PXD058199-1

PXD058199 is an original dataset announced via ProteomeXchange.

Title	Construction, debugging and iterative redesign of synXVI, a 903-kb synthetic chromosome of Saccharomyces cerevisiae
Description	Assembly and debugging of the 902,994-bp synthetic Saccharomyces cerevisiae chromosome synXVI of the Sc2.0 project is described. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5’ UTR of genes required for optimal growth and were identified as a systematic cause of defective growth. Based on lessons learned from analysis of Sc2.0 defects and synXVI, an in-silico redesign of the synXVI chromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. The in-silico redesign of synXVI includes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs. This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_05:01:24.460.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paige Erpf
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-24 16:03:33	ID requested
⏵ 1	2025-05-07 05:01:25	announced

10.1038/s41467-024-55318-3;

Goold HD, Kroukamp H, Erpf PE, Zhao Y, Kelso P, Calame J, Timmins JJB, Wightman ELI, Peng K, Carpenter AC, Llorente B, Hawthorne C, Clay S, van Wyk N, Daniel EL, Harrison F, Meier F, Willows RD, Cai Y, Walker RSK, Xu X, Espinosa MI, Stracquadanio G, Bader JS, Mitchell LA, Boeke JD, Williams TC, Paulsen IT, Pretorius IS, kb synthetic Saccharomyces cerevisiae chromosome. Nat Commun, 16(1):841(2025) [pubmed]

submitter keyword: yeast 2.0, SCRaMbLE,synthetic genome, yeast

Ian T Paulsen
contact affiliation	School of Natural Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia. The Australian Genome Foundry, Sydney, Australia.
contact email	ian.paulsen@mq.edu.au
lab head
Paige Erpf
contact affiliation	Macquarie Univeristy
contact email	paige.erpf@mq.edu.au
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/2025/05/PXD058199

PRIDE project URI

• PRIDE
  1. PXD058199
     1. Label: PRIDE project
     2. Name: Construction, debugging and iterative redesign of synXVI, a 903-kb synthetic chromosome of Saccharomyces cerevisiae