Identification of fungal secreted proteins
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus Niger
SUBMITTER: 
Guodong Liu
PROVIDER: PXD020432 | iProX | Sun Jul 19 00:00:00 BST 2020
REPOSITORIES: iProX
Publications
Deletion of the middle region of the transcription factor ClrB in <i>Penicillium oxalicum</i> enables cellulase production in the presence of glucose.
Gao Liwei L Xu Yanning Y Song Xin X Li Shiying S Xia Chengqiang C Xu Jiadi J Qin Yuqi Y Liu Guodong G Qu Yinbo Y
The Journal of biological chemistry 20191028 49
Enzymes that degrade lignocellulose to simple sugars are of great interest in research and for biotechnology because of their role in converting plant biomass to fuels and chemicals. The synthesis of cellulolytic enzymes in filamentous fungi is tightly regulated at the transcriptional level, with the transcriptional activator ClrB/CLR-2 playing a critical role in many species. In <i>Penicillium oxalicum</i>, <i>clrB</i> overexpression could not relieve the dependence of cellulase expression on c ...[more]
Similar Datasets
Project description:Normal and cirrhotic LSECs can influence hepatic stellate cells (HSCs) differently. This project aims to determine the set of proteins secreted by LSECs from healthy and cirrhotic livers, and identify the protein(s) that promote HSC activation.
2018-11-06 | PXD009010 | Pride
Project description:Despite widespread advances in DNA sequencing in the past decade, the functional consequences of most rare genetic variants remain poorly understood, severely limiting our ability to connect variants to their consequences on protein function, identify biochemical mechanisms by which variation causes disease, and interpret variant pathogenicity. Multiplexed Assays of Variant Effect (MAVEs), which can measure the function of tens of thousands variants, are beginning to address this problem. However, existing MAVEs cannot be applied to the approximately 10% of human genes encoding secreted proteins, about a quarter of which are associated with disease. We developed a flexible and scalable human cell surface display method, Multiplexed Surface Tethering of Extracellular Proteins (MultiSTEP), that can simultaneously measure the functional effects of tens of thousands of variants in secreted proteins. We used MultiSTEP to study the consequences of missense variation in coagulation factor IX (FIX), a vitamin K-dependent plasma serine protease where variation can cause FIX deficiency and the bleeding disorder hemophilia B. We used a panel of antibodies to detect FIX secretion or FIX post-translational modification, measuring a total of 45,024 effects for 9,007 variants. 43.8% of all possible F9 missense variants impact FIX secretion, post-translational modification or both. We also identify new signals of functional constraint on secretion including within the signal peptide, folded domains, and for nearly all variants that caused gain or loss of cysteine. FIX secretion scores correlate strongly with FIX levels in patient plasma and also reveal that most F9 missense variants causing severe hemophilia do so by profoundly impacting secretion. We integrate the secretion and post-translational modification data to develop a F9 variant classifier that can identify loss of function variants with high specificity. We use the resulting classifications to reinterpret and upgrade 62 of 97 F9 variants of uncertain significance (VUS) in the MyLifeOurFuture hemophilia genotyping project to likely pathogenic. Lastly, we show that MultiSTEP can be applied to a wide variety of secreted proteins, ranging from small signaling proteins like insulin to large proteins like factor VIII. Thus, we establish a multiplexed, multimodal, and generalizable method for systematically assessing variant effects for secreted proteins at scale, paving the way for improved understanding of biochemical mechanisms of disease and clinical variant interpretation.
2025-01-14 | GSE242805 | GEO
Project description:Transcriptional profiles were carried out for four transcription factors and two receptor-like kinases mutants, corresponding to genes that are co-expressed in silico with the CESA7 gene in Arabidopsis. These mutants show enhanced disease susceptibility to the necrotrophic fungal pathogen Plecthosphaerella cucmerina. Several gene families of small secreted peptides, some of them with known hormone or signalling implications, were commonly up-regulated in all of the 6 genotypes, unveiling a functional implication of these secreted peptides in the defence pathway against fungi.
2015-01-20 | GSE36308 | GEO
Project description:Multiplex, multimodal mapping of variant functional effects in secreted proteins
| PRJNA1014772 | ENA
Project description:Transcriptional profiles were carried out for four transcription factors and two receptor-like kinases mutants, corresponding to genes that are co-expressed in silico with the CESA7 gene in Arabidopsis. These mutants show enhanced disease susceptibility to the necrotrophic fungal pathogen Plecthosphaerella cucmerina. Several gene families of small secreted peptides, some of them with known hormone or signalling implications, were commonly up-regulated in all of the 6 genotypes, unveiling a functional implication of these secreted peptides in the defence pathway against fungi. Transcriptomics of 6 mutant plants, including four transcription factors and two receptor-like kinases, were compared to their background Col-0 accession. For this porpoise, plants were grown as described and leaves from three plants of each genotype were mixed and extracted as one single replicate. Three replicates from three different sets of plants were analysed for each genotype.
