Quantitative proteomics analysis of moderate high pressure superdormant spores and comparison to the initial dormant spore population
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Bacillus Subtilis
SUBMITTER: 
Alessia Delbrück
LAB HEAD: Alexander Mathys
PROVIDER: PXD027768 | Pride | 2021-12-13
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 13 |
Similar Datasets
Project description:Moorella thermoacetica spores are the most heat-resistant so far retrieved in food industry and we previously showed that the resistance properties of these spores to wet- heat and biocides were lower when spores were produced at low limit temperature than at optimal temperature. By electron microcopy, we observed that the ultrastructure of the spore coat differed according to the sporulation temperature, with spores produced at 55 °C mainly exhibiting lamellar inner coat tightly associated to diffuse outer coat, while spores produced at 45 °C showing an inner and outer coat separated by a less electron- dense zone. Moreover, misarranged coat structures were more frequently observed when spores were produced at low limit temperature. We analyzed the proteome of spore ob- tained at 45° and 55 °C and focused our data analysis on putative spore coat, exosporium proteins or proteins playing a role in spore resistance. Some putative spore coat proteins, such as CotSA, were only identified in spores produced at 55 °C, while some other puta- tive exosporium and coat proteins were significantly less abundant in spores produced at 45 °C. Altogether, our results suggest that sporulation temperature affects the structure and the protein composition of M. thermoacetica spores.
2022-02-17 | PXD029621 | Pride
Project description:The members of the genus Clostridium, such as the other spore-forming anaerobic bacteria, have a complex and strictly regulated life-cycle but very little is known about genetic pathways involved at different stages. Clostridium sporogenes, Gram positive bacterium usually involved in food spoilage and frequently isolated from late blowed cheese is genetically indistinguishable from proteolytic Clostridium botulinum and is the non-neurotoxigenic counterpart often used as exemplar for the toxic subtypes. In this work we have performed a microscopy study combined with a custom array-based analysis of C. sporogenes cycle, from dormant spores to early stationary phase. We identified in spores a total of 211 transcripts validating the ipothesis that mRNAs are abundant and strikingly different from those present in growing cells. The spores transcripts included genes responsible of different life-sustaining functions, suggesting the theory of transcripts entrapment or of a basic poly-functional genes activation for future steps. In addition, after three hours from the beginning of the germination process, a 20% of the total up-regulated genes were temporally expressed in germinating spores. The vegetative condition appears to be the more active in terms of gene transcription and protein synthesis and also genes for germination and sporulation factors seem to be expressed at this point. These results suggest that spores are not silent entities and a wider knowledge about genetic pathways involved in Clostridium life cycle could be of help for a better understanding also of pathogenic clostridia types. RNA was isolated from spores, germinating spores (3h), outgrowth/transitional mid-log vegetative cells and early stationary cells of Clostridium sporogenes UC9000 previously isolated from milk. There were 3 biological replicates (independent cultures) for each condition. Probes corresponding to 3400 genomic CDSs of C. botulinum A ATCC 3502 were synthesized in three replicates randomly distributed on the chip.
2012-06-12 | E-GEOD-38619 | biostudies-arrayexpress
Project description:Mucormycosis is a life-threatening disease especially in immunocompromised patients that was caused my mucoralean fungi. The rate of mortality is tremendously increased in the last decades due to the lack of appropriate diagnostic tools, insufficient knowledge about the immune response toward the mucormycosis and unavailability of specific antifungal drugs. Several species of mucoralean fungi cause mucormycosis such as Lichtheimia, Rhizopus, and Mucor. Lichtheimia species ranks the second and third cause of mucormycosis in Europe and the USA, respectively. In this study, we investigated the receptors present on the surface of immune cells that bind to the spores of Lichtheimia. We focus on two strains of L. corymbifera (FSU:9682 and FSU:10164) using resting and heat-killed spores. Additionally, we choose alveolar macrophages (MH-S) to carry out our experiment. MH-S is the first line of defense in the lung and the major component in the innate immune system. MH-S surface proteins were biotinylated and incubated with Lichtheimia spores. The surface proteins and putative binding partners were enriched by streptavidin. LC-MS/MS analysis showed that several proteins are highly expressed in presence of Lichtheimia spores, of which the heat shock protein family A (HSPA8) was one of the most abundant proteins. FACS analysis and immunofluorescence examination confirmed that HSPA8 is highly abundant on the surface of the MH-S, but not on the surface of Lichtheimia spores. Moreover, our study showed that the intensity of HSPA8 on the surface of MH-S depends on the multiplicity of infection (MOI). Additionally, the blocking with anti-HSPA8 antibody reduced the capability of MH-S to engulf the Lichtheimia spores, but not Aspergillus fumigatus spores. This confirms that HSPA8 is specific to Lichtheimia. THis is the first study addressing the determination of surface receptors of alveolar macrophages that in the context of Mucoralean fungi.
