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Sveholm E, Mattila H, Aro N, Valkonen M, Paasela T, Pakula TM. Transcriptomic and metabolic changes in Trichoderma reesei caused by mutation in xylanase regulator 1 (xyr1). BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:106. [PMID: 39030601 PMCID: PMC11265206 DOI: 10.1186/s13068-024-02556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Trichoderma reesei is known for its ability to produce large amounts of extracellular proteins and is one of the most important industrially used filamentous fungus. Xylanase regulator 1 (XYR1) is the master regulator responsible for the activation of cellulase and hemicellulase gene expression under inducing conditions. It has been reported that strains with point mutations in certain areas of xyr1 bypass the need for inducing carbon source, allowing high (hemi)cellulase production even in the presence of glucose. These mutations also change the profile of produced proteins, shifting it more towards xylanase production, and increase the overall protein production in inducing conditions. However, how these mutations alter the metabolism and other cellular processes to cause these changes remains unclear. RESULTS In this study, we aimed to explore changes caused by a point mutation in xyr1 on transcriptomic and metabolic level to better understand the reasons behind the increased protein production in both repressing glucose and inducing lactose conditions. As expected, the expression of many carbohydrate-active enzyme (CAZy) genes was increased in the xyr1 mutant in both conditions. However, their induction was higher under inducing conditions. The xyr1 mutant strain built more biomass and produced more extracellular proteins during growth on lactose compared to the wild type xyr1 strain. Genes involved in oxidoreductive D-galactose catabolism pathway were upregulated in the xyr1 mutant strain, potentially contributing to the more efficient utilization of lactose. In addition to CAZy genes, clustering and enrichment analysis showed over-representation of mitochondria-related Gene Ontology terms in clusters where gene expression was higher in the xyr1 mutant, indicating that mitochondria play a role in the altered metabolic state associated with the xyr1 mutation. Metabolomics revealed that free tyrosine was more abundant in the xyr1 mutant strain in all measured timepoints, whereas multiple fatty acids were less abundant in the mutant strain on glucose. CONCLUSIONS The results contribute to more in-depth knowledge on T. reesei physiology growing under inducing and repressing carbon sources and gives new insights on the function of the master regulator XYR1. The vast data generated serve as a source for new targets for improved protein production.
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Affiliation(s)
- Emmi Sveholm
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Hans Mattila
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Nina Aro
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Mari Valkonen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Tanja Paasela
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland.
| | - Tiina M Pakula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
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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.
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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.
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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.
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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.)
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Botrytis cinerea Transcription Factor BcXyr1 Regulates (Hemi-)Cellulase Production and Fungal Virulence. mSystems 2022; 7:e0104222. [PMID: 36468854 PMCID: PMC9765177 DOI: 10.1128/msystems.01042-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Botrytis cinerea is an agriculturally notorious plant-pathogenic fungus with a broad host range. During plant colonization, B. cinerea secretes a wide range of plant-cell-wall-degrading enzymes (PCWDEs) that help in macerating the plant tissue, but their role in pathogenicity has been unclear. Here, we report on the identification of a transcription factor, BcXyr1, that regulates the production of (hemi-)cellulases and is necessary for fungal virulence. Deletion of the bcxyr1 gene led to impaired spore germination and reduced fungal virulence and reactive oxygen species (ROS) production in planta. Secreted proteins collected from the bcxyr1 deletion strain displayed a weaker cell-death-inducing effect than the wild-type secretome when infiltrated to Nicotiana benthamiana leaves. Transcriptome sequencing (RNA-seq) analysis revealed 41 genes with reduced expression in the Δbcxyr1 mutant compared with those in the wild-type strain, of which half encode secreted proteins that are particularly enriched in carbohydrate-active enzyme (CAZyme)-encoding genes. Among them, we identified a novel putative expansin-like protein that was necessary for fungal virulence, supporting the involvement of BcXyr1 in the regulation of extracellular virulence factors. IMPORTANCE PCWDEs are considered important components of the virulence arsenal of necrotrophic plant pathogens. However, despite intensive research, the role of PCWDEs in the pathogenicity of necrotrophic phytopathogenic fungi remains ambiguous. Here, we demonstrate that the transcription factor BcXyr1 regulates the expression of a specific set of secreted PCWDE-encoding genes and that it is essential for fungal virulence. Furthermore, we identified a BcXyr1-regulated expansin-like gene that is required for fungal virulence. Our findings provide strong evidence for the importance of PCWDEs in the pathogenicity of B. cinerea and highlight specific PCWDEs that might be more important than others.
