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Related Experiment Videos

Simple sequence proteins in prokaryotic proteomes.

Mekapati Bala Subramanyam1, Muthiah Gnanamani, Srinivasan Ramachandran

  • 1G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall road, Delhi-110007, India. baloomek@yahoo.com

BMC Genomics
|June 10, 2006
PubMed
Summary

Simple Sequence Proteins (SSPs) are influenced by genomic factors like base composition and duplications. Their amino acid preferences are linked to low biosynthetic costs, with SSPs favoring cell surface functions over metabolism.

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Simple Sequence Proteins (SSPs) are characterized by non-globularity, disease association, signaling roles, and post-translational modifications.
  • SSPs contribute to genetic and phenotypic variation.
  • Analysis of 249 prokaryotic proteomes provides insights into SSP genomic properties.

Purpose of the Study:

  • To examine the genomic properties of Simple Sequence Proteins (SSPs) across a diverse range of prokaryotic proteomes.
  • To investigate the factors influencing the proportion and characteristics of SSPs within different species.

Main Methods:

  • Comparative genomic analysis of 249 prokaryotic proteomes.
  • Examination of proteome size, genomic GC content, mutational bias, and lifestyle factors.

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  • Analysis of amino acid composition and functional associations of SSPs.

    • Main Results:

    • SSPs are a minority protein group whose proportion increases with proteome size, influenced by genomic base composition and duplications.
    • Amino acid preferences in SSPs show a trend towards low biosynthetic cost; specific amino acids like Alanine, Glycine, Leucine, and Valine are abundant across varying GC content.
    • SSPs are preferentially associated with cell surface, cell membrane, and transport functions, with a negative association with metabolism.

    Conclusions:

    • Genomic forces, including base compositional bias and duplications, significantly shape SSP growth and patterns.
    • Amino acid preferences in SSPs are driven by biosynthetic cost, evolutionary age, and codon composition, with restricted abundance of charged amino acids.
    • SSPs are functionally linked to cell surface and interface roles, contrasting with the preference for globular proteins in metabolism.