2020-07-17 | PXD014197 | Pride
Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.
2012-05-31 | E-GEOD-37124 | biostudies-arrayexpress
Project description:Spermatophyte pollen tubes and root hairs have been used as single-cell-type model systems toward understanding the molecular processes underlying polar growth of plant cells. Horsetail (Equisetum arvense L.) is a perennial herb species in Equisetopsida, which creates separately growing spring and summer stems in its life cycle. The mature chlorophyllous spores produced from spring stems can germinate without dormancy. Here we report the cellular features and protein expression patterns in five stages of horsetail spore germination (mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Using 2-DE combined with mass spectrometry, 80 proteins were found to be differentially expressed upon spore germination. Among them, proteins involved in photosynthesis, protein turnover, and energy supply were over-represented. Thirteen proteins appeared as isoforms on the gels, indicating the potential importance of post-translational modification. In addition, the dynamic changes of ascorbate peroxidase, peroxiredoxin, and dehydroascorbate reductase implied that reactive oxygen species homeostasis is critical in regulating cell division and tip-growth. The time course of germination and diverse expression patterns of proteins in photosynthesis, energy supply, lipid and amino acid metabolism indicated that heterotrophic and autotrophic metabolism were necessary in light-dependent germination of the spores. Twenty-six proteins were involved in protein synthesis, folding, and degradation, indicating that protein turnover is vital to spore germination and rhizoid tip-growth. Furthermore, the altered abundance of small G protein Ran1, 14-3-3 protein, actin, and Caffeoyl-CoA O-methyltransferase revealed that signaling transduction, vesicle trafficking, cytoskeleton dynamics, and cell wall modulation were critical to cell division and polar growth. These findings provide up-to-date evidences for understanding fern spore asymmetric division and rhizoid polar growth.
2016-12-23 | PXD002218 | Pride
Project description:Pathogenic species belonging to Bacillus cereus sensu lato group possess a high evolutionary advantage in the environment and in food matrices thanks to their capacity to survive as silent spores to harsh environmental insults and grow at relatively low temperatures. Ready to re-heat products are at severe risk for contamination by members of Bacillus cereus s.l. group if not stored at proper conditions. In this work, the goal was to assess, by means of a genome-wide transcriptional assay, the isolated strain Bacillus cereus UC10070 gene expression behind the process of spore germination and consequent outgrowth in an artificially contaminated vegetable-based food model. A vegetable food model subjected to a heat treatment was determined to present favourable conditions for spores germination. Microscopic analyses together with OD measurements were applied to select the key steps of B. cereus cell cycle to be used for the microarray analysis. Using this approach we found a total of 1,646 probe sets differentially expressed and modulated during the entire B. cereus life cycle in the vegetable foodstuff. RNA was isolated from the dormant spores (DS), germinating spores at 40 minutes (GSP), early-log phase at 2h (C2h) and late log phase cells at 12 hours (C12h) after thermal treatment of B. cereus UC10070 previously isolated froma biofilm on a spoiled vegetable-based puree. There were 3 biological replicates (independent cultures) for each condition. Complete genome sequence of B. thuringiensis sv konkukian str. 97-27 (NCBI Reference Sequence: NC_005957.1) was chosen for its high homology with B. cereus s.l. UC10070, to design probes corresponding to 5,197 genes spotted in duplicates onto ElectraSenseH 12K microarrays chip.