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Shen L, Yan A, Wang Y, Wang Y, Liu H, Zhong Y. Tailoring the expression of Xyr1 leads to efficient production of lignocellulolytic enzymes in Trichoderma reesei for improved saccharification of corncob residues. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:142. [PMID: 36528622 PMCID: PMC9759857 DOI: 10.1186/s13068-022-02240-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei is extensively used for the industrial-scale cellulase production. It has been well known that the transcription factor Xyr1 plays an important role in the regulatory network controlling cellulase gene expression. However, the role of Xyr1 in the regulation of cellulase expression has not been comprehensively elucidated, which hinders further improvement of lignocellulolytic enzyme production. RESULTS Here, the expression dosage of xyr1 was tailored in T. reesei by differentially overexpressing the xyr1 gene under the control of three strong promoters (Pegl2, Pcbh1, and Pcdna1), and the transcript abundance of xyr1 was elevated 5.8-, 12.6-, and 47.2-fold, respectively. We found expression of cellulase genes was significantly increased in the Pegl2-driven xyr1 overexpression strain QE2X, whereas relatively low in the Pcbh1- and Pcdna1-driven overexpression strains. We also found that the Pegl2-driven overexpression of xyr1 caused a more significant opening of chromatin in the core promoter region of the prominent cellulase genes. Furthermore, the cellulase activity showed a 3.2-fold increase in the strain QE2X, while insignificant improvement in the Pcbh1- and Pcdna1-driven strains. Finally, the saccharification efficiency toward acid-pretreated corncob residues containing high-content lignin by the crude enzyme from QE2X was increased by 57.2% compared to that from the parental strain. Moreover, LC-MS/MS and RT-qPCR analysis revealed that expression of accessory proteins (Cip1, Cip2, Swo1, and LPMOs) was greatly improved in QE2X, which partly explained the promoting effect of the Pegl2-driven overexpression on enzymatic hydrolysis of lignocellulose biomass. CONCLUSIONS Our results underpin that the precise tailoring expression of xyr1 is essential for highly efficient cellulase synthesis, which provide new insights into the role of Xyr1 in regulating cellulase expression in T. reesei. Moreover, these results also provides a prospective strategy for strain improvement to enhance the lignocellulolytic enzyme production for use in biorefinery applications.
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Affiliation(s)
- Linjing Shen
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Aiqin Yan
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yifan Wang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yubo Wang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Hong Liu
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yaohua Zhong
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
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Havukainen S, Pujol-Giménez J, Valkonen M, Hediger MA, Landowski CP. Functional characterization of a highly specific L-arabinose transporter from Trichoderma reesei. Microb Cell Fact 2021; 20:177. [PMID: 34496831 PMCID: PMC8425032 DOI: 10.1186/s12934-021-01666-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lignocellulose biomass has been investigated as a feedstock for second generation biofuels and other value-added products. Some of the processes for biofuel production utilize cellulases and hemicellulases to convert the lignocellulosic biomass into a range of soluble sugars before fermentation with microorganisms such as yeast Saccharomyces cerevisiae. One of these sugars is l-arabinose, which cannot be utilized naturally by yeast. The first step in l-arabinose catabolism is its transport into the cells, and yeast lacks a specific transporter, which could perform this task. Results We identified Trire2_104072 of Trichoderma reesei as a potential l-arabinose transporter based on its expression profile. This transporter was described already in 2007 as d-xylose transporter XLT1. Electrophysiology experiments with Xenopus laevis oocytes and heterologous expression in yeast revealed that Trire2_104072 is a high-affinity l-arabinose symporter with a Km value in the range of \documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼ 0.1–0.2 mM. It can also transport d-xylose but with low affinity (Km\documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼ 9 mM). In yeast, l-arabinose transport was inhibited slightly by d-xylose but not by d-glucose in an assay with fivefold excess of the inhibiting sugar. Comparison with known l-arabinose transporters revealed that the expression of Trire2_104072 enabled yeast to uptake l-arabinose at the highest rate in conditions with low extracellular l-arabinose concentration. Despite the high specificity of Trire2_104072 for l-arabinose, the growth of its T. reesei deletion mutant was only affected at low l-arabinose concentrations. Conclusions Due to its high affinity for l-arabinose and low inhibition by d-glucose or d-xylose, Trire2_104072 could serve as a good candidate for improving the existing pentose-utilizing yeast strains. The discovery of a highly specific l-arabinose transporter also adds to our knowledge of the primary metabolism of T. reesei. The phenotype of the deletion strain suggests the involvement of other transporters in l-arabinose transport in this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01666-4.
