PXD052373-2

PXD052373 is an original dataset announced via ProteomeXchange.

Title	Diribonuclease activity eliminates toxic diribonucleotide accumulation
Description	RNA degradation is a central process in cells that is vital for transcriptional regulation. The degradation process is initiated by endoribonucleolytic fragmentation of long RNA polymers, followed by exoribonucleolytic cleavage to release mononucleotides from the fragment ends. In this process, the degradation of short oligonucleotides, especially diribonucleotides, into mononucleotides requires specific enzymatic activity, which in Gram-negative bacteria is provided by oligoribonuclease (Orn). Orn is unique in that it is the only essential exoribonuclease in Escherichia coli. Recent studies have shown that Orn cleaves only diribonucleotides under physiological conditions, suggesting that the accumulation of dinucleotides poisons cells. Yet, related organisms, such as Pseudomonas aeruginosa, display a growth defect but are viable without Orn, contesting its essentiality. Here, we took advantage of P. aeruginosa orn mutants to elucidate the mechanisms of their survival. Genetic screening for suppressors that restored colony morphology identified yciV. Purified YciV exhibited diribonuclease activity. YciV is present in all g-proteobacteria, suggesting that YciV from P. aeruginosa is distinct from its E. coli ortholog. Phylogenetic analysis revealed differences between the two orthologs that were mapped to the active site of the enzyme and correlated with differences in substrate profiles. The expression of P. aeruginosa YciV in E. coli eliminated the necessity of orn. Similarly, the deletion of yciV from P. aeruginosa caused orn to become essential. Together, these results show that diribonuclease activity is required in g-proteobacteria and that diribonucleotides are utilized to monitor the efficacy of RNA degradation. Because Orn is found in higher eukaryotes, these observations indicate a conserved mechanism for monitoring RNA degradation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:58:42.174.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD052373
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Conor Jenkins
SpeciesList	scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Pseudomonas aeruginosa PA14; NCBI TaxID: 652611;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-19 06:14:01	ID requested
1	2024-09-16 12:15:48	announced
⏵ 2	2024-10-22 06:58:42	announced	2024-10-22: Updated project metadata.

10.6019/PXD052373;

10.1016/j.celrep.2024.114759;

Kim SK, Orr MW, Turdiev H, Jenkins CC, Lormand JD, Myers TM, Burnim AA, Carter JA, Kung WC, Jiang X, Sondermann H, Winkler WC, Lee VT, Diribonuclease activity eliminates toxic diribonucleotide accumulation. Cell Rep, 43(9):114759(2024) [pubmed]

submitter keyword: Orn,RNA degradation, YCIV, LCMS, Bacteria, Pseudomonas aeruginosa

Vincent T. Lee
contact affiliation	University of Maryland - College Park Molecular & Cellular Biology
contact email	vtlee@umd.edu
lab head
Conor Jenkins
contact affiliation	US Army DEVCOM CBC
contact email	conor.c.jenkins.civ@army.mil
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD052373
     1. Label: PRIDE project
     2. Name: Diribonuclease activity eliminates toxic diribonucleotide accumulation