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Functional analysis of Mpk1-mediated cell wall integrity signaling pathway in the thermotolerant methylotrophic yeast Hansenula polymorpha

ABSTRACT: Functional analysis of Mpk1-mediated cell wall integrity signaling pathway in the thermotolerant methylotrophic yeast Hansenula polymorpha

PROVIDER: PRJNA418241 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6288015_1.fastq.gz	Fastqsanger.gz
	SRR6288015_2.fastq.gz	Fastqsanger.gz
	SRR6288016_1.fastq.gz	Fastqsanger.gz
	SRR6288016_2.fastq.gz	Fastqsanger.gz

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Functional analysis of Mpk1-mediated cell wall integrity signaling pathway in the thermotolerant methylotrophic yeast Hansenula polymorpha

Project description:Purpose: To identify the downstream gene sets regulated by Mpk1p in H. polymorpha under normal and caffeine-treated conditions, we compared the RNA-seq based transcriptional profiles. Methods: Total RNA was isolated according to the hot phenol extraction method and all procedure for RNA sequencing were conducted by ChunLab. More than 1.5-fold regulated genes are functionally classified using the Munich Information Center for Protein Sequences (MIPS) FunCat. Results: Transcriptome analysis of the DL1-L strain revealed that caffeine significantly increased expression of a subset of cell-wall related genes in an Mpk1p-dependent manner, but most of which were not Rlm1-target genes. Conclusion: Our results support the essential role of Mpk1p in maintaining cell wall integrity upon several stress conditions of H. polymorpha.

2018-11-14 | GSE106861 | GEO

Transcriptome profiling of Hansenula polymorpha in response to sulfur starvation and cadmium stress

2014-07-31 | GSE31197 | GEO

Investigation of the contribution of Complex I to respiratory energy-coupling in glucose-grown cultures of the Crabtree-negative yeast Ogataea parapolymorpha

Project description:The methylotrophic, thermotolerant yeast Ogataea parapolymorpha (formerly Hansenula polymorpha) is an industrially relevant production host and exhibits a respiratory metabolism in the presence of oxygen. It possesses a branched respiratory chain with multiple entry points for NADH-derived electrons that differ in complexity and degree of energy conservation: proton-translocating respiratory Complex I and three putative alternative NADH dehydrogenases. To investigate the physiological importance of Complex I, wild type O. parapolymorpha and a Complex I-disrupted mutant were cultured in glucose-grown bioreactor experiments in batch, chemostat and retentostat cultivations which allowed quantitative characterization of the strains over a wide range of growth rates in the presence and absence of excess substrate.

2020-05-12 | GSE140480 | GEO

Transcriptome profiling of H. polymorpha in response to Cd exposure.

Project description:To gain insight into the basic mechanism of Cd detoxification in the methylotrophic yeast, H. polymorpha, we analyzed temporal changes in transcriptional profiles in response to Cd exposure. We used H. polymorpha whole-genome cDNA microarrays, which contain 98% of all H. polymorpha ORFs in duplicate or triplicate. Keywords: time course, cadmium

2007-08-30 | GSE6989 | GEO

An Omics approach on Marchantia polymorpha single FERONIA and MARIS homologs confirms links between cell wall integrity and abscisic acid

Project description:Plant cells are surrounded by an extracellular cell wall that shields them from their abiotic and biotic environment. To coordinate their growth with their cell wall status, they have developed cell wall integrity mechanisms at the center of which lies the transmembrane Malectin-like receptor kinase FERONIA (FER). FER controls a myriad of plant developmental processes including sexual reproduction, cell growth and morphogenesis, often intersecting with phytohormones-dependent pathways such as abscisic acid (ABA) or plant immunity. Interestingly, FER and its downstream receptor-like cytoplasmic kinase MARIS (MRI) were shown to cooperate similarly in the control of root hair and rhizoid integrity for the vascular model Arabidopsis and the early diverging bryophyte model Marchantia polymorpha, respectively. Here, we carried out comparative transcriptomics and proteomics approach on Mpfer-1 and Mpmri-1 knock-down mutant plants and the wild-type strains Tak-1 and Tak-2. Our -omics analyses revealed that globally, MpFER and MpMRI largely cooperate to negatively regulate transcriptional and translational networks in particular those related to plant defense and ABA responses. Moreover, Mpfer-1 plants were found to be hypersensitive to ABA-dependent growth inhibition indicating that FER’s function of negatively regulating ABA-related growth responses is conserved between bryophytes and vascular plants.

