Gene copy analysis of the F1 haploid progeny generated by Hypocrea jecorina CBS999.97 sexual development
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ABSTRACT:
ORGANISM(S): Trichoderma reesei
PROVIDER: GSE59350 | GEO | 2015/01/07
SECONDARY ACCESSION(S): PRJNA255121
REPOSITORIES: GEO
Similar Datasets
Project description:H. jecorina undergoes a heterothallic reproductive cycle, and the mating yields asci with 16 linearly arranged ascospores. The sixteen ascospores are generated via two rounds of postmeiotic mitosis following the two meiotic divisions. We have discovered that viable aneuploid ascosporesare are frequently (~90%) generated due to a net gain of a conserved ~500 kbp genomic segment. Here we have compared whole genome gene copy number changes in the aneuploid F1 progeny, euploid F1 progeny, parental strains and the F1 progeny of RTU strain backcross with CBS999.97 .
2015-01-07 | GSE41965 | GEO
Project description:H. jecorina undergoes a heterothallic reproductive cycle, and the mating yields asci with 16 linearly arranged ascospores. The sixteen ascospores are generated via two rounds of postmeiotic mitosis following the two meiotic divisions. We have discovered that viable aneuploid ascosporesare are frequently (~90%) generated due to a net gain of a conserved ~500 kbp genomic segment. Here we have compared whole genome gene copy number changes in the aneuploid F1 progeny, euploid F1 progeny, parental strains and the F1 progeny of RTU strain backcross with CBS999.97 . We determined genome-wide gene copy number in the genomes of ascospores generated from haploid wild-type strain. We also determined genome-wide gene copy number in the genomes of the F1 progeny of CBS999.97 wild type.
2015-01-07 | E-GEOD-41965 | biostudies-arrayexpress
Project description:Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach.
2014-04-01 | GSE53629 | GEO
Project description:Interest in generating lignocellulosic biofuels through enzymatic hydrolysis continues to rise as nonrenewable fossil fuels are depleted. The high cost of producing cellulases, hydrolytic enzymes that cleave cellulose into fermentable sugars, currently hinders economically viable biofuel production. Here, we report the crystal structure of a prevalent endoglucanase in the biofuels industry, Cel5A from the filamentous fungus Hypocrea jecorina. The structure reveals a general fold resembling that of the closest homolog with a high-resolution structure, Cel5A from Thermoascus aurantiacus. Consistent with previously described endoglucanase structures, the H. jecorina Cel5A active site contains a primarily hydrophobic substrate binding groove and a series of hydrogen bond networks surrounding two catalytic glutamates. The reported structure, however, demonstrates stark differences between side-chain identity, loop regions, and the number of disulfides. Such structural information may aid efforts to improve the stability of this protein for industrial use while maintaining enzymatic activity through revealing nonessential and immutable regions.
| S-EPMC3267957 | biostudies-literature
Project description:Comparison of T. reesei grown on lactose fed chemostat cultivations in different growth rates and cell densities The analysis is further described in paper Correlation of gene expression and protein production rate - a system wide study. Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivistoinen, Paula Jouhten, Erno Lindfors, Marilyn Wiebe, Merja Penttilä and Markku Saloheimo, Submitted. Abstract: Background:Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Saccharomyces cerevisiae chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus Trichoderma reesei (Hypocrea jecorina) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype. Results: We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of T. reesei. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response. Conclusions: Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR).
2011-12-22 | GSE30458 | GEO
Project description:Investigation of whole genome gene expression level changes in response to different light conditions of the H. jecorina CBS999.97(MAT1-2) parental strain (W) and the deletion strain delta-env1 (E). These two strains were grown on malt extract agar(Merck) at 25M-bM-^DM-^C in four different conditions: (1) 24L: constant light illumination (24L); (2) 12L12D: in a 12h light/dark cycle and then 6h light illumination; (3) 12D12L: in a 12h dark/light cycle and then 6h constant darknes; (4) 24D: constant darkness. The wild-type strain is potent for sexual development in 12D12L, 12L12D and 24D, whereas the delta-env1 mutant undergo sexual development only in 24D. By contrast, the wild-type strain is female sterile in 24L, and the delta-env1 mutant is female sterile in 12D12L, 12L12D and 24D. Our results reveal that conidation-specific genes, mating locus gene, h-type maitng pheromone genes, and genes invovled in processing and secretion of h-type mating pheromone are significantly upregulated in all four female sterile conditions (W-24L, E-12L12D, E-12D12L and E-24L). We used two biological replicates of two H. jecorina CBS999.97 (MAT1-2) strains, wild-type (W) and delta-env(E) on the cellophane-covered malt extract agar (MEA) plate at 25M-bM-^DM-^C for 7.25 days.
