title: Simple sequence proteins in prokaryotic proteomes.
abstract: BACKGROUND
  The structural and functional features associated with Simple Sequence Proteins (SSPs) are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs.
  
  
  RESULTS
  SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in genomic GC, mutational bias, life style, and pathogenicity. Their proportion in each proteome is strongly influenced by genomic base compositional bias. In most species simple duplications is favoured, but in a few cases such as Mycobacteria, large families of duplications occur. Amino acid preference in SSPs exhibits a trend towards low cost of biosynthesis. In SSPs and in non-SSPs, Alanine, Glycine, Leucine, and Valine are abundant in species widely varying in genomic GC whereas Isoleucine and Lysine are rich only in organisms with low genomic GC. Arginine is abundant in SSPs of two species and in the non-SSPs of Xanthomonas oryzae. Asparagine is abundant only in SSPs of low GC species. Aspartic acid is abundant only in the non-SSPs of Halobacterium sp NRC1. The abundance of Serine in SSPs of 62 species extends over a broader range compared to that of non-SSPs. Threonine(T) is abundant only in SSPs of a couple of species. SSPs exhibit preferential association with Cell surface, Cell membrane and Transport functions and a negative association with Metabolism. Mesophiles and Thermophiles display similar ranges in the content of SSPs.
  
  
  CONCLUSIONS
  Although SSPs are a minority, the genomic forces of base compositional bias and duplications influence their growth and pattern in each species. The preferences and abundance of amino acids are governed by low biosynthetic cost, evolutionary age and base composition of codons. Abundance of charged amino acids Arginine and Aspartic acid is severely restricted. SSPs preferentially associate with cell surface and interface functions as opposed to metabolism, wherein proteins of high sequence complexity with globular structures are preferred. Mesophiles and Thermophiles are similar with respect to the content of SSPs. Our analysis serves to expand the commonly held views on SSPs.
authors.affiliation: G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall road, Delhi-110007, India. baloomek@yahoo.com
authors.forename: Mekapati Bala
authors.initials: MB
authors.lastname: Subramanyam
authors.forename: Muthiah
authors.initials: M
authors.lastname: Gnanamani
authors.forename: Srinivasan
authors.initials: S
authors.lastname: Ramachandran
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D019843:Archaeal Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D001482:Base Composition / Q000235:genetics; D020440:Gene Duplication; D020745:Genome, Archaeal / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D