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Alharake J, Bidard F, Aouam T, Sénamaud-Beaufort C, Margeot A, Heiss-Blanquet S. Effect of the res2 transcription factor gene deletion on protein secretion and stress response in the hyperproducer strain Trichoderma reesei Rut-C30. BMC Microbiol 2023; 23:374. [PMID: 38036984 PMCID: PMC10687790 DOI: 10.1186/s12866-023-03125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND The fungus Trichoderma reesei is one of the most used industrial cellulase producers due to its high capacity of protein secretion. Strains of T. reesei with enhanced protein secretion capacity, such as Rut-C30, have been obtained after several rounds of random mutagenesis. The strain was shown to possess an expanded endoplasmic reticulum, but the genetic factors responsible for this phenotype remain still unidentified. Recently, three new transcription factors were described in Neurospora crassa which were demonstrated to be involved in protein secretion. One of them, RES2, was involved in upregulation of secretion-related genes. The aim of our present study was therefore to analyze the role of RES2, on protein secretion in the T. reesei Rut-C30 strain. RESULT Deletion of the res2 gene in Rut-C30 resulted in slightly slower growth on all substrates tested, and lower germination rate as well as lower protein secretion compared to the parental strain Rut-C30. Transcriptomic analysis of the Rut-C30 and the Δres2 mutant strain in secretion stress conditions showed remarkably few differences : 971 genes were differentially expressed (DE) in both strains while 192 genes out of 1163 (~ 16.5%) were DE in Rut-C30 only and 693 out of 1664 genes (~ 41.6%) displayed differential expression solely in Δres2. Notably, induction of protein secretion by cultivating on lactose and addition of secretion stress inducer DTT induced many genes of the secretion pathway similarly in both strains. Among the differentially expressed genes, those coding for amino acid biosynthesis genes, transporters and genes involved in lipid metabolism were found to be enriched specifically in the Δres2 strain upon exposure to lactose or DTT. Besides, redox homeostasis and DNA repair genes were specifically upregulated in the Δres2 strain, indicating an altered stress response. CONCLUSION These results indicate that in the T. reesei Rut-C30 strain, RES2 does not act as a master regulator of the secretion pathway, but it contributes to a higher protein secretion by adjusting the expression of genes involved in different steps of protein synthesis and the secretion pathway.
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Affiliation(s)
- Jawad Alharake
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Thiziri Aouam
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Catherine Sénamaud-Beaufort
- Département de biologie, GenomiqueENS, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, École normale supérieure, Paris, 75005, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, Rueil-Malmaison Cedex, 92852, France.
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Reyre JL, Grisel S, Haon M, Xiang R, Gaillard JC, Armengaud J, Guallar V, Margeot A, Arragain S, Berrin JG, Bissaro B. Insights into peculiar fungal LPMO family members holding a short C-terminal sequence reminiscent of phosphate binding motifs. Sci Rep 2023; 13:11586. [PMID: 37463979 DOI: 10.1038/s41598-023-38617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are taxonomically widespread copper-enzymes boosting biopolymers conversion (e.g. cellulose, chitin) in Nature. White-rot Polyporales, which are major fungal wood decayers, may possess up to 60 LPMO-encoding genes belonging to the auxiliary activities family 9 (AA9). Yet, the functional relevance of such multiplicity remains to be uncovered. Previous comparative transcriptomic studies of six Polyporales fungi grown on cellulosic substrates had shown the overexpression of numerous AA9-encoding genes, including some holding a C-terminal domain of unknown function ("X282"). Here, after carrying out structural predictions and phylogenetic analyses, we selected and characterized six AA9-X282s with different C-term modularities and atypical features hitherto unreported. Unexpectedly, after screening a large array of conditions, these AA9-X282s showed only weak binding properties to cellulose, and low to no cellulolytic oxidative activity. Strikingly, proteomic analysis revealed the presence of multiple phosphorylated residues at the surface of these AA9-X282s, including a conserved residue next to the copper site. Further analyses focusing on a 9 residues glycine-rich C-term extension suggested that it could hold phosphate-binding properties. Our results question the involvement of these AA9 proteins in the degradation of plant cell wall and open new avenues as to the divergence of function of some AA9 members.
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Affiliation(s)
- Jean-Lou Reyre
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, 13009, Marseille, France
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Sacha Grisel
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, 13009, Marseille, France
- INRAE, Aix Marseille University, 3PE Platform, 13009, Marseille, France
| | - Mireille Haon
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, 13009, Marseille, France
- INRAE, Aix Marseille University, 3PE Platform, 13009, Marseille, France
| | - Ruite Xiang
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, 30200, Bagnols-Sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, 30200, Bagnols-Sur-Cèze, France
| | - Victor Guallar
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Simon Arragain
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, 13009, Marseille, France.
- INRAE, Aix Marseille University, 3PE Platform, 13009, Marseille, France.
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, 13009, Marseille, France.
