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Pattern analysis of 5S rRNA.

M Eigen, B Lindemann, R Winkler-Oswatitsch

    Proceedings of the National Academy of Sciences of the United States of America
    |April 1, 1985
    PubMed
    Summary
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    Analysis of 200 5S ribosomal RNA (rRNA) sequences reveals a biased base triplet pattern in evolutionary relationships. This pattern, strongest in eubacteria and archaebacteria, shows a preference for guanine and cytosine across all sequences.

    Area of Science:

    • Molecular Biology
    • Evolutionary Biology
    • Bioinformatics

    Background:

    • 5S ribosomal RNA (rRNA) is a crucial component of ribosomes across all domains of life.
    • Understanding the evolutionary relationships and sequence features of 5S rRNA can provide insights into cellular evolution.

    Purpose of the Study:

    • To analyze evolutionary kinship and sequential features of approximately 200 5S rRNA sequences.
    • To identify group-specific base occupation patterns and their evolutionary implications.

    Main Methods:

    • Comparative sequence analysis of 5S rRNA from diverse organisms (eubacteria, chloroplasts, mitochondria, archaebacteria, eukaryotes).
    • Development of group-specific occupation schemes for 149 aligned positions.
    • Statistical analysis of base triplet frequencies and patterns in different reading frames.

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    Main Results:

    • A strongly biased base triplet pattern was observed in one of three reading frames across various 5S rRNA sequences.
    • This bias was most pronounced in eubacterial, chloroplastic, and archaebacterial sequences, but also detectable in mitochondrial and eukaryotic cytoplasmic sequences.
    • Triplet frequencies followed the order RNY > RNR > YNY > YNR, with a strong preference for guanine or cytosine at all positions.

    Conclusions:

    • The observed base triplet patterns are a conserved feature across diverse 5S rRNA sequences, reflecting evolutionary constraints.
    • These findings suggest underlying selection pressures influencing 5S rRNA sequence composition and evolution.
    • The study provides a detailed framework for understanding 5S rRNA sequence evolution and functional constraints.