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Global transcriptional regulation by small non-coding RNAs is required for the response to injury of a filamentous fungus

ABSTRACT: Global transcriptional regulation by small non-coding RNAs is required for the response to injury of a filamentous fungus

PROVIDER: PRJNA508370 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8280330.fastq.gz	Fastqsanger.gz
	SRR8280340.fastq.gz	Fastqsanger.gz
	SRR8280350.fastq.gz	Fastqsanger.gz
	SRR8280360.fastq.gz	Fastqsanger.gz
	SRR8280331.fastq.gz	Fastqsanger.gz

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Global transcriptional regulation by small non-coding RNAs is required for the response to injury of a filamentous fungus

Project description:The ability to respond to injury is essential for the survival of an organism and involves analogous mechanisms in animals and plants. Such mechanisms integrate coordinated genetic and metabolic reprogramming events requiring fine tuned regulation by small RNAs for adequate healing of the wounded area. We previously reported that in response to injury, the filamentous fungus Trichoderma atroviride uses molecular mechanisms very similar to those of plants and animals. These processes lead to the formation of new hyphae and the development of asexual reproduction structures (conidiophores). Here we show that regulation by sRNAs of nitrogen metabolic processes and the cellular redox balance is necessary to carry out the correct response to injury. We further discover microRNA-like RNAs (milRNAs) related with the development of conidiophores. Finally, using a loss-of-function and transcriptomic approach, we demonstrate that a milRNA plays a central role in growth and hyphal regeneration in the filamentous fungus T. atroviride, which regulates signaling and cell proliferation at the transcriptional level. Although many classes of small RNAs have been profiled in fungi, and showed to be important for contending with different types of stress, this is the first report showing a physiological function of a milRNA in fungi.

2018-12-05 | GSE123330 | GEO

Identification of microRNA-like RNAs in the filamentous fungus Trichoderma reesei by Solexa sequencing

Project description:MicroRNAs (miRNAs) are small non-coding RNAs capable of negatively regulating gene expression. Trichoderma reesei is an industrial filamentous fungus that can secrete abundant hydrolases for cellulosic biofuels. Recently, microRNA-like RNAs (milRNAs) were discovered in several filamentous fungi rather than T. reesei. The purpose of this study was to explore the presence of milRNA in T. reesei, to characterize the differential expression of T. reesei milRNA under cellulose induction, and to reveal the target genes of milRNA involved in cellulase production. Two small RNA libraries of cellulose induction (IN) or non-induction (CON) were generated and sequenced using Solexa sequencing technology. A total of 664,463 and 529,545 unique sequences, representing 1,271 and 1,021 unique small RNAs, were obtained from the IN and CON samples, respectively. Thirteen milRNAs were finally identified in T. reesei using the hairpin structure analysis. The milRNAs profiles obtained in deep sequencing were validated by RT-qPCR assay. The miRanda program predicts a number of potential targets for T. reesei milRNAs, including several hydrolases and carbon catabolite repressor Cre1.The presence and differential expression of T. reesei milRNAs, along with their predicted targets indicate that milRNAs might play a regulatory role in cellulase induction. This work lays foundation for further functional study of fungal milRNAs and their industrial application.

2014-12-31 | GSE46679 | GEO

Phosphoproteome of filamentous fungus Aspergillus nidulans

Project description:We describe thephosphoproteome of filamentous fungus Aspergillus nidulans. Phosphopeptides were enriched using affinity enrichment using titanium dioxide and separated using a convenient ultralong gradient separations on c18 reverse phase columns. Over 1637 phosphopeptides corresponding to 647 phosphoproteins were identified using using a “high-high” strategy using HCD on the novel Q-exactive platform

2014-11-18 | PXD000715 | Pride

Comparison of extracellular vesicle and filamentous cell transcriptomes of Ustilago maydis

Project description:The coding transcriptomes of filamentous cultures of the maize smut fungus Ustilago maydis and their extracellular vesicles (EVs) were compared. Protein-coding transcripts relatively enriched in EVs versus filament cells were identified and examined to identify potentially functional mRNA cargos of U. maydis EVs.

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PFK2/FBPase-2 is a potential target for metabolic engineering in the filamentous fungus Myceliophthora thermophila

Project description:The PFK-2/ FBPase-2 are important regulatory enzymes in the glycolytic and are present in all major eukaryotic taxa. However, unlike the well-studied animal and plant PFK-2/ FBPase-2, their functions in filamentous fungi remain little investigated. As a typical filamentous fungus and industrial microorganisms, M. thermophila was choose to investigate the functions of this gene. At the same time, the application of regulating this gene in improving metabolites production was also studied.

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Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum

Project description:Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum

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Establishment of TurboID proximity proteomics in the filamentous fungus Sordaria macrospora

Project description:Biotin identification (BioID) is a proximity-dependent labeling technique to study protein-protein co-localization in vivo. Although BioID has been applied in animal cells, plants and yeast, the method remained to be established in filamentous fungi. In this study, we established BioID for the filamentous fungus Sordaria macrospora using the well-characterized striatin interacting phosphatase and kinase (STRIPAK) complex as a proof of principle. In detail, the STRIPAK complex interactor 1 (SCI1) was fused to a codon-optimized TurboID biotin ligase. This SCI1-TurboID fusion protein complemented the Δsci1 deletion strain phenotype. The identification of the already known SmSTRIPAK components PRO11, SmMOB3, SmPP2Ac1 and PRO22 in a BioID experiment with SCI1-TurboID demonstrated its successful application in S. macrospora. The technique will provide a powerful proteomics tool for fungal biologists.

2022-10-25 | PXD034217 | Pride

Identification of the calcium-responsive genes dependent on CrzA in the filamentous fungus Aspergillus nidulans

Project description:Microarray analysis was used to identify the calcium-responsive genes dependent on CrzA in the filamentous fungus Aspergillus nidulans. In order to identify such genes, we conducted the two types of experiment. One was a comparison between wild type with calcium treatment and wild type without calcium treatment. Another was a comparison between wild type with calcium treatment and crzA mutant with calcium treatment. From a comparison between the results of these experiments, we could identify the genes whose expression was induced or repressed in response to calcium in a manner dependent on CrzA. KEY WORD; Aspergillus nidulans, calcium response, crzA

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Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum [II]

Project description:Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum [II]

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Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum [I]

Project description:Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum [I]

| PRJNA429633 | ENA