Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Searching N-terminal modifications of proteins starting with Gly in Arabidopsis thaliana

ABSTRACT: Characterization of Myristoylated proteins in Arabidopsis thaliana Col 0 wild type

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Rosette

SUBMITTER: Willy Bienvenut

LAB HEAD: Willy Bienvenut

PROVIDER: PXD008663 | Pride | 2018-06-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20130111_WIB_At-WT-Rep1_SCX_Frac-02.dat	Other
	20130111_WIB_At-WT-Rep1_SCX_Frac-02.mgf	Mgf
	20130111_WIB_At-WT-Rep1_SCX_Frac-02.raw	Raw
	20130111_WIB_At-WT-Rep1_SCX_Frac-03.dat	Other
	20130111_WIB_At-WT-Rep1_SCX_Frac-03.mgf	Mgf

Items per page:

1 - 5 of 831

Publications

Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern.

Castrec Benoit B Dian Cyril C Ciccone Sarah S Ebert Coralie L CL Bienvenut Willy V WV Le Caer Jean-Pierre JP Steyaert Jean-Marc JM Giglione Carmela C Meinnel Thierry T

Nature chemical biology 20180611 7

An organism's entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes. The crystal structures of human modifier NMT1 complexed with reactive and nonreactive target-mimicking peptide ligands revealed unexpected binding clefts and a modifier recognition pattern. This information allowed integrated mapping of myristoylomes u ...[more]

PMID: 29892081

Similar Datasets

Tracking the N-Myristoylated N-termini in human cell line lysates (soluble fraction) to highlight this protein modification at the proteome level

Project description:Characterization of N-Myristoylated proteins in the soluble fraction of four human cell lines (HUVEC, U87, K562 and HCT116) using large-scale proteomics approaches.

2018-06-18 | PXD008666 | Pride

Large scale investigation of the phage Vp16 PDF activity

Project description:Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this cotranslational mechanism. Recent genome sequencing and annotation studies highlighted over 2x104 putative peptide deformylase sequences. Furthermore, unpredicted modified bacterial PDF genes have been retrieved from many phages. Sequence comparisons with other known PDFs reveal that viral PDFs are devoid of the key ribosome-interacting C-terminal region. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity in vitro or in vivo. This investigation determines the activity of the recombinant Vp16 PDF in E. coli PDF defective cell to remove the N-formyl group at the protein N-terminus.

2017-09-25 | PXD006008 | Pride

Reference dataset for EnCOUNTer tool development

Project description:Reference dataset used for the development of the EnCOUNTEr tool to both (i) score all characterized peptides using discriminant parameters to evidence mature protein N-termini and (ii) determine the N-terminus acetylation yield for the most reliable ones.

2017-03-14 | PXD005720 | Pride

Molecular Hydrogen Impact on Chalcopyrite Bioleaching by the Extremely Thermoacidophilic Archaeon Metallosphaera sedula

Project description:Hydrogen served as a competitive inorganic energy source, impacting the CuFeS2 bioleaching efficiency of the extremely thermoacidophilic archaeon Metallosphaera sedula. Open reading frames encoding key terminal oxidase and electron transport chain components were triggered by CuFeS2. Evidence of heterotrophic metabolism was noted after extended periods of bioleaching, presumably related to cell lysis. One 3 slide loop for Mse cells includes 3 conditions: M. sedula inoculum prior to introduction to chalcopyrite (d0~day 0), M. sedula after 3 days on chalcopyrite (d3~day 3), and M. sedula after 9 days on chalcopyrite (d9~day 9). Half of an RNA sample for one condition (consisting of pools of RNA from multiple cultures) was labeled with Cy3 while the other half was labeled with Cy5. The two differently labeled samples were run on different slides. Each probe is spotted on each slide 5 times (5 spots/slide x 2 slides = 10 technical replicates per condition; spot intensities for all replicates on slide provided in associated raw data file).

