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Adaptive evolution in LINE-1 retrotransposons.

S Boissinot1, A V Furano

  • 1Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA.

Molecular Biology and Evolution
|November 24, 2001
PubMed
Summary
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Human evolution saw active LINE-1 (L1) retrotransposons evolve through five families over 25 Myr. Positive selection initially drove changes in the L1 ORF1 protein

Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Genomics

Background:

  • LINE-1 (L1) retrotransposons are mobile genetic elements active in the human genome.
  • Understanding L1 evolution provides insights into genome dynamics and host-parasite interactions.

Purpose of the Study:

  • To investigate the sequence evolution of the active human LINE-1 (L1) retrotransposon lineage over the past 25 million years.
  • To identify periods of positive and purifying selection acting on specific L1 protein domains.

Main Methods:

  • Comparative sequence analysis of five major L1 element families (L1PA5 to L1PA1).
  • Analysis of substitution rates (nonsynonymous vs. synonymous) in different L1 open-reading frames (ORFs).
  • Statistical assessment of selection pressures on L1 protein domains.

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Main Results:

  • A single lineage of L1 elements evolved through five families (L1PA5-L1PA1) over ~25 Myr.
  • The coiled coil region of ORF1p experienced positive selection from L1PA5 to L1PA3B, indicating adaptation.
  • This region showed reduced change from L1PA3B to L1PA1, suggesting a shift in selective pressure.

Conclusions:

  • Selective pressure on the L1 coiled coil region has changed over evolutionary time.
  • Rapid amino acid replacement in the coiled coil region may reflect adaptation to genomic or host factors.
  • Other L1 domains, including ORF2 and the ORF1 nucleic acid-binding domain, are highly conserved under purifying selection.