Pecoramyces ruminantium strain:C1A
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ABSTRACT:
PROVIDER: PRJNA284193 | ENA |
REPOSITORIES: ENA
Dataset's files
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| SRR2033890.fastq.gz | Fastqsanger.gz |
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Project description:Pecoramyces ruminantium strain:C1A Transcriptome or Gene expression
| PRJNA392419 | ENA
Project description:Pecoramyces ruminantium strain:C1A Genome sequencing and assembly
| PRJNA200719 | ENA
Project description:Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.
| S-EPMC5796279 | biostudies-literature
Project description:Genomic analysis of the model lignocellulosic biomass degrading bacteria C. phytofermentans indicates that it can degrade, transport, and utilize a wide-range of carbohydrates as possible growth substrates. Previous experiments characterized the expression of the degradation and transport machinery using custom whole genome oligonucleotide microarrays. The results indicate that C. phytofermentans utilizes ATP-binding cassette (ABC) transporters for carbohydrate uptake and does not use the sole phosphoenolpyruvate-phosphotransferase system (PTS) for any of the tested substrates. While some ABC transporters are specific for a single carbohydrate, the expression profiles indicate that others may be capable of transporting multiple substrates. Distinct sets of Carbohydrate Active Enzymes (CAZy) genes were also up-regulated on specific substrates indicative of C. phytofermentans ability to selectively degrade plant biomass. We also identified a highly expressed cluster of genes which includes seven extracellular glycoside hydrolases and two ABC transporters with unknown specificity. These results lead to the hypothesis that when grown on plant biomass, C. phytofermentans is capable of degrading and transporting all major carbohydrate components of the plant cell. To test this, C. phytofermentans was grown on cornstover and switchgrass. Results from this expression data and HPLC analysis indicates that C. phytofermentans is utilizing multiple substrates. with multiple sugar ABC transporter clusters and glycoside hydrolases being expressed. Interestingly all of the transporters were initially identified on disaccharides or oligio-saccharides, and none of the transporters identified as monosaccharide specific transporters were expressed. This could be an indication that C. phytofermentans prefers to transport oligiosacchrides over monosaccharides. The results presented here corroborate the genomic data which indicates the breath of the carbohydrate degradation, transport, and utilization machinery of C. phytofermentans.
2013-11-20 | GSE52498 | GEO
Project description:Genomic analysis of the model lignocellulosic biomass degrading bacteria C. phytofermentans indicates that it can degrade, transport, and utilize a wide-range of carbohydrates as possible growth substrates. Previous experiments characterized the expression of the degradation and transport machinery using custom whole genome oligonucleotide microarrays. The results indicate that C. phytofermentans utilizes ATP-binding cassette (ABC) transporters for carbohydrate uptake and does not use the sole phosphoenolpyruvate-phosphotransferase system (PTS) for any of the tested substrates. While some ABC transporters are specific for a single carbohydrate, the expression profiles indicate that others may be capable of transporting multiple substrates. Distinct sets of Carbohydrate Active Enzymes (CAZy) genes were also up-regulated on specific substrates indicative of C. phytofermentans ability to selectively degrade plant biomass. We also identified a highly expressed cluster of genes which includes seven extracellular glycoside hydrolases and two ABC transporters with unknown specificity. These results lead to the hypothesis that when grown on plant biomass, C. phytofermentans is capable of degrading and transporting all major carbohydrate components of the plant cell. To test this, C. phytofermentans was grown on cornstover and switchgrass. Results from this expression data and HPLC analysis indicates that C. phytofermentans is utilizing multiple substrates. with multiple sugar ABC transporter clusters and glycoside hydrolases being expressed. Interestingly all of the transporters were initially identified on disaccharides or oligio-saccharides, and none of the transporters identified as monosaccharide specific transporters were expressed. This could be an indication that C. phytofermentans prefers to transport oligiosacchrides over monosaccharides. The results presented here corroborate the genomic data which indicates the breath of the carbohydrate degradation, transport, and utilization machinery of C. phytofermentans. C. phytofermentans was cultured anaerobically on switchgrass and corn stover to determine specific expression patterns. The data in this series consists three independent RNA preparations from replicate cultures.
2013-11-20 | E-GEOD-52498 | biostudies-arrayexpress
Project description:Heterobasidion annosum gene expression from mycelium grown on different substrates
| PRJNA176693 | ENA
Project description:Purpose: Identify the effect of substrate stiffness on gene expression Methods:Evaluating for differentially expressed mRNAs in the SKOV-3 cells grown on the different substrates via High-throughput sequence Results: We found that the general direction of changes in gene expression of cells grown on the different substrates and the most significant signalling pathways and the expression of gene orthologs broadly involved in platinum drug resistance, apoptosis, cell cycle. Conclusions: Our study represents the first detailed analysis of the effects of substrate stiffness on gene expression of ovarian cancer cells.
2021-06-26 | GSE178888 | GEO
Project description:HvPap-1 is a C1A cysteine protease from barley that has been associated to endogenous processes and responds to abiotic and biotic stresses. Overexpressing and silencing lines were constructed to test the response of plants with variations in the levels of HvPap-1 to different stresses. RNA-seq analyses were done to know how changes in HvPap-1 expression levels affect the expression of other genes and the effect of these changes in the response of the plant.
2017-09-29 | E-MTAB-5963 | biostudies-arrayexpress
Project description:The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds.
2018-01-29 | GSE98572 | GEO