PXD006502

PXD006502 is an original dataset announced via ProteomeXchange.

Title	Reduced protein expression in a virus attenuated by codon deoptimization
Description	A general means of viral attenuation involves the extensive recoding of synonymous codons in the viral genome. The mechanistic underpinnings of this approach remain unclear, however. Using quantitative proteomics and RNA sequencing, we explore the molecular basis of attenuation in a strain of bacteriophage T7 whose major capsid gene was engineered to carry 182 suboptimal codons. We do not detect transcriptional effects from recoding. Proteomic observations reveal that translation is halved for the recoded major capsid gene, and a more modest reduction applies to several co-expressed downstream genes. We observe no changes in protein abundances of other co-expressed genes that are encoded upstream. Viral burst size, like capsid protein abundance, is also decreased by half. Together, these observations suggest that, in this virus, reduced translation of an essential polycistronic transcript and diminished virion assembly form the molecular basis of attenuation.
HostingRepository	PRIDE
AnnounceDate	2018-10-24
AnnouncementXML	Submission_2018-10-24_13:36:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Benjamin Jack
SpeciesList	scientific name: Escherichia coli (strain K12); NCBI TaxID: 83333; scientific name: Enterobacteria phage T7; NCBI TaxID: 10760;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-05-12 01:00:47	ID requested
⏵ 1	2018-10-24 13:36:29	announced

Jack BR, Boutz DR, Paff ML, Smith BL, Bull JJ, Wilke CO, Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization. G3 (Bethesda), 7(9):2957-2968(2017) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Codon deoptimization, viral attenuation, codon usage

Claus O. Wilke
contact affiliation	University of Texas at Austin, Department of Integrative Biology
contact email	wilke@austin.utexas.edu
lab head
Benjamin Jack
contact affiliation	University of Texas at Austin
contact email	b.jack@utexas.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006502
     1. Label: PRIDE project
     2. Name: Reduced protein expression in a virus attenuated by codon deoptimization