Comparison of gene expression in M. tuberculosis TrxB2-DUC mutant treated or not with atc
ABSTRACT: M. tuberculosis thioredoxin reductase (TrxB2) is essential for bacterial survival in vitro and in vivo. To gain insight into the mechanisms underlying lethality caused by TrxB2 depletion, we compared the mRNA profiles of TrxB2-DUC mutant in the presence and absence of atc. We grew bacteria in 7H9 medium to an OD of 0.5~0.6 and then added atc to a final concentration of 400ng/ml. Samples were collected 6 h and 24 h after atc treatment.
Project description:M. tuberculosis thioredoxin reductase (TrxB2) is essential for Mtb physiology and pathogenesis. To gain insight into its biological functions, we generated the TrxB2-TetON-tetO mutants, in which TrxB2 is partially depleted in the absence of atc without impairing bacterial viability. We grew TrxB2-TetON-tetO-WT in 7H9 medium with 400 ng/ml atc, until the OD reached 0.5~0.6. Then Mtb was washed with 7H9 medium 3 times and suspended in 7H9 medium with or without atc. Then samples were taken 24, 48, 72 and 120 hrs later.
Project description:M. tuberculosis thioredoxin reductase (TrxB2) is essential for bacterial survival in vitro and in vivo. To gain insight into the pathways dependent on TrxB2, we compared the mRNA profiles of TrxB2-DUC mutant in the presence and absence of atc and DTT. We grew bacteria in 7H9 medium to an OD of 0.5~0.6. We then added atc to a final concentration of 800 ng/ml and DTT to a final concentration of 2 mM. Samples were collected 24 hr after treatment.
Project description:Transcriptional profiling of Mycobacterium smegmatis comparing a strain undergoing I-SceI generated DNA damage at a single genomic locus versus a control strain with no I-SceI recognition sequence in its genome (and thus not undergoing double strand DNA breaks Gene designations are from the original annotation, not the updated Five conditions investigated: Log phase cultures without induction of I-SceI expression (T=0, -Atc), Log phase cultures induced to express I-SceI by the addition of ATc for 45 minutes (T=45, +ATc), Stationary cultures control without induction of I-SceI expression (T=0, -Atc), Stationary phase cultures induced to express I-SceI by the addition of ATc for 15 minutes (T=15, +ATc), and Stationary cultures induced to express I-SceI for 45 minutes by the addition of ATc (T=45, +ATc). 3 biological replicates of each strain for each experiment.
Project description:In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine-containing protein, HPr) binds to operator sites called catabolite responsive elements, cre. Depending on the cre box position relative to the promoter, the CcpA/HPr-Ser-P complex can either act as a positive or a negative regulator. The cre boxes are highly degenerate semi-palindromes with a lowly conserved consensus sequence. So far, studies aimed at revealing how CcpA can bind such diverse sites were focused on the analysis of single cre boxes. In this study, a genome-wide analysis of cre sites was performed in order to identify differences in cre sequence and position, which determine their binding affinity. The transcriptomes of B. subtilis cultures with three different CcpA expression levels were compared. The higher the amount of CcpA in the cells, the more operons possessing cre sites were differentially regulated. The cre boxes that mediated regulation at low CcpA levels were designated as strong (high affinity) and those which responded only to high amounts of CcpA, as weak (low affinity). Differences in the sequence and position in relation to the transcription start site between strong and weak cre boxes were revealed. Certain residues at specific positions in the cre box as well as, to a certain extent, a more palindromic nature of cre sequences and the location of cre in close vicinity to the transcription start site contribute to the strength of CcpA-dependent regulation. The main factors contributing to cre regulatory efficiencies, enabling subtle differential control of various subregulons of the CcpA regulon, are identified. Bacillus subtilis strain MP902 [strain MP901 (Ptet-ccpA, KmR) carrying pWH119 (Pxyl-tetR, EmR)] was grown in presence of three different concentrations of Ptet inducer, anhydrotetracycline (ATc), leading to three levels of ccpA expression induction. The control culture was grown in absence of ATc. The total RNA for transcriptome analyses was isolated at OD600 = 0.8 from 16 ml culture. Three independent cultures of each strain (target strains and controls) were used, and cells were sampled for microarray experiment.