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Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
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Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
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Pirayre A, Duval L, Blugeon C, Firmo C, Perrin S, Jourdier E, Margeot A, Bidard F. Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30. BMC Genomics 2020; 21:885. [PMID: 33302864 PMCID: PMC7731781 DOI: 10.1186/s12864-020-07281-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungus Trichoderma reesei. Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network of T. reesei Rut-C30. RESULTS Experimental results on the Rut-C30 hyperproducing strain confirmed the impact of sugar mixtures on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network built using BRANE Cut software reveals three sub-networks related to i) a positive correlation between lactose concentration and cellulase production, ii) a particular dependence of the lactose onto the β-glucosidase regulation and iii) a negative regulation of the development process and growth. CONCLUSIONS This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration of xyr1, clr2 and ace3 for cellulase and hemicellulase induction and production, a fine regulation of the β-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains in industry-like conditions.
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Affiliation(s)
- Aurélie Pirayre
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France.
| | - Laurent Duval
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
- Laboratoire d'Informatique Gaspard-Monge (LIGM), ESIEE Paris, Université-Gustave Eiffel, Marne-la-Vallée, F-77454, France
| | - Corinne Blugeon
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Cyril Firmo
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Sandrine Perrin
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Etienne Jourdier
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Frédérique Bidard
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
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Paës G, Navarro D, Benoit Y, Blanquet S, Chabbert B, Chaussepied B, Coutinho PM, Durand S, Grigoriev IV, Haon M, Heux L, Launay C, Margeot A, Nishiyama Y, Raouche S, Rosso MN, Bonnin E, Berrin JG. Tracking of enzymatic biomass deconstruction by fungal secretomes highlights markers of lignocellulose recalcitrance. Biotechnol Biofuels 2019; 12:76. [PMID: 30976326 PMCID: PMC6442405 DOI: 10.1186/s13068-019-1417-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/23/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Lignocellulose biomass is known as a recalcitrant material towards enzymatic hydrolysis, increasing the process cost in biorefinery. In nature, filamentous fungi naturally degrade lignocellulose, using an arsenal of hydrolytic and oxidative enzymes. Assessment of enzyme hydrolysis efficiency generally relies on the yield of glucose for a given biomass. To better understand the markers governing recalcitrance to enzymatic degradation, there is a need to enlarge the set of parameters followed during deconstruction. RESULTS Industrially-pretreated biomass feedstocks from wheat straw, miscanthus and poplar were sequentially hydrolysed following two steps. First, standard secretome from Trichoderma reesei was used to maximize cellulose hydrolysis, producing three recalcitrant lignin-enriched solid substrates. Then fungal secretomes from three basidiomycete saprotrophs (Laetisaria arvalis, Artolenzites elegans and Trametes ljubarskyi) displaying various hydrolytic and oxidative enzymatic profiles were applied to these recalcitrant substrates, and compared to the T. reesei secretome. As a result, most of the glucose was released after the first hydrolysis step. After the second hydrolysis step, half of the remaining glucose amount was released. Overall, glucose yield after the two sequential hydrolyses was more dependent on the biomass source than on the fungal secretomes enzymatic profile. Solid residues obtained after the two hydrolysis steps were characterized using complementary methodologies. Correlation analysis of several physico-chemical parameters showed that released glucose yield was negatively correlated with lignin content and cellulose crystallinity while positively correlated with xylose content and water sorption. Water sorption appears as a pivotal marker of the recalcitrance as it reflects chemical and structural properties of lignocellulosic biomass. CONCLUSIONS Fungal secretomes applied to highly recalcitrant biomass samples can further extend the release of the remaining glucose. The glucose yield can be correlated to chemical and physical markers, which appear to be independent from the biomass type and secretome. Overall, correlations between these markers reveal how nano-scale properties (polymer content and organization) influence macro-scale properties (particle size and water sorption). Further systematic assessment of these markers during enzymatic degradation will foster the development of novel cocktails to unlock the degradation of lignocellulose biomass.