2015-01-20 | E-GEOD-36308 | biostudies-arrayexpress
Project description:Invasive fungal pathogens are major causes of human mortality and morbidity1,2. While numerous secreted effector proteins that reprogram innate immunity to promote virulence have been identified in pathogenic bacteria, there are no examples of analogous secreted effector proteins produced by human fungal pathogens. Cryptococcus neoformans, the most common cause of fungal meningitis and a major AIDS pathogen, induces a pathogenic type 2 response characterized by pulmonary eosinophilia and alternatively activated macrophages3-8. Here, we identify Cpl1 as an effector protein secreted by C. neoformans that drives alternative activation (also known as M2 polarization) of macrophages to enable pulmonary infection. We observed that Cpl1-enhanced macrophage polarization requires Toll-like receptor 4, best known as a receptor for bacterial endotoxin, but is also a poorly understood mediator of allergen-induced type 2 responses9-12. We show that this effect is due to Cpl1 itself and not contamination by lipopolysaccharide. Cpl1 is essential for virulence, drives polarization of interstitial macrophages in vivo, and requires type 2 cytokine signaling for its impact on infectivity. Strikingly, C. neoformans selectively associates with polarized interstitial macrophages during infection, suggesting a mechanism by which C. neoformans generates its own intracellular replication niche within the host. This work identifies a novel circuit whereby a secreted effector protein produced by a human fungal pathogen reprograms innate immunity, revealing an unexpected role for Toll-like receptor 4 in pathogenesis of infectious disease.
2022-08-12 | GSE203483 | GEO
Project description:Background. Bacillus subtilis is a favorable host for the production of industrially relevant proteins because of its capacity of secreting proteins into the medium to high levels, its GRAS (Generally Recognized As Safe) status, its genetic accessibility and its capacity to grow in large fermentations. However, production of heterologous proteins still faces limitations. Results. This study aimed at the identification of bottlenecks in secretory protein production by analyzing the response of B. subtilis at the transcriptome level to overproduction of eight secretory proteins of endogenous and heterologous origin and with different subcellular or extracellular destination: secreted proteins (NprE and XynA of B. subtilis, Usp45 of Lactococcus lactis, TEM-1beta -lactamase of Escherichia coli), membrane proteins (LmrA of L. lactis and XylP of Lactobacillus pentosus) and lipoproteins (MntA and YcdH of B. subtilis). Responses specific for proteins with a common localization as well as more general stress responses were observed. The latter include upregulation of genes encoding intracellular stress proteins (groES/EL, CtsR regulated genes). Specific responses include upregulation of the liaIHGFSR operon under Usp45 and TEM-1 beta-lactamase overproduction; cssRS, htrA and htrB under all secreted proteins overproduction; sigW and SigW-regulated genes mainly under membrane proteins overproduction; and ykrL (encoding an HtpX homologue) specifically under membrane proteins overproduction. Conclusions. The results give better insights into B. subtilis responses to protein overproduction stress and provide potential targets for genetic engineering in order to further improve B. subtilis as a protein production host. Samples for transcriptome analyses were induced at the exponential-growth phase (OD600 = 0.7) with 0.1% subtilin (subtilin containing supernatant of subtilin producing B. subtilis strain ATCC 6633). Cells were harvested 30 min after induction. Three or four independent cultures of each strain (target strains and controls) were used, and cells were sampled for microarray experiment.
2012-05-24 | E-GEOD-34505 | biostudies-arrayexpress
Project description:Toxoplasma gondii is an obligate intracellular parasite which can cause toxoplasmosis. Surface and secreted proteins of T. gondii play important roles in infection and immunity, and also are antigen targets in immunological diagnosis and vaccine development. However, it is difficult to investigate identities and antigenicities of surface and secreted proteins due to limitation of surface protein extraction methods. In this study, a total of 785 potential surface and secreted proteins of T. gondii RH tachyzoites were identified using a method combination of biotin labeling, avidin chromatography isolation, and high flux proteomics (LC-MS/MS). Among the highly-expressed 65 proteins, 43 proteins (66%) were originally annotated as surface or secreted proteins in the released T. gondii genomes, which proved the method combination to be a credible strategy. Furthermore, the transcriptomic responses and cytokine secretions induced by the isolated proteins, the live T. gondii RH tachyzoites infection, and the live pathogenic E. coli infection, in the human peripheral blood monocyte THP-1 cell lines, were comparatively analyzed to reveal antigenicities and immunobiological properties of T. gondii surface and secreted proteins. The transciptomic profiles induced by the isolated proteins were similar to those induced by the live bacterium infection, but were different from those induced by the live parasite infection. Contrary to the low cytokine secretion induced by the live parasite infection, the isolated proteins induced significant cytokine and chemokines secretion. Especially, the secretions of several chemokines induced by the isolated proteins were even higher than those induced by the live bacterium infection. These data suggested that T. gondii surface and secreted proteins were effective antigens, while the live parasite could evade the host innate immunity. This study comprehensively revealed the identities and antigenicities of T. gondii surface and secreted proteins, which laid foundation for further screening new T. gondii antigens, developing immunological diagnosis methods, and studying host immune response to T. gondii infection.
2017-09-20 | GSE103985 | GEO
Project description:Proteins are secreted from cells to send information to neighboring cells or distant tissues. Because of the highly integrated nature of energy balance systems, there has been particular interest in myokines and adipokines. These are challenging to study through proteomics because serum or plasma contain highly abundant proteins that limit the detection of proteins with lower abundance. We show here that extracellular fluid (EF) from muscle and fat tissues of mice show a different protein composition than either serum or tissues. Mass spectrometry analyses of EFs from mice with physiological perturbations, like exercise or cold exposure, allowed quantification of many potentially novel myokines and adipokines. Using this approach, we identify prosaposin as a secreted product of muscle and fat. Prosaposin expression stimulates thermogenic gene expression and induces mitochondrial respiration in primary fat cells. These studies together illustrate the utility of EF isolation as a discovery tool for adipokines and myokines.
2023-01-20 | GSE216094 | GEO
Project description:This project aims at identifying secreted proteins that modulate plant immunity from Ustilaginoidea virens, which infects rice panicles and is the causal agent of rice false smut (RFS). The identified proteins will be expressed in plant and test whether they can induce cell death, induce plant immunity or suppress plant immunity.
2021-04-23 | PXD024541 | Pride