Root transcriptional responses of two melon (Cucumis melo) genotypes with contrasting tolerance to Monosporascus cannonballus infection
Ontology highlight
ABSTRACT:
ORGANISM(S): Cucumis melo
DISEASE(S): mock-inoculated
SUBMITTER: Gabino Rios
PROVIDER: E-MEXP-3732 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Filamentous fungi including mushrooms frequently and spontaneously degenerate during subsequent culture maintenance on artificial media, which shows the loss or reduction abilities of asexual sporulation, sexuality, fruiting and production of secondary metabolites, thus leading to economic losses during mass production. To better understand the underlying mechanisms of fungal degeneration, the model fungus Aspergillus nidulans was employed in this study for comprehensive analyses. First, linkage of oxidative stress to culture degeneration was evident in A. nidulans. Taken together with the verifications of cell biology and biochemical data, a comparative mitochondrial proteome analysis revealed that, unlike the healthy wild type, a spontaneous fluffy sector culture of A. nidulans demonstrated the characteristics of mitochondrial dysfunctions. Relative to the wild type, the features of cytochrome c release, calcium overload and up-regulation of apoptosis inducing factors evident in sector mitochondria suggested a linkage of fungal degeneration to cell apoptosis. However, the sector culture could still be maintained for generations without the signs of growth arrest. Up-regulation of the heat shock protein chaperones, anti-apoptotic factors and DNA repair proteins in the sector could account for the compromise in cell death. The results of this study not only shed new lights on the mechanisms of spontaneous degeneration of fungal cultures but will also provide alternative biomarkers to monitor fungal culture degeneration. Label-free quantitative proteomic analysis of the WT and Sec mt proteins was performed as described previously. Briefly, purified mitochondrial proteins (100 ug) were diluted in the lysis buffer to a concentration of 5 g/ul and carboxyamidomethylated in 50 mM iodoacetamide for 40 min at room temperature in the dark. The proteins were digested with an endoprotease Lys-C (Roche Applied Science, Indianapolis, IN) at a final substrate/enzyme ratio of 100:1 (w/w) at 37 C for 3 h. The Lys-C digests were further treated with modified sequencing grade trypsin (Roche Applied Science, Indianapolis, IN) at a final substrate/enzyme ratio of 50:1 (w/w) at 37 C for 20 h. After digestion, the peptide mixture was passed through an ultra-filter unit (Millipore, Billerica, MA) with a molecular weight cut-off of 10 kDa and acidified by formic acid (0.1% final concentration) for mass spectrum analysis. A linear ion trap-orbitrap liquid chromatography-tandem mass spectrometry system (LTQ-Orbitrap, Thermo Fisher Scientific, San Josse, CA) equipped with a nanospray ion source was used for full MS scan analysis followed by five MS/MS scans in the LTQ on the five most intense ions from the MS spectrum. Three parallel runs were performed consecutively for each sample. The software DeCyder MS (ver 2.0) (GE Healthcare, Pittsburgh, PA) was used to generate the peak lists from all the runs and the data were then automatically searched using the SEQUEST (ver. 2.7) (Thermo Fisher Scientific, San Josse, CA) against the A. nidulans genome archive (ver. S03-M05-R01, containing 10,644 protein entries) at AspGD database (www.aspgd.org) with the following parameters: peptide mass tolerance set to 10 ppm; fragment tolerance set to 0.8 Da, and two missed trypsin cleavages. Carbamidomethylation of cysteine was searched as a fixed modification, whereas N-acetyl protein and oxidation of methionine were searched as variable modifications. For protein identification, all peptide matches were filtered by a maximum false discovery rate (FDR) index less than 0.01, delta Cn larger than 0.1 and Xcorr scores of greater than 1.7, 2.0 and 3.0 for +1, +2, and +3 charged ions, respectively. The peptides were discarded for further analysis if mapped to more than two different proteins. A protein was considered identifiable with at least one unique peptide detected for more than twice in the three replicates of each sample. The MS data have been deposited in the PRIDE proteomics identification database under accession numbers ? List of the identified peptides and matched proteins is provided in Supplemental Table 1. Quantification of proteins was performed by estimating the normalized spectral index (SIN) for each protein, which combines the features of peptide count, spectral count, fragment-ion intensity and protein length as described by Griffin et al.. Reliability of technical repeats was analyzed by calculating the multivariate Pearson correlation coefficients using the software SigmaPlot (ver. 8.0). FDR estimation of differentially expressed proteins was conducted using a mixture model-based method. Heat mapping analysis was conducted using the program Matlab (R2009a). The significance of differentially expressed proteins between the samples was tested with the cutoff values of P less than or equal to 0.05 and FDR less than or equal to 0.05.
2019-11-25 | PXD000422 | Pride
Project description:We used microarrays to find out carbon souce responsive genes of A. oryzae with 1hr induction with galactose, glucose, and sorbitol. The A.oryzae RIB40 was cultured for 24hr in glucose as a carbon source, then shifted to galactose, glucose, and sorbitol containing medium and cultured for 1hr. Two biological replicates in each conditions were used for the microarray analysis.
2016-06-30 | E-GEOD-76534 | biostudies-arrayexpress
Project description:Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions: The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high. Detection of gene expression variance among Frankia HfpCci3 (Cci3) cells grown in ammonium chloride for three days, five days and HfpCci3 cells grown in nitrogen fixing conditions for three days using mRNA-seq
2011-07-15 | E-GEOD-30680 | biostudies-arrayexpress
Project description:Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues however, little is known about how R. solani causes disease. This study capitalises on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification.
2016-01-28 | PXD002806 | Pride
Project description:A self-designed Trichoderma high density oligonuclotide (HDO) microarray (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 13,443 EST-derived transcripts (Trichochip-1) and the genomes of T. atroviride (11,100 genes) and T. virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum) under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (VizcaÃno et al., 2006). The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032) T. atroviride P1 mycelium grown (approximately for 24h) at 25ºC on a cellophane sheet on PDA (Difco) plates before contact (at a distance of 5 mm) a R. solani colony grown under identical conditions in the same plate was compared with T. atroviride P1 mycelium after contact (5 mm) the above R. solani colony (mycoparasitic interaction). RNAs from both conditions were extracted and the corresponding cDNAs were use to hybridize by triplicate the Trichoderma HDO microarray.
2010-04-22 | E-GEOD-20516 | biostudies-arrayexpress
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Paxillus involutus ectomycorrhizal roots compared to mycelium patches . Mycorrhizal roots were harvested after 4 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Paxillus involutus ectomycorrhizal roots and mycelium patches were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.
2015-02-06 | E-GEOD-63924 | biostudies-arrayexpress
Project description:CHL1 functions as a nitrate sensor and also is one of major nitrate transporters responsible for nitrate responses and uptake. ANI is a protein phosphatase particiates in temporal nitrate response, its influence was analyzed in a global transcriptome study using Affymetrix ATH1 array. Two biological replicates of 10-day-old Arabidopsis root tissue from wild-type and ani1 plants were performed to explore differences in gene expression between the wild-type and ani1 mutants exposed to 200 μM nitrate for 0h (T0), 0.5h (T0.5), or 16h (T16) using Affymetrix ATH1 microarray.
2014-10-26 | E-GEOD-33242 | biostudies-arrayexpress
Project description:Using a 3′-tiling microarray covering the whole F. graminearum genes, we carried out genome-wide expression analyses of F. graminearum infected with FgV-DK21 (Mycovirus) at two different time stages (36 h and 120 h). Our study is the first report which elucidated the global alternation of the prominent cellular pathways in fungal host by FgV1-DK21 virus infection. A total of 12 chips were used for microarray. At 36 h and 120 h, total RNAs were extracted from virus free Fusarium and virus infected Fusarium with three biological replicates.
2012-03-01 | E-GEOD-30545 | biostudies-arrayexpress
Project description:Gene expression analysis of S. coelicolor M145 wild type strain, and mutants delta0877 and delta 7173. RNA samples were extracted from 48 h culture samples during growth in flasks in defined mineral medium MG supplemented with 5% of yeast extract. Cy5 labelled genomic DNA was used as the common reference.
2009-04-17 | E-MEXP-2132 | biostudies-arrayexpress
Project description:Background: Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers [GSE33852]. Results: In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. Conclusions: By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production. Six samples in total consisting of duplicate shake flask Aspergillus niger cultures from three conditions: glucose 48 h, willow 24 h, willow 24 h + glucose 5 h
2015-04-13 | E-GEOD-62284 | biostudies-arrayexpress