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Affiliation(s)
- Gabriel Paës
- FARE Laboratory, INRA, Université de Reims Champagne-Ardenne, Reims, France
| | - David Navarro
- INRA, Aix Marseille Univ., UMR1163, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- INRA, Aix-Marseille Univ., UMR1163, CIRM-CF, Marseille, France
| | - Yves Benoit
- IFP Energies Nouvelles, Rueil-Malmaison, France
| | | | - Brigitte Chabbert
- FARE Laboratory, INRA, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Pedro M. Coutinho
- CNRS, Aix-Marseille Univ., UMR7857 AFMB, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Sylvie Durand
- INRA, UR1268 Biopolymères Interactions Assemblages, Nantes, France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Mireille Haon
- INRA, Aix Marseille Univ., UMR1163, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Laurent Heux
- CNRS, Univ. Grenoble Alpes, CERMAV, Grenoble, France
| | - Charlène Launay
- INRA, UR1268 Biopolymères Interactions Assemblages, Nantes, France
| | | | | | - Sana Raouche
- INRA, Aix Marseille Univ., UMR1163, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Marie-Noëlle Rosso
- INRA, Aix Marseille Univ., UMR1163, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Estelle Bonnin
- INRA, UR1268 Biopolymères Interactions Assemblages, Nantes, France
| | - Jean-Guy Berrin
- INRA, Aix Marseille Univ., UMR1163, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
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Filiatrault-Chastel C, Navarro D, Haon M, Grisel S, Herpoël-Gimbert I, Chevret D, Fanuel M, Henrissat B, Heiss-Blanquet S, Margeot A, Berrin JG. AA16, a new lytic polysaccharide monooxygenase family identified in fungal secretomes. Biotechnol Biofuels 2019; 12:55. [PMID: 30923563 PMCID: PMC6420742 DOI: 10.1186/s13068-019-1394-y] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lignocellulosic biomass is considered as a promising alternative to fossil resources for the production of fuels, materials and chemicals. Efficient enzymatic systems are needed to degrade the plant cell wall and overcome its recalcitrance. A widely used producer of cellulolytic cocktails is the ascomycete Trichoderma reesei, but this organism secretes a limited set of enzymes. To improve the saccharification yields, one strategy is to upgrade the T. reesei enzyme cocktail with enzymes produced by other biomass-degrading filamentous fungi isolated from biodiversity. RESULTS In this study, the enzymatic cocktails secreted by five strains from the genus Aspergillus (Aspergillus japonicus strains BRFM 405, 1487, 1489, 1490 and Aspergillus niger strain BRFM 430) were tested for their ability to boost a T. reesei reference cocktail for the saccharification of pretreated biomass. Proteomic analysis of fungal secretomes that significantly improved biomass degradation showed that the presence of proteins belonging to a putative LPMO family previously identified by genome analysis and awaiting experimental demonstration of activity. Members of this novel LPMO family, named AA16, are encountered in fungi and oomycetes with life styles oriented toward interactions with plant biomass. One AA16 protein from Aspergillus aculeatus (AaAA16) was produced to high level in Pichia pastoris. LPMO-type enzyme activity was demonstrated on cellulose with oxidative cleavage at the C1 position of the glucose unit. AaAA16 LPMO was found to significantly improve the activity of T. reesei CBHI on cellulosic substrates. CONCLUSIONS Although Aspergillus spp. has been investigated for decades for their CAZymes diversity, we identified members of a new fungal LPMO family using secretomics and functional assays. Properties of the founding member of the AA16 family characterized herein could be of interest for use in biorefineries.
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Affiliation(s)
- Camille Filiatrault-Chastel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - David Navarro
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Mireille Haon
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Sacha Grisel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Isabelle Herpoël-Gimbert
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Didier Chevret
- Plateforme d’Analyse Protéomique de Paris Sud-Ouest, Institut Micalis, UMR1319, INRA, Agro-ParisTech, Jouy-En-Josas, France
| | - Mathieu Fanuel
- UR1268, INRA, Biopolymères Interactions Assemblages, Nantes, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257, CNRS, Aix Marseille Université, Marseille, France
- USC1408, INRA, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
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Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F. Correction to: Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes. Biotechnol Biofuels 2018; 11:163. [PMID: 29942348 PMCID: PMC5998568 DOI: 10.1186/s13068-018-1161-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
[This corrects the article DOI: 10.1186/s13068-017-0837-6.].
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Affiliation(s)
- Etienne Jourdier
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Preau, 92852 Rueil-Malmaison, France
| | - Lyam Baudry
- Groupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut Pasteur, 75015 Paris, France
- UMR 3525, CNRS, 75015 Paris, France
| | - Dante Poggi-Parodi
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Preau, 92852 Rueil-Malmaison, France
| | - Yoan Vicq
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Preau, 92852 Rueil-Malmaison, France
| | - Romain Koszul
- Groupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut Pasteur, 75015 Paris, France
- UMR 3525, CNRS, 75015 Paris, France
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Preau, 92852 Rueil-Malmaison, France
| | - Martial Marbouty
- Groupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut Pasteur, 75015 Paris, France
- UMR 3525, CNRS, 75015 Paris, France
| | - Frédérique Bidard
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Preau, 92852 Rueil-Malmaison, France
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Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F. Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes. Biotechnol Biofuels 2017; 10:151. [PMID: 28616075 PMCID: PMC5469131 DOI: 10.1186/s13068-017-0837-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/31/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND The presence of low complexity and repeated regions in genomes often results in difficulties to assemble sequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to several investigations, regarding for instance the evolution of entire clades, the analysis of chromosome rearrangements, and is pivotal to sexual crossing studies. In non-conventional but industrially relevant model organisms, such as the ascomycete Trichoderma reesei, a complete genome assembly is seldom available. RESULTS The chromosome scaffolds of T. reesei QM6a and Rut-C30 strains have been generated using a contact genomic/proximity ligation genomic approach. The original reference assembly, encompassing dozens of scaffolds, was reorganized into two sets of seven chromosomes. Chromosomal contact data also allowed to characterize 10-40 kb, gene-free, AT-rich (76%) regions corresponding to the T. reesei centromeres. Large chromosomal rearrangements (LCR) in Rut-C30 were then characterized, in agreement with former studies, and the position of LCR breakpoints used to assess the likely chromosome structure of other T. reesei strains [QM9414, CBS999.97 (1-1, re), and QM9978]. In agreement with published results, we predict that the numerous chromosome rearrangements found in highly mutated industrial strains may limit the efficiency of sexual reproduction for their improvement. CONCLUSIONS The GRAAL program allowed us to generate the karyotype of the Rut-C30 strain, and from there to predict chromosome structure for most T. reesei strains for which sequence is available. This method that exploits proximity ligation sequencing approach is a fast, cheap, and straightforward way to characterize both chromosome structure and centromere sequences and is likely to represent a popular convenient alternative to expensive and work-intensive resequencing projects.
