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A rendezvous of two second messengers: The c-di-AMP receptor protein DarB controls (p)ppGpp synthesis in Bacillus subtilis

ABSTRACT: DarB is a cyclic di-AMP binding protein consisting of two CBS (Cystathionine-beta synthase) domains. To reveal the global role of the second-messenger, understanding the function of the receptor proteins is fundamental. In order to do so, we aimed to identify potential binding partners of DarB in vitro with an unbiased protein pulldown experiment. In this study, we identified the (p)ppGpp synthetase/ hydrolase RelA as the binding partner of DarB and could confirm these findings with an in vivo interaction experiment.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Bacillus Subtilis Subsp. Subtilis Str. 168

SUBMITTER: Oliver Valerius

LAB HEAD: Jörg Stülke

PROVIDER: PXD018087 | Pride | 2021-01-12

REPOSITORIES: Pride

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			Action	DRS
	LK_Q_25.msf	Msf
	LK_Q_25.raw	Raw
	LK_Q_26.msf	Msf
	LK_Q_26.raw	Raw
	LK_Q_27.msf	Msf

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Publications

A meet-up of two second messengers: the c-di-AMP receptor DarB controls (p)ppGpp synthesis in Bacillus subtilis.

Krüger Larissa L Herzberg Christina C Wicke Dennis D Bähre Heike H Heidemann Jana L JL Dickmanns Achim A Schmitt Kerstin K Ficner Ralf R Stülke Jörg J

Nature communications 20210222 1

Many bacteria use cyclic di-AMP as a second messenger to control potassium and osmotic homeostasis. In Bacillus subtilis, several c-di-AMP binding proteins and RNA molecules have been identified. Most of these targets play a role in controlling potassium uptake and export. In addition, c-di-AMP binds to two conserved target proteins of unknown function, DarA and DarB, that exclusively consist of the c-di-AMP binding domain. Here, we investigate the function of the c-di-AMP-binding protein DarB i ...[more]

PMID: 33619274

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The human cholesterogenic enzymes DHCR14 and LBR are differentially regulated transcriptionally and post-translationally

Project description:Cholesterol synthesis is a tightly regulated process, both transcriptionally and post-translationally. Transcriptional control of cholesterol synthesis is relatively well understood. However, of the ~20 enzymes in cholesterol biosynthesis, post-translational regulation has only been examined for a small number. Three of the four sterol reductases, DHCR7, DHCR14 and LBR, share evolutionary ties with a high level of sequence homology and predicted structural homology. Despite their homology and that they uniquely share the same 14 reductase activity in cholesterol biosynthesis, little is known about the post-translational regulation of DHCR14 and LBR. Using CHO-7 cells stably expressing epitope tagged DHCR14 or LBR we investigated the post-translational regulation of these enzymes. We found that DHCR14 and LBR undergo differential post translational regulation, with DHCR14 being rapidly turned over, triggered by cholesterol and other sterol intermediates while LBR remained stable. DHCR14 is degraded via the ubiquitin-proteasome system and we identified several DHCR14 and DHCR7 putative interaction partners including the E3 ligase WWP2, which plays a role in the basal and cholesterol-mediated regulation of DHCR14. Interestingly, we found that gene expression across an array of human tissues showed that the C14-SRs gene expression is negatively related; one enzyme or the other tends to be predominately expressed in each tissue. Overall, our findings indicate that while LBR tends to be the constitutively active C14-SR, DHCR14 levels are tuneable, responding to the local cellular demands for cholesterol.

2020-01-15 | PXD016417 | Pride

Identification of Bacillus subtilis YjoB-binding proteins using AP-MS

Project description:Bacillus subtilis YjoB has been an uncharacterized AAA+ ATPase which consists of a single ATPase domain and a unique N-terminal domain. To understand the molecular function of YjoB, we identified YjoB-binding proteins through proteomics approaches, and analyzed the relationship between YjoB and its binding proteins. YjoB was coeluted with catalase and iron-sulfur cluster proteins in affinity purification and enhanced the activity of a catalase by specifically preventing heat-induced aggregation of catalase.

2022-10-12 | PXD032982 | Pride

Proteomic Profiling of cFeimin Interaction Proteins

Project description:In this study, we undertook a comprehensive characterization of proteins interacting with cFeimin. Through rigorous analysis of mass spectrometry data, we discerned candidates for potential interaction partners of cFeimin. Notably, the protein Foxc2 emerged with heightened possibilities of being a binding partner, suggesting a probable functional association with cFeimin.

