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Castañeda-Casasola CC, Nieto-Jacobo MF, Soares A, Padilla-Padilla EA, Anducho-Reyes MA, Brown C, Soth S, Esquivel-Naranjo EU, Hampton J, Mendoza-Mendoza A. Unveiling a Microexon Switch: Novel Regulation of the Activities of Sugar Assimilation and Plant-Cell-Wall-Degrading Xylanases and Cellulases by Xlr2 in Trichoderma virens. Int J Mol Sci 2024; 25:5172. [PMID: 38791210 PMCID: PMC11121469 DOI: 10.3390/ijms25105172] [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: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-α or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-α. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.
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Affiliation(s)
- Cynthia Coccet Castañeda-Casasola
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Centro Nacional de Referencia Fitosanitaria, Tecamac 55740, Mexico
| | | | - Amanda Soares
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Emir Alejandro Padilla-Padilla
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 04510, Mexico
| | - Miguel Angel Anducho-Reyes
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
| | - Chris Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
| | - Sereyboth Soth
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Edgardo Ulises Esquivel-Naranjo
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, Queretaro 76230, Mexico
| | - John Hampton
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Artemio Mendoza-Mendoza
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
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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.
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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
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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.
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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
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Hirasawa H, Shioya K, Furukawa T, Tani S, Sumitani JI, Kawaguchi T, Morikawa Y, Shida Y, Ogasawara W. Engineering of the Trichoderma reesei xylanase3 promoter for efficient enzyme expression. Appl Microbiol Biotechnol 2018; 102:2737-2752. [DOI: 10.1007/s00253-018-8763-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
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Li CX, Zhao S, Zhang T, Xian L, Liao LS, Liu JL, Feng JX. Genome sequencing and analysis of Talaromyces pinophilus provide insights into biotechnological applications. Sci Rep 2017; 7:490. [PMID: 28352091 PMCID: PMC5428652 DOI: 10.1038/s41598-017-00567-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/03/2017] [Indexed: 11/09/2022] Open
Abstract
Species from the genus Talaromyces produce useful biomass-degrading enzymes and secondary metabolites. However, these enzymes and secondary metabolites are still poorly understood and have not been explored in depth because of a lack of comprehensive genetic information. Here, we report a 36.51-megabase genome assembly of Talaromyces pinophilus strain 1-95, with coverage of nine scaffolds of eight chromosomes with telomeric repeats at their ends and circular mitochondrial DNA. In total, 13,472 protein-coding genes were predicted. Of these, 803 were annotated to encode enzymes that act on carbohydrates, including 39 cellulose-degrading and 24 starch-degrading enzymes. In addition, 68 secondary metabolism gene clusters were identified, mainly including T1 polyketide synthase genes and nonribosomal peptide synthase genes. Comparative genomic analyses revealed that T. pinophilus 1-95 harbors more biomass-degrading enzymes and secondary metabolites than other related filamentous fungi. The prediction of the T. pinophilus 1-95 secretome indicated that approximately 50% of the biomass-degrading enzymes are secreted into the extracellular environment. These results expanded our genetic knowledge of the biomass-degrading enzyme system of T. pinophilus and its biosynthesis of secondary metabolites, facilitating the cultivation of T. pinophilus for high production of useful products.
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Affiliation(s)
- Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Liang Xian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Jun-Liang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China.
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Transcription factor Xpp1 is a switch between primary and secondary fungal metabolism. Proc Natl Acad Sci U S A 2017; 114:E560-E569. [PMID: 28074041 DOI: 10.1073/pnas.1609348114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fungi can produce a wide range of chemical compounds via secondary metabolism. These compounds are of major interest because of their (potential) application in medicine and biotechnology and as a potential source for new therapeutic agents and drug leads. However, under laboratory conditions, most secondary metabolism genes remain silent. This circumstance is an obstacle for the production of known metabolites and the discovery of new secondary metabolites. In this study, we describe the dual role of the transcription factor Xylanase promoter binding protein 1 (Xpp1) in the regulation of both primary and secondary metabolism of Trichoderma reesei Xpp1 was previously described as a repressor of xylanases. Here, we provide data from an RNA-sequencing analysis suggesting that Xpp1 is an activator of primary metabolism. This finding is supported by our results from a Biolog assay determining the carbon source assimilation behavior of an xpp1 deletion strain. Furthermore, the role of Xpp1 as a repressor of secondary metabolism is shown by gene expression analyses of polyketide synthases and the determination of the secondary metabolites of xpp1 deletion and overexpression strains using an untargeted metabolomics approach. The deletion of Xpp1 resulted in the enhanced secretion of secondary metabolites in terms of diversity and quantity. Homologs of Xpp1 are found among a broad range of fungi, including the biocontrol agent Trichoderma atroviride, the plant pathogens Fusarium graminearum and Colletotrichum graminicola, the model organism Neurospora crassa, the human pathogen Sporothrix schenckii, and the ergot fungus Claviceps purpurea.
