Transcriptional profiling of Neurospora crassa conidia undergoing germling fusion: M-NM-^Tpp-1 vs WT
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ABSTRACT:
ORGANISM(S): Neurospora crassa OR74A
SUBMITTER: Abby Leeder
PROVIDER: E-GEOD-50446 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose. N. crassa was pregrown in Sucrose and transferred to Avicel (cellulose), Cellobiose, Sucrose or media with no carbon added. Biological triplicates used to identify differentially expressed genes in WT on Avicel. Single libraries for mutant strains identify which genes show similair expression on cellobiose as in the WT on cellulose.
2012-04-04 | E-GEOD-36719 | biostudies-arrayexpress
Project description:CDT-1 and CDT-2 are two cellodextrin transporters discovered in the filamentous fungus Neurospora crassa. Previous studies focused on characterizing the role of these transporters in only a few conditions, including cellulose degradation, and the function of these two transporters is not yet completely understood. In this study, we show that deletion of cdt-2, but not cdt-1, results in growth defects not only on Avicel but also on xylan. cdt-2 can be highly induced by xylan, and this mutant has a xylodextrin consumption defect. Transcriptomic analysis of the cdt-2 deletion strain on Avicel and xylan showed that major cellulase and hemicellulase genes were significantly down-regulated in the cdt-2 deletion strain and artificial over expression of cdt-2 in N. crassa increased cellulase and hemicellulase production. Together, these data clearly show that CDT-2 plays a critical role in hemicellulose sensing and utilization. This is the first time a sugar transporter has been assigned a function in the hemicellulose degradation pathway. Furthermore, we found that the transcription factor XLR-1 is the major regulator of cdt-2, while cdt-1 is primarily regulated by CLR-1. These results deepen our understanding of the functions of both cellodextrin transporters, particularly for CDT-2. Our study also provides novel insight into the mechanisms for hemicellulose sensing and utilization in N. crassa, and may be applicable to other cellulolytic filamentous fungi. N. crassa was pregrown in Sucrose and transferred to Avicel (cellulose) or Xylan(hemicellulose) media. Up regulated and down regulated genes expressions were compared with wild type strain on two conditions (Avicel and xylan) respectively.
2014-09-25 | E-GEOD-44673 | biostudies-arrayexpress
Project description:Transcriptional profiling with next-generation sequencing methods refined our understanding of the N. crassa transcriptional response to cellulose and demonstrated that the newly characterized transcription factors clr-1 and clr-2 were required for the bulk of that response including induction all major cellulase and some major hemicellulase genes. N. crassa pregrown in Sucrose and transferred to Avicel (cellulose), Sucrose or media with no carbon added. Biological triplicates used to identify differentially expressed genes in WT. Single libraries for mutant strains identify which genes show deficient regulation in response to Avicel. Note: Samples named "cdr1" and "cdr2" correspond to the genes clr-1 and clr-2 respectively.
