Molecular mechanisms of Acanthamoeba castellanii response to different sources of oxidative stress.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF Pro 2
ORGANISM(S): Acanthamoeba Castellanii
SUBMITTER: 
Guillaume CHEVREUX
LAB HEAD: Robert Sutak
PROVIDER: PXD052473 | Pride | 2025-01-21
REPOSITORIES: pride
Dataset's files
Items per page: 5 1 - 5 of 84 |
Similar Datasets
Project description:Ciliates undergo developmentally programmed genome elimination, in which small RNAs direct the removal of target DNA segments, including transposable elements. At each sexual generation, the development of the macronucleus (MAC) requires massive and reproducible elimination of a large proportion of the germline micronuclear (MIC) genome, leading to a highly streamlined somatic MAC genome. 25-nt long scnRNAs are produced from the entire germline MIC genome during meiosis, and this initial complex small RNA population is then transported to the maternal MAC, where selection of scnRNAs corresponding to germline (MIC)-specific sequences is thought to take place. Selected scnRNAs, loaded onto the PIWI protein Ptiwi09, guide the deposition of histone H3 post-translational modifications (H3K9me3 and H3K27me3) onto transposable elements in the developing macronucleus, ultimately triggering their specific elimination. How germline-specific MIC scnRNAs are selected remains to be determined. Here, we provide important mechanistic insights into the scnRNA selection pathway by identifying a Paramecium homolog of Gametocyte specific factor 1 (Gtsf1) as essential for the selective degradation of scnRNAs corresponding to retained somatic MAC sequences. Consistently, we also show that Gstf1 is exclusively localized in the maternal macronucleus, where scnRNA selection is presumed to occur, and associates with the scnRNA-binding protein Ptiwi09. Furthermore, Gtsf1 is necessary for DNA elimination and correct H3K9me3 and H3K27me3 localization in the new developing macronucleus, demonstrating that the scnRNA selection process is important for genome elimination. We propose that Gtsf1 is required for the coordinated degradation of Ptiwi09-scnRNA complexes that pair with nascent RNA transcribed from the maternal MAC genome, similarly to the mechanism suggested for microRNA target-directed degradation in metazoans.
2024-10-17 | PXD045214 | Pride
Project description:Candida albicans is an opportunist pathogen responsible for a large spectrum of infections, from superficial mycosis to systemic diseases known as candidiasis. C. albicans can grow in various morphological forms, including unicellular budding yeasts, filamentous pseudophyphae and true hyphae, and the ability to switch from yeast to hyphal forms is a key survival mechanism in the adaptation of the pathogen to the microenvironments encountered within the host. The filamentation is regulated by multiple signalling pathways and can be induced, in vitro, in several growth media, often leading to contradictory results in the literature. In this study, we use quantitative proteomic analyses to compare the response of C. albicans yeast cells grown in the minimal medium YNB to four media widely used in the literature to induce the yeast to hyphae transition: YNB-Serum, YNB-N-Acetyl-glucosamine (YNB-NAG), Lee medium and the rich Spider medium. We show here that each growth medium induces a unique pattern of response in C. albicans cells, and that some conditions trigger an original and specific metabolic adaptive response. Moreover, comparison of the proteomic profiles indicates modifications of the thiol-dependent oxidative stress status of the cells, especially in YNB-Serum and Lee medium, and, to a lesser extent, in Spider medium, confirming the role of oxidative stress in the filamentation process. Overall, our data indicate that some hypha-inducing media routinely used in the literature are associated with significant changes in in proteomic signature and that should be more often taken account when exploring the filamentation process of the pathogen.