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Affiliation(s)
- Etienne Jourdier
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Lyam Baudry
- Groupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut Pasteur, 75015 Paris, France
- UMR 3525, CNRS, 75015 Paris, France
| | - Dante Poggi-Parodi
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Yoan Vicq
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Romain Koszul
- Groupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut Pasteur, 75015 Paris, France
- UMR 3525, CNRS, 75015 Paris, France
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Martial Marbouty
- Groupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut Pasteur, 75015 Paris, France
- UMR 3525, CNRS, 75015 Paris, France
| | - Frédérique Bidard
- IFP Energies nouvelles, 1 et 4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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9
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Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F. Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. Biotechnol Biofuels 2017; 10:209. [PMID: 28912831 PMCID: PMC5588705 DOI: 10.1186/s13068-017-0897-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/29/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype. RESULTS Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions. CONCLUSION We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.
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Affiliation(s)
- Christa Ivanova
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- Present Address: Genetics of Biofilms Unit, Department of Microbiology, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jonas Ramoni
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Thiziri Aouam
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Alexa Frischmann
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Stéphane Le Crom
- Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, 75005 Paris, France
| | - Sophie Lemoine
- École normale supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l’École normale supérieure (IBENS), Plateforme Génomique, 75005 Paris, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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10
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Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP. Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics 2015; 16:725. [PMID: 26395946 PMCID: PMC4580284 DOI: 10.1186/s12864-015-1917-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 11/10/2022] Open
Affiliation(s)
- Alexander Lichius
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Franziska Buchholz
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Stéphane Le Crom
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), FR 3631, Département des Plateforme, F-75005, Paris, France
| | - Joel Martin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Tina Austerlitz
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria.
| | - Christian P Kubicek
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
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11
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Ghassemi S, Lichius A, Bidard F, Lemoine S, Rossignol MN, Herold S, Seidl-Seiboth V, Seiboth B, Espeso EA, Margeot A, Kubicek CP. The ß-importin KAP8 (Pse1/Kap121) is required for nuclear import of the cellulase transcriptional regulator XYR1, asexual sporulation and stress resistance in Trichoderma reesei. Mol Microbiol 2015; 96:405-18. [PMID: 25626518 PMCID: PMC4390390 DOI: 10.1111/mmi.12944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 11/26/2022]
Abstract
The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes, and serves as a prime model for their genetic regulation. Most of its (hemi-)cellulolytic enzymes are obligatorily dependent on the transcriptional activator XYR1. Here, we investigated the nucleo-cytoplasmic shuttling mechanism that transports XYR1 across the nuclear pore complex. We identified 14 karyopherins in T. reesei, of which eight were predicted to be involved in nuclear import, and produced single gene-deletion mutants of all. We found KAP8, an ortholog of Aspergillus nidulans KapI, and Saccharomyces cerevisiae Kap121/Pse1, to be essential for nuclear recruitment of GFP-XYR1 and cellulase gene expression. Transformation with the native gene rescued this effect. Transcriptomic analyses of Δkap8 revealed that under cellulase-inducing conditions 42 CAZymes, including all cellulases and hemicellulases known to be under XYR1 control, were significantly down-regulated. Δkap8 strains were capable of forming fertile fruiting bodies but exhibited strongly reduced conidiation both in light and darkness, and showed enhanced sensitivity towards abiotic stress, including high osmotic pressure, low pH and high temperature. Together, these data underscore the significance of nuclear import of XYR1 in cellulase and hemicellulase gene regulation in T. reesei, and identify KAP8 as the major karyopherin required for this process.
