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Laboratory Evolution Experiments Help Identify a Predominant Site of ΔrnhA-dnaA Constitutive Stable DNA Replication Initiation

ABSTRACT: The study evaluated the effect of cSDR on gene expression by comparing the gene expression states in ΔrnhA-dnaA and evolved suppressor mutants

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE135706 | GEO | 2019/09/10

REPOSITORIES: GEO

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Laboratory Evolution Experiments Help Identify a Predominant Site of ΔrnhA-dnaA Constitutive Stable DNA Replication Initiation

Project description:Laboratory Evolution Experiments Help Identify a Predominant Site of ΔrnhA-dnaA Constitutive Stable DNA Replication Initiation

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Laboratory Evolution Experiments Help Identify a Predominant Region of Constitutive Stable DNA Replication Initiation.

Project description: Not available

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Expression profiles of dnaA null, rok null, and dnaA null; rok null mutants

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Project description:Supporting data for Hottes et al., "DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus" The microarray component of this work monitors mRNA expression during the cell cycle of synchronized populations of Caulobacter crescentus cells. Transcription during the normal cell cycle is compared with transcription during a cell cycle where expression of dnaA, which encodes a key DNA replication initiation factor, is delayed. Keywords: time course, cell cycle, metabolism

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Structures reveal DnaA domain I dimer conserved across Actinomycetes: implications for replication initiation

Project description:DNA replication is a fundamental process in biology with initiation marking its key, first step. In bacteria, DNA replication is initiated by the DnaA protein. DnaA exhibits multidomain architecture, consisting of an N-terminal domain I, linker region, AAA+ family ATPase cassette, and C-terminal DNA-binding motif. Taxon-specific regulatory functions are primarily coordinated by the DnaA domain I, which exhibits substantial sequence variation across bacteria. Notably, although the DnaA domain I has been shown to be essential, its contributions to initiation are not completely understood. Importantly, studies have indicated a role for DnaA domain I dimerization in the cooperative assembly of the initiation complex at the origin. However, the mechanism(s) and molecular basis of DnaA domain I dimerization have proved elusive. Here, we report structures of the DnaA domain I from ten Actinobacterial species. Strikingly, all structures reveal the same, unique dimer, and key elements which support DnaA domain I self-interaction are broadly conserved across the class Actinomycetes. Further, a suite of biochemical oligomerization assays and HDX-MS studies support the structural dimer. These findings suggest weak dimerization, as mediated by the DnaA domain I, acts a fine-tuned trigger in cooperative oriC assembly and that this is a broadly conserved biological mechanism for replication initiation in the class Actinomycetes.

2026-05-27 | PXD074705 | Pride

Expression profiles of dnaA null, rok null, and dnaA null; rok null mutants

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).

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Project description: Not available

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Project description:DNA replication initiation is orchestrated in bacteria by the replication initiator DnaA. Two models for regulation of DnaA activity in Escherichia coli have been proposed: the switch between an active and inactive form and the titration of DnaA on the chromosome. Although proposed decades ago, experimental evidence of a titration-based control mechanism is still lacking. Here, we first identified a conserved high-density region of binding motifs near the origin of replication, an advantageous trait for titration of DnaA. We then investigated the mobility of DnaA by visualising single proteins inside single cells of wild-type and deletion mutants E. coli strains, while monitoring cellular size and DNA content. Our results indicate that the chromosome of E. coli controls the free amount of DnaA in a growth rate-dependent fashion. Moreover, they address long-standing questions on the relevance of DnaA titration in stabilising DNA replication by preventing re-initiation events during slow growth.

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