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Affiliation(s)
- Sami Havukainen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
| | - Mari Valkonen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
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Ijoma GN, Heri SM, Matambo TS, Tekere M. Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. J Fungi (Basel) 2021; 7:700. [PMID: 34575737 PMCID: PMC8464691 DOI: 10.3390/jof7090700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.
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Affiliation(s)
- Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Sylvie M. Heri
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Tonderayi S. Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Memory Tekere
- Department of Environmental Science, College of Agricultural and Environmental Science, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa;
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Integrative Analysis of Selected Metabolites and the Fungal Transcriptome during the Developmental Cycle of Ganoderma lucidum Strain G0119 Correlates Lignocellulose Degradation with Carbohydrate and Triterpenoid Metabolism. Appl Environ Microbiol 2021; 87:e0053321. [PMID: 33893114 DOI: 10.1128/aem.00533-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To systemically understand the biosynthetic pathways of bioactive substances, including triterpenoids and polysaccharides, in Ganoderma lucidum, the correlation between substrate degradation and carbohydrate and triterpenoid metabolism during growth was analyzed by combining changes in metabolite content and changes in related enzyme expression in G. lucidum over 5 growth phases. Changes in low-polarity triterpenoid content were correlated with changes in glucose and mannitol contents in fruiting bodies. Additionally, changes in medium-polarity triterpenoid content were correlated with changes in the lignocellulose content of the substrate and with the glucose, trehalose, and mannitol contents of fruiting bodies. Weighted gene coexpression network analysis (WGCNA) indicated that changes in trehalose and polyol contents were related to carbohydrate catabolism and polysaccharide synthesis. Changes in triterpenoid content were related to expression of the carbohydrate catabolic enzymes laccase, cellulase, hemicellulase, and polysaccharide synthase and to the expression of several cytochrome P450 monooxygenases (CYPs). It was concluded that the products of cellulose and hemicellulose degradation participate in polyol, trehalose, and polysaccharide synthesis during initial fruiting body formation. These carbohydrates accumulate in the early phase of fruiting body formation and are utilized when the fruiting bodies mature and a large number of spores are ejected. An increase in carbohydrate metabolism provides additional precursors for the synthesis of triterpenoids. IMPORTANCE Most studies of G. lucidum have focused on its medicinal function and on the mechanism of its activity, whereas the physiological metabolism and synthesis of bioactive substances during the growth of this species have been less studied. Therefore, theoretical guidance for cultivation methods to increase the production of bioactive compounds remains lacking. This study integrated changes in the lignocellulose, carbohydrate, and triterpenoid contents of G. lucidum with enzyme expression from transcriptomics data using WGCNA. The findings helped us better understand the connections between substrate utilization and the synthesis of polysaccharides and triterpenoids during the cultivation cycle of G. lucidum. The results of WGCNA suggest that the synthesis of triterpenoids can be enhanced not only through regulating the expression of enzymes in the triterpenoid pathway, but also through regulating carbohydrate metabolism and substrate degradation. This study provides a potential approach and identifies enzymes that can be targeted to regulate lignocellulose degradation and accelerate the accumulation of bioactive substances by regulating substrate degradation in G. lucidum.
