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Related Experiment Videos

Exploiting protein structure data to explore the evolution of protein function and biological complexity.

Russell L Marsden1, Juan A G Ranea, Antonio Sillero

  • 1Department of Biochemistry, University College London Gower Street, London WC1E 6BT, UK. marsden@biochem.ucl.ac.uk

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|March 10, 2006
PubMed
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Genome sequencing and structural genomics reveal universal protein domain families. Analysis shows expanded families in bacteria, particularly in metabolism and regulation, contributing to organismal complexity.

Area of Science:

  • Genomics
  • Structural Biology
  • Bioinformatics

Background:

  • Genome sequencing provides protein repertoires across life.
  • Structural genomics and advanced technologies expand knowledge of protein structures and families.
  • Sensitive methods detect remote sequence similarities, enabling domain mapping onto genomes.

Purpose of the Study:

  • To map protein domain structures from completed genomes to known families in the CATH database.
  • To analyze the distribution and evolutionary behavior of these domain families across different organisms.
  • To understand the contribution of domain families to functional repertoires and biological complexity.

Main Methods:

  • Utilized robust protocols to assign genome sequences to domain structures in the CATH database.

Related Experiment Videos

  • Analyzed the distribution of domain families across bacterial genomes.
  • Compared domain family distributions across all kingdoms of life.
  • Performed structural analyses of metabolic families.

    • Main Results:

    • Up to 60% of domain sequences in genomes could be assigned to known structural families.
    • Identified over 300 universal domain families in bacteria, with some significantly expanded.
    • Expanded bacterial families are primarily involved in metabolism and regulation.
    • Found approximately 140 universal domain families across all life kingdoms, with protein biosynthesis families being the largest conserved component.
    • Identified innovative families (metabolism, regulation) with complex evolutionary histories.

    Conclusions:

    • Protein domain families are widely distributed and contribute significantly to organismal functional repertoires and complexity.
    • Specific domain families, particularly those involved in metabolism and regulation, show significant expansion and innovation in bacteria.
    • Evolutionary analysis reveals diverse strategies, including altered domain partnerships and structural modifications, driving functional innovation in protein families.