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Single-Frame, Multiple-Frame and Framing Motifs in Genes.

Christian J Michel1

  • 1Theoretical bioinformatics, ICube, CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67400 Illkirch, France. c.michel@unistra.fr.

Life (Basel, Switzerland)
|February 13, 2019
PubMed
Summary

This study introduces novel gene motif classes, single-frame (SF) and multiple-frame (MF) motifs, revealing complementarity

Keywords:
antiparallel and parallel sequencesearly life genesframing motifsgene codingmultiple-frame motifssingle-frame motifs

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Area of Science:

  • Genomics and Molecular Biology
  • Bioinformatics and Computational Biology
  • Origin of Life Studies

Background:

  • The distribution and properties of gene motifs, particularly novel classes, remain underexplored.
  • Understanding gene coding mechanisms requires analyzing sequence patterns and their decoding properties.
  • The role of specific sequence motifs in the early evolution of the genetic code is debated.

Purpose of the Study:

  • To investigate the distribution of newly defined single-frame (SF) and multiple-frame (MF) gene motifs.
  • To analyze the impact of constraints like codons and complementarity on motif distributions.
  • To explore the potential role of these motifs in the origin and evolution of the genetic code.

Main Methods:

  • Definition and classification of SF and MF motifs based on trinucleotide occurrences in different reading frames.
  • Computational analysis of motif distributions with and without constraints (initiation/stop codons, periodic codons, complementarity).
  • Investigation of SF and MF dipeptides associated with their respective dicodons.

Main Results:

  • Identified and analyzed distributions of SF and MF motifs, including 5' unambiguous (5'U) motifs.
  • Demonstrated that complementarity (antiparallel and parallel) is fundamental for unambiguous trinucleotide decoding.
  • SF and MF motifs, along with framing (F) motifs, may have played roles in early gene coding and the development of the genetic code.

Conclusions:

  • Complementarity is a key property for gene coding, enabling unambiguous trinucleotide decoding.
  • SF and F motifs could be crucial for understanding the evolution of the genetic code, potentially acting before anticodon-amino acid interactions.
  • The study of SF and MF dipeptides offers insights into early biology and the origin of life.