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Affiliation(s)
- Sara Ghassemi
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Alexander Lichius
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Fréderique Bidard
- IFP Energies nouvelles1-4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Sophie Lemoine
- Ecole Normale Supérieure, Institut de Biologie de l'ENSIBENS, Plateforme Génomique, Paris, F-75005, France
| | - Marie-Noëlle Rossignol
- Ecole Normale Supérieure, Institut de Biologie de l'ENSIBENS, Plateforme Génomique, Paris, F-75005, France
| | - Silvia Herold
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
- ACIB GmbH, c/o Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Antoine Margeot
- IFP Energies nouvelles1-4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Christian P Kubicek
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
- *For correspondence. E-mail ; Tel. (+ 1) 43 1 58801 166085; Fax (+ 1) 43 1 58801 17299
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12
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Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R. High-quality genome (re)assembly using chromosomal contact data. Nat Commun 2014; 5:5695. [PMID: 25517223 PMCID: PMC4284522 DOI: 10.1038/ncomms6695] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023] Open
Abstract
Closing gaps in draft genome assemblies can be costly and time-consuming, and published genomes are therefore often left ‘unfinished.’ Here we show that genome-wide chromosome conformation capture (3C) data can be used to overcome these limitations, and present a computational approach rooted in polymer physics that determines the most likely genome structure using chromosomal contact data. This algorithm—named GRAAL—generates high-quality assemblies of genomes in which repeated and duplicated regions are accurately represented and offers a direct probabilistic interpretation of the computed structures. We first validated GRAAL on the reference genome of Saccharomyces cerevisiae, as well as other yeast isolates, where GRAAL recovered both known and unknown complex chromosomal structural variations. We then applied GRAAL to the finishing of the assembly of Trichoderma reesei and obtained a number of contigs congruent with the know karyotype of this species. Finally, we showed that GRAAL can accurately reconstruct human chromosomes from either fragments generated in silico or contigs obtained from de novo assembly. In all these applications, GRAAL compared favourably to recently published programmes implementing related approaches. The correct assembly of genomes from sequencing data remains a challenge due to difficulties in correctly assigning the location of repeated DNA elements. Here the authors describe GRAAL, an algorithm that utilizes genome-wide chromosome contact data within a probabilistic framework to produce accurate genome assemblies.
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Affiliation(s)
- Hervé Marie-Nelly
- 1] Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France [2] CNRS, UMR 3525, 75015 Paris, France [3] Institut Pasteur, Unité Imagerie et Modélisation, 75015 Paris, France [4] CNRS, URA 2582, 75015 Paris, France [5] Sorbonne Universités, UPMC Univ Paris06, IFD, 4 place Jussieu, 75252 Paris, France
| | - Martial Marbouty
- 1] Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France [2] CNRS, UMR 3525, 75015 Paris, France
| | - Axel Cournac
- 1] Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France [2] CNRS, UMR 3525, 75015 Paris, France
| | - Jean-François Flot
- Max Planck Institute for Dynamics and Self-Organization, Group Biological Physics and Evolutionary Dynamics, Bunsenstr. 10, 37073 Göttingen, Germany
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France
| | - Dante Poggi Parodi
- 1] Sorbonne Universités, UPMC Univ Paris06, IFD, 4 place Jussieu, 75252 Paris, France [2] IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Sylvie Syan
- Institut Pasteur, Unité Cell Biology of Parasitism, 75015 Paris, France
| | - Nancy Guillén
- Institut Pasteur, Unité Cell Biology of Parasitism, 75015 Paris, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Christophe Zimmer
- 1] Institut Pasteur, Unité Imagerie et Modélisation, 75015 Paris, France [2] CNRS, URA 2582, 75015 Paris, France
| | - Romain Koszul
- 1] Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France [2] CNRS, UMR 3525, 75015 Paris, France
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13
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Poggi-Parodi D, Pirayre A, Portnoy T, Mathis H, Aouam T, Bidard F, Le Crom S, Margeot A. The cellulase induction system in Trichoderma reesei strains remains well conserved despite several generations of random mutagenesis and screening. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Poggi-Parodi D, Bidard F, Pirayre A, Portnoy T, Blugeon C, Seiboth B, Kubicek CP, Le Crom S, Margeot A. Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain. Biotechnol Biofuels 2014; 7:173. [PMID: 25550711 PMCID: PMC4279801 DOI: 10.1186/s13068-014-0173-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/18/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. RESULTS We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. CONCLUSIONS This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
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Affiliation(s)
- Dante Poggi-Parodi
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- />Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France
| | - Frédérique Bidard
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Aurélie Pirayre
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Thomas Portnoy
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Plateforme Génomique, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Inserm, U1024, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France
| | - Corinne Blugeon
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Plateforme Génomique, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Inserm, U1024, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France
| | - Bernhard Seiboth
- />Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Getreidemarkt 9/166, A- 1060 Vienna, Austria
| | | | - Stéphane Le Crom
- />Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Plateforme Génomique, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Inserm, U1024, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France
| | - Antoine Margeot
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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15
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Portnoy T, Margeot A, Linke R, Atanasova L, Fekete E, Sándor E, Hartl L, Karaffa L, Druzhinina IS, Seiboth B, Le Crom S, Kubicek CP. The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation. BMC Genomics 2011; 12:269. [PMID: 21619626 PMCID: PMC3124439 DOI: 10.1186/1471-2164-12-269] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 05/27/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known. RESULTS Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) by profiling transcription in a wild-type and a delta-cre1 mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes. CONCLUSIONS Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.
