PXD068223

PXD068223 is an original dataset announced via ProteomeXchange.

Title	Probing the genomic and proteomic basis of encystment in Oxytricha granulifera
Description	Protozoan encystment is a crucial survival strategy for resisting environmental stresses, yet its molecular mechanisms remain poorly understood due to limited genomic resources and lack of integrated multi-omics analyses in model ciliates. In this study, we aimed to elucidate the molecular mechanisms underlying the encystment process in Oxytricha granulifera by sequencing and assembled its genome, and by conducting comprehensive transcriptome, proteome and morphology analyses to reveal gene expression and morphologic changes between vegetative and cyst stages. Morphological observation revealed ciliary dedifferentiation and cyst-wall formation during encystment, events respectively supported by the downregulation of microtubule dynamics related genes and the upregulation of vesicle transport related genes in cyst stage. Expanded gene families for carbohydrate metabolism, autophagy and cellular acidification align with the species’ mucocyst signature and their observed autophagic clearance, hinting at previously unrecognized mechanisms underlying cyst formation. Elevated expression of the ubiquitin-proteasome system and autophagy pathways facilitates protein turnover, and upregulation of antioxidant enzymes genes helps mitigate oxidative damage, while a rewired post-transcriptional regulation that increases spliceosome activity and alternative splicing frequency—each trend validated at the protein level. Concurrently, the methyltransferases responsible for DNA N6-adenine methylation (6mA), with homologous genes of AMT1 and AMT6/7 significantly downregulated. These results suggesting a multilayered regulation of ciliate encystment and the first integrated evidence that alternative splicing modulates dormancy. Our findings establish the first multi-omics framework for O. granulifera encystment, offering baseline data and tentative clues to the dormancy mechanism that will inform future inquiries into how single-celled eukaryotes endure adverse environments.
HostingRepository	PRIDE
AnnounceDate	2026-04-14
AnnouncementXML	Submission_2026-04-14_00:13:27.485.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juan Yang
SpeciesList	scientific name: Oxytricha granulifera; NCBI TaxID: NEWT:5947;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-09 04:06:27	ID requested
⏵ 1	2026-04-14 00:13:27	announced

10.1128/MSYSTEMS.01757-25;

submitter keyword: 6mA, spliceosome, transcriptomic,cyst, mucocyst

Xiao Chen
contact affiliation	Shandong University
contact email	alpha67@163.com
lab head
Juan Yang
contact affiliation	Shandong University
contact email	yangjuan5721@163.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD068223
     1. Label: PRIDE project
     2. Name: Probing the genomic and proteomic basis of encystment in Oxytricha granulifera