PXD060688

PXD060688 is an original dataset announced via ProteomeXchange.

Title	DdiA, an XRE family transcriptional regulator, regulates a LexA-independent DNA damage response in Myxococcus xanthus
Description	Repair of DNA damage is essential for genome integrity. DNA damage elicits a DNA damage response (DDR) that includes error-free and error-prone, i.e. mutagenic, repair. The SOS response is a widely conserved system in bacteria that regulates the DDR and depends on the recombinase RecA and the transcriptional repressor LexA. However, RecA/LexA-independent DDRs have been identified in several bacterial species. Here, using a whole-cell, label-free quantitative proteomics approach, we map the proteomic response in Myxococcus xanthus to mitomycin C treatment and the lack of LexA. In doing so, we confirm a LexA-independent DDR in M. xanthus. Using a candidate approach, we identify DdiA, a transcriptional regulator of the XRE family, and demonstrate that it regulates a subset of the LexA-independent DDR genes. Further, we show that ddiA expression is activated heterogeneously in a subpopulation of cells in the absence of exogenous genotoxic stress and is reversibly activated population-wide in response to such stress. We show that DdiA, indirectly or directly, activates the expression of dnaE2, which encodes the DnaE2 error-prone DNA polymerase, and inhibits the expression of recX, which encodes RecX, a negative regulator of RecA. Accordingly, the ΔddiA mutant has a lower mutation frequency than the wild-type but also a fitness defect, suggesting that DdiA mediates a trade-off between fitness and mutagenesis. We speculate that the DdiA-dependent response is tailored to counter replication stress, thereby preventing the induction of the complete RecA/LexA-dependent DDR in the absence of exogenous genotoxic stress.
HostingRepository	PRIDE
AnnounceDate	2025-02-12
AnnouncementXML	Submission_2025-02-12_00:43:50.671.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Timo Glatter
SpeciesList	scientific name: Myxococcus xanthus DK 1622; NCBI TaxID: 246197;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-11 08:46:56	ID requested
⏵ 1	2025-02-12 00:43:51	announced

Dataset with its publication pending

submitter keyword: Myxococcus xanthus ,DNA damage

Timo Glatter
contact affiliation	Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany
contact email	timo.glatter@mpi-marburg.mpg.de
lab head
Timo Glatter
contact affiliation	Max Planck Institute for Terrestrial Microbiology Marburg
contact email	timo.glatter@mpi-marburg.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060688
     1. Label: PRIDE project
     2. Name: DdiA, an XRE family transcriptional regulator, regulates a LexA-independent DNA damage response in Myxococcus xanthus