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Propensity for proto-gene emergence in bacteria.

Md Hassan Uz-Zaman1, Howard Ochman2

  • 1Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.

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|October 22, 2025
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Summary
This summary is machine-generated.

New genes arise from non-coding DNA through proto-genes, but these rarely evolve into functional genes. While proto-genes emerge uniformly across bacteria, most show neutral evolution, limiting their role as gene precursors.

Keywords:
BacteriaDe novo gene evolutionMass spectrometryProto-genes

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Gene birth from non-coding DNA is thought to involve a proto-gene phase.
  • Proto-genes lack clear function but are abundant in bacterial genomes.
  • The frequency of proto-gene emergence and their role as gene precursors remain unclear.

Purpose of the Study:

  • Investigate the emergence and evolutionary fate of proto-genes in bacteria.
  • Determine if proto-genes act as precursors for new functional genes.
  • Analyze the rate and regulation of proto-gene origination across bacterial taxa.

Main Methods:

  • Combined transcriptomic, proteomic, and comparative genomic analyses.
  • Identification and characterization of novel, unannotated bacterial protein-coding genes.
  • Assessment of sequence properties and evolutionary rates of novel proteins.

Main Results:

  • Hundreds of novel bacterial proteins, many conserved, were identified.
  • Most novel proteins exhibit neutral evolution, similar to non-coding DNA.
  • Only one de novo proto-gene emergence was rigorously confirmed in Escherichia coli.
  • Proto-genes emerge at a uniform rate across diverse bacterial taxa.
  • Taxon-specific mechanisms appear to regulate proto-gene origination and persistence.

Conclusions:

  • Proto-genes frequently emerge in bacterial populations.
  • Proto-gene sequence properties provide limited evidence for their role as new gene precursors.
  • Detecting de novo gene birth via proto-genes is challenging in bacterial genomes.