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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomic analysis of cellulolytic fungus Penicillium oxalicum and transcription factor mutant strains in response to different carbon sources

ABSTRACT: RNA-seq was used to compare the responses of Penicillium oxalicum strains to different carbon sources including carbon-starvation, glucose and cellulose. The wild-type strain and transcription facor (ClrB, CreA and AmyR) mutants were studied. A total of 24 samples were analzyed, which include biological triplicates. The wild-type strain cultured without carbon source was considered as a reference.

ORGANISM(S): Penicillium oxalicum

SUBMITTER: Guodong Liu

PROVIDER: E-GEOD-69298 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptomic analysis of cellulolytic fungus Penicillium oxalicum and its sporogenesis related genes deletion strains

Project description:RNA-seq was used to compare differential gene expressions for Penicillium oxalicum wild type strain (M12) and sporognesis related genes knock out strains.The goals of this study are to construct the sporogenesis regulation pathway of Penicillium oxalicum. Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and nine mutant strains (flbA knoutout strain, flbB knoutout strain, flbC knoutout strain, flbD knoutout strain, flbE knoutout strain,wetA knoutout strain, abaA knoutout strain,stuA knoutout strain, swi6 knoutout strain)

2015-09-01 | E-GEOD-72523 | biostudies-arrayexpress

Transcriptomic analysis of fungus Penicillium oxalicum and its laeA and creA deletion strains

Project description:The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), laeA knockout strain (M-NM-^TlaeA), creA knockout strain (M-NM-^TcreA), and double genes knockout strain (M-NM-^TlaeAM-NM-^TcreA). The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inM-NM-^TlaeA. The deletion of creA upregulated genes involved in hydrolase activity, acting on glycosyl bonds. Many genes involved in conidiation were drastically regulated inM-NM-^TlaeAM-NM-^TcreA. This study provides the information that combined laeA and creA function are required in conidiation and hydrolase activity of P. oxalicum. Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and three mutant strains (laeA knockout strain, creA knockout strain and double genes knockout strain). qRTM-bM-^@M-^SPCR validation was performed using SYBR Green assays.

2014-11-19 | E-GEOD-63408 | biostudies-arrayexpress

Transcriptomic analysis of cellulolytic fungus Penicillium oxalicum and transcription factor mutant strains in response to different carbon sources

Project description:RNA-seq was used to compare the responses of Penicillium oxalicum strains to different carbon sources including carbon-starvation, glucose and cellulose. The wild-type strain and transcription facor (ClrB, CreA and AmyR) mutants were studied.

2015-05-28 | GSE69298 | GEO

Transcriptomic analysis of fungus Penicillium decumbens and brlA deletion strains in different culture medium

Project description:Transcriptomic analysis of fungus Penicillium decumbens and brlA deletion strains in liquid medium and solid medium respectivelly Examination of differential gene expressions by Penicillium decumbens strains 114-2 and brlA deletion stains in liquid medium and solid medium

2013-04-09 | E-GEOD-45855 | biostudies-arrayexpress

CreA phosphorylation sites are important for the regulation of carbon catabolite repression in filamentous fungi

Project description:Saprobic microorganisms, such as filamentous fungi of the genus Aspergillus, are of particular interest for biotechnological applications due to their natural capacity to secrete plant cell wall-degrading enzymes that are known as carbohydrate-active enzymes (CAZy). The presence of easily metabolizable sugars such as glucose, whose concentrations increase during plant biomass hydrolysis, results in the repression of CAZy-encoding genes, in a process known as carbon catabolite repression (CCR), which is undesired for the purpose of large-scale enzyme production. To date, the C2H2 transcription factor CreA has been described as the major CC-repressor in Aspergillus spp. Although CreA-mediated CCR has been extensively studied, less is known about the regulation of CreA itself and the role of post-translational modifications in this process. In this work, phosphorylation sites were identified by mass spectrometry on A. nidulans CreA and subsequently four sites, S262, S268, T308 and S319, were chosen to be mutated to non-phosphorylatable residues before their effects on CCR in both CC-repressing and de-repressing conditions were studied. Sites S262, S268 and T308 are important for CreA protein accumulation and cellular localization and repression of enzyme activities. In contrast, site S319 is key for CreA degradation and induction of enzyme activities. All sites were shown to be important for glycogen and trehalose metabolism. This study highlights the importance of CreA phosphorylation sites for the regulation of CCR. Furthermore, these sites are interesting targets for biotechnological strain engineering without the need to delete essential genes which can result in undesired side effects.

