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

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

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Willy Bienvenut

LAB HEAD: Willy Bienvenut

PROVIDER: PXD008666 | Pride | 2018-06-18

REPOSITORIES: Pride

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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

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

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

2018-06-18 | PXD008663 | 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

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

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

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

2015-07-22 | PXD001983 | 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

Proteome imprinting by N-terminal acetylation is a vital hormone-regulated master switch during stress

Project description:N-terminal acetylation (NTA) catalyzed by N-terminal acetyltransferases (Nats) is among the most common protein modifications in eukaryotes, but its significance is still enigmatic. Characterization of the plant NatA complex reveals evolutionary conservation of NatA biochemical properties within higher eukaryotes and uncovers specific and essential functions of NatA for regulation of development, numerous biosynthetic pathways and stress responses in plants. We show that NTA decreases significantly in case of drought stress, since NatA abundance is rapidly down-regulated by the phytohormone abscisic acid. Accordingly, down-regulation of NatA by genetic engineering is sufficient for induction of the drought stress response and results in strikingly drought resistant plants. Thus, NTA by the NatA complex is a vital cellular surveillance mechanism during stress. We conclude that imprinting of the proteome by NatA is a master switch for control of metabolism, development and cellular stress responses and integrates stress signals by perceiving the hormone abscisic acid.

2016-06-14 | PXD002069 | Pride

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

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

plasma membrane anchored NAA60 N-terminal acetylation profiling in Arabidopsis thaliana

Project description:N-terminal acetylation (NTA) is one of the most abundant protein modifications in eukaryotes and is catalysed in humans by seven N-acetyltransferases. AtNAA60 localizes to the plasma membrane in vivo by an α-helical membrane anchor at its C-terminus. In this study, we investigated the Arabidopsis thaliana N-terminal acetylome in leaf cells of naa60-1 to identify AtNAA60 substrates in vivo using the SILProNAQ approach.

2020-07-15 | PXD016494 | Pride

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