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Shida Y, Furukawa T, Ogasawara W. Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus. Biosci Biotechnol Biochem 2016; 80:1712-29. [DOI: 10.1080/09168451.2016.1171701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.
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Affiliation(s)
- Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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Amores GR, Guazzaroni ME, Arruda LM, Silva-Rocha R. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories. Curr Genomics 2016; 17:85-98. [PMID: 27226765 PMCID: PMC4864837 DOI: 10.2174/1389202917666151116212255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/23/2015] [Accepted: 06/01/2015] [Indexed: 01/03/2023] Open
Abstract
Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant
biomass and this feature has a tremendous potential for biofuel production from renewable sources.
The past decades have been marked by a remarkable progress in the genetic engineering of fungi to
generate industry-compatible strains needed for some biotech applications. In this sense, progress in
this field has been marked by the utilization of high-throughput techniques to gain deep understanding
of the molecular machinery controlling the physiology of these organisms, starting thus the Systems
Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized
promoters in order to construct new expression systems with enhanced performance under the conditions of
interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of
fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms
relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction
of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered
promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact
in the final performance of the process of interest. We expect to provide here some new directions to drive future research
directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.
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Druzhinina IS, Kubicek CP. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:69-147. [PMID: 27261782 DOI: 10.1016/bs.aambs.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.
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Affiliation(s)
- I S Druzhinina
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - C P Kubicek
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
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Mello-de-Sousa TM, Rassinger A, Pucher ME, dos Santos Castro L, Persinoti GF, Silva-Rocha R, Poças-Fonseca MJ, Mach RL, Nascimento Silva R, Mach-Aigner AR. The impact of chromatin remodelling on cellulase expression in Trichoderma reesei. BMC Genomics 2015; 16:588. [PMID: 26248555 PMCID: PMC4528718 DOI: 10.1186/s12864-015-1807-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 08/03/2015] [Indexed: 01/31/2023] Open
Abstract
Background Trichoderma reesei is used for industry-scale production of plant cell wall-degrading enzymes, in particular cellulases, but also xylanases. The expression of the encoding genes was so far primarily investigated on the level of transcriptional regulation by regulatory proteins. Otherwise, the impact of chromatin remodelling on gene expression received hardly any attention. In this study we aimed to learn if the chromatin status changes in context to the applied conditions (repressing/inducing), and if the presence or absence of the essential transactivator, the Xylanase regulator 1 (Xyr1), influences the chromatin packaging. Results Comparing the results of chromatin accessibility real-time PCR analyses and gene expression studies of the two prominent cellulase-encoding genes, cbh1 and cbh2, we found that the chromatin opens during sophorose-mediated induction compared to D-glucose-conferred repression. In the strain bearing a xyr1 deletion the sophorose mediated induction of gene expression is lost and the chromatin opening is strongly reduced. In all conditions the chromatin got denser when Xyr1 is absent. In the case of the xylanase-encoding genes, xyn1 and xyn2, the result was similar concerning the condition-specific response of the chromatin compaction. However, the difference in chromatin status provoked by the absence of Xyr1 is less pronounced. A more detailed investigation of the DNA accessibility in the cbh1 promoter showed that the deletion of xyr1 changed the in vivo footprinting pattern. In particular, we detected increased hypersensitivity on Xyr1-sites and stronger protection of Cre1-sites. Looking for the players directly causing the observed chromatin remodelling, a whole transcriptome shotgun sequencing revealed that 15 genes encoding putative chromatin remodelers are differentially expressed in response to the applied condition and two amongst them are differentially expressed in the absence of Xyr1. Conclusions The regulation of xylanase and cellulase expression in T. reesei is not only restricted to the action of transcription factors but is clearly related to changes in the chromatin packaging. Both the applied condition and the presence of Xyr1 influence chromatin status.
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Affiliation(s)
- Thiago M Mello-de-Sousa
- Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria.
| | - Alice Rassinger
- Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria.
| | - Marion E Pucher
- Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria.
| | - Lilian dos Santos Castro
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil.
| | - Gabriela F Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil.
| | - Rafael Silva-Rocha
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil.
| | - Marcio J Poças-Fonseca
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia, Brasília, DF, Brazil.
| | - Robert L Mach
- Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil.
| | - Astrid R Mach-Aigner
- Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria.
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Novel Strategies for Genomic Manipulation of Trichoderma reesei with the Purpose of Strain Engineering. Appl Environ Microbiol 2015; 81:6314-23. [PMID: 26150462 PMCID: PMC4542242 DOI: 10.1128/aem.01545-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/29/2015] [Indexed: 01/18/2023] Open
Abstract
The state-of-the-art procedure for gene insertions into Trichoderma reesei is a cotransformation of two plasmids, one bearing the gene of interest and the other a marker gene. This procedure yields up to 80% transformation efficiency, but both the number of integrated copies and the loci of insertion are unpredictable. This can lead to tremendous pleiotropic effects. This study describes the development of a novel transformation system for site-directed gene insertion based on auxotrophic markers. For this purpose, we tested the applicability of the genes asl1 (encoding an enzyme of the l-arginine biosynthesis pathway), the hah1 (encoding an enzyme of the l-lysine biosynthesis pathway), and the pyr4 (encoding an enzyme of the uridine biosynthesis pathway). The developed transformation system yields strains with an additional gene at a defined locus that are prototrophic and ostensibly isogenic compared to their parental strain. A positive transformation rate of 100% was achieved due to the developed split-marker system. Additionally, a double-auxotrophic strain that allows multiple genomic manipulations was constructed, which facilitates metabolic engineering purposes in T. reesei. By employing goxA of Aspergillus niger as a reporter system, the influence on the expression of an inserted gene caused by the orientation of the insertion and the transformation strategy used could be demonstrated. Both are important aspects to be considered during strain engineering.
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Derntl C, Rassinger A, Srebotnik E, Mach RL, Mach-Aigner AR. Xpp1 regulates the expression of xylanases, but not of cellulases in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:112. [PMID: 26246855 PMCID: PMC4526299 DOI: 10.1186/s13068-015-0298-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/24/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND The ascomycete Trichoderma reesei is industrially used for the production of cellulases. During the production process xylanases are co-secreted, which uses energy and nutrients. Cellulases and xylanases share the same main regulators, which makes a knowledge-based strain design difficult. However, previously a cis-element in the promoter of the main xylanase-encoding gene was identified as binding site for a putative repressor. Subsequently, three candidate repressors were identified in a pull-down approach. The expression of the most promising candidate, Xpp1 (Xylanase promoter-binding protein 1), was reported to be up-regulated on the repressing carbon source d-glucose and to bind the cis-element in vitro. RESULTS In this study, Xpp1 was deleted and over-expressed in T. reesei. An in vivo DNA-footprint assay indicated that Xpp1 binds a palindromic sequence in the xyn2 promoter. Comparison of the deletion, the over-expression, and the parent strain demonstrated that Xpp1 regulates gene expression of xylanolytic enzymes at later cultivation stages. Xpp1 expression was found to be up-regulated, additionally to d-glucose, by high d-xylose availability. These findings together with the observed xyn2 transcript levels during growth on xylan suggest that Xpp1 is the mediator of a feedback mechanism. Notably, Xpp1 has neither influence on the d-xylose metabolism nor on the expression of cellulases. CONCLUSIONS Xpp1 as regulator acting on the expression of xylanases, but not cellulases, is a highly promising candidate for knowledge-based strain design to improve the cellulases-to-xylanases ratio during industrial cellulase production.
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Affiliation(s)
- Christian Derntl
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Alice Rassinger
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Ewald Srebotnik
- />Department of Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Robert L Mach
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Astrid R Mach-Aigner
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
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13
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Gorsche R, Jovanovic B, Gudynaite-Savitch L, Mach RL, Mach-Aigner AR. A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements. Nucleic Acids Res 2013; 42:e1. [PMID: 24097437 PMCID: PMC3874196 DOI: 10.1093/nar/gkt883] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Knowing which regions of a gene are targeted by transcription factors during induction or repression is essential for understanding the mechanisms responsible for regulation. Therefore, we re-designed the traditional in vivo footprinting method to obtain a highly sensitive technique, which allows identification of the cis elements involved in condition-dependent gene regulation. Data obtained through DMS methylation, HCl DNA cleavage and optimized ligation-mediated PCR using fluorescent labelling followed by capillary gel electrophoresis are analysed by ivFAST. In this work we have developed this command line-based program, which is designed to ensure automated and fast data processing and visualization. The new method facilitates a quantitative, high-throughput approach because it enables the comparison of any number of in vivo footprinting results from different conditions (e.g. inducing, repressing, de-repressing) to one another by employing an internal standard. For validation of the method the well-studied upstream regulatory region of the Trichoderma reesei xyn1 (endoxylanase 1) gene was used. Applying the new method we could identify the motives involved in condition-dependent regulation of the cbh2 (cellobiohydrolase 2) and xyn2 (endoxylanase 2) genes.
