Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affinity chromatography-based identification of sRNA protein partners in Rhizobia

ABSTRACT: This project aims to identify novel protein partners of conserved trans-sRNAs in the α-proteobacterium Sinorhizobium meliloti. Trans-sRNAs (AbcR2, NfeR1 and EcpR1) were tagged at their 5’ ends with the MS2 aptamer. To identify the proteins associated with the trans-sRNAs we: i) expressed and purified the MS2 coat protein fused to maltose-binding protein (MS2-MBP); ii) purified MS2 tagged sRNAs conjugated with MS2-MBP via amylase column; and iii) subjected retained proteins to mass spectrometry analysis. To discard unspecific interactions we also analysed several control samples: i) samples expressing untagged trans-sRNAs; ii) samples expressing an MS2 tagged Rho-independent transcriptional terminator.

INSTRUMENT(S): amaZon Speed ETD

ORGANISM(S): Rhizobium Meliloti (ensifer Meliloti) (sinorhizobium Meliloti)

SUBMITTER: Ana Matia Gonzalez

LAB HEAD: José Ignacio Jiménez Zurdo

PROVIDER: PXD006410 | Pride | 2020-10-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ABCR2.dat	Other
	ABCR2.yep	Other
	ABCR2_MSII.dat	Other
	ABCR2_MSII.yep	Other
	ECPR1.dat	Other

Items per page:

1 - 5 of 14

Publications

Synthetase of the methyl donor S-adenosylmethionine from nitrogen-fixing α-rhizobia can bind functionally diverse RNA species.

Robledo Marta M García-Tomsig Natalia I NI Matia-González Ana M AM García-Rodríguez Fernando M FM Jiménez-Zurdo José I JI

RNA biology 20201010 8

Function of bacterial small non-coding RNAs (sRNAs) and overall RNA metabolism is largely shaped by a vast diversity of RNA-protein interactions. However, in non-model bacteria with defined non-coding transcriptomes the sRNA interactome remains almost unexplored. We used affinity chromatography to capture proteins associated <i>in vivo</i> with MS2-tagged <i>trans</i>-sRNAs that regulate nutrient uptake (AbcR2 and NfeR1) and cell cycle (EcpR1) mRNAs by antisense-based translational inhibition in ...[more]

PMID: 33043803

Similar Datasets

Identification of sRNA binding to ITSmetZW and ITSmetWV using MS2-affinity purification coupled with RNA sequencing (MAPS) technology

Project description:During ribosomal and transfer RNA maturation, external transcribed spacer (ETS) and internal transcribed spacer (ITS) sequences are excised and, as non-functional by-products, are rapidly degraded. The 3’ETS of the glyW-cysT-leuZ polycistronic tRNA precursor was highly and specifically enriched by co-purification with at least two different small regulatory RNAs (sRNAs), RyhB and RybB. Both sRNAs were shown to base pair with the same region in the 3’ETS of leuZ (3’ETSleuZ). Disrupting the pairing by mutating 3’ETSleuZ significantly increased the activity of sRNAs, even under non-inducing conditions. Our results indicate that 3’ETSleuZ prevents sRNA-dependent remodeling of tricarboxylic acid (TCA) cycle fluxes and increases antibiotic sensitivity when sRNAs are transcriptionally repressed. This suggests that 3’ETSleuZ functions as a sponge to absorb transcriptional noise from repressed sRNAs. Finally, the fact that RybB and MicF sRNAs are co-purified with ITSmetZ-metW and ITSmetW-metV strongly suggests a much broader phenomenon. Identification of sRNAs co-purified with MS2-ITSmetZW and MS2-ITSmetWV. ITSmetZW and ITSmetWV (without MS2) were used as control

2015-04-16 | E-GEOD-66517 | biostudies-arrayexpress

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RyhB sRNA targetome

Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RyhB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RyhB in a rne131 ?ryhB strain. RyhB (without MS2) was used as control

2015-04-16 | E-GEOD-66519 | biostudies-arrayexpress

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RybB sRNA targetome

Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RybB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RybB in a rne131 ΔrybB strain. RybB (without MS2) was used as control

2015-04-16 | E-GEOD-66518 | biostudies-arrayexpress

Gene expression profiles of MBP-specific T cells during experimental autoimmune encephalomyelitis

Project description:2nd generation sequencing was used to compare expression profiles of MBP-specific T cells retrieved from blood, CSF, spinal cord meninges and parenchyma. The overall expression profiles were found to be very similar.However, genes regulated during T cell activation were found to be upregulated in T cells from spinal cord meninges and parenchyma compared to blood and CSF. 2nd generation sequencing of MBP-specific T cells retrieved from blood and CNS compartments during experimental autoimmune encephalomyelitis

