PXD032398-1

PXD032398 is an original dataset announced via ProteomeXchange.

Title	For origin melting Rep nucleoprotein complex accommodates both dsDNA and ssDNA of DUE
Description	The replication initiation proteins interact dsDNA located at replication origin and ssDNA of DNA unwinding element (DUE), formed as a result of the destabilization of the double-stranded helix of AT-rich origin region. It is a critical step in the DNA replication initiation; however, the structure of nucleoprotein complex involving initiator protein, dsDNA and/or ssDNA is still elusive and different models are proposed. In this work, based on crosslinking combined with mass spectrometry (MS), structural and bioinformatic analysis, we defined amino acid residues in plasmid Rep proteins, TrfA and RepE, that are essential for interaction with ssDNA. The study of Rep mutant proteins containing single amino acid substitutions affecting DNA interaction reveals the importance of Rep-ssDNA complexes formation for a dsDNA melting at DUE. Furthermore, the crystal structures obtained for complex of RepE protein with DUE ssDNA, and, RepE complexed with both DUE ssDNA and dsDNA containing RepE specific binding site (iteron) revealed that the plasmid initiator can not only bind iterons and ssDNA DUE separately but also can form a tripartite nucleoprotein complex bringing together specific sequences of replication origin. The presented data strongly supports the loop-back model in which a replication initiator molecule interacts with dsDNA and ssDNA.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:39:05.073.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paulina Czaplewska
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	5800 TOF/TOF; TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-18 09:13:26	ID requested
⏵ 1	2024-10-08 11:39:10	announced
2	2024-10-22 06:25:30	announced	2024-10-22: Updated project metadata.

Wegrzyn K, Oliwa M, Nowacka M, Zabrocka E, Bury K, Purzycki P, Czaplewska P, Pipka J, Giraldo R, Konieczny I, Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation. Nucleic Acids Res, 51(19):10551-10567(2023) [pubmed]

10.1093/nar/gkad740;

submitter keyword: DNA replication, Rep proteins, protein-DNA interaction, replication initiators, origin opening

Paulina Czaplewska
contact affiliation	Universuty of Gdansk, Intercollegiate Faculty of Biotechnology, Laboratory of Mass Spectrometry
contact email	paulina.czaplewska@ug.edu.pl
lab head
Paulina Czaplewska
contact affiliation	University of Gdansk
contact email	paulina.czaplewska@ug.edu.pl
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/2024/01/PXD032398

PRIDE project URI

• PRIDE
  1. PXD032398
     1. Label: PRIDE project
     2. Name: For origin melting Rep nucleoprotein complex accommodates both dsDNA and ssDNA of DUE