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Transcriptome profiling of Hansenula polymorpha in response to sulfur starvation and cadmium stress

Project description:Transcriptome profiling analysis of the Hansenula polymorpha MET4 gene deletion strain have been carried out to obtain comprehensive information on the HpMet4p-mediated regulatory networks in association with the cadmium (Cd) detoxification and sulfur regulation in H. polymorpha. Total RNA samples were collected from H. polymorpha wild type, and HpMET4 deletion strain, under sulfur starvation or Cd (0.6 mM) stress conditions. The differential fluorescence intensities of each RNA sample were measured after labeling with Cy3 or Cy5. For all analyses, we performed dye swapping experiments to avoid dye bias. Thus, four intensity values were generated for each ORF and averaged for analysis.

2014-07-31 | E-GEOD-31197 | biostudies-arrayexpress

Transcriptome profiling of H. polymorpha in response to hydrogen peroxide exposure

2015-02-28 | GSE43048 | GEO

Transcriptome profiling of H. polymorpha in response to hydrogen peroxide exposure

Project description:To gain insight into the basic mechanism of Hydrogen peroxide detoxification in the methylotrophic yeast, H. polymorpha, we analyzed changes in transcriptional profiles in response to hydrogen peroxide exposure. Total RNA samples were collected from H. polymorpha cells after 30 min incubation with 0.5mM hydrogen peroxide. Using the RNA sample obtained prior to hydrogen peroxide addition as a reference, the differential fluorescence intensities of each RNA sample prepared at the indicated time was measured after labeling with Cy3 or Cy5 fluorochromes. For all analyses, we performed dye swapping experiments to avoid dye bias.

2015-02-28 | E-GEOD-43048 | biostudies-arrayexpress

A seven-membered cell wall related transglycosylase gene family in Aspergillus niger is relevant for cell wall integrity in cell wall mutants with reduced α-glucan or galactomannan

Project description:Chitin is an important fungal cell wall component that is cross-linked to β-glucan for structural integrity. Acquisition of chitin to glucan cross-links has previously been shown to be performed by transglycosylation enzymes in S. cerevisiae, called Congo Red hypersensitive (Crh) enzymes. Here, we characterized the impact of deleting all seven gene members of the crh gene family (crhA-G) in Aspergillus niger on cell wall integrity, cell wall composition and genome-wide gene expression. In this study, we show that the seven-fold knockout strain shows slightly compact plate growth, but no increased sensitivity to cell wall perturbing compounds. Additionally, we found that the cell wall composition of this knockout strain was virtually identical to that of the wild type. In congruence with these data, genome-wide expression analysis revealed very limited changes in gene expression and no signs of activation of the cell wall integrity response pathway. However, deleting the entire crh gene family in cell wall mutants that are deficient in either galactofuranose (ΔugmA) or α-glucan (ΔagsE and ΔagsA, ΔagsE), resulted in a synthetic growth defect and an increased sensitivity towards Congo Red compared the parental strains. Altogether, these results indicate that loss of the crh gene family in A. niger does not trigger the cell wall integrity response in itself, but does play an important role in ensuring cell wall integrity in mutant strains with reduced galactofuranose or α-glucan.

2019-12-21 | GSE142461 | GEO

Transcriptome analysis of isoxaben-induced loss of cell wall integrity in Arabidopsis nia1/2 mutant

Project description:Plant cell walls maintain their functional integrity during growth, defense and turgor generation through a dedicated cell wall integrity (CWI) maintenance mechanism. Upon detection of integrity impairment due to cell wall damage (CWD) compensatory responses are activated to maintain CWI. Responses include production of salicylic acid (SA), jasmonic acid (JA) and lignin as well as growth inhibition. Here we investigated the processes responsible for inducing growth inhibition upon CWD in Arabidopsis thaliana seedlings. Genetic studies implicated NITRATE REDUCTASE1 2 (NIA1 2) in the response to CWD. RNAseq-based transcriptomics showed that nearly all the CWD-induced transcript changes detectable in Col-0 were absent in nia1 2 seedlings.

2018-01-25 | GSE109613 | GEO

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