PXD062120

PXD062120 is an original dataset announced via ProteomeXchange.

Title	Propensity for proto-gene emergence in bacteria
Description	The birth of new genes from non-coding sequences has been postulated to be preceded by a proto-gene phase, in which a sequence is translated into protein but does not exhibit hallmarks of a clear function. Despite the abundance of such proto-genes in bacterial genomes, the frequency of their emergence and whether they actually act as precursors of new genes in natural populations are still open questions. To address these issues, we applied a combination of transcriptomic, proteomic and comparative genomic approaches to identify and analyze hundreds of novel bacterial protein-coding genes that have previously escaped annotation. These novel proteins, including many that are widely conserved across genera, display sequence properties indistinguishable from the non-coding regions of the genome, suggesting that the vast majority are evolving neutrally. We provide evidence of de novo emergence of three proto-genes within the history of the E. coli species; however, most such elements are formed via the mutational modification of existing open reading frames. Contrary to expectations, we discover that proto-genes emerge at a uniform rate across distant bacterial taxa despite significant differences in their genomic characteristics, suggesting the presence of taxon-specific mechanisms that regulate their origination and persistence.
HostingRepository	PRIDE
AnnounceDate	2025-09-19
AnnouncementXML	Submission_2025-09-19_10:01:37.758.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD062120
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Md Hassan uz-Zaman
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Thermo Scientific instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-21 08:06:04	ID requested
⏵ 1	2025-09-19 10:01:38	announced

10.6019/PXD062120;

submitter keyword: Proto-genes, mass spectrometry, bacteria, De novo gene evolution

Howardh Ochman
contact affiliation	Molecular Biosciences, University of Texas at Austin
contact email	howard.ochman@austin.utexas.edu
lab head
Md Hassan uz-Zaman
contact affiliation	Postdoctoral Fellow, Molecular Biosciences, University of Texas at Austin
contact email	h.uzzaman@utexas.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062120
     1. Label: PRIDE project
     2. Name: Propensity for proto-gene emergence in bacteria