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Daranagama ND, Suzuki Y, Shida Y, Ogasawara W. Involvement of Xyr1 and Are1 for Trichodermapepsin Gene Expression in Response to Cellulose and Galactose in Trichoderma reesei. Curr Microbiol 2020; 77:1506-1517. [DOI: 10.1007/s00284-020-01955-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
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10
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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.
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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.
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11
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Wang L, Yang R, Cao Y, Zheng F, Meng X, Zhong Y, Chen G, Zhang W, Liu W. CLP1, a Novel Plant Homeo Domain Protein, Participates in Regulating Cellulase Gene Expression in the Filamentous Fungus Trichoderma reesei. Front Microbiol 2019; 10:1700. [PMID: 31447796 PMCID: PMC6691364 DOI: 10.3389/fmicb.2019.01700] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023] Open
Abstract
The stringent regulatory network of cellulase gene expression in the filamentous fungus Trichoderma reesei involves multiple transcriptional regulators. However, identification and mechanistic investigation of these regulators are still insufficient. Here, we identified a novel transcriptional regulator, CLP1, a plant homeo domain (PHD) Protein that participates in regulating T. reesei cellulase gene expression. Phylogenetic analyses demonstrated that CLP1 homologs are widely distributed in filamentous fungi including Trichoderma, Penicillium, Fusarium, Neurospora, and Aspergillus species. We demonstrated that CLP1 is a nuclear protein and lack of CLP1 significantly impaired the induced expression of cellulase genes. ChIP experiments showed CLP1 binding to the cellulase gene promoters specifically under cellulose conditions and compromised XYR1 occupancy on the same promoters in the absence of CLP1 at the early induction stage. XYR1 overexpression fully rescued the defect in cellulase production but not the defect in conidia formation in the clp1 null mutant. Further analysis showed that the PHD is required for the CLP1 appropriate subcellular localization as well as the induced cellulase gene expression and conidiation. Taken together, these data demonstrated an important role of CLP1 in the regulation of cellulase and xylanase gene expression in T. reesei.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Renfei Yang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yanli Cao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Fanglin Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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12
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Wang L, Lv X, Cao Y, Zheng F, Meng X, Shen Y, Chen G, Liu W, Zhang W. A novel transcriptional regulator RXE1 modulates the essential transactivator XYR1 and cellulase gene expression in Trichoderma reesei. Appl Microbiol Biotechnol 2019; 103:4511-4523. [DOI: 10.1007/s00253-019-09739-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/26/2019] [Accepted: 03/03/2019] [Indexed: 12/20/2022]
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13
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Benocci T, Aguilar-Pontes MV, Kun RS, Lubbers RJM, Lail K, Wang M, Lipzen A, Ng V, Grigoriev IV, Seiboth B, Daly P, de Vries RP. Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:81. [PMID: 31007715 PMCID: PMC6454604 DOI: 10.1186/s13068-019-1422-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/03/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Trichoderma reesei is one of the major producers of enzymes for the conversion of plant biomass to sustainable fuels and chemicals. Crude plant biomass can induce the production of CAZymes in T. reesei, but there is limited understanding of how the transcriptional response to crude plant biomass is regulated. In addition, it is unknown whether induction on untreated recalcitrant crude plant biomass (with a large diversity of inducers) can be sustained for longer. We investigated the transcriptomic response of T. reesei to the two industrial feedstocks, corn stover (CS) and soybean hulls (SBH), over time (4 h, 24 h and 48 h), and its regulatory basis using transcription factor deletion mutants (Δxyr1 and Δara1). We also investigated whether deletion of a xylulokinase gene (Δxki1) from the pentose catabolic pathway that converts potential inducers could lead to increased CAZyme gene expression. RESULTS By analyzing the transcriptomic responses using clustering as well as differential and cumulative expression of plant biomass degrading CAZymes, we found that corn stover induced a broader range and higher expression of CAZymes in T. reesei, while SBH induced more pectinolytic and mannanolytic transcripts. XYR1 was the major TF regulating CS utilization, likely due to the significant amount of d-xylose in this substrate. In contrast, ARA1 had a stronger effect on SBH utilization, which correlates with a higher abundance of l-arabinose in SBH that activates ARA1. Blocking pentose catabolism by deletion of xki1 led to higher expression of CAZyme encoding genes on both substrates at later time points. Surprisingly, this was also observed for Δara1 at later time points. Many of these genes were XYR1 regulated, suggesting that inducers for this regulator accumulated over time on both substrates. CONCLUSION Our data demonstrates the complexity of the regulatory system related to plant biomass degradation in T. reesei and the effect the feedstock composition has on this. Furthermore, this dataset provides leads to improve the efficiency of a T. reesei enzyme cocktail, such as by the choice of substrate or by deleting xki1 to obtain higher production of plant biomass degrading CAZymes.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roland Sándor Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ronnie J. M. Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598 USA
