Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response

Pastor-Flores, Daniel; Ferrer-Dalmau, Jofre; Bahí, Anna; Boleda, Martí; Biondi, Ricardo M.; Casamayor, Antonio

doi:10.1186/s12864-015-1903-8

Cited by 3 publications

(1 citation statement)

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“…In the yeast S. cerevisiae , three PKH genes encode Pkh1, Pkh2, and Pkh3. None are essential alone, but a triple mutant is inviable . Depletion of Pkh2 from yeast cells deleted for both PKH1 and PKH3 revealed a chronic stress phenotype.…”

Section: Stress‐responsive Regulation Of Mrna Decay: An Additional Lementioning

confidence: 99%

mRNA decay: an adaptation tool for the environmental fungal pathogen Cryptococcus neoformans

2017

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Fungi are ubiquitous in the environment and humans constantly encounter them in the soil, air, water, and food. The vast majority of these interactions are inconsequential. However, in the context of immunodeficiency precipitated by HIV infection, hematologic malignancy, or transplantation, a small subset of fungi can cause devastating, systemic infection. The most deadly of the opportunistic environmental fungi, Cryptococcus neoformans, is estimated to cause hundreds of thousands of deaths per year, mostly in the context of HIV co-infection. The cellular processes that mediate adaptation to the host environment are of great interest as potential novel therapeutic targets. One such cellular process important for host adaptation is mRNA decay, which mediates the specific degradation of subsets of functionally related mRNAs in response to stressors relevant to pathogenesis, including human core body temperature, carbon limitation, and reactive oxygen stress. Thus, for C. neoformans, host adaptation requires mRNA decay to mediate rapid transcriptome remodeling in the face of stressors encountered in the host. Several nodes of stress-responsive signaling that govern the stress-responsive transcriptome also control the decay rate of mRNAs cleared from the ribosome during stress, suggesting an additional layer of coupling between mRNA synthesis and decay that allows C. neoformans to be a successful pathogen of humans. WIREs RNA 2017, 8:e1424. doi: 10.1002/wrna.1424 For further resources related to this article, please visit the WIREs website.

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Section: Stress‐responsive Regulation Of Mrna Decay: An Additional Lementioning

confidence: 99%

mRNA decay: an adaptation tool for the environmental fungal pathogen Cryptococcus neoformans

2017

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Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme

et al. 2019

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BRANEnet: embedding multilayer networks for omics data integration

et al. 2022

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Background Gene expression is regulated at different molecular levels, including chromatin accessibility, transcription, RNA maturation, and transport. These regulatory mechanisms have strong connections with cellular metabolism. In order to study the cellular system and its functioning, omics data at each molecular level can be generated and efficiently integrated. Here, we propose BRANEnet, a novel multi-omics integration framework for multilayer heterogeneous networks. BRANEnet is an expressive, scalable, and versatile method to learn node embeddings, leveraging random walk information within a matrix factorization framework. Our goal is to efficiently integrate multi-omics data to study different regulatory aspects of multilayered processes that occur in organisms. We evaluate our framework using multi-omics data of Saccharomyces cerevisiae, a well-studied yeast model organism. Results We test BRANEnet on transcriptomics (RNA-seq) and targeted metabolomics (NMR) data for wild-type yeast strain during a heat-shock time course of 0, 20, and 120 min. Our framework learns features for differentially expressed bio-molecules showing heat stress response. We demonstrate the applicability of the learned features for targeted omics inference tasks: transcription factor (TF)-target prediction, integrated omics network (ION) inference, and module identification. The performance of BRANEnet is compared to existing network integration methods. Our model outperforms baseline methods by achieving high prediction scores for a variety of downstream tasks.

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Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response

Cited by 3 publications

References 74 publications

mRNA decay: an adaptation tool for the environmental fungal pathogen Cryptococcus neoformans

mRNA decay: an adaptation tool for the environmental fungal pathogen Cryptococcus neoformans

Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme

BRANEnet: embedding multilayer networks for omics data integration

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