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Affiliation(s)
- Thomas Portnoy
- IFP Energies nouvelles, Département Biotechnologie, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
- École normale supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France. Inserm, U1024, Paris, F-75005 France. CNRS, UMR 8197, Paris, F-75005 France
| | - Antoine Margeot
- IFP Energies nouvelles, Département Biotechnologie, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Rita Linke
- Austrian Center of Industrial Biotechnology, c/o Institute of Chemical Engineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Lea Atanasova
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4010, P.O.Box 56, Debrecen, Hungary
| | - Erzsébet Sándor
- Department of Plant Protection, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, H-4032 Böszörményi út 138., Debrecen, Hungary
| | - Lukas Hartl
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4010, P.O.Box 56, Debrecen, Hungary
| | - Irina S Druzhinina
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Stéphane Le Crom
- École normale supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France. Inserm, U1024, Paris, F-75005 France. CNRS, UMR 8197, Paris, F-75005 France
| | - Christian P Kubicek
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
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16
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Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 2011; 12:R40. [PMID: 21501500 PMCID: PMC3218866 DOI: 10.1186/gb-2011-12-4-r40] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/28/2011] [Accepted: 04/18/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. CONCLUSIONS The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
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Affiliation(s)
- Christian P Kubicek
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Verena Seidl-Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Diego A Martinez
- Broad Institute of MIT and Harvard, 301 Binney St, Cambridge, MA 02142, USA
| | - Irina S Druzhinina
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Michael Thon
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Susanne Zeilinger
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Sergio Casas-Flores
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Mala Mukherjee
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Luis D Alcaraz
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Andrea Aerts
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Zsuzsanna Antal
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Lea Atanasova
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Mayte G Cervantes-Badillo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Jean Challacombe
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Olga Chertkov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Fanny Coulpier
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Nandan Deshpande
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Hans von Döhren
- TU Berlin, Institut für Chemie, FG Biochemie und Molekulare Biologie OE2, Franklinstr. 29, 10587 Berlin, Germany
| | - Daniel J Ebbole
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Edgardo U Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Michel Flipphi
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Apartado de Correos 73, Burjassot (Valencia) E-46100, Spain
| | - Fabian Glaser
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Elida Y Gómez-Rodríguez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Sabine Gruber
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Cliff Han
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Rosa Hermosa
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Idit Kosti
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Stéphane Le Crom
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Erika Lindquist
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Susan Lucas
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mette Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Peter S Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Antoine Margeot
- Biotechnology Department, IFP Energies nouvelles, 1-4 avenue de Bois Préau, Rueil-Malmaison, 92852, France
| | - Benjamin Metz
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Monica Misra
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Helena Nevalainen
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Markus Omann
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Nicolle Packer
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Edith E Uresti-Rivera
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Asaf Salamov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Monika Schmoll
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Harris Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Serenella Sukno
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Juan Antonio Tamayo-Ramos
- Wageningen University, Systems and Synthetic Biology, Fungal Systems Biology Group, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Doris Tisch
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Aric Wiest
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Heather H Wilkinson
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Michael Zhang
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Enrique Monte
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Scott E Baker
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Ayrinhac C, Margeot A, Ferreira NL, Chaabane FB, Monot F, Ravot G, Sonet JM, Fourage L. Improved Saccharification of Wheat Straw for Biofuel Production Using an Engineered Secretome of Trichoderma reesei. Org Process Res Dev 2010. [DOI: 10.1021/op100218a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Céline Ayrinhac
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
| | - Antoine Margeot
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
| | - Nicolas Lopes Ferreira
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
| | - Fadhel Ben Chaabane
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
| | - Frédéric Monot
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
| | - Gilles Ravot
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
| | - Jean-Marie Sonet
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
| | - Laurent Fourage
- Protéus SA, 70, allée Graham Bell, Parc scientifique Georges Besse, 30035 Nimes Cedex 1, France, and IFP Energies Nouvelles, 1 et 4, avenue de Bois-Préau, 92852 Rueil Malmaison Cedex, France
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18
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Jourdren L, Duclos A, Brion C, Portnoy T, Mathis H, Margeot A, Le Crom S. Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments. Nucleic Acids Res 2010; 38:e117. [PMID: 20176570 PMCID: PMC2879536 DOI: 10.1093/nar/gkq110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to deal with this problem, but each program is developed with its own strategy, which makes the choice of the best solution difficult. Here we describe Teolenn, a universal probe design workflow developed with a flexible and customizable module organization allowing fixed or variable length oligonucleotide generation. In addition, our software is able to supply quality scores for each of the designed probes. In order to assess the relevance of these scores, we performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. We show that our scoring pipeline correlates with signal quality for 97.2% of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities. This result is useful in discarding any bad scoring probes during the design step in order to get high-quality microarrays. Teolenn is available at http://transcriptome.ens.fr/teolenn/.
