Global Transcriptome Characterization and Assembly of thermophilic ascomycete Chaetomium thermophilum
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ABSTRACT:
PROVIDER: PRJNA480310 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7502540.fastq.gz | Fastqsanger.gz | |||
| SRR7502541.fastq.gz | Fastqsanger.gz | |||
| SRR7502539.fastq.gz | Fastqsanger.gz |
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Project description:A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is limited to open reading frames (ORFs) of genes and contains only a few noncoding transcripts. In this study, we identified and annotated by deep RNA sequencing full-length transcripts of C.thermophilum. We identified 7044 coding genes and a large number of noncoding genes (n=4567). Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help understanding the gene regulatory landscape in C.thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species. The new genome annotation of the GTF file can be found here.
2019-12-31 | GSE116834 | GEO
Project description:The thermophilic fungus Chaetomium thermophilum has been successfully used in the past for biochemical and high resolution structural studies of protein complexes, but subsequent functional analysis of these assemblies were hindered due to the lack of genetic tools in this thermophile, which are typically amenable in several other mesophilic eukaryotic model organisms, in particular the yeast Saccharomycers cerevisiae. Hence, we aimed to develop a regulatable gene-expression system in C. thermophilum, which might facilitate such in vivo studies, based on what we know about the galactose-inducible GAL promoter in yeast. To identify sugar-regulatable promoters in C. thermophilum, we performed comparative xylose- versus glucose-dependent gene expression studies, which uncovered a number of enzymes induced by xylose but repressed by glucose. Subsequently, we cloned the promoters of the two most stringently regulated genes, the xylosidase-like gene (XYL) and xylitol dehydrogenase (XDH), obtained from this genome-wide analysis in front of the thermostable YFP (yellow fluorescent protein) reporter. In this way, we could demonstrate xylose-dependent YFP expression by either western blotting or life cell imaging fluorescence microscopy. Prompted by these results, we finally expressed a well-characterized dominant-negative ribosome assembly factor mutant, rsa4 E117>D, under the control of the XDH promoter, which allowed us to induce a nuclear export defect of the pre-60S subunit when C. thermophilum cells were grown in xylose but not glucose containing medium. Altogether, our study recognized xylose-regulatable promoters in Chaetomium thermophilum, which may foster functional studies of genes of interest in this thermophilic eukaryotic model organism.
2022-09-26 | GSE214043 | GEO
Project description:A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is essentially limited to open reading frames (ORFs) of protein coding genes and contains only a few noncoding transcripts. In this study, we identified and annotated full-length transcripts of C. thermophilum by deep RNA sequencing. We annotated 7044 coding genes and 4567 noncoding genes. Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes as well as 2878 novel noncoding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help to understand the gene regulatory landscape in C. thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species.
| S-EPMC8535861 | biostudies-literature
Project description:Mitochondrial complex I is a redox-driven proton pump that generates most of the proton-motive force powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic eukaryote Chaetomium thermophilum, determined by electron cryo-microscopy to 2.4 A resolution in the open and closed conformation. Complex I has two arms, the peripheral and membrane arm, forming an L-shape. The two conformations differ in the relative position of the two arms. The open-to-closed transition is accompanied by substantial conformational changes in the Q-binding cavity and the E-channel, and by the formation of an aqueous connection between the E-channel and an extensive aqueous passage inside the membrane arm. The observed similarities provide strong support for a conserved, common mechanism that applies across all species from fungi to mammals. Furthermore, the complex is inhibited by the detergent DDM, which binds reversibly to two sites in the Q-binding cavity.
