Not just an alternative nitrogenase: The Fe-nitrogenase system belongs to the NifA regulon in Rhodobacter capsulatus
ABSTRACT: The diazotrophic bacterium Rhodobacter capsulatus synthesizes a molybdenum nitrogenase and an alternative iron-only nitrogenase, enabling growth with molecular dinitrogen as sole nitrogen source. Regulation of nitrogen fixation was analyzed by proteome profiling of wild-type and mutant strains lacking the transcriptional regulators NifA, AnfA, and MopAB.
Project description:The diazotrophic bacterium Rhodobacter capsulatus is able to synthesize two nitrogenases, a molybdenum-dependent and an alternative Mo-free iron-only nitrogenase, enabling growth with molecular dinitrogen (N2) as sole nitrogen source. The Mo response of the wild type and a mutant lacking the high-affinity molybdate transporter, ModABC, were analyzed by proteome profiling.
Project description:Chelocardin is an atypical tetracycline and its mechanism of action is discussed controversially in literature. Therefore, we analyzed the bacterial response of Bacillus subtilis to chelocardin and as a control for classical tetracyclines to tetracycline by proteomic profiling. The induced marker proteins mirror the damage in the cell due the antibiotic stress. Proteomic profiling was carried out by 2D-PAGE and spot identification by nUPLC-ESI-MS/MS. The proteomic profile of chelocardin demonstrates a dual mechanism of action with protein biosynthesis inhibition and membrane damage.
Project description:Based on UPLC-Q-TOF-MS metabolomics technology, urine samples of 1072 subjects from 9 centers, including normal control, phlegm and blood stasis (PBS) syndrome and Qi and Yin deficiency (QYD) syndrome, and other syndromes of CHD, were conducted to find biomarkers. Among them, the discovery set (n = 125) and the test set (n = 337) were used to identify and validate biomarkers, and the validation set (n = 610) was used for the application and evaluation of the support vector machine (SVM) prediction model.
Project description:Recent studies have shown that Pelagibacter oxidize a wide range of one carbon (C1) and methylated compounds that are ubiquitous in the oceans. However, the metabolic pathways used to oxidize and assimilate these compounds are complex and have been only partly described. To understand the metabolism of these compounds in Pelagibacter and to identify candidate genes involved in these pathways, we used microarray to study changes in gene expression in response to five different compounds (trimethylamine N-oxide (TMAO), methylamine, dimethylsulfoniopropionate (DMSP), methanol, and glycine betaine (GBT)) in Pelagibacter strain HTCC1062. This project will examine the transcriptional response of the marine microorganism Pelagibacter HTCC1062 to five methylated compounds. To do this, 18 flasks were innoculated with cells - 3 flasks without any methylated compounds and rest of 15 treated with different methylated compounds respectively (TMAO (trtmA), methylamine (trtmB), DMSP (trtmC), methanol (trtmD) and glycine betaine (trtmE)). Cells were all harvested at the same timepoint in the exponential phase.
Project description:Comparison at two different timepoints of expression profiles of wild_type Bacillus and a deletion mutant of the PlcR regulator. Additional processed data can be found in the FTP directory for this experiment <a href="ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-1472/">ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-1472/</a>
Project description:Transcriptome analysis was used to investigate the global stress response of the Gram-positive bacterium Bacillus subtilis caused by overproduction of the well-secreted AmyQ α-amylase from Bacillus amyloliquefaciens. Analyses of the control and overproducing strains were carried out at the end of exponential growth and in stationary phase, when protein secretion from B. subtilis is optimal. Among the genes that showed increased expression were htrA and htrB, which are part of the CssRS regulon that responds to high-level protein secretion and heat stress. The analysis of the transcriptome profiles of a cssS mutant compared to the wild-type, under identical secretion stress conditions, revealed several genes with altered transcription in a CssRS-dependent manner, for example citM, ylxF, yloA, ykoJ and several genes of the flgB operon. However, a high affinity CssR-binding was only observed for htrA and htrB, and possibly for citM. In addition, the DNA macroarray approach reveal that several genes of the sporulation pathway are downregulated by AmyQ overexpression, and a group of motility-specific (σD-dependent) transcripts were clearly upregulated. Subsequent flow cytometric analyses demonstrate that upon overproduction of AmyQ as well as a non-secretable variant of the α-amylase, the process of sporulation is severely inhibited. The same experiments were implemented to investigate the expression levels of the hag promoter, a well-established reporter for σD-dependent gene expression. This approach confirmed the observations based on our DNA macroarray analyses and led us to conclude that expression levels of several genes involved in motility are maintained at high levels under all conditions of α-amylase overproduction. Secretion stress was applied by overproducing the well-secreted AmyQ α-amylase (pKTH10 vector) from B. amyloliquefaciens. Besides examining secretion stress in wild-type cells, we compared transcriptome profiles of a cssS mutant strain under conditions of high-level AmyQ production. Samples for transcriptome analyses were collected at the late exponential growth stage (one hour before the transition point) and 3 hours upon entry in the stationary growth phase. Three independent cultures of each strain were used and cells were sampled for macroarray experiments. Duplicate spots were averaged in Array-Pro software (Media Cybernetics, Inc.) and the signal was normalized after background subtraction by calculation of the percentage of total signal per gene using Microsoft Excel.
Project description:Bio-active peptides are involved in the regulation of most if not all physiological processes in the body. Classical bio-active peptides (CBAPs) are mostly cleaved from a larger precursor protein and stored in secretion vesicles from which they are released in the extracellular space to exert there (signaling) activity. Only recently, another non-classical type of bio-active peptides (NCBAPs) is being discovered. These typically are not secreted but instead appear to be translated from short open reading frames (sORF) and released directly into the cytoplasm. In contrast to CBAPs, they appear to be involved in the regulation of intra-cellular processes such as transcriptional control, calcium handling and DNA repair. However, bio-chemical evidence for the translation of these sORFs remains elusive. Comprehensive analysis of these sORF-encoded polypeptides (SEPs) by peptidomic approach is hampered by a number of methodological and biological challenges: the low molecular mass of SEPs (many are in the range of 4-10 KDa), their low abundance, their transient expression and many complications in data analysis to confidently identify these peptides. In this study, we developed a strategy to address these issues as much as possible. Since translation of these predicted sORFs is still controversial, our data-analysis strategy is aimed not to maximize the number of identifications but rather to exclude as much as possible false positive identifications. Applying this strategy to a mouse brain striatum sample, we identified 981 neuropeptides originated from 50 known (neuro)peptide precursors, demonstrating the sensitivity of the method applied. In addition, five SEPs were identified including NoBody, a SEP that was previously discovered in humans and four novel SEPS from 5’ untranslated transcript regions (UTRs).
Project description:It was analyzed whole genome microarray data to describe the changes in gene transcription profile in human MCF-7 cancer cells under the influence of fatty acid extracts from CLA-enriched and non-enriched egg yolks.Those results might be found useful in assessing the application of CLA-enriched egg as a nutraceutics in cancer prevention. Six-condition experiment: CLA, KT, cis9,trans11-CLA, trans10,cis12-CLA, KT+cis9,trans11-CLA and KT+trans10,cis12-CLA vs MCF-7 adenocarcinoma cell line. Two control of expreriment. Three biological replicates and three technical replicates.