2024-10-10 | PXD045263 | Pride

A non-canonical function of tyrosyl-tRNA synthetase in actin bundling

Project description:Aminoacyl-tRNA synthetases are the largest protein family implicated in Charcot-Marie-Tooth disease (CMT), the most common inherited peripheral neuropathy that is currently incurable. These essential enzymes catalyze the attachment of amino acids to their cognate tRNAs, thereby enabling the protein biosynthesis in every cell. Surprisingly, loss of aminoacylation is not a prerequisite for CMT to occur, suggesting a disease mechanism associated with a gain of neurotoxic function. Via an unbiased genetic modifier screen in a Drosophila model of tyrosyl-tRNA synthetase (YARS) -induced CMT, we established a link between the tRNA-ligase and regulators of actin cytoskeleton. By investigating the interactome of YARS in cellulo we found this synthetase to be enriched in protein complexes containing actin and actin-modifying proteins. Follow up in vitro and in vivo studies demonstrated that YARS itself has not only actin binding- but also actin-bundling properties independent of its aminoacylation function. These non-canonical activities are evolutionary conserved and contribute to the organization of actin cytoskeleton in Drosophila neurons and in patient-derived cells. An enzymatically active YARSCMT mutant caused stronger actin bundling in vitro, disorganization of actin bundle-rich stress fibers in patient-derived cells and impaired multiple actin-based steps of the synaptic vesicle cycle in fly neurons. Genetic modulation of the F-actin organization state restored synaptic vesicle mobility and rescued hallmark electrophysiological and morphological features in the neurons of fruit flies expressing different YARSCMT mutations. Thus, we uncover a role of tyrosyl-tRNA synthetase in actin organization that is implicated in the CMT neuropathy.

2023-01-09 | PXD037630 | Pride

Quantitative Rps2 BioID to monitor Asc1-dependent rearrangement at the head region of the 40S ribosome

Project description:In a previous study we applied a quantitative proximity-labeling technique called Biotin Identification (BioID, Roux et al., 2012) to analyze the microenvironment of the Gβ-like scaffold protein Asc1 (Opitz et al., 2017). The WD40-repeat protein Asc1 binds to the head region of the small 40S ribosomal (hr40S) subunit. In this study, we analyzed the hr40S from the perspective of Rps2, a ribosomal neighbor of Asc1. We intended to confirm proteins of the Asc1 proxiOME at the hr40S and to observe changes when Asc1 was absent. References: Roux K.J., Kim D.I., Raida M., Burke B. 2012. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol 196:801-810 Opitz N., Schmitt K., Hofer-Pretz V., Neumann B., Krebber H., Braus G.H., Valerius O. 2017. Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast. Mol Cell Proteomics 16:2199-2218

2019-11-07 | PXD015611 | Pride

Mitochondrial small heat-shock proteins are essential for normal growth of Arabidopsis thaliana

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2021-01-28 | PXD019603 | Pride

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Project description:Chromatin immunoprecipitation of FOXK2 (tagged with Flag and His tags) in U2OS cells detected by SOLiD sequencing. ***Correction March 2014: The sample “FOXK2_Dox_treated” has been renamed, it was originally named “FOXK2_rep2”. A new sample “FOXK2_rep2” has been added, with new files. It has come to our attention that one of the FOXK2 ChIP-seq replicates 'FOXK2_rep2' that we used in our paper recent paper (Ji, Z., Donaldson, I.J., Liu, J., Hayes, A., Zeef, L.A.H. and Sharrocks, A.D. (2012) The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation. Mol. Cell. Biol. 32, 385-398. doi:10.1128/MCB.05504-11) was incorrect. The replicate was actually treated with doxorubicin prior to ChIP-seq analysis resulting in the loss of many FOXK2 binding events.***

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Project description:Nitrogen limitation imposes a major transition in the life-style of non-diazotrophic cyanobacteria, which is regulated via a complex interplay of regulatory factors, involving, the nitrogen-specific transcription factor NtcA and the pervasive signal processor PII. Immediately upon nitrogen-limitation, newly fixed carbon is re-directed towards glycogen synthesis. How operation of the metabolic switch for distributing fixed carbon to either glycogen or cellular building blocks was poorly understood. Here we identify from Synechocystis sp. PCC 6803 a novel PII interactor, PirC, (Sll0944) that controls 3-phosphoglycerate mutase (PGAM), the enzyme that deviates newly fixed CO2 towards lower glycolysis. PirC acts as competitive inhibitor of PGAM and this interaction is tuned by PII/2-oxoglutarate. High oxoglutarate release PirC from PII-complex to inhibit PGAM. Accordingly, PirC deficient mutant, as compared to the wild-type, shows strongly reduced glycogen levels upon nitrogen deprivation whereas polyhydroxybutyrate granules are over-accumulated. Metabolome analysis revealed an imbalance in 3-phosphoglycerate to pyruvate levels in the PirC mutant, conforming that PirC controls the carbon flux in cyanobacteria via mutually exclusive interaction with either PII or PGAM.

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