2024-10-31 | PXD052475 | Pride
Project description:Orthohantaviruses are rodent-borne emerging viruses known to cause severe diseases in humans but no apparent pathology in their small mammal reservoirs. However, the mechanisms leading to tolerance or pathogenicity in humans and persistence in rodent reservoirs are poorly understood, as is the manner in which they spread within and between organisms. Here, we used a range of cellular and molecular approaches to investigate the interactions of three different orthohantaviruses – Puumala virus (PUUV), responsible for a mild form of hemorrhagic fever in humans, Tula virus (TULV) with low pathogenicity, and nonpathogenic Prospect Hill virus (PHV) – with human and rodent host cell lines. We showed that the three orthohantaviruses were able to infect Vero E6 and HuH7 cells but only the former secreted infectious particles. In cells derived from the PUUV reservoir (Myodes glareolus), PUUV achieved complete viral cycling, while TULV did not enter the cells and PHV infected them but did not produce infectious particles, reflecting some differences in host specificity. A search for mature virions by electron microscopy revealed that TULV assembly occurred in part at the plasma membrane, whereas PHV particles were trapped in autophagic vacuoles in cells of the heterologous rodent host. The interaction of orthohantaviruses with cellular factors was investigated by studying the colocalization of viral nucleocapsids with markers of cell compartments, identifying interactors of viral proteins by mass spectrometry analysis, and measuring the regulation of gene expression by transcriptomic analysis in infected cells. Overall, our study highlighted the complexity of the host-virus relationship, demonstrated that orthohantaviruses were restricted at different levels of the viral cycle, and provided different levels of analysis to further investigate how these viruses differ in their interactions with cells to evade innate immunity and how this depends on the tissue and host species.
2022-10-04 | PXD032365 | Pride
Project description:Extracellular vesicles (EVs) are nanoparticles containing various bioactive cargos, e.g., proteins, RNAs, and lipids, that are released into the environment by all cell types. They are involved in, amongst others, intercellular communication. This article presents studies on EVs produced by the probiotic yeast Saccharomyces boulardii CNCM I-745. The size distribution and concentration of EVs in the liquid culture of yeast were estimated. Moreover, the vesicles of S. boulardii were tested for their cytotoxicity against three model human intestinal cell lines. This study did not show any significant negative effect of yeast EVs on these cells under tested conditions. In addition, EVs of S. boulardii were verified for their ability to internalize in vitro with human cells and transfer their cargo. The yeast vesicles were loaded with doxorubicin, an anticancer agent, and added to the cellular cultures. Subsequently, microscopic observations revealed that these EVs transferred the chemotherapeutic to human intestinal cell lines. A cytotoxicity test confirmed the activity of the transferred doxorubicin. Detailed information about the proteins present in EVs might be important in terms of exploring yeast EVs as carriers of active molecules. Thus, proteomic analysis of the EV content was also conducted within the present study, and it allowed to identify 541 proteins after matching to the Saccharomyces Genome Database (SGD). Altogether, this study provides strong evidence that the EVs of the probiotic CNCM I-745 strain could be considered a drug delivery system.
2023-06-29 | PXD042660 | Pride
Project description:Here we provide proteomic datasets of pairs of cortical and trabecular bone from six Early Holocene Caprinae rib fragments from the site of La Draga, Spain, using shotgun proteomics. Our observations on proteome size and protein, peptide, and amino acid degradation have implications for the sampling of archaeological skeletal remains in highly degraded proteomic contexts, where preference should be given to the sampling of cortical bone in order to maximise the retrieval of larger and better-preserved skeletal proteomes.
2024-07-12 | PXD047126 | Pride
Project description:Marine brown algae produce the highly recalcitrant polysaccharide fucoidan, contributing to long-term oceanic carbon storage and climate regulation. Fucoidan is degraded by specialized heterotrophic bacteria, which promote ecosystem function and global carbon turnover using largely uncharacterized mechanisms. Here, we isolate and study two Planctomycetota strains from the microbiome associated with the alga Fucus spiralis, which grow efficiently on chemically diverse fucoidans. One of the strains appears to internalize the polymer, while the other strain degrades it extracellularly. Multi-omic approaches show that fucoidan breakdown is mediated by the expression of divergent polysaccharide utilization loci, and endo-fucanases of family GH168 are strongly upregulated during fucoidan digestion. Enzymatic assays and structural biology studies reveal how GH168 endo-fucanases degrade various fucoidan cores from brown algae, assisted by auxiliary hydrolytic enzymes. Overall, our results provide insights into fucoidan processing mechanisms in macroalgal-associated bacteria.
