PXD005798

PXD005798 is an original dataset announced via ProteomeXchange.

Title	Quantitative chemical proteomic analysis of YnMyr-tagged proteins in HeLa cells infected with RV16
Description	Rhinovirus causes the common cold and drives exacerbation in asthma and COPD, leading to substantial morbidity and healthcare cost. The single positive strand RNA genome of this non-enveloped virus is translated into a single polyprotein that is processed by virus 3C protease to form three structural capsid proteins VP0, VP1 and VP3, and other proteins required for viral life cycle completion. Capsid proteins assemble into the 5S capsid protomer, five of which form a 14S pentamer, and 12 pentamers then assemble to form the 150S icosahedral provirion into which the viral genome is incorporated. During the final step of viral maturation, VP0 is cleaved into VP2 and VP4. VP4 is encoded at the N-terminus of the viral polyprotein, and in many Picornaviruses is N-myristoylated by host cell N-myristoyltransferase (NMT). We have explored the impact of IMP-1088 (the first sub-nanomolar IC50 dual inhibitor of human N-myristoyl transferases HsNMT1 and HsNMT2) on HRV capsid myristoylation in cells. Global identification of proteins for which myristoylation is selectively inhibited by IMP-1088 was performed by quantitative chemical proteomic analysis of YnMyr-tagged proteins in HeLa cells infected with RV16 treated with 50 nM IMP-1088 or vehicle (DMSO). Proteins were subjected to ligation to AzRB, an azide capture reagent bearing a trypsin-cleavable linker and biotin dual label followed by affinity enrichment on Neutravidin beads, on-bead digestion with trypsin, nanoLC-MS/MS analysis of tryptic peptides, and data processing by label-free protein quantification (LFQ) in MaxQuant. 60 N-myristoylated proteins were identified, including the RV16 polyprotein which responded to IMP-1088 inhibition, with no significant change in protein abundances across the whole proteome in the presence of inhibitor. The majority of viral capsid peptides identified in the pull-down mapped to the VP0 domain of the polyprotein, and the N-terminal YnMyr-tagged peptide was readily identified by MS/MS. These data provide the first direct evidence for HRV capsid myristoylation in human cells, and demonstrate that this lipid modification is highly susceptible to inhibition by a selective NMT inhibitor.
HostingRepository	PRIDE
AnnounceDate	2018-05-09
AnnouncementXML	Submission_2018-05-23_00:37:50.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005798
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Julia Morales Sanfrutos
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-01-28 04:07:13	ID requested
1	2018-05-09 00:09:10	announced
⏵ 2	2018-05-23 00:37:51	announced	Updated publication reference for PubMed record(s): 29760414.

Mousnier A, Bell AS, Swieboda DP, Morales-Sanfrutos J, P, é, rez-Dorado I, Brannigan JA, Newman J, Ritzefeld M, Hutton JA, Gued, á, n A, Asfor AS, Robinson SW, Hopkins-Navratilova I, Wilkinson AJ, Johnston SL, Leatherbarrow RJ, Tuthill TJ, Solari R, Tate EW, Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Nat Chem, 10(6):599-606(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: HeLa, RV16, myristoylation, NMT inhibition, proteomics

Edward W. Tate
contact affiliation	Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
contact email	e.tate@imperial.ac.uk
lab head
Julia Morales Sanfrutos
contact affiliation	Imperial College London
contact email	j.morales-sanfrutos@imperial.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005798
     1. Label: PRIDE project
     2. Name: Quantitative chemical proteomic analysis of YnMyr-tagged proteins in HeLa cells infected with RV16