2010-05-05 | E-GEOD-20554 | biostudies-arrayexpress

Identification and characterization of the first Nα-acetyltransferase in plastids

Project description:Protein Nα-terminal acetylation represents one of the most abundant protein modifications of higher eukaryotes. In humans, six Nα-acetyltransferases (Nats) are responsible for the acetylation of approximately 80% of the cytosolic proteins. N-terminal protein acetylation has not been evidenced in organelles of metazoans, but in higher plants, it is a widespread modification not only in the cytosol but also in the chloroplast. In this study, we identify and characterize the first organellar-localized Nat in eukaryotes. A primary sequence-based search in Arabidopsis thaliana revealed seven putatively plastid-localized Nats of which AT2G39000 (AtNAA70) showed the highest conservation of the acetyl-CoA binding pocket. The chloroplastic localization of AtNAA70 was demonstrated by transient expression of AtNAA70:YFP in Arabidopsis mesophyll protoplasts. Homology modeling uncovered a significant conservation of tertiary structural elements between human HsNAA50 and AtNAA70. The in vivo acetylation activity of AtNAA70 was demonstrated on a number of distinct protein N alpha-termini with a newly established Nat-activity global profiling after expression of AtNAA70 in E. coli. AtNAA70 predominately acetylated proteins starting with M, A, S, and T, providing an explanation for most protein N-termini acetylation events found in chloroplasts.

2015-06-29 | PXD001947 | Pride

Large scale profiling of the physiological impact of a potent anti-cancer agent inhibiting early protein maturation

Project description:Fumagillin and its derivatives are therapeutically-useful compounds for their capacity to reduce cancer progression. Fumagillin exerts a specific proliferation inhibition on endothelial cell lines and on several tumor lines. The specific molecular target of fumagillin is MetAP2, one of the two cytosolic MetAPs. MetAPs are in charge of N-terminal Methionine Excision, an essential pathway of cotranslational protein maturation. Why the inhibition of MetAP2 causes cell growth arrest in a subset class of cells is yet unknown. Here, we focus on a global large scale characterization of the N-terminal Methionine Excision pathway and the inhibition of one of its enzymes by fumagillin in a number of lines including cancer cell lines. N-termini profiling of responsive and unresponsive cells to fumagillin treatment was conducted using large scale proteomics approach

2017-01-02 | PXD002690 | Pride

Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition

Project description:A proteome-wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of the antibiotic actinonin specifically inhibiting peptide deformylase (PDF). A new strategy and tool suite (SILProNaQ) was employed to provide large scale N-terminus acetylation yield quantitation. In control conditions, more than 1000 N-termini could be identified with 56 % Met removal, and additional modifications involving partial or complete N-acetylation (10%) and formyl retention (5%). Among the proteins undergoing these N-terminal modifications, some translocated membrane proteins were highlighted. The early time-course impact of actinonin was followed after the addition of bacteriostatic concentrations of the drug immediately slowing down the growth rate. Under these conditions, 25% of all proteins remain formylated after 10 min, a value reaching more than 60% of all characterized proteins after 40 min of treatment. The N-formylation rate on individual proteins increased with the same trend. Upon PDF inhibition, we finally show that two major categories of proteins retain their formyl group: a large number of inner membrane proteins and proteins involved in protein synthesis including many factors assisting the nascent chains in co-translational events.

2015-07-21 | PXD002012 | Pride

Cracking the code of an elusive key protein modification at structural and genome scales

Project description:Characterization of Myristoylated proteins in human brain and liver samples.

2018-06-18 | PXD008625 | Pride

Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state

2015-07-22 | PXD001983 | Pride

Expression data from mouse limb tendon cells during development.

Project description:We have undertaken a screen of mouse limb tendon cells in order to identify molecular pathways involved in tendon development. Mouse limb tendon cells were isolated based on Scleraxis (Scx) expression at different stages of development: E11.5, E12.5 and E14.5 Microarray comparisons were carried out between tendon progenitor and differentiated stages. Forelimbs from E11.5, E12.5 and E14.5 Scx-GFP embryos were collected and dissociated with trypsin to obtain cell suspensions. Scx-positive tendon cells were isolated by FACS. RNA was extracted and Fragmented biotin-labelled cRNA samples were hybridized on Affymetrix Gene Chip Mouse Genome 430 2.0 arrays.

2014-01-18 | E-GEOD-54207 | 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