PXD058665

PXD058665 is an original dataset announced via ProteomeXchange.

Title	Proteomic analyses of V. cholerae phage ICP1 and the phage satellite PLE11
Description	ICP1 is a predominant lytic phage of the Vibrio cholerae, the causative pathogen of diarrheal disease of cholera. A mobile genetic element called PLE (Phage inducible chromosomal island-like element) is often integrated into the V. cholerae chromosome, which is activated to excise only upon ICP1. PLE then redirects the ICP1 machinery to promote its own replication, packaging, and propagation while inhibiting ICP1 at multiple stages of infection. Thus, PLEs act as ‘phage satellites’ that parasitize ICP1 and provide anti-ICP1 phage defense to the V. cholerae population. The ICP1 and PLE virions have similar overall morphologies: an icosahedral capsid and a contractile tail. However, PLE does not encode a full suite of structural proteins. PLE remodels ICP1 capsid components to assemble a smaller capsid fitted for its shorter genomic DNA (Boyd C.M. et al., eLife 12, RP87611, 2024). This agrees with models of phage satellite assembly in the literature, which also propose that phage satellites hijack unmodified tails of the phages they parasitize. Surveillance of V. cholerae in cholera patient stool samples from 2019 to 2023 revealed PLE11, a novel PLE variant that potently inhibits ICP1 by the activity of a gene, Rta, which causes the production of tailless ICP1 particles. Genetic screening of escape mutations indicates the ICP1’s tape measure protein (TMP) as a probable target. However, PLE11 virions have functional contractile tails despite Rta-mediated inhibition of ICP1 tails. Further, bioinformatic analyses indicate PLE genomes encode a subset of tail protein, including a tail assembly chaperone and tape measure protein. Thus, we inquired whether PLE manipulates the ICP1 tail assembly to create hybrid PLE tails. In this proteomics study, we analyzed proteins constituting purified virions of ICP1 and PLE11 to decipher their structural compositions. The data identifies all predicted ICP1 structural proteins in ICP1 virions at expected abundances and demonstrates that PLE11 tails are hybrid, comprising PLE11-encoded TMP, baseplate hub, two proteins of unknown function, and the remaining tail proteins hijacked from ICP1. Together, the data substantiate the findings from our genetics and molecular biology approaches to uncover a novel phenomenon of tail assembly pathway manipulation by a phage satellite. Here, samples YM1 and YM4 are purified PLE11 and ICP1_2006_Dha_E virions (respectively), and the resulting peptides were searched against the translated genomes of ICP1 (Accession code: MH310934), V. cholerae (Accession code: N16961), and PLE11 (available on request). A combined database with fasta formatted sequences of the three proteomes is also provided with the data.
HostingRepository	PRIDE
AnnounceDate	2026-01-08
AnnouncementXML	Submission_2026-01-08_12:50:15.842.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD058665
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kimberley Seed
SpeciesList	scientific name: Vibrio phage ICP1_2006_E; NCBI TaxID: NEWT:1296591; scientific name: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961); NCBI TaxID: NEWT:243277;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-07 14:56:37	ID requested
⏵ 1	2026-01-08 12:50:16	announced

10.6019/PXD058665;

submitter keyword: None

Kimberley Seed
contact affiliation	Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
contact email	kseed@berkeley.edu
lab head
Kimberley Seed
contact affiliation	University of California Berkeley
contact email	kseed@berkeley.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD058665
     1. Label: PRIDE project
     2. Name: Proteomic analyses of V. cholerae phage ICP1 and the phage satellite PLE11