2024-11-22 | PXD057797 | Pride
Project description:Firefly larvae are highly specialized predators of snails, which utilize midgut secretions to incapacitate and pre-digest their much larger prey. With the current analysis we aim to shed light on the composition of the midgut secretion of these larvae utilizing a proteo-transcriptomic approach.
2024-07-03 | PXD052900 | Pride
Project description:Many mammals can temporally uncouple conception from parturition by pacing down their development around the blastocyst stage. In mice, this dormant state is achieved by decreasing the activity of the growth-regulating mTOR signaling pathway1. It is unknown whether this ability is conserved in mammals in general and in humans in particular. Here we show that decreasing the activity of the mTOR signaling pathway induces human pluripotent stem cells (hPSCs) and blastoids to enter a dormant state with limited proliferation, developmental progression, and capacity to attach to endometrial cells. These in vitro assays show that, similar to other species, the ability to enter dormancy is active in human cells around the blastocyst stage and is reversible at both functional and molecular levels. The pacing of human blastocyst development has potential implications for reproductive therapies.
2024-09-26 | PXD036258 | Pride
Project description:Neural communication requires both fast-acting neurotransmitters and neuromodulators that function on slower timescales to communicate. Endogenous bioactive peptides, often called “neuropeptides,” comprise the largest and most diverse class of neuromodulators that mediate crosstalk between the brain and peripheral tissues to regulate physiology and behaviors conserved across the animal kingdom. Neuropeptide signaling can be terminated through receptor binding and internalization or degradation by extracellular enzymes called neuropeptidases. Inactivation by neuropeptidases can shape the dynamics of signaling in vivo by specifying both the duration of signaling and the anatomic path neuropeptides can travel before they are degraded. For most neuropeptides, the identity of the relevant inactivating peptidase(s) is unknown. Here, we established a screening platform in C. elegans utilizing mass spectrometry-based peptidomics to discover neuropeptidases and simultaneously profile the in vivo specificity of these enzymes against each of more than 250 endogenous peptides. We identified NEP-2, a worm ortholog of the mammalian peptidase neprilysin-2, and demonstrated that it regulates specific neuropeptides, including those in the egg-laying circuit. We found that NEP-2 is required in muscle cells to regulate signals from neurons to modulate both behavior and health in the reproductive system. Taken together, our results demonstrate that peptidases, which are an important node of regulation in neuropeptide signaling, affect the dynamics of signaling to impact behavior, physiology, and aging.
2024-10-11 | PXD050464 | Pride
Project description:Nearly all cellular functions are mediated by protein-protein interactions and mapping the interactome provides fundamental insights into the regulation and structure of biological systems. In principle, affinity purification coupled to mass spectrometry (APMS) is an ideal and scalable tool, however, it has been difficult to identify low copy number complexes, membrane complexes and those disturbed by protein-tagging. As a result, our current knowledge of the interactome is far from complete, and assessing the reliability of reported interactions is challenging. Here we develop a sensitive, high-throughput, and highly reproducible AP-MS technology combined with a quantitative two-dimensional analysis strategy for comprehensive interactome mapping of Saccharomyces cerevisiae. We reduced required cell culture volumes thousand-fold and employed 96-well formats throughout, allowing replicate analysis of the endogenous green fluorescent protein (GFP) tagged library covering the entire expressed yeast proteome. The 4159 pull-downs generated a highly structured network of 3,909 proteins connected by 29,710 interactions. Compared to previous large-scale studies, we double the number of proteins (nodes in the network) and triple the number of reliable interactions (edges), including very low abundant epigenetic complexes, organellar membrane complexes and non-taggable complexes interfered by abundance correlation. This nearly saturated interactome reveals that the vast majority of yeast proteins are highly connected, with an average of 15 interactors, the majority of them unreported so far. Similar to social networks between humans, the average shortest distance is 4.2 interactions. A web portal (www.yeastinteractome.org) enables exploration of our dataset by the network and biological communities and variations of our AP-MS technology can be employed in any organism or dynamic conditions.
2023-09-11 | PXD031940 | Pride