2021-02-18 | PXD018967 | Pride

Transcriptomic analysis of fungus Penicillium oxalicum and its laeA and creA deletion strains

Project description:The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), laeA knockout strain (ΔlaeA), creA knockout strain (ΔcreA), and double genes knockout strain (ΔlaeAΔcreA). The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inΔlaeA. The deletion of creA upregulated genes involved in hydrolase activity, acting on glycosyl bonds. Many genes involved in conidiation were drastically regulated inΔlaeAΔcreA. This study provides the information that combined laeA and creA function are required in conidiation and hydrolase activity of P. oxalicum.

2014-11-19 | GSE63408 | GEO

A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production

Project description:Comparative transcriptional profiling of N. crassa grown on five major crop straws of China (barley, corn, rice, soybean and wheat straws) revealed a highly overlapping group of 430 genes, the Biomass commonly Induced Core Set (BICS). A large proportion of induced carbohydrate-active-enzyme (CAZy) genes (82 out of 113) were also conserved across the five plant straws. Excluding 178 genes within the BICS that were also up-regulated under no-carbon conditions, the remaining 252 genes were defined as the Biomass Regulon (BR). Interestingly, 88 genes were only induced by plant biomass and not by three individual polysaccharides (Avicel, xylan, and pectin); these were denoted as the Biomass Unique Set (BUS). Deletion of one BUS gene, the transcriptional regulator rca-1, significantly improved lignocellulase production using plant biomass as the sole carbon source, possibly functioning via de-repression of the regulator clr-2. Thus, this result suggests that rca-1 is a potential engineering target for biorefineries, especially for plant biomass direct microbial conversion processes. Conidia of Neurospora crass wild type were inoculated at 10^6 conidia/mL into 100 mL 1×Vogel’s salts with 2% (w/w) ground crop straws, barley straw, corn straw, rice straw, soybean straw and wheat straw respectively for 30 h or 2% sucrose for 16 h. Then, mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN). The qualified RNA was prepared with standard protocol from Shenzhen BGI (China) and sequenced on the Illumina HiSeqTM 2000 platform.

2015-01-21 | E-GEOD-60986 | biostudies-arrayexpress

The effects of ClrB internal mutant overexpression and creA deletion on the transcriptome of Penicillium oxalicum

Project description:The synthesis of cellulolytic enzymes by filamentous fungi are mainly regulated at the transcriptional level. The essential role of transcriptional activator ClrB/CLR-2 in the induction of cellulase genes has been reported in several fungal species. In this study, we identified the C-terminal region of ClrB in Penicillium oxalicum as a transcriptional activation domain using a yeast reporter gene system. Overexpression of a mutant ClrBID fusing the DNA-binding and transcriptional activation domains of ClrB together enabled cellulase production under cellulase non-inducing conditions. Strikingly, the ClrBID-overexpression strain produced cellulase in the presence of glucose at a level similar to that of reference strain on cellulose. Combination of ClrBID overexpression and deletion of carbon catabolite-repressor gene creA suggested an additive effect of the two manipulations on carbon catabolite de-repression. A similar modification of ClrB in Aspergillus niger also resulted in cellulase production on glucose. The results indicated that the post-transcriptional control of ClrB activity involves its central region, and provided a potential strategy for engineering Penicillium and Aspergillus strains for cellulase production on easy-to-use carbon sources.

2019-01-01 | GSE120416 | GEO

The metabolic regulation of sporulation and parasporal crystal formation in Bacillus thuringiensis revealed by transcriptomics and proteomics

Project description:Proteomics on B. thuringiensis CT_43 cells in GYS medium. Two biological replicate cell samples were collected at time points of 7 h, 9 h, 13 h and 22 h, respectively. The crude proteins were purified using the ReadyPrep 2-D Cleanup Kit, underwent the reductive alkylation, tryptically digested, and were labeled with 8-plex iTRAQ reagents as follows: 7 h-1, 113; 7 h-2, 114; 9 h-1, 115; 9 h-2, 116; 13 h-1, 117; 13 h-2, 118; 22 h-1, 119; and 22 h-2, 121. The labeled samples were pooled and resolved into 12 fractions, which were loaded onto LC-MSMS.

2019-11-22 | PXD000020 | Pride

Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose

Project description:D-glucose, D-xylose and L-arabinose are three major monosaccharides in the plant cell wall. Complete utilization of all three sugars is still a bottleneck for second-generation cellulolytic bioethanol production, especially for L-arabinose. However, little is known about the gene expression profiles during L-arabinose utilization in fungi at genome-wide level and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. To better understand the microbial response and utilization of L-arabinose for subsequent microbial engineering for co-fermentation all three sugars, we performed transcriptome analysis of N. crassa grown on L-arabinose, compared with that on D-xylose and D-glucose. RNA was extracted from cultures of N. carassa in early growth stage growing with D-glucose, L-arabinose or D-xylose as carbon source; duplicate cultures were sampled in some conditions.

2014-03-17 | E-GEOD-51091 | biostudies-arrayexpress

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