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Affiliation(s)
- Laurent Jourdren
- Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 75005 Paris, France
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19
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Margeot A, Hahn-Hagerdal B, Edlund M, Slade R, Monot F. New improvements for lignocellulosic ethanol. Curr Opin Biotechnol 2009; 20:372-80. [DOI: 10.1016/j.copbio.2009.05.009] [Citation(s) in RCA: 280] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 05/12/2009] [Accepted: 05/14/2009] [Indexed: 11/29/2022]
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Herpoël-Gimbert I, Margeot A, Dolla A, Jan G, Mollé D, Lignon S, Mathis H, Sigoillot JC, Monot F, Asther M. Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains. Biotechnol Biofuels 2008; 1:18. [PMID: 19105830 PMCID: PMC2631499 DOI: 10.1186/1754-6834-1-18] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 12/23/2008] [Indexed: 05/05/2023]
Abstract
BACKGROUND Due to its capacity to produce large amounts of cellulases, Trichoderma reesei is increasingly been researched in various fields of white biotechnology, especially in biofuel production from lignocellulosic biomass. The commercial enzyme mixtures produced at industrial scales are not well characterized, and their proteinaceous components are poorly identified and quantified. The development of proteomic methods has made it possible to comprehensively overview the enzymes involved in lignocellulosic biomass degradation which are secreted under various environmental conditions. RESULTS The protein composition of the secretome produced by industrial T. reesei (strain CL847) grown on a medium promoting the production of both cellulases and hemicellulases was explored using two-dimensional electrophoresis and MALDI-TOF or LC-MS/MS protein identification. A total of 22 protein species were identified. As expected, most of them are potentially involved in biomass degradation. The 2D map obtained was then used to compare the secretomes produced by CL847 and another efficient cellulolytic T. reesei strain, Rut-C30, the reference cellulase-overproducing strain using lactose as carbon source and inducer of cellulases. CONCLUSION This study provides the most complete mapping of the proteins secreted by T. reesei to date. We report on the first use of proteomics to compare secretome composition between two cellulase-overproducing strains Rut-C30 and CL847 grown under similar conditions. Comparison of protein patterns in both strains highlighted many unexpected differences between cellulase cocktails. The results demonstrate that 2D electrophoresis is a promising tool for studying cellulase production profiles, whether for industrial characterization of an entire secretome or for a more fundamental study on cellulase expression at genome-wide scale.
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Affiliation(s)
- Isabelle Herpoël-Gimbert
- INRA, UMR1163, Biotechnologie des Champignons Filamenteux, F-13000 Marseille, France
- Universités Aix-Marseille I & II, UMR1163, BCF, F-13000 Marseille, France
| | - Antoine Margeot
- IFP, Biotechnology Department, Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Alain Dolla
- IMR, FRE3083 – CNRS, Institut de Biologie Structurale et Microbiologie, Chemin Joseph-Aiguier, 13402 Marseille cedex 20, France
| | - Gwénaël Jan
- INRA, UMR1253, Science et Technologie du Lait et de l'Oeuf, F-35000 Rennes, France
- Agrocampus Rennes, UMR1253, STLO, F-35000 Rennes, France
| | - Daniel Mollé
- INRA, UMR1253, Science et Technologie du Lait et de l'Oeuf, F-35000 Rennes, France
- Agrocampus Rennes, UMR1253, STLO, F-35000 Rennes, France
| | - Sabrina Lignon
- Plate-forme protéomique, Institut de Biologie structurale et Microbiologie, Chemin Joseph-Aiguier, 13402 Marseille cedex 20, France
| | - Hughes Mathis
- IFP, Biotechnology Department, Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Jean-Claude Sigoillot
- INRA, UMR1163, Biotechnologie des Champignons Filamenteux, F-13000 Marseille, France
- Universités Aix-Marseille I & II, UMR1163, BCF, F-13000 Marseille, France
| | - Frédéric Monot
- IFP, Biotechnology Department, Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Marcel Asther
- INRA, UMR1163, Biotechnologie des Champignons Filamenteux, F-13000 Marseille, France
- Universités Aix-Marseille I & II, UMR1163, BCF, F-13000 Marseille, France
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Margeot A, Garcia M, Wang W, Tetaud E, di Rago JP, Jacq C. Why are many mRNAs translated to the vicinity of mitochondria: A role in protein complex assembly? Gene 2005; 354:64-71. [PMID: 15979254 DOI: 10.1016/j.gene.2005.04.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 04/15/2005] [Indexed: 11/28/2022]
Abstract
The longstanding question of the presence of mitochondria-bound polysomes has been recently revisited using new approaches. Genome-wide analyses provided evidence that many genes are actually translated on mitochondria-bound polysomes and GFP-labeling techniques have shown that, in vivo, the 3'UTR sequence of these genes contains signals which can target hybrid RNA molecules to the proximity of mitochondria. Evolutionary conservation of some of these signals will be presented. Interestingly, class I mRNA which are translated on free polysomes and class II mRNA which are translated on mitochondria-bound polysomes have, mostly, eukaryotic and prokaryotic origins respectively. Using ATP2, a typical prokaryotic-derived gene, as a model for class II mRNA, we showed that its 3'UTR sequence is essential both for a correct addressing of mRNA to mitochondria proximity and to a proper production of functional ATP synthases. These different observations suggest that prokaryotic-derived genes are, like the contemporary mitochondrial genes, translated near mitochondrial membranes. In both cases this locus specific translation process might be connected to a correct complex assembly program and the cases of ATP synthase and cytochrome c oxidase complexes will be considered in this respect.
