Ypr1-fusion transcription factor could induce xylanase production rates on glycerol to outstanding extents, and hence could be deployed in the future to utilize crude glycerol, the main co-product of the biodiesel production process.
Collapse
Affiliation(s)
- Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| |
Collapse
|
49
|
Hirasawa H, Shioya K, Mori K, Tashiro K, Aburatani S, Shida Y, Kuhara S, Ogasawara W. Cellulase productivity of Trichoderma reesei mutants developed in Japan varies with varying pH conditions. J Biosci Bioeng 2019; 128:264-273. [DOI: 10.1016/j.jbiosc.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 01/08/2023]
|
50
|
Wang Q, Chen L, Fang C, Wang H, Shi Y, Zhao Y. The overexpression of one single cbh gene making Trichoderma asperellum T-1 a better cellulase producer. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01458-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|