2012-12-31 | E-GEOD-39111 | biostudies-arrayexpress
Project description:Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach. T. reesei (QM9414) was grown in Mandels-Andreotti medium, supplemented with 1% of cellulose, 2% of glucose or 1mM of sophorose. The cultures were incubated on an orbital shaker (200 rpm) at 28M-BM-0C for 24, 48 and 72 hours using cellulose as carbon source; for 24 and 48 hours with glucose as the carbon; and 2, 4 and 6 hours with sophorose as the carbon source. In the latter, the mycelium was previously grown on glycerol for 24 hours and then transferred to 20 mL of Mandels-Andreotti medium without peptone. All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80M-BM-0C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzolM-BM-. reagent. RNA-seq experiments were performed by LGC Genomics GmbH (Berlin/Germany) using the platform Illumina/HiSeq2000.
2014-04-01 | E-GEOD-53629 | biostudies-arrayexpress
Project description:Two major xylanases (XYN I and XYN II) of the filamentous fungus Hypocrea jecorina (Trichoderma reesei) are simultaneously expressed during growth on xylan but respond differently to low-molecular-weight inducers. In vivo footprinting analysis of the xylanase1 (xyn1) promoter revealed three different nucleotide sequences (5'-GGCTAAATGCGACATCTTAGCC-3' [an inverted repeat of GGCTAA spaced by 10 bp], 5'-CCAAT-3', and 5'-GGGGTCTAGACCCC-3' [equivalent to a double Cre1 site]) used to bind proteins. Binding to the Cre1 site is only observed under repressed conditions, whereas binding to the two other motifs is constitutive. Applying heterologously expressed components of the H. jecorina cellulase regulators Ace1 and Ace2 and the xylanase regulator Xyr1 suggests that Ace1 and Xyr1 but not Ace2 contact both GGCTAA motifs. H. jecorina transformants containing mutated versions of the xyn1 promoter, leading to elimination of protein binding to the left or the right GGCTAA box revealed either strongly reduced or completely eliminated induction of transcription. Elimination of Cre1 binding to its target released the basal transcriptional level from glucose repression but did not influence the inducibility of xyn1 expression. Mutation of the CCAAT box prevents binding of the Hap2/3/5 complex in vitro and is partially compensating for the loss of transcription caused by the mutation of the right GGCTAA box. Finally, evidence for a competition of Ace1 and Xyr1 for the right GGCTAA box is given. These data prompted us to hypothesize that xyn1 regulation is based on the interplay of Cre1 and Ace1 as a general and specific repressor with Xyr1 as transactivator.
| S-EPMC1398055 | biostudies-literature
Project description:Comparison of T. reesei grown on lactose fed chemostat cultivations in different growth rates and cell densities The analysis is further described in paper Correlation of gene expression and protein production rate - a system wide study. Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivistoinen, Paula Jouhten, Erno Lindfors, Marilyn Wiebe, Merja Penttilä and Markku Saloheimo, Submitted. Abstract: Background:Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Saccharomyces cerevisiae chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus Trichoderma reesei (Hypocrea jecorina) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype. Results: We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of T. reesei. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response. Conclusions: Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR). A nine chip study using total RNA recovered from three separate cultures of T. reesei RutC-30 grown with growth rate 0.03, three separate cultures grown with growth rate 0.06 and three separate cultures grown with growth rate 0.03 in high cell density.
2011-12-22 | E-GEOD-30458 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in response to different light conditions of the H. jecorina CBS999.97(MAT1-2) parental strain (W) and the deletion strain delta-env1 (E). These two strains were grown on malt extract agar(Merck) at 25℃ in four different conditions: (1) 24L: constant light illumination (24L); (2) 12L12D: in a 12h light/dark cycle and then 6h light illumination; (3) 12D12L: in a 12h dark/light cycle and then 6h constant darknes; (4) 24D: constant darkness. The wild-type strain is potent for sexual development in 12D12L, 12L12D and 24D, whereas the delta-env1 mutant undergo sexual development only in 24D. By contrast, the wild-type strain is female sterile in 24L, and the delta-env1 mutant is female sterile in 12D12L, 12L12D and 24D. Our results reveal that conidation-specific genes, mating locus gene, h-type maitng pheromone genes, and genes invovled in processing and secretion of h-type mating pheromone are significantly upregulated in all four female sterile conditions (W-24L, E-12L12D, E-12D12L and E-24L).
2012-12-31 | GSE39111 | GEO