Cell cycle-associated expression patterns predict gene function in mycobacteria
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ABSTRACT:
ORGANISM(S): Mycobacterium tuberculosis
PROVIDER: GSE147345 | GEO | 2020/08/31
REPOSITORIES: GEO
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Project description:Purified NK cells were co-cultured with M. bovis BCG or M. tuberculosis H37Rv (1:1) in the presence of IL-2 (100U/ml) or IL-12 (10pg/ml) for 24h before trizol extraction. We used microarrays to detail the global gene expression underlying NK cell activation by mycobacteria.
2011-07-27 | GSE30950 | GEO
Project description:Purified NK cells were co-cultured with M. bovis BCG or M. tuberculosis H37Rv (1:1) in the presence of IL-2 (100U/ml) or IL-12 (10pg/ml) for 24h before trizol extraction. We used microarrays to detail the global gene expression underlying NK cell activation by mycobacteria. NK cell were isolated from the blood of 6 independent donors and activated with different mycobacteria and cytokines in order to study their transcriptional profiles according to mycobacterial virulence.
2011-07-26 | E-GEOD-30950 | biostudies-arrayexpress
Project description:During cytokinesis in the budding yeast Saccharomyces cerevisiae, contraction of the cytokinetic ring and primary septum synthesis by chitin synthase II (Chs2p) are coupled processes. Myosin II (Myo1p), is involved in the actomyosin ring formation, required for proper cytokinesis, while Chs2p is responsible for the chitin primary septum formation which is necessary to stabilize the cytokinetic ring during its contraction. Morphological phenotypes of myo1∆ and chs2∆ mutants are therefore similar particularly in that both are unable to complete normal cytokinesis. A comparison between the global mRNA transcription profiles of myo1∆ and chs2∆ strains was conducted using oligonucleotide microarrays to establish if these cytokinesis mutants exhibited similar mRNA expression patterns and signature profiles were later generated from gene set enrichment analysis (GSEA). Genetic experiments were conducted to further test predictions based on the GSEA results. As reported previously in myo1∆ strains, a significant number of protein biosynthesis and RNA processing genes that may be attributed to regulation by cell integrity pathway(s) were also down-regulated in the chs2∆ strain. Genes coding for proteins involved in autophagy were coordinately upregulated only in the chs2∆ strain yet an ATG9 genetic knockout that completely blocks autophagy was viable in chs2∆ and myo1∆ genetic backgrounds.. However, the chs2∆ strain was significantly more susceptible to lysis by B-1,3-glucanase than myo1∆ and fks1 control strains. We interpret this result to indicate that these two cytokinesis mutant strains possess different cell wall properties. This interpretation was further supported by the observation that Slt2p hyperphosphorylation was detected in the chs2∆ strain yet expression of SLT2 was not required for cell viability. We conclude that in contrast to myo1∆ strains, chs2∆ strains do not activate the cell integrity pathway.
2009-05-21 | GSE12994 | GEO
Project description:Escherichia coli coordinates replication and division cycles by initiating replication at a narrow range of cell sizes. By tracking replisomes in individual cells through thousands of division cycles in wild-type and mutant strains, we were able to compare the relative importance of previously described control systems. We found that accurate triggering of initiation does not require synthesis of new DnaA. The initiation size increased only marginally as DnaA was diluted by growth after dnaA expression had been turned off. This suggests that the conversion of DnaA between its active ATP- and inactive ADP-bound states is more important for initiation size control than the total free concentration of DnaA. In addition, we found that the known ATP/ADP-converters DARS and datA compensate for each other, although the removal of them makes the initiation size more sensitive to the concentration of DnaA. Only disruption of the regulatory inactivation of DnaA (RIDA) mechanism had a radical impact on replication initiation. This result was corroborated by the finding that termination of one round of replication correlates with the next initiation at intermediate growth rates, as would be the case if RIDA-mediated conversion from DnaA-ATP to DnaA-ADP abruptly stops at termination and DnaA-ATP starts accumulating.
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Project description:To identify potential targets of co-regulation by DnaA and Rok, we compared the transcriptional profiles of dnaA null, rok null, and dnaA null rok null mutants. Because a dnaA null mutant requires an oriC- strain background, we used an oriC- oriN+ background for all strains, to allow direct comparisons.
2015-06-13 | GSE69788 | GEO
Project description:To identify potential targets of co-regulation by DnaA and Rok, we compared the transcriptional profiles of dnaA null, rok null, and dnaA null rok null mutants. Because a dnaA null mutant requires an oriC- strain background, we used an oriC- oriN+ background for all strains, to allow direct comparisons. We compared biological triplicates for each of the following strains: dnaA null (CAL2074), rok null (CAS196), dnaA null rok null (CAS192), and dnaA+ rok+ (CAL2083; control).
2015-06-13 | E-GEOD-69788 | biostudies-arrayexpress
Project description:Initiation of DNA replication requires binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. In low G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB are also required to load the replicative helicase outside of oriC during replication restart, in a DnaA-independent manner. DnaA also binds to many sites around the chromosome, outside of oriC, and acts as a transcription factor at several of these. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in vivo in Bacillus subtilis. This association was dependent on DnaA and the order of recruitment was the same as that at oriC, but was independent of a functional oriC. The presence of DnaD and DnaB at the secondary (non-oriC) targets of DnaA in the absence of helicase loading indicates a possible role for DnaD and DnaB in modulating the activity of DnaA.
2010-12-07 | GSE23686 | GEO
Project description:Initiation of DNA replication requires binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. In low G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB are also required to load the replicative helicase outside of oriC during replication restart, in a DnaA-independent manner. DnaA also binds to many sites around the chromosome, outside of oriC, and acts as a transcription factor at several of these. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in vivo in Bacillus subtilis. This association was dependent on DnaA and the order of recruitment was the same as that at oriC, but was independent of a functional oriC. The presence of DnaD and DnaB at the secondary (non-oriC) targets of DnaA in the absence of helicase loading indicates a possible role for DnaD and DnaB in modulating the activity of DnaA. The genome-wide binding profiles of DnaA, DnaD, DnaB and DnaC were determined. Binding profiles were determined in exponentially growing cells with and without HPUra treatment. Three biological replicates were analyzed per protein/treatment (one per array). Enrichment in immunoprecipitated samples versus total genomic DNA were determined.
2010-12-07 | E-GEOD-23686 | biostudies-arrayexpress
Project description:The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.
2010-06-12 | GSE22296 | GEO