Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus niger Aspergillus niger CBS 513.88
PROVIDER: GSE17641 | GEO | 2009/09/17
SECONDARY ACCESSION(S): PRJNA118585
REPOSITORIES: GEO
Similar Datasets
Project description:Reconstruction of signaling networks regulating fungal morphogenesis by the expression profiling of wild-type and the temperature sensitive morphological ramosa-1 mutant. Aspergillus niger wildtype versus Ramosa mutant for 1h at 37 under controlled growth condition in 5L bioreactor
2010-05-05 | E-GEOD-17641 | biostudies-arrayexpress
Project description:Coordinated control of hyphal elongation and branching is essential for sustaining mycelial growth of filamentous fungi. In order to study the molecular machinery ensuring polarity control in the industrial fungus Aspergillus niger, we took advantage of the temperature-sensitive (ts) apical-branching ramosa-1 mutant. We show here that this strain serves as an excellent model system to study critical steps of polar growth control during mycelial development and report for the first time a transcriptomic fingerprint of apical branching for a filamentous fungus. This fingerprint indicates that several signal transduction pathways, including TORC2, phospholipid, calcium, and cell wall integrity signaling, concertedly act to control apical branching. We furthermore identified the genetic locus affected in the ramosa-1 mutant by complementation of the ts phenotype. Sequence analyses demonstrated that a single amino acid exchange in the RmsA protein is responsible for induced apical branching of the ramosa-1 mutant. Deletion experiments showed that the corresponding rmsA gene is essential for the growth of A. niger, and complementation analyses with Saccharomyces cerevisiae evidenced that RmsA serves as a functional equivalent of the TORC2 component Avo1p. TORC2 signaling is required for actin polarization and cell wall integrity in S. cerevisiae. Congruently, our microscopic investigations showed that polarized actin organization and chitin deposition are disturbed in the ramosa-1 mutant. The integration of the transcriptomic, genetic, and phenotypic data obtained in this study allowed us to reconstruct a model for cellular events involved in apical branching.
| S-EPMC2772408 | biostudies-literature
Project description:Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics
| PRJNA118585 | ENA
Project description:The capacity to sense and transduce temperature signals pervades all aspects of biology, and temperature exerts powerful control over the development and virulence of diverse pathogens. In the leading fungal pathogen of humans, Candida albicans, temperature has a profound impact on morphogenesis, a key virulence trait. Many cues that induce the transition from yeast to filamentous growth are contingent on a minimum temperature of 37ºC, while further elevatation to 39ºC serves as an independent inducing cue. The molecular chaperone Hsp90 is a key regulator of C. albicans temperature-dependent morphogenesis, as induction of filamentous growth requires relief from Hsp90-mediated repression of the morphogenetic program. Compromise of Hsp90 function genetically, pharmacologically, or by elevated temperature induces filamentation in a manner that depends on protein kinase A (PKA) signaling, but is independent of the terminal transcription factor, Efg1. Here, we determine that despite morphological and regulatory differences, inhibition of Hsp90 induces a transcriptional profile similar to that induced by other filamentation cues, and does so in a manner that is independent of Efg1. Further, we identify Hms1 as a transcriptional regulator required for morphogenesis induced by elevated temperature or compromise of Hsp90 function. Hms1 functions downstream of the cyclin Pcl, and the cyclin-dependent kinase Pho85, both of which are required for temperature-dependent filamentation. Upon Hsp90 inhibition, Hms1 binds to DNA elements involved in filamentous growth, including UME6 and RBT5, and regulates their expression, providing a mechanism through which Pho85, Pcl1, and Hms1 govern morphogenesis. Consistent with the importance of morphogenetic flexibility with virulence, deletion of C. albicans HMS1 attenuates virulence in a metazoan model of infection. Thus, we establish a new mechanism through which Hsp90 orchestrates C. albicans morphogenesis, and define novel regulatory circuitry governing a temperature-dependent developmental program, with broad implications for temperature sensing and virulence of microbial pathogens. Two-color experimental design testing the effect of geldanamycin on wild type of delta-efg1 cells. RNA from each replicate came from independent cultures.
2012-03-20 | E-GEOD-34255 | biostudies-arrayexpress
Project description:Morphogenetic transitions are prevalent in the fungal kingdom. For a leading human fungal pathogen, Candida albicans, the capacity to transition between yeast and filaments is key for virulence. For the model yeast Saccharomyces cerevisiae, filamentation enables nutrient acquisition. A recent functional genomic screen in S. cerevisiae identified Mfg1 as a regulator of morphogenesis that acts in complex with Flo8 and Mss11 to enable transcriptional responses crucial for filamentation. In C. albicans, Mfg1 also interacts physically with Flo8 and Mss11 and is critical for filamentation in response to diverse cues, but the mechanisms through which it regulates morphogenesis remained elusive. Here, we explored the consequences of perturbation of Mfg1, Flo8, and Mss11 on C. albicans morphogenesis, and identified functional divergence of complex members. We observed that C. albicans Mss11 was dispensable for filamentation, and that overexpression of FLO8 caused constitutive filamentation even in the absence of Mfg1. Epistasis experiments suggested that Mfg1 acts downstream of protein kinase A, as does Flo8. Harnessing transcriptional profiling and chromatin immunoprecipitation coupled to microarray analysis, we identified divergence between transcriptional targets of Mfg1 and Flo8 in C. albicans. A key direct transcriptional target of Mfg1 is TEC1, for which overexpression was sufficient to restore filamentation in the absence of Mfg1. To identify additional Mfg1 downstream effectors, we employed a novel strategy to select for mutations that restore filamentation in the absence of Mfg1. Whole genome sequencing of filamentation-competent mutants revealed chromosome 6 amplification as a conserved adaptive mechanism. A key determinant of the amplification on chromosome 6 is FLO8, as deletion of one allele blocked morphogenesis, and chromosome 6 was not amplified in evolved lineages for which FLO8 was re-located to a different chromosome. Thus, this work highlights rewiring of key morphogenetic regulators over evolutionary time and aneuploidy as an adaptive mechanism driving fungal morphogenesis.
