The WOPR protein Ros1 is a master regulator of sporogenesis and effector gene expression in the maize pathogen Ustilago maydis
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ABSTRACT:
ORGANISM(S): Ustilago maydis
SUBMITTER: Marie Tollot
PROVIDER: E-GEOD-76231 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Goals: characterization of the transcription factor Ros1 in Ustilago maydis Methods: generation of deletion mutants, microscopic observations, ectopic expression of ros1, identification of Ros1 regulated genes by RNAseq and ChIP sequencing Results: Ros1 is not involved in plant colonization but is essential to trigger sporogenesis during late stages of infection. Premature expression of ros1 revealed that Ros1 counteracts the b-dependent filamentation program and induces morphological alterations resembling the early steps of sporogenesis. Transcriptional profiling and ChIP seq analyses revealed that Ros1 affects the expression of about 30 % of all U. maydis genes with 40% being direct targets. Cell wall remodeling and plasma membrane modifications are among the processes affected by Ros1 dependent regulation. Interestingly a large number of b-dependent genes including transcription factors and effector genes involved in biotrophy establishment were downregulated by Ros1 while a subset of novel â??late effectorsâ?? were upregulated. Taken together our results indicate that Ros1 is a master regulator of sporogenesis in U. maydis and that the switch to sporogenesis is accompanied by the differential regulation of 75% of the effector genes. 4 samples were analyzed in triplicate. The first two samples correspond to input and output DNA obtained from ChIP carried out on plant material infected with U. maydis strains expressing Ros1 with an HA tag. The other two other samples correspond to input and output DNA from ChIP carried out on plant material infected with U. maydis strains expressing Ros1 without a tag (control samples).
2016-06-24 | E-GEOD-76230 | biostudies-arrayexpress
Project description:Goals: characterization of the transcription factor Ros1 in Ustilago maydis Methods: generation of deletion mutants, microscopic observations, ectopic expression of ros1, identification of Ros1 regulated genes by RNAseq and ChIP sequencing Results: Ros1 is not involved in plant colonization but is essential to trigger sporogenesis during late stages of infection. Premature expression of ros1 revealed that Ros1 counteracts the b-dependent filamentation program and induces morphological alterations resembling the early steps of sporogenesis. Transcriptional profiling and ChIP seq analyses revealed that Ros1 affects the expression of about 30 % of all U. maydis genes with 40% being direct targets. Cell wall remodeling and plasma membrane modifications are among the processes affected by Ros1 dependent regulation. Interestingly a large number of b-dependent genes including transcription factors and effector genes involved in biotrophy establishment were downregulated by Ros1 while a subset of novel â??late effectorsâ?? were upregulated. Taken together our results indicate that Ros1 is a master regulator of sporogenesis in U. maydis and that the switch to sporogenesis is accompanied by the differential regulation of 75% of the effector genes. Two samples corresponding to plant material infected with either U. maydis wild type strains FB1 x FB2 or the ros1 deletion strains FB1Dros1 x FB2Dros1 were analyzed in triplicate.
2016-06-24 | E-GEOD-76229 | biostudies-arrayexpress
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
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Project description:Urea can serve as nitrogen source for coral holobionts and plays a cruscial role in coral calcification, although the degradation of urea by coral symbionts is not fully understood. In this study, we investigated the urea utilized pathway and the responses of the Symbiodiniaceae family to urea under high temperature conditions. Genome screening revealed that all Symbiodiniaceae species contain the urease (URE) and DUR2 subunit of urea amidolyase (UAD) system. However, only three speciesCladocopium goreaui, Cladopium c92, and Symbiodinium pilosum possess a complete UAD system, including both DUR1 and DUR2. Phylogentic analyses revealed that the UAD system in Symbiodiniaceae clusters more closely with symbiotic bacteria, indicating that horizontal gene transfer of UAD system has occured in coral symbionts. Physiology analysis showed that the symbiodiniacean species Cladocopium goreaui, which containing both URE and UAD, grew better under urea than ammonium conditions, as indicated by higher maximum specific growth rates. Furthermore, most genes of Symbiodiniaceae involved in urea utilization appeared to be stable under various conditions such as heat stress (HS), low light density, and nitrogen deficiency, wheras in ammonium and nitrate transporters were significantly regulated. These relatively stable molecular regulatory properties support sustained urea absorption by Symbiodiniaceae, as evidenced by an increase in δ15N2-urea absorption and the decreases in δ5N-NO3-, and δ15N-NH4+ from cultural environment to Symbiodiniaceae under HS conditions. Token together, this study reveals two distinct urea utilization systems in coral ecosystem and highlights the importance of the urea cycle in coral symbionts when facing fluctuating nitrogen environment in future warming ocean.
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Project description:While insulin replacement therapy restores the health and prevents the onset of diabetic complications (DC) for many decades, some T1D patients have elevated hemoglobin A1c values suggesting poor glycemic control, a risk factor of DC. We surveyed the stool microbiome and urinary proteome of a cohort of 220 adolescents and children, half of which had lived with T1D for an average of 7 years and half of which were healthy siblings. Phylogenetic analysis of the 16S rRNA gene did not reveal significant differences in gut microbial alpha-diversity comparing the two cohorts. The urinary proteome of T1D patients revealed increased abundances of several lysosomal proteins that correlated with elevated HbA1c values. In silico protein network analysis linked such proteins to extracellular matrix components and the glycoprotein LRG1. LRG1 is a prominent inflammation and neovascularization biomarker. We hypothesize that these changes implicate aberrant glycation of macromolecules that alter lysosomal function and metabolism in renal tubular epithelial cells, cells that line part of the upper urinary tract.
2019-03-28 | PXD012413 | Pride
Project description:GalNAc-transferase (GalNAc-T) isoforms modify distinct subsets of the O-glycoproteome and GalNAc-type O-glycosylation is found on most proteins trafficking through the secretory pathway in metazoan cells. The O-glycoproteome is regulated by up to 20 polypeptide GalNAc-Ts and the contributions and biological functions of individual GalNAc-Ts are poorly understood. Here, we used a zinc-finger nuclease (ZFN)-directed knockout strategy to probe the contributions of the major GalNAc-Ts (GalNAc-T1 and T2) in liver cells, and explore how the GalNAc-T repertoire quantitatively affects the O-glycoproteome. We demonstrate that the majority of the O-glycoproteome is covered by redundancy, whereas distinct subsets of substrates are modified by non-redundant functions of GalNAc-T1 and T2. Differential transcriptomic analysis indicates that loss of function of a GalNAc-T induces specific transcriptional response. The non-redundant O-glycoproteome subsets for and the transcriptional responses for each isoform appeared to be related to different cellular processes, and for the GalNAc-T2 isoform supporting a role in lipid metabolism. The results demonstrate that GalNAc-Ts have non-redundant glycosylation functions, and that these may affect distinct cellular processes. The data provides a comprehensive resource for unique substrates for individual GalNAc-Ts. Our study provides a new view on the regulation of the O-glycoproteome, suggesting that the plurality of GalNAc-Ts arose to regulate distinct protein functions and cellular processes.
2015-08-21 | PXD002770 | Pride
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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