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
| | - Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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14
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Zou G, Jiang Y, Liu R, Zhu Z, Zhou Z. The putative β-glucosidase BGL3I regulates cellulase induction in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:314. [PMID: 30473732 PMCID: PMC6240962 DOI: 10.1186/s13068-018-1314-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina) displays increased cellulase expression while growing on inducers such as lactose or cellulose. However, the mechanism of cellulase induction in T. reesei is not yet completely characterized. Here, a protein annotated as β-glucosidase (BGL3I) was found to be involved in cellulase induction in T. reesei. The effects of BGL3I on cellulase production have not yet been fully understood. RESULTS Deletion of the bgl3i gene had no influence on the growth of T. reesei, but significantly increased its cellulase activities. Deletion of bgl3i also resulted in decreased extracellular galactosidase activity, but significantly increased transcription of lactose permeases, which might be involved in lactose transport. Furthermore, deletion of bgl3i enhanced the transcription levels of intracellular β-glucosidases cel1a, cel1b and the regulator xyr1, which are all essential for lactose induction in T. reesei. BGL3I was found to have a relatively high ability to hydrolyze sophorose, which is proposed to be the strongest natural inducer of cellulase synthesis in T. reesei. CONCLUSIONS BGL3I may take part in the complex regulating system of cellulase induction. The deletion of bgl3i offers a new strategy to improve T. reesei strain performance.
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Affiliation(s)
- Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 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 Agriculture Science, 1000 Jinqi Rd, Fengxian, 201403 Shanghai China
| | - Yanping Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
- Southwest Jiaotong University, Chengdu, 611756 Sichuan China
| | - Rui Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 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, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
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15
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Borin GP, Carazzolle MF, Dos Santos RAC, Riaño-Pachón DM, Oliveira JVDC. Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30. Front Bioeng Biotechnol 2018; 6:151. [PMID: 30406095 PMCID: PMC6204389 DOI: 10.3389/fbioe.2018.00151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022] Open
Abstract
The biomass-degrading fungus Trichoderma reesei has been considered a model for cellulose degradation, and it is the primary source of the industrial enzymatic cocktails used in second-generation (2G) ethanol production. However, although various studies and advances have been conducted to understand the cellulolytic system and the transcriptional regulation of T. reesei, the whole set of genes related to lignocellulose degradation has not been completely elucidated. In this study, we inferred a weighted gene co-expression network analysis based on the transcriptome dataset of the T. reesei RUT-C30 strain aiming to identify new target genes involved in sugarcane bagasse breakdown. In total, ~70% of all the differentially expressed genes were found in 28 highly connected gene modules. Several cellulases, sugar transporters, and hypothetical proteins coding genes upregulated in bagasse were grouped into the same modules. Among them, a single module contained the most representative core of cellulolytic enzymes (cellobiohydrolase, endoglucanase, β-glucosidase, and lytic polysaccharide monooxygenase). In addition, functional analysis using Gene Ontology (GO) revealed various classes of hydrolytic activity, cellulase activity, carbohydrate binding and cation:sugar symporter activity enriched in these modules. Several modules also showed GO enrichment for transcription factor activity, indicating the presence of transcriptional regulators along with the genes involved in cellulose breakdown and sugar transport as well as other genes encoding proteins with unknown functions. Highly connected genes (hubs) were also identified within each module, such as predicted transcription factors and genes encoding hypothetical proteins. In addition, various hubs contained at least one DNA binding site for the master activator Xyr1 according to our in silico analysis. The prediction of Xyr1 binding sites and the co-expression with genes encoding carbohydrate active enzymes and sugar transporters suggest a putative role of these hubs in bagasse cell wall deconstruction. Our results demonstrate a vast range of new promising targets that merit additional studies to improve the cellulolytic potential of T. reesei strains and to decrease the production costs of 2G ethanol.
