PXD036040

PXD036040 is an original dataset announced via ProteomeXchange.

Title	Recognition of DNA damage lesions across the tree of life
Description	Protecting the integrity of their genome is critical to all species. The surveillance and maintenance of the genome of every organism is orchestrated by a highly regulated combination of DNA damage response and specific DNA repair pathways. Two of these critical pathways are base excision repair (BER) and ribonucleotide excision repair (RER). Here, we investigate the phylogenetic diversity in the recognition and repair of three well-established DNA lesions, primarily repaired by BER or RER: 1) 8-oxoguanine, 2) an abasic site, and 3) incorporated ribonucleotide in DNA in E. coli, B. subtilis, H. salinarum, T. brucei, T. thermophila, S. cerevisiae, S. pombe, C. elegans, human HeLa and HEK293 cells, A. thaliana, and Z. mays. Using quantitative mass spectrometry, we identified 337 enriched interactors across these species. Of these proteins, 140 were previously characterized to be involved in DNA repair, and 39 proteins were newly identified due to their homology to previously studied repair proteins. For 10 of the 11 species, we identify unique, uncharacterized proteins that lack homology to any protein within the included 11 species. Our study emphasizes strong crosstalk between RER and BER and highlights the evolutionary conservation of this cross recognition across all domains of life.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:56:48.745.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	F Butter
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Halobacterium salinarum; NCBI TaxID: 2242; scientific name: Trypanosoma brucei; NCBI TaxID: 5691; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Zea mays (Maize); NCBI TaxID: 4577; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-12 13:39:14	ID requested
1	2023-07-20 12:36:51	announced
2	2023-11-14 09:03:58	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:56:53	announced	2024-10-22: Updated project metadata.

10.1016/j.isci.2023.106778;

Nischwitz E, Schoonenberg VAC, Fradera-Sola A, Dejung M, Vydzhak O, Levin M, Luke B, Butter F, Scheibe M, DNA damage repair proteins across the Tree of Life. iScience, 26(6):106778(2023) [pubmed]

submitter keyword: LC-MS/MS

Falk Butter
contact affiliation	Institute of Molecular Biology (IMB)
contact email	f.butter@imb.de
lab head
F Butter
contact affiliation	Quantitative Proteomics Institute of Molecular Biology (IMB)
contact email	f.butter@imb-mainz.de
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/2023/07/PXD036040

PRIDE project URI

• PRIDE
  1. PXD036040
     1. Label: PRIDE project
     2. Name: Recognition of DNA damage lesions across the tree of life