Project description:Combined script for the generation of images within paper. Three experiments in total 1) Phosphopeptide enrichment of Three biological replicates of each condition (uninfected, WT infected , detla NleH1 NleH2 infected, pNleH1 infected and pNleH2 infection) 2) Total proteome analysis to complement phosphoproteomic study aimed at identifying the substrate of NleH1/2 3) In vitro assays of EPS8 with catalytically active and inactive NleH1 and NleH2.
Project description:dKDM4A is a Drosophila H3 K9/K36 me2/me3 demethylase, which has been disrupted here by P-element insertion. We compare whole-genome ChIP-chip in mutant and WT to look for target genes of dKDM4A.
Project description:dKDM4A is a Drosophila H3 K9/K36 me2/me3 demethylase, which has been disrupted here by P-element insertion. We compare whole-genome ChIP-chip in mutant and WT to look for target genes of dKDM4A. Two samples, WT and dkDM4A mutant. 2 biological replicates each. 2 arrays.
Project description:Aims: To compare the transcriptional profiles of an AtHAP5 (AtNF-YC, AtCBF-C) triple mutant vs. a Constans mutant. Background Information on Mutants: AtHAP5 triple mutant created by cross between the following SALK TDNA inserts: SALK_034838, SALK_058903, SALK_032163; these correspond to At1G54830, At1G08970, At5G63470, respectively. co-SAIL TDNA insertion SAIL_24_H04 corresponds to AT5G15840. Tissue: Above-ground whole plants grown for 10 days, under 16 hr light 8 hrs dark at constant 22C. Tissue collected 14 hrs after lights on. RT-PCR analysis on test RNA confirmed FT levels reduced in mutants lines compared to wild-type.
Project description:An analysis of purified Cx32 wt, W3S and R22G mutations. The three different proteins were expressed, digested and measured in DIA.
Project description:Transcriptional profiling of Arabidopsis comparing wild type with vim1,2,3 triple mutant to investigate epigenetic function of VIM family genes
Project description:Aims: To compare the transcriptional profiles of an AtHAP5 (AtNF-YC, AtCBF-C) triple mutant vs. a Constans mutant. Background Information on Mutants: AtHAP5 triple mutant created by cross between the following SALK TDNA inserts: SALK_034838, SALK_058903, SALK_032163; these correspond to At1G54830, At1G08970, At5G63470, respectively. co-SAIL TDNA insertion SAIL_24_H04 corresponds to AT5G15840. Tissue: Above-ground whole plants grown for 10 days, under 16 hr light 8 hrs dark at constant 22C. Tissue collected 14 hrs after lights on. RT-PCR analysis on test RNA confirmed FT levels reduced in mutants lines compared to wild-type. 9 samples were used in this experiment.
Project description:Ferric uptake regulator (Fur) is the major regulator of iron acquisition in Escherichia coli and other bacteria. In the present study, the role of Fur in anaerobic S. enterica serovar Typhimurium was determined by transcriptome analysis, reporter assays, and enzymatic assays. In anaerobic Δfur, 298 genes were differentially expressed. In general, Fur repressed genes required for iron acquisition/storage, metabolism, electron transport, oxidative/nitrosative stress, and modulators of virulence. There were 73 genes whose expression required Fur, eleven of which contain a putative Fur box 5‟ of the gene. Transcription of sodA was >9-fold higher in Δfur but there was no corresponding increase in the activity of SodA.
Project description:Background: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that must successfully adapt to the broad fluctuations in the concentration of dissolved dioxygen encountered in the host. In Escherichia coli, ArcA (Aerobic Respiratory Control) helps the cells to sense and respond to the presence of dioxygen. The global role of ArcA in E. coli is well characterized; however, little is known about its role in anaerobically grown S. Typhimurium. Results: We compared the transcriptional profiles of the virulent wild-type (WT) strain (ATCC 14028s) and its isogenic arcA mutant grown under anaerobic conditions. We found that ArcA directly or indirectly regulates 392 genes (8.5% of the genome); of these, 138 genes are poorly characterized. Regulation by ArcA in S. Typhimurium is similar, but distinct from that in E. coli. Thus, genes/operons involved in core metabolic pathways (e.g., succinyl-CoA, fatty acid degradation, cytochrome oxidase complexes, flagellar biosynthesis, motility, and chemotaxis) were regulated similarly in the two organisms. However, genes/operons present in both organisms, but regulated differently by ArcA in S. Typhimurium included those coding for ethanolamine utilization, lactate transport and metabolism, and succinate dehydrogenases. Salmonella-specific genes/operons regulated by ArcA included those required for propanediol utilization, flagellar genes (mcpAC, cheV), Gifsy-1 prophage genes, and a few SPI-3 genes (mgtBC, slsA, STM3784). In agreement with our microarray data, the arcA mutant was non-motile, lacked flagella, and was as virulent in mice as the WT. Furthermore, we identified a set of 120 genes whose regulation was shared with the anaerobic redox regulator, Fnr. Conclusion(s): We have identified the ArcA regulon in anaerobically grown S. Typhimurium. Our results demonstrated that in S. Typhimurium, ArcA serves as a transcriptional regulator coordinating cellular metabolism, flagella biosynthesis, and motility. Furthermore, ArcA and Fnr share in the regulation of 120 S. Typhimurium genes.
Project description:The PAQosome is composed of the HSP90/R2TP chaperone and a prefoldin-like module. It promotes the biogenesis of cellular machineries but it is unclear how it discriminates closely related client proteins. Among the main PAQosome clients are C/D snoRNPs and in particular their core protein NOP58. Using NOP58 mutants and proteomic experiments, we identify different assembly intermediates and show that C12ORF45, which we rename NOPCHAP1, acts as a bridge between NOP58 and PAQosome. NOPCHAP1 makes direct physical interactions with the CC-NOP domain of NOP58 and the RUVBL1/RUVBL2 AAA+ ATPases. Interestingly, NOPCHAP1 binds several RUVBL1/2 mutants except those unable to hydrolyze ATP. Moreover, while it robustly binds both yeast and human NOP58, it makes only weak interactions with NOP56 and PRPF31, two other closely related CC-NOP proteins. Transient expression of NOP58, but not NOP56 or PRPF31, is decreased in NOPCHAP1 KO cells. We propose that NOPCHAP1 is a client-loading PAQosome cofactor that select NOP58 to promote box C/D snoRNP assembly.