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Related Experiment Videos

RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins.

Noel G Faux1, Gavin A Huttley, Khalid Mahmood

  • 1Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.

Genome Research
|June 15, 2007
PubMed
Summary
This summary is machine-generated.

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Single amino acid repeats are common in proteins and linked to diseases. Genomic analysis reveals specific codon biases and mutation mechanisms, with conserved repeats under strong purifying selection.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Over 3% of human proteins contain single amino acid repeats (repeat-containing proteins, RCPs).
  • Expansion of certain repeats, like poly-Q and poly-A, is linked to neurological diseases.
  • Previous research suggested G+C-rich tracts and replication slippage drive homopeptide formation.

Purpose of the Study:

  • To conduct a large-scale genomic analysis of genes encoding RCPs across 13 species.
  • To develop an online database for comparing RCPs, homopeptides, and genetic tracts.
  • To investigate the variation and evolutionary pressures on homopeptides.

Main Methods:

  • Large-scale genomic analysis of RCP-encoding genes in 13 species.
  • Development of an online database (http://repeats.med.monash.edu.au/genetic_analysis/) for data access and analysis.

Related Experiment Videos

  • Comparative analysis of homopeptide composition, codon usage, and genetic variation.

    • Main Results:

    • A bias for a small subset of reiterated codons within homopeptides was observed, with no G+C or A+T bias relative to the transcriptome.
    • Single base pair transversions from homocodons are common, potentially reducing homopeptide mutation rates.
    • Conserved homopeptides are under stronger purifying selection than nonconserved ones.

    Conclusions:

    • Homopeptide formation is influenced by specific codon reiteration and unique mutation mechanisms.
    • Conserved homopeptides are evolutionarily constrained, indicating functional importance.
    • The developed database provides a valuable resource for studying repeat-containing proteins across species.