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Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
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16
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Liu J, Zhang J, Wang J, Zhang J, Miao H, Jia C, Wang Z, Xu B, Jin Z. MuMADS1 and MaOFP1 regulate fruit quality in a tomato ovate mutant. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:989-1001. [PMID: 28944538 PMCID: PMC5902769 DOI: 10.1111/pbi.12843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/11/2017] [Accepted: 09/20/2017] [Indexed: 05/11/2023]
Abstract
Fruit ripening and quality are common botanical phenomena that are closely linked and strictly regulated by transcription factors. It was previously discovered that a banana MADS-box protein named MuMADS1 interacted with an ovate family protein named MaOFP1 to regulate banana fruit ripening. To further investigate the role of MuMADS1 and MaOFP1 in the regulation of fruit quality, a combination of genetic transformation and transcriptional characterization was used. The results indicated that the co-expression of MuMADS1 and MaOFP1 in the ovate mutant could compensate for fruit shape and inferior qualities relating to fruit firmness, soluble solids and sugar content. The number of differentially expressed genes (DEGs) was 1395 in WT vs. ovate, with 883 up-regulated and 512 down-regulated genes, while the numbers of DEGs gradually decreased with the transformation of MuMADS1 and MaOFP1 into ovate. 'Starch and sucrose metabolism' constituted the primary metabolic pathway, and the gene numbers in this pathway were obviously different when MuMADS1 and MaOFP1 were integrated into ovate. A series of metabolic genes involved in cell wall biosynthesis were up-regulated in the WT vs. ovate, which probably resulted in the firmer texture and lower sugar contents in the ovate fruit. These results demonstrate that MuMADS1 and MaOFP1 are coregulators of fruit quality, facilitating the dissection of the molecular mechanisms underlying fruit quality formation.
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Affiliation(s)
- Juhua Liu
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jing Zhang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jingyi Wang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Hongxia Miao
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Caihong Jia
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Zhuo Wang
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Biyu Xu
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop BiotechnologyMinistry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Key Laboratory of Genetic Improvement of BananasHainan ProvinceHaikou Experimental StationChinese Academy of Tropical Agricultural SciencesHaikouChina
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17
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Liu J, Zhang J, Miao H, Jia C, Wang J, Xu B, Jin Z. Elucidating the Mechanisms of the Tomato ovate Mutation in Regulating Fruit Quality Using Proteomics Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10048-10057. [PMID: 29120173 DOI: 10.1021/acs.jafc.7b03656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The ovate mutation has frequently been used to study changes in fruit shape but not fruit quality. A deterioration in fruit quality associated with the ovate mutation was discovered in this study. To elucidate how ovate influences the quality of fruit, we performed a proteomics analysis of the fruits of the ovate mutant (LA3543) and wild-type ("Ailsa Craig", LA2838A) using tandem mass tag analysis. The results indicated that the ovate mutation significantly influences fruit quality in a number of ways, including by reducing the expression of 1-aminocyclopropane-1-carboxylic acid oxidase 3 (ACO3) in ethylene biosynthesis, improving firmness by reducing the amount of pectinesterase and polygalacturonase, reducing sugar accumulation by downregulating the abundance of mannan endo-1,4-β-mannosidase 4, β-galactosidase, and β-amylase, and reducing the malic acid content by downregulating the accumulation of malic enzymes and malate synthase. These findings could inform future improvements in fruit quality.
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Affiliation(s)
- Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Jing Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
- Key Laboratory of Genetic Improvement of Bananas, Chinese Academy of Tropical Agricultural Sciences , Haikou Experimental Station, Haikou, Hainan Province 570102, China
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18
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Conservation and diversity of the regulators of cellulolytic enzyme genes in Ascomycete fungi. Curr Genet 2017; 63:951-958. [DOI: 10.1007/s00294-017-0695-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 01/08/2023]
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