PXD035658

PXD035658 is an original dataset announced via ProteomeXchange.

Title	Prioritization of antimicrobial targets by CRISPR-based oligo recombineering
Description	Nucleophilic amino acids are important in covalent drug development yet underutilized as antimicrobial targets. Over recent years, several chemoproteomic technologies have been developed to mine chemically-accessible residues via their intrinsic reactivity toward electrophilic probes. However, these approaches cannot discern which reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based Oligo Recombineering (CORe) platform to systematically prioritize reactive amino acids according to their contribution to protein function. Our approach directly couples protein sequence and function with biological fitness. Here, we profile the reactivity of >1,000 cysteines on ~700 proteins in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. We competitively compared the fitness effect of 370 codon switches at 74 cysteines and identify functional sites in a diverse range of proteins. In our proof of concept, CORe performed >800 times faster than a standard genetic workflow. Reactive cysteines decorating the ribosome were found to be critical for parasite growth, with subsequent target-based screening validating the apicomplexan translation machinery as a target for covalent ligand development. CORe is system-agnostic, and supports expedient identification, functional prioritization, and rational targeting of reactive sites in a wide range of organisms and diseases.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:18:04.817.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julia Falco
SpeciesList	scientific name: Toxoplasma gondii RH; NCBI TaxID: 383379;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Discovery

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-01 01:58:46	ID requested
⏵ 1	2024-10-08 11:18:05	announced

10.1038/S41564-022-01249-Y;

submitter keyword: Toxoplasma Gondii, Oligo Recombineering, Proteomics

Eranthie Weerapana
contact affiliation	Weerpana Lab Boston College Chemistry Department Chestnut Hill, MA, USA
contact email	eranthie@bc.edu
lab head
Julia Falco
contact affiliation	Boston College
contact email	falcoju@bc.edu
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/2022/10/PXD035658

PRIDE project URI

• PRIDE
  1. PXD035658
     1. Label: PRIDE project
     2. Name: Prioritization of antimicrobial targets by CRISPR-based oligo recombineering