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Affiliation(s)
- Rita Gorsche
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Str. 1 a, A-1060 Vienna, Austria and Department of Biology, University of Ottawa, Gendron Hall, 30 Marie Curie, Ottawa, ON, K1N6N5, Canada
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14
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Liu G, Zhang L, Wei X, Zou G, Qin Y, Ma L, Li J, Zheng H, Wang S, Wang C, Xun L, Zhao GP, Zhou Z, Qu Y. Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PLoS One 2013; 8:e55185. [PMID: 23383313 PMCID: PMC3562324 DOI: 10.1371/journal.pone.0055185] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/19/2012] [Indexed: 02/06/2023] Open
Abstract
Many Penicillium species could produce extracellular enzyme systems with good lignocellulose hydrolysis performance. However, these species and their enzyme systems are still poorly understood and explored due to the lacking of genetic information. Here, we present the genomic and secretomic analyses of Penicillium decumbens that has been used in industrial production of lignocellulolytic enzymes in China for more than fifteen years. Comparative genomics analysis with the phylogenetically most similar species Penicillium chrysogenum revealed that P. decumbens has evolved with more genes involved in plant cell wall degradation, but fewer genes in cellular metabolism and regulation. Compared with the widely used cellulase producer Trichoderma reesei, P. decumbens has a lignocellulolytic enzyme system with more diverse components, particularly for cellulose binding domain-containing proteins and hemicellulases. Further, proteomic analysis of secretomes revealed that P. decumbens produced significantly more lignocellulolytic enzymes in the medium with cellulose-wheat bran as the carbon source than with glucose. The results expand our knowledge on the genetic information of lignocellulolytic enzyme systems in Penicillium species, and will facilitate rational strain improvement for the production of highly efficient enzyme systems used in lignocellulose utilization from Penicillium species.
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Affiliation(s)
- Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Lei Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaomin Wei
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Gen Zou
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuqi Qin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong, China
| | - Liang Ma
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jie Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Shengyue Wang
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Chengshu Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zhihua Zhou
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong, China
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15
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Weissmann S, Brutnell TP. Engineering C4 photosynthetic regulatory networks. Curr Opin Biotechnol 2012; 23:298-304. [PMID: 22261559 DOI: 10.1016/j.copbio.2011.12.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 11/25/2022]
Abstract
C4 photosynthesis is a complex metabolic pathway responsible for carbon fixation in major feed, food and bioenergy crops. Although many enzymes driving this pathway have been identified, regulatory mechanisms underlying this system remain elusive. C4 photosynthesis contributes to photosynthetic efficiency in major bioenergy crops such as sugarcane, Miscanthus, switchgrass, maize and sorghum, and international efforts are underway to engineer C4 photosynthesis into C3 crops. A fundamental understanding of the C4 network is thus needed. New experimental and informatics methods can facilitate the accumulation and analysis of high-throughput data to define components of the C4 system. The use of new model plants, closely related to C4 crops, will also contribute to our understanding of the mechanisms that regulate this complex and important pathway.
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Affiliation(s)
- Sarit Weissmann
- Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY 14853, United States
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16
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Seiboth B, Herold S, Kubicek CP. Metabolic engineering of inducer formation for cellulase and hemicellulase gene expression in Trichoderma reesei. Subcell Biochem 2012; 64:367-90. [PMID: 23080260 DOI: 10.1007/978-94-007-5055-5_18] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The filamentous fungus T. reeseiis today a paradigm for the commercial scale production of different plant cell wall degrading enzymes mainly cellulases and hemicellulases. Its enzymes have a long history of safe use in industry and well established applications are found within the pulp, paper, food, feed or textile processing industries. However, when these enzymes are to be used for the saccharification of cellulosic plant biomass to simple sugars which can be further converted to biofuels or other biorefinery products, and thus compete with chemicals produced from fossil sources, additional efforts are needed to reduce costs and maximize yield and efficiency of the produced enzyme mixtures. One approach to this end is the use of genetic engineering to manipulate the biochemical and regulatory pathways that operate during enzyme production and control enzyme yield. This review aims at a description of the state of art in this area.
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Affiliation(s)
- Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, 166-5, A-1060, Vienna, Austria
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