PXD064682

PXD064682 is an original dataset announced via ProteomeXchange.

Title	The contribution of the transcription factors Crz1 and Rim101 to the response to alkalinization in Komagataella phaffii
Description	In the industrially relevant yeast Komagataella phaffii, as in other yeasts, alkalinization of the medium results in fast and extensive transcriptional remodeling. This response has been useful to design novel methanol-free, regulatable platforms for heterologous protein expression. However, its molecular bases are fully unknown. Crz1 and Rim101/PacC are transcription factors known to contribute to the alkaline pH transcriptional responses in many fungi. We identified here the transcription factors Crz1 and Rim1 in K. phaffii and used CRISPR/Cas9 techniques to create single and double mutant strains. Phenotypic characterization shows that crz1 cells are strongly sensitive to Ca2+ ions, mildly sensitive to alkaline pH and hypertolerant to SDS. In contrast, rim101 cells are markedly hypersensitive to Na+ and Li+ ions, to alkaline pH and to SDS. RNA-seq transcriptomic analysis revealed that mutation of RIM101 affects 55% of genes whose expression is altered at pH 8.0, whereas lack of Crz1 alters only 11% of these. Thirty-eight genes are co-regulated by both Crz1 and Rim101. The PMC1 vacuolar Ca+2-ATPase is regulated by Crz1, whereas the ENA2 Na+-ATPase, the PHO89 and PHO84 phosphate transporters, and diverse genes involved in iron homeostasis are Rim101-dependent. These effects were confirmed by proteomic analyses after 3 h of alkalinization. Therefore, while Rim101 appears as a major player in the transcriptional response to alkalinization, nearly 40% of the alkaline pH transcriptional response in K. phaffii is controlled still unknown pathways.
HostingRepository	PRIDE
AnnounceDate	2025-10-20
AnnouncementXML	Submission_2025-10-20_06:26:26.005.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Komagataella phaffii; NCBI TaxID: NEWT:460519;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-05 06:28:39	ID requested
1	2025-09-02 07:30:12	announced
⏵ 2	2025-10-20 06:26:27	announced	2025-10-20: Updated project metadata.

10.1038/s41598-025-20192-6;

Albacar M, Casamayor A, Zekhnini A, Schmidt A, Gonz, á, lez A, Ari, ñ, o J, Signaling pathways contributing to the transcriptional response to alkalinization in Komagataella phaffii: role of the transcription factors Crz1 and Rim101. Sci Rep, 15(1):35841(2025) [pubmed]

submitter keyword: LC-MS,Crz1, LFQ

Alexander Schmidt
contact affiliation	Biozentrum, University of Basel, Switzerland
contact email	alex.schmidt@unibas.ch
lab head
Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/09/PXD064682

PRIDE project URI

• PRIDE
  1. PXD064682
     1. Label: PRIDE project
     2. Name: The contribution of the transcription factors Crz1 and Rim101 to the response to alkalinization in Komagataella phaffii