Browse
Submit Data
Databases
API
Help

Dataset Information

279 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Large scale investigation of the phage Vp16 PDF activity

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Escherichia Coli

SUBMITTER: Willy Bienvenut

LAB HEAD: Willy Vincent Bienvenut

PROVIDER: PXD006008 | Pride | 2017-09-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation.

Grzela Renata R Nusbaum Julien J Fieulaine Sonia S Lavecchia Francesco F Bienvenut Willy V WV Dian Cyril C Meinnel Thierry T Giglione Carmela C

Scientific reports 20170908 1

Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identifie ...[more]

PMID: 28887476

Similar Datasets

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

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

System-wide analyses reveal essential roles of N-terminal protein modification in bacterial physiology

Project description:Removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria that impacts over 90% of the proteome. PDF is essential and a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. In this work, we used system-wide and time-resolved analyses of the E. coli translatome and proteome to investigate the consequences of PDF inhibition at different stages. We found that PDF inhibition results in the rapid activation of cellular stress responses, especially those associated with defects in protein folding and perturbations at the bacterial inner membrane, followed by a global downregulation of metabolic pathways. Functional assays reveal the rapid hyperpolarization of the plasma membrane and impaired membrane integrity upon PDF inhibition, suggesting that disruption of plasma membrane is the most immediate and primary consequence of formyl group retention on nascent proteins. Our work resolves the physiological function of a ubiquitous N-terminal protein modification and uncovers its crucial role in maintaining the proper structure and function of the bacterial membrane.

2022-07-20 | PXD032725 | Pride

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

Whole lysate and ribosome enriched fractions analyses of the amino terminal status of Escherichia coli at the steady state and upon deformylation inhibition

2015-07-21 | PXD001979 | Pride

System-wide analyses reveal essential roles of N-terminal protein modification in bacterial physiology

2022-07-20 | GSE199360 | GEO

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

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

Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo

Project description:As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting and folding factors. Here we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone Trigger Factor (TF) reveal that, while TF can interact with many polypeptides, Î²-barrel outer membrane proteins are the most prominent substrates. Loss of TF leads to broad outer membrane defects and premature, cotranslational protein translocation. While in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting ad folding factors. Examination of translation in the Gram-negative bacterium Escherichia coli, as well as an analysis of the interactions between nascent chains and the molecular chaperone Trigger Factor.

2011-12-09 | E-GEOD-33671 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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