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Affiliation(s)
- A Margeot
- Laboratoire de Génétique Moléculaire CNRS, UMR 8541, Ecole Normale Supérieure, 46 rue d'Ulm. 75230 Paris Cedex 05, France
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Sylvestre J, Margeot A, Jacq C, Dujardin G, Corral-Debrinski M. The role of the 3' untranslated region in mRNA sorting to the vicinity of mitochondria is conserved from yeast to human cells. Mol Biol Cell 2003; 14:3848-56. [PMID: 12972568 PMCID: PMC196577 DOI: 10.1091/mbc.e03-02-0074] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2003] [Revised: 05/12/2003] [Accepted: 05/12/2003] [Indexed: 11/11/2022] Open
Abstract
We recently demonstrated, using yeast DNA microarrays, that mRNAs of polysomes that coisolate with mitochondria code for a subset of mitochondrial proteins. The majority of these mRNAs encode proteins of prokaryotic origin. Herein, we show that a similar association occurs between polysomes and mitochondria in human cells. To determine whether mRNA transport machinery is conserved from yeast to human cells, we examined the subcellular localization of human OXA1 mRNA in yeast. Oxa1p is a key component in the biogenesis of mitochondrial inner membrane and is conserved from bacteria to eukaryotic organelles. The expression of human OXA1 cDNA partially restores the respiratory capacity of yeast oxa1- cells. In this study, we demonstrate that 1) OXA1 mRNAs are remarkably enriched in mitochondrion-bound polysomes purified from yeast and human cells; 2) the presence of the human OXA1 3' untranslated region (UTR) is required for the function of the human Oxa1p inside yeast mitochondria; and 3) the accurate sorting of the human OXA1 mRNA to the vicinity of yeast mitochondria is due to the recognition by yeast proteins of the human 3' UTR. Therefore, it seems that the recognition mechanism of OXA1 3' UTR is conserved throughout evolution and is necessary for Oxa1p function.
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Affiliation(s)
- J Sylvestre
- Laboratoire de Génétique Moléculaire, Unité Mixte Recherche Centre National de la Recherche Scientifique 8541, Ecole Normale Supérieure, Paris, France
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Margeot A, Blugeon C, Sylvestre J, Vialette S, Jacq C, Corral-Debrinski M. In Saccharomyces cerevisiae, ATP2 mRNA sorting to the vicinity of mitochondria is essential for respiratory function. EMBO J 2002; 21:6893-904. [PMID: 12486010 PMCID: PMC139110 DOI: 10.1093/emboj/cdf690] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2002] [Revised: 10/23/2002] [Accepted: 10/31/2002] [Indexed: 11/13/2022] Open
Abstract
We recently demonstrated that polysome-associated mRNAs that co-isolate with mitochondria encode a subset of mitochondrial proteins, and that the 3' UTRs of these transcripts are essential for their localization to the vicinity of the organelle. To address the question of the involvement of the mRNA targeting process in mitochondrial biogenesis, we studied the role of ATP2 3' UTR. An altered ATP2 allele in which the 3' UTR was replaced by the ADH1 3' UTR exhibits properties supporting the importance of mRNA localization to the vicinity of mitochondria: (i) the mutated strain presents a respiratory dysfunction; (ii) mitochondrial import of the protein translated from the altered gene is strongly reduced, even though the precursor is addressed to the organelle surface; (iii) systematic deletions of ATP2 3' UTR revealed a 100 nucleotide element presenting RNA targeting properties. Additionally, when the ATM1 3' UTR was replaced by the ADH1 3' UTR, we obtained cells in which ATM1 mRNA is also delocalized, and presenting a respiratory dysfunction. This demonstrates that mRNA localization to the vicinity of mitochondria plays a critical role in organelle biogenesis.
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Affiliation(s)
| | | | | | | | | | - Marisol Corral-Debrinski
- Laboratoire de Génétique Moléculaire, UMR CNRS 8541, Ecole Normale Supérieure, 46 rue d’Ulm, 75230 Paris Cedex 05, France
Corresponding author e-mail:
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Marc P, Margeot A, Devaux F, Blugeon C, Corral-Debrinski M, Jacq C. Genome-wide analysis of mRNAs targeted to yeast mitochondria. EMBO Rep 2002; 3:159-64. [PMID: 11818335 PMCID: PMC1083966 DOI: 10.1093/embo-reports/kvf025] [Citation(s) in RCA: 243] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2001] [Revised: 11/28/2001] [Accepted: 12/06/2001] [Indexed: 11/12/2022] Open
Abstract
It is agreed that nuclear-encoded mitochondrial proteins are post-translationally targeted to mitochondria, even if, in some cases, a co-translational phase can assist the import of precursor proteins. We used yeast DNA microarrays to analyse the mRNA populations associated with free and mitochondrion-bound polysomes. As expected, many mRNAs, known to encode mitochondrial proteins, are localized to free cytoplasmic polysomes, but many are localized to mitochondrion-bound polysomes. Furthermore, the 3'-UTR of six randomly chosen mitochondrion-bound mRNAs contains sufficient information to target, in vivo, non-translatable RNA to the vicinity of mitochondria. Interestingly, genes producing mRNAs that are targeted to mitochondria are mainly of ancient bacterial origin, whereas those producing mRNAs that are translated in the cytoplasm are mainly of eukaryotic origin. These observations, which support the recent hypotheses concerning the dual origin of the mitochondrial proteome, provide new insights into the biogenesis of mitochondria.
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Affiliation(s)
- Philippe Marc
- Laboratoire de Génétique Moléculaire (UMR CNRS 8541), Ecole Normale Supérieure, 46 rue d'Ulm, F-75005 Paris, France
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