PXD013407-1

PXD013407 is an original dataset announced via ProteomeXchange.

Title	Systems biology decodes herpes simplex virus 1
Description	Since the genome of herpes simplex virus 1 (HSV-1) was first sequenced more than 30 years ago, the 84 genes it was thought to encode have been intensively studied. Here, we unravel the full complement of viral transcription and translation during lytic infection with base-pair resolution by computational integration of multi-omics data. This includes a total of 201 viral transcripts and 296 open reading frames (ORFs), comprising all known large ORFs, 55 large novel ORFs including a novel spliced ORF in the ICP0 locus that initiates from a non-AUG start codon and a novel strongly translated ORF in the ICP34.5 locus as well as multiple short ORFs. By defining viral gene modules, we link translation of ORFs to the expression of transcript isoforms. This explained translation of the vast majority of viral ORFs as well as N-terminal extensions and truncations thereof. We show that N-terminal extensions initiating from non-AUG start codons govern subcellular protein localization and packaging of key viral regulators and structural proteins. This work has great implications for future functional studies, vaccine design and novel oncolytic therapies.
HostingRepository	PRIDE
AnnounceDate	2020-05-22
AnnouncementXML	Submission_2020-05-21_23:59:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Guido Mastrobuoni
SpeciesList	scientific name: Herpes simplex virus unknown type; NCBI TaxID: 126283; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-08 08:14:18	ID requested
⏵ 1	2020-05-21 23:59:49	announced

Whisnant AW, J, ü, rges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, G, ö, bel M, D, ö, ring K, Menegatti J, Antrobus R, Matheson NJ, K, ü, nzig FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Gr, ä, sser F, Lehner PJ, Friedel CC, Erhard F, D, ö, lken L, Integrative functional genomics decodes herpes simplex virus 1. Nat Commun, 11(1):2038(2020) [pubmed]

submitter keyword: genome annotation, systems biology, shotgun proteomics

Stefan Kempa
contact affiliation	Berlin Institute for Medical System Biology @ Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association Hannoversche Str. 28, 10115 Berlin Germanyt
contact email	stefan.kempa@mdc-berlin.de
lab head
Guido Mastrobuoni
contact affiliation	Berlin Institute for Medical Systems Biology at the Max Delbrueck Centrum for Molecular Medicine
contact email	guido.mastrobuoni@mdc-berlin.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD013407
     1. Label: PRIDE project
     2. Name: Systems biology decodes herpes simplex virus 1