2012-04-23 | E-GEOD-35227 | biostudies-arrayexpress
Project description:Filamentous fungi are powerful producers of hydrolytic enzymes for the deconstruction of plant cell wall polysaccharides. However, the central question of how these sugars are perceived in the context of the complex cell wall matrix remains largely elusive. To address this question in a systematic fashion we performed an extensive comparative systems analysis of how the model filamentous fungus Neurospora crassa responds to the three main cell wall polysaccharides: pectin, hemicellulose and cellulose. We found the pectic response to be largely independent of the cellulolytic one with some overlap to hemicellulose, and in its extent surprisingly high, suggesting advantages for the fungus beyond being a mere carbon source. Our approach furthermore allowed us to identify carbon source-specific adaptations, such as the induction of the unfolded protein response on cellulose, and a commonly induced set of 29 genes likely involved in carbon scouting. Moreover, by hierarchical clustering we generated a co-expression matrix useful for the discovery of new components involved in polysaccharide utilization. This is exemplified by the identification of lat-1, which we demonstrate to encode for the physiologically relevant arabinose transporter in Neurospora. The analyses presented here are an important step towards understanding fungal degradation processes of complex biomass. Our data are based on carbon source transfer experiments. For this, N. crassa pregrown in sucrose for 16 hrs was washed in media without carbon and then transferred to either pectin, orange peel powder (OPP), xylan, Avicel (cellulose), sucrose, or media without carbon (NoC) for another 4 hrs. Biological triplicates (pectin, Avicel, sucrose, NoC) or duplicates (OPP) were used to identify differentially expressed genes in WT. For xylan only a single library was prepared, which was found to correlate well with previously published microarray data (Sun et al. 2012; doi: 10.1128/EC.05327-11)
2013-11-27 | E-GEOD-42692 | biostudies-arrayexpress
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
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
Project description:Purpose: To explore the function of VIB1 in regulating cellulase production in Neurospora crassa. Method: mRNA from vib-1 mutants were collected after a culture shift from sucrose to Avicel (crystaline cellulose) or carbon-free media. Expression profiles of vib-1 mutants were compared with published profiles of wild type created under the same conditions. Results: We found that many genes that specifically upregulated in wild type upon exposure to Avicel were expressed at low levels in M-bM-^HM-^Fvib-1 and many other genes involved in metabolism and energy were expressed at high levels compared to wild type. Conclusions: Our study shows that VIB1 is required for suppression of glucose response and carbon catabolite repression to allow proper expression of clr-2 and subsequent cellulase production in response to cellulosic induction. Biological triplicates of liquid culture N. crassa were harvested at 4 hours after a switch from sucrose media to media of interest. Global mRNA abundances were measured by sequencing on the Illumina Genome Analyzer Iix and HiSeq2000 platforms.
2014-07-08 | E-GEOD-52316 | biostudies-arrayexpress
Project description:Cellulose, particularly the major cellulolytic product cellobiose, can induce the production of enzymes associated with deconstruction of lignocellulose in filamentous fungi. However, the detailed mechanisms underlying this biotechnologically important process remain to be disclosed. Here, the proteome response to cellobiose, crystalline cellulose (Avicel), and carbon starvation of a Neurospora crassa triple β-glucosidase mutant were compared using tandem mass tag (TMT)-based proteome quantification. Improved quantification accuracy was achieved with synchronous precursor selection (SPS)-based MS3 technology compared to MS2 using a high resolution tribrid mass spectrometer. Exposure to carbon starvation, cellobiose or Avicel induced the production of cellulase and lytic polysaccharide monooxygenase enzymes in N. crassa, as well as a cellobionic acid transporter, indicating their functional roles in the early adaptation to plant cell wall. In particular, cellobiose specifically induced the production of proteins in the functional categories of protein processing and export as well as cell wall organization. The data presented here integrates the signaling pathway associated with cellobiose transporters CDT-1 and/or CDT-2 with the direct targets of the transcription factors CLR-1, CLR-2, and XLR-1, the unfolded protein response (UPR) mediated by Ire-1/Hac-1, as well as calcium homeostasis and cell wall organization. The cellobiose-dependent response network will be useful for rational strain improvement to facilitate the production of lignocellulases in filamentous fungi and plant biomass-based products.
2020-05-15 | PXD011598 | Pride
Project description:U251 gliolbastoma cells were treated with vehicle (DMSO) or G-TPP, a mitochondrial targeted version of 17-AAG. 6 hours after treatment RNA was harvested and subjected to microarray analysis on Human Gene 1.0 ST Array.
2010-12-28 | GSE26313 | GEO
Project description:We performed microarray analysis in order to evaluate the combination effect of the mitochondrial matrix chaperone inhibitor gamitrinib-triphenylphosphonium (G-TPP) and Liver X receptor agonist LXR623 on gene expression in stem cell like glioma cells (NCH644).
2019-09-25 | GSE104272 | GEO