2016-02-12 | E-GEOD-75488 | biostudies-arrayexpress

Identification of RNA interacting with the sRNA sponge 3'ETSleuZ

Project description:During glyW-cysT-leuZ polycistronic tRNA maturation, the 3’external transcribed spacer (3’ETS) sequence is excised and act as a sRNA sponge (Lalaouna et al., 2015). Using MS2-affinity purification coupled with RNA sequencing (MAPS), we demonstrated that 3’ETSleuZ was highly and specifically enriched by co-purification with at least two different small regulatory RNAs (sRNAs), RyhB and RybB. Both sRNAs were shown to base pair with the same region in 3’ETSleuZ. Here, we use MS2-3’ETSleuZ as bait to co-purify all interacting sRNAs and confirm 3’ETSleuZ/RyhB and 3’ETSleuZ/RybB interactions.

2017-11-28 | GSE79278 | GEO

Internally Tagged Ubiquitin: a Tool to Identify Linear Polyubiquitin-modified Proteins by Mass Spectrometry

Project description:Even though ubiquitination controls a plethora of cellular processes, modifications by linear polyubiquitin have so far only been linked with acquired and innate immunity, lymphocyte development and genotoxic stress response. Until now, a single E3 ligase complex (LUBAC), one specific deubiquitinase (Otulin) and a very few substrates have been identified. The existing methods for the study of lysine-based polyubiquitination are not suitable for the detection of linear polyubiquitin-modified proteins. Here, we present a novel approach to discovering linear polyubiquitin-modified substrates by combining lysine-less internally tagged ubiquitin (INT-Ub.7KR) with SILAC-based mass spectrometry. We applied our approach in TNFα-stimulated T-Rex HEK293T cells and afterwards validated newly identified linear polyubiquitin targets. Moreover, we demonstrated that linear polyubiquitination of the novel LUBAC substrate TRAF6 is essential for the NFkappaB signalling. Overall, we have established a powerful method for the detection of linear polyubiquitin substrates.

2017-03-21 | PXD005878 | Pride

Alterations in liver proteome caused by bisphenol A and the bisphenol A metabolite, MBP, in males of Cyprinodon variegatus

Project description:Fifteen adult male Cyprinodon variegatus were exposed individually to 10µg/L of bisphenol A (BPA) for 7 days in 1.8L vessels and other fifteen to 10 µg/L of BPA metabolite, 4-methyl-2,4-bis(4-hydroxyphenyl)pent-1-ene (MBP) under the same conditions. Dimethyl sulfoxide (DMSO) was used as a carrier at 1µL/100mL and was added at the same concentration to the solvent control (n = 15). 90% daily water renewal was done after monitoring the culture conditions, that were: temperature 18.8 ± 0.2°C, pH 7.94±0.03, dissolved oxygen saturation 99.3% ± 1.1 and 16:8 hours of light:dark photoperiod. BPA, MBP and DMSO concentrations were adjusted daily after water renewal.

2022-02-23 | PXD029244 | Pride

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaI sRNA targetome

Project description:The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non coding RNAs (sRNAs). Most of the sRNAs regulate gene expression through base-pairings with mRNAs. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaI sRNA of S. aureus.

2018-11-02 | GSE122065 | GEO

Project description:Host AGO1-associated trans-kingdom sRNAs

| PRJNA794992 | ENA

Exon Expression Changes in the Spinal Cords of Lewis Rats with Myelin Basic Protein-Induced Experimental Autoimmune Encephalomyelitis (EAE)

Project description:Myelin Basic Protein (MBP) induced experimental autoimmune encephalomyelitis (EAE) in the Lewis rat, produces an an acute weakness, or paralysis of the tail and hind limb ataxia ,weakness or paralysis associated with increased permiability of the blood brain barrier, inflammation and demyelination in central nervous system (CNS). Clinical symptoms , ascending weakness or paralysis of the tail followed by the hind limbs and in rare cases the fore limbs occurs 8 and 14 days post immunisation (dpi) and is generally resolved completely by day 20 dpi. We have carried out transcriptome analysis of total RNA from the spinal cords of female Lewis rats at the peak of disease (EAE) and age matched healthy controls to identify exon expression changes associated with the disease. In these data sets we include the exon expression data obtained from total RNA preparations from the spinal cords of female Lewis rats sacrificed at the clinical peak of MBP induced EAE and age matched , untreated, healthy controls. 8 total RNA samples were prepared. A two way ANOVA comparison carried out in Partek Genomics Suite was used to detect differences in exon expression in the spinal cord of female lewis rats with MBP induced EAE and age matched healthy controls.

2013-06-30 | E-GEOD-39120 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data