2018-07-24 | GSE117477 | GEO
Project description:The capacity to sense and transduce temperature signals pervades all aspects of biology, and temperature exerts powerful control over the development and virulence of diverse pathogens. In the leading fungal pathogen of humans, Candida albicans, temperature has a profound impact on morphogenesis, a key virulence trait. Many cues that induce the transition from yeast to filamentous growth are contingent on a minimum temperature of 37ºC, while further elevatation to 39ºC serves as an independent inducing cue. The molecular chaperone Hsp90 is a key regulator of C. albicans temperature-dependent morphogenesis, as induction of filamentous growth requires relief from Hsp90-mediated repression of the morphogenetic program. Compromise of Hsp90 function genetically, pharmacologically, or by elevated temperature induces filamentation in a manner that depends on protein kinase A (PKA) signaling, but is independent of the terminal transcription factor, Efg1. Here, we determine that despite morphological and regulatory differences, inhibition of Hsp90 induces a transcriptional profile similar to that induced by other filamentation cues, and does so in a manner that is independent of Efg1. Further, we identify Hms1 as a transcriptional regulator required for morphogenesis induced by elevated temperature or compromise of Hsp90 function. Hms1 functions downstream of the cyclin Pcl, and the cyclin-dependent kinase Pho85, both of which are required for temperature-dependent filamentation. Upon Hsp90 inhibition, Hms1 binds to DNA elements involved in filamentous growth, including UME6 and RBT5, and regulates their expression, providing a mechanism through which Pho85, Pcl1, and Hms1 govern morphogenesis. Consistent with the importance of morphogenetic flexibility with virulence, deletion of C. albicans HMS1 attenuates virulence in a metazoan model of infection. Thus, we establish a new mechanism through which Hsp90 orchestrates C. albicans morphogenesis, and define novel regulatory circuitry governing a temperature-dependent developmental program, with broad implications for temperature sensing and virulence of microbial pathogens. Genome-wide occupancy experiments (Chip-CHIP) of FLAG-tagged Hms1p from cells grown in the presence or absence of geldanamycin (GldA). Co-precipitating genomic DNA was labelled and hybridized to whole-genome tiling arrays.
2012-03-20 | E-GEOD-34938 | biostudies-arrayexpress
Project description:eDNA metabarcoding versus morphological fungal community analysis.
| PRJEB29665 | ENA
Project description:We here used the technology of RNA interference or selective treatment of the ESR1 and cDNA microarrays to reconstruct a network between genes known to be disregulated in ER-positive breast cancer diseases. Therefor single genes of high importance were silenced and the effect of this pertubation was measured with cDNA microarrays. Keywords: Network Reconstruction, RNAi, siRNA, Interaction Network
2009-07-29 | GSE12291 | GEO
Project description:We have focused our investigation on the characterization of the role of the fungal specific SWI/SNF subunit, Snf6. Our data show that, although the C. albicans subunit has only limited sequence similarity to other fungal orthologs, Snf6 was copurified with SWI/SNF complex subunits including the catalytic ATPase subunit, Snf2. We show that Snf6 plays a critical role in biological processes that are essential for fungal pathogenesis including carbon metabolic flexibility, stress response and morphogenesis. The Snf6 regulon was determined by combining both genome-wide location (ChIP-chip) and transcriptional profiling (microarrays) to identify targets of the SWI/SNF complex under both yeast- and hyphal-promoting conditions.
2017-10-28 | GSE106278 | GEO
Project description:Elucidating regulatory relationships between transcription factors (TFs) and target genes is fundamental to understanding how cells control their identity and behavior. To overcome the limited scope and scalability of experimental methods in mapping this control, computational GRN reconstruction methods have been developed to infer relationships from transcriptomic data. We developed a new computational GRN reconstruction tool called Epoch, which takes advantage of single-cell RNA sequencing to address a number of shortcomings of existing tools including low precision, low sensitivity, and the limited ability to describe network topology changes over time. We used Epoch to identify the dynamic networks and key transcriptional regulators underpinning directed differentiation of mouse embryonic stem cells, and further demonstrate that modulating signaling pathways drives topological network changes that shape cell fate potential. By integrating signaling pathways with GRN structures, we traced how Wnt activation and PI3K suppression govern mesoderm and endoderm specification, respectively.
2022-01-27 | GSE177051 | GEO