2022-11-29 | PXD033234 | Pride
Project description:Thermophilic fungi are eukaryotic species that grow at high temperatures, but little is known about the thermophily of thermophilic fungi. Here the proteome and N-glycoproteome of Chaetomium thermophilum at varying culture temperatures (30℃, 50℃, and 55℃) were studied using hydrophilic interaction liquid chromatography enrichment and high-resolution liquid chromatography–tandem mass spectroscopy analysis. In proteome, the numbers of differentially expressed proteins were 1274, 1374, and 1063 in T50/T30, T55/T30, and T55/T50, respectively. The up-regulated proteins were involved in biological processes, such as protein folding and carbohydrate metabolism. Most down-regulated proteins were involved in molecular functions, such as structural constituent of the ribosome and structural activity. For N-glycoproteome, the numbers of differentially expressed N-glycoproteins were 160, 176, and 128 in T50/T30, T55/T30, and T55/T50, respectively. The differential glycoproteins were mainly involved in various types of N-glycan biosynthesis, mRNA surveillance pathway, and protein processing in the endoplasmic reticulum. These results indicated that an efficient protein homeostasis pathway plays an essential role in the thermophily of C. thermophilum, and N-glycosylation is involved by affecting related proteins. This is the first study to reveal thermophilic fungi's physiological response to high-temperature adaptation using omics analysis, facilitating the exploration of the thermophily mechanism of thermophilic fungi.
2021-05-17 | PXD023311 | Pride
Project description:TMT-labeled LC-MSMS was performed to identify and quantify proteins from three different TAP-purification pull-outs from Chaetomium thermophilum. The aim was to identify interaction partners and to study, whether the two tagged proteins (Naa50 and Naa15) are likely to interact, as they do in other organisms. CtNaa50 is a special homolog of known Naa50 proteins and in this case, it does not interact with Naa15, but other identified proteins.
2022-10-14 | PXD035320 | Pride
Project description:The thermophilic filamentous fungi Myceliophthora thermophila (Sporotrichum thermophile) and Thielavia terrestris are proficient decomposers of cellulose, suggesting that they will be a rich source of thermostable industrial enzymes for lignocellulose degradation. To identify the genes and proteins involved in this process, we explored the transcriptomes of M. thermophila and T. terrestris growing at 45 ºC on either glucose, alfalfa, or barley straw by short-read sequencing of extracted mRNA. To better understand the adaptations that allow these fungi to grow at elevated temperatures, we compared their transcriptomes when growing at 34C to their transcritomes at 45C, and also to the transcriptome of the related fungus Chaetomium globosum, which does not grow at 45C.
2011-08-08 | GSE27323 | GEO
Project description:Identification and characterization of sugar regulated promoters in Chaetomium thermophilum
| PRJNA883678 | ENA
Project description:The thermophilic filamentous fungi Myceliophthora thermophila (Sporotrichum thermophile) and Thielavia terrestris are proficient decomposers of cellulose, suggesting that they will be a rich source of thermostable industrial enzymes for lignocellulose degradation. To identify the genes and proteins involved in this process, we explored the transcriptomes of M. thermophila and T. terrestris growing at 45 ºC on either glucose, alfalfa, or barley straw by short-read sequencing of extracted mRNA. To better understand the adaptations that allow these fungi to grow at elevated temperatures, we compared their transcriptomes when growing at 34C to their transcritomes at 45C, and also to the transcriptome of the related fungus Chaetomium globosum, which does not grow at 45C. RNA was extracted from cultures in early growth stage growing with glucose, alfalfa, or barley straw as carbon source at 34C or 45C (M. thermophila and T. terrestris); duplicate cultures were sampled in some conditions.
2011-08-08 | E-GEOD-27323 | biostudies-arrayexpress
Project description:Glycerol is an organic compound that can be utilized as an alternative source of carbon by various organisms. One of the ways to assimilate glycerol by the cell is the phosphorylative catabolic pathway in which its activation is catalyzed by glycerol kinase (GK) and glycerol-3-phosphate (G3P) is formed. To date, several GK crystal structures from bacteria, archaea, and unicellular eukaryotic parasites have been solved. Herein, we present a series of crystal structures of GK from Chaetomium thermophilum (CtGK) in apo and glycerol-bound forms. In addition, we show the feasibility of an ADP-dependent glucokinase (ADPGK)-coupled enzymatic assay to measure the CtGK activity. New structures described in our work provide structural insights into the GK catalyzed reaction in the filamentous fungus and set the foundation for understanding the glycerol metabolism in eukaryotes.
| S-EPMC7765489 | biostudies-literature