2015-01-26 | E-GEOD-65259 | biostudies-arrayexpress
Project description:It has been reported that repeated intra-tracheal instillation of S. chartarum spores induced significant pulmonary arterial remodeling in mice, which resulted in pathological changes like human pulmonary arterial hypertension (PAH) and elevation right ventricle systolic pressure. Then, we used microarrays to know the complex molecular mechanisms that underlie pathogenesis of PAH. Isolates of Stachybotrys chartarum were used. Ddy mice were anesthetized and the spore suspension was intratracheally injected 12 times, i.e. 1×104 spores into each mouse at 4-5 day intervals for 8 weeks. Mice were sacrificed one week after the final injection and then examined. Lung tissue specimens from mice model of PAH (n=3) and normal controls (n=3) were obtained. RNA targets preparation were performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix). One hundred nanograms of total RNA was converted into double-stranded cDNA template for transcription. In vitro transcription synthesized amplified RNA (aRNA) and incorporated a biotin-conjugated nucleotide. After purification and fragmentation of aRNA, 12.5 ug of them was hybridized to GeneChip(R) Mouse Genome 430 2.0 Array (Affymetrix).The Probe Array was scanned using a GeneChip(R) Scanner 3000 7G.
2010-07-28 | E-GEOD-23178 | biostudies-arrayexpress
Project description:Sorbic acid (SA) is widely used as a preservative, but the effect of SA on spore germination and outgrowth has gained limited attention up to now. Therefore, the effect of sorbic acid on germination of spores of B. cereus strain ATCC 14579 was analyzed both at phenotype and transcriptome level. Spore germination and outgrowth was assessed at pH 5.5 without and with 0.75, 1.5 and 3.0mM (final concentrations) undissociated sorbic acid (HSA). This resulted in distinct HSA concentration-dependent phenotypes, varying from delays in germination and outgrowth to complete blockage of germination at 3.0mM HSA. The phenotypes reflecting different stages in the germination process could be confirmed using flow cytometry and could be recognized at transcriptome level by distinct expression profiles. In the absence and presence of 0.75 and 1.5mM HSA, similar cellular ATP levels were found up to the initial stage of outgrowth, suggesting that HSA-induced inhibition of outgrowth is not caused by depletion of ATP. Transcriptome analysis revealed the presence of a limited number of transcripts in dormant spores, outgrowth related expression, and genes specifically associated with sorbic acid stress, including alterations in cell envelope and multi-drug resistance. The potential role of these HSA-stress associated genes in spore outgrowth is discussed. Per concentration of undissociated sorbic acid (0, 0.75, and 1.5mM) four exposure times (10, 30, 60, and 120 minutes) were each compared with dormant spores (i.e., t0). The experiments were performed in duplicate and the duplicate samples were hybridized with a dye-swap
2010-11-01 | E-GEOD-19186 | biostudies-arrayexpress
Project description:The establishment of seeds is considered a milestone in plant evolution. A major proportion of the protein networks underpinning desiccation tolerance, the accumulation of storage compounds, and the regulation of dormancy have probably evolved much earlier, however. The same is likely to be the case for the molecular program that drives the transition from heterotrophic offspring to the autotrophic plant. We hypothesized that a comparison with a bryophyte representing a distinct evolutionary lineage to seed plants may reveal the origin of components of the “seed program”. Therefore, we investigated the proteome of five timepoints of moss (P. patens) spore germination as well as protonemata and gametophores, and compared it to Arabidopsis proteome data during seedling establishment. This quantitative comparison showed that not only spores are functionally related to seeds but also the functional similarity of germinating spores and young seedlings. We observed remarkable similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and the metabolic pathways that transform fatty acids into sugars. However, there were also striking differences. For example, the spores of P. patens did not harbor any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss.
2023-12-15 | PXD043767 | Pride
Project description:Using RNA-Seq data from the mycelium of Fusarium graminearum, we found weakly expressed regions on all of the four chromosomes that exactly matched with non-conserved regions. Comparison of gene expression between two different developmental stages (spores and mycelium) showed that the expression of genes in conserved regions is stable, while gene expression in non-conserved regions is much more influenced by developmental stage. Examination of gene expression in two developmental stages (spores and mycelium). Three biological replicates were performed for each stage.
2014-03-01 | E-GEOD-55477 | biostudies-arrayexpress