Project description:BACKGROUND: Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. RESULTS: We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. CONCLUSIONS: We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-143]
Project description:Background: The CRISPR/Cas9 toolbox has recently been expanded to include approaches for modulating gene expression. To successfully build on this work, and apply it for answering biological questions, it is important to establish it in a broad range of circumstances. Genome-scale CRISPR interference (CRISPRi) has been used in human cells lines, however the rules for designing effective guide RNAs (gRNAs) in different organisms are not well known. We sought to determine rules that determine gRNA effectiveness at transcriptional repression in Saccharomyces cerevisiae. Results: We created an inducible single plasmid CRISPRi system for gene repression in yeast, and used it to analyze fitness effects of gRNAs under 18 small molecule treatments. Our approach correctly identified previously-described chemical-genetic interactions, as well as a new mechanism of suppressing fluconazole toxicity by repression of the ERG25 gene. Assessment of multiple target loci across treatments allowed us to determine generalizable features associated with gRNA efficacy. Guides that target regions with low nucleosome occupancy and high chromatin accessibility were clearly more effective. We also found the best region to target gRNAs was between the transcription start site (TSS) and 200bp upstream of the TSS. Finally, unlike nuclease-proficient Cas9 in human cells, point mutations were tolerated equally well by truncated (18 nt specificity sequence) and full length (20 nt) gRNAs, however, 18 nt gRNAs were generally less potent than full length gRNAs. Conclusions: Our results establish a powerful functional genomics screening method, provide rules for designing effective gRNAs for gene repression, and show that 18 nt and 20 nt gRNAs exhibit similar tolerance to mismatches in the target sequence. These findings will enable effective library design and genome-wide screening in many genetic backgrounds. An expression construct was created for inducible CRISPRi in yeast. Key features include ORFs expressing dCas9-Mxi1 and the tetracycline repressor (TetR), as well as a tetracycline inducible gRNA locus containing the RPR1 promoter with a TetO site, a NotI site for cloning new gRNA specificity sequences, and the constant part of the gRNA. When yeast containing this plasmid are grown in the absence of anhydrotetracycline (ATc) TetR binds the gRNA promoter and prevents PolIII from binding and transcribing the gRNA. This in turn prevents dCas9-Mxi1 from binding the target site. In the presence of ATc, TetR dissociates and gRNA is expressed, allowing dCas9-Mxi1 to bind its target locus, and repress gene expression. gRNA libraries were cloned into this construct and transformed into yeast to create pools. Experiments were conducted in which yeast pools were grown in inducing (+ATc) and non-inducing conditions (-ATc) in the presence of different drugs. After multiple generations of growth in these conditions, yeast plasmids were minipreped and the gRNA locus was PCRed and sequenced via MiSeq. Counts of each gRNA were compared in different conditions.
Project description:During aging, the kidney undergoes functional and physiological changes that are closely affiliated with chronic kidney disease (CKD). There is increasing evidence supporting the role of lipid or lipid-derived mediators in the pathogenesis of CKD and other aging-related diseases. To understand the role of lipids in various metabolic processes during kidney aging, we conducted MALDI imaging mass spectrometry (MALDI-IMS) analysis in kidneys harvested from young (2 months old, n=3) and old mice (24 months old, n=3). MALDI-IMS analysis showed an increase in ceramide level and a decrease in sphingomyelin (SM) and phosphatidylcholine (PC) levels in kidneys of old mice. The increased expression of cPLA2 and SMPD1 protein in aged kidney was confirmed by immunohistochemistry and western blot analysis. Our MALDI-IMS data showed the altered distribution of lipids in aged kidney as indicative of aging-related functional changes of the kidney. Combined analysis of MALDI-IMS and IHC confirmed lipidomic changes and expression levels of responsible enzymes as well as morphological changes.
Project description:Transcriptional profiling of Mycobacterium smegmatis comparing strains undergoing I-SceI generated DNA damage at a single genomic locus Gene designations are the updated annotation Four comparisons were made, all with log phase cultures and no ATc added. Darr Site(+) with an empty vector compared to wild-type M. smegmatis Site(+), Darr Site(+) with a vector expressing WT Arr compared to wild-type M. smegmatis Site(+), Darr Site(+) with a vector expressing ArrH18A compared to wild-type M. smegmatis Site(+), Darr Site(+) with a vector expressing Arr D83A compared to wild-type M. smegmatis Site(+). 3 biological replicates of each strain for each experiment.
Project description:We have created a global map of the effects of polymorphism on gene expression in 550 children from families recruited through a proband with atopic dermatitis. We genotyped >300,000 SNPs and identified expression quantitative trait loci from measurements of 16,487 probes representing 15,576 genes in Epstein-Barr virus¨Ctransformed lymphoblastoid cell lines. We executed genome-wide association scans for these traits.