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Allosteric activation mechanism of DriD, a WYL-domain containing transcription regulator

ABSTRACT: This project aims to understand the ssDNA-mediated allosteric activation mechanism of DriD, a novel Caulobacter crescentus transcription activator. Using LC-MS/MS, the major proteolytic cleavage site within DriD was identified, providing insight into its solvent accessible regions.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Caulobacter Vibrioides

SUBMITTER: Emily Cannistraci

LAB HEAD: Maria A Schumacher

PROVIDER: PXD062430 | Pride | 2025-04-14

REPOSITORIES: Pride

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			Action	DRS
	10346_021524.sf3	Other
	ID111698_01_FSN20560_10346_021424.raw	Raw
	ID111699_01_FSN20560_10346_021424.raw	Raw
	ID111700_01_FSN20560_10346_021424.raw	Raw
	ID111701_01_FSN20560_10346_021424.raw	Raw

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Contribution of ShkA dysregulation to the cdG0 phenotype

Project description:The ShkA-ShpA-TacA phosphorelay regulates stalk biogenesis and G1-S phase transition in Caulobacter crescentus. Histidine kinase activity of ShkA is c-di-GMP dependent and a strain lacking c-di-GMP (cdG0) shows a number of phenotypic aberrations. In this project, we aim at disentangling the contribution of ShkA-ShpA-TacA pathway dysregulation to the cdG0 phenotype by profiling the proteomes of mutants that constitutively activate or deactivate TacA target gene expression.

2019-12-16 | PXD012739 | Pride

Identification of substrates of LarA-activated Lon protease and Identification of Lon protease interactome

Project description:With this analysis we aim to identify proteins that are substrates of LarA-activated Lon protease in Caulobacter crescentus. We will compare samples of wild type cells either harboring an empty vector (vector control, VC) or overexpressing 3xFLAG-tagged LarA (F-LarA). Based on our previous data we hypothesize that proteins affected by LarA-overexpression which results in Lon protease activation will decrease in levels compared to the vector control sample. The aim of this analysis is the identification of the interactome of the Lon protease in Caulobacter crescentus. It is a follow-up analysis of a project in which we were looking for novel substrates of the Lon protease in Caulobacter crescentus. To narrow down the list of potential substrates we obtained through the first analysis, we have purified the protease (Lon WT) as well an inactive TRAP mutant and interacting proteins using a Twin-Strep-tag (Iba lifesciences). As a control, a cell lysate without Strep-tag containing protein was included in the purification set-up. The aim is to identify the proteins that specifically interact with the Lon protease by mass spectrometry.

2023-10-25 | PXD036514 | Pride

Caulobacter crescentus starved for carbon

Project description:This SuperSeries is composed of the following subset Series: GSE25996: Expression data from Caulobacter crescentus starved for carbon GSE25997: Expression data from Caulobacter crescentus (syn. C. vibrioides) swarmer and stalked cells starved for carbon GSE25998: Expression data from WT, DSigT and DSigU Caulobacter crescentus (syn. C. vibrioides) starved for carbon Refer to individual Series

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Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (ChIP-seq)

Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism. An allele of phoB bearing a C-terminal 3x-flag tag was integrated at its native locus, and ChIP followed by deep sequencing on Illumina MiSeq was performed on samples grown in rich medium, phosphate-limited medium, and in a pstS::Tn5 mutant background in rich medium.

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Expression analysis of Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) [DccrM] vs Caulobacter crescentus NA1000 wild type [WT]

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2014-01-08 | E-GEOD-52375 | biostudies-arrayexpress

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Project description:The goal of this study was to measure the effects of nitric oxide exposure (using DETA NONOate as a nitric oxide donor) on transcription in Caulobacter. Untreated Caulobacter crescentus were grown to a density of 0.3 (at OD660) in PYE medium (pH 7) in rolled culture tubes. DETA-NONOate treated Caulobacter crescentus were grown to a density of 0.3 (at OD660), and then treated with 100 mM DETA NONOate for 30 minutes.

2010-06-20 | E-GEOD-21139 | biostudies-arrayexpress

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Project description:Influence of the Heme Nitric Oxide / Oxygen Binding Protein (H-NOX) on cell cycle regulation in Caulobacter crescentus

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Expression analysis of Caulobacter crescentus NA1000 bearing a CCNA_00690 (cdnL) deletion [dcdnL] vs Caulobacter crescentus NA1000 wild type [wt]

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Expression analysis of Caulobacter crescentus NA1000 Plac::CCNA_00382 (ccrM) vs Caulobacter crescentus

Project description:Investigation of whole genome gene expression level changes in a Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain cause the CcrM DNA methyltransferase to be overexpressed and the chromosome to be constitutively methylated at the adenine at GANTC motifs. References of strains: CcrMOE: Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. A six chip study using total RNA recovered from three separate wild-type cultures of Caulonacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive. Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.

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2020-02-06 | PXD015525 | Pride

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