PXD050621

PXD050621 is an original dataset announced via ProteomeXchange.

Title	Total proteome of AB1157 with RA-inducing plasmid pTn5053
Description	Bacterial defence systems are tightly regulated to avoid autoimmunity. In Type I restriction-modification (R-M) systems, a specific mechanism called restriction alleviation (RA) controls the activity of the restriction module. In the case of the Escherichia coli Type I R-M system EcoKI, RA proceeds through ClpXP-mediated proteolysis of restriction complexes bound to non-methylated sites that appear after replication or reparation of host DNA. Here, we show that RA is also induced in the presence of plasmids carrying EcoKI recognition sites, a phenomenon we refer to as plasmid-induced RA. Further, we show that the anti-restriction behavior of plasmid-borne non-conjugative transposons such as Tn5053, previously attributed to their ardD loci, is due to plasmid-induced RA. Plasmids carrying both EcoKI and Chi sites induce RA in RecA- and RecBCD-dependent manner. However, inactivation of both RecA and RecBCD restores RA, indicating that there exists an alternative, RecA-independent, homologous recombination pathway that is blocked in the presence of RecBCD. Indeed, plasmid-induced RA in a RecBCD-deficient background does not depend on the presence of Chi sites. We propose that processing of random dsDNA breaks in plasmid DNA via homologous recombination generates non-methylated EcoKI sites, which attract EcoKI restriction complexes channeling them for ClpXP-mediated proteolysis.
HostingRepository	PRIDE
AnnounceDate	2024-06-23
AnnouncementXML	Submission_2024-06-23_01:26:31.616.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Artem Isaev
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-14 09:25:41	ID requested
⏵ 1	2024-06-23 01:26:32	announced

10.1093/nar/gkae243;

Skutel M, Yanovskaya D, Demkina A, Shenfeld A, Musharova O, Severinov K, Isaev A, RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation. Nucleic Acids Res, 52(9):5195-5208(2024) [pubmed]

submitter keyword: restriction alleviation. E. coli, AB1157, EcoKI

Artem Isaev
contact affiliation	Skolkovo Institute of Science and Technology, Moscow, Russia
contact email	tcft18@gmail.com
lab head
Artem Isaev
contact affiliation	Skolkovo Institute of Science and Tecgnology
contact email	tcft18@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD050621
     1. Label: PRIDE project
     2. Name: Total proteome of AB1157 with RA-inducing plasmid pTn5053