PXD023992

PXD023992 is an original dataset announced via ProteomeXchange.

Title	Spotlight on alternative frame coding: two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection
Description	The existence of overlapping genes (OLGs) with significant coding overlaps revolutionises our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the medically important Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing data. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically highly restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.
HostingRepository	PRIDE
AnnounceDate	2022-03-21
AnnouncementXML	Submission_2022-03-21_07:04:03.593.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christina Ludwig
SpeciesList	scientific name: Pseudomonas aeruginosa PAO1; NCBI TaxID: 208964;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-04 04:05:18	ID requested
⏵ 1	2022-03-21 07:04:04	announced

Kreitmeier M, Ardern Z, Abele M, Ludwig C, Scherer S, Neuhaus K, are translated and under purifying selection. iScience, 25(2):103844(2022) [pubmed]

submitter keyword: mass spectrometry, orphan genes, ribosome profiling, overprinting,Overlapping genes, de novo gene origin

Christina Ludwig
contact affiliation	Bavarian Center for Biomolecuar Mass Spectrometry (BayBioMS, Technical University of Munich (TUM), Freising, Germany
contact email	tina.ludwig@tum.de
lab head
Christina Ludwig
contact affiliation	TU Munich
contact email	tina.ludwig@tum.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023992
     1. Label: PRIDE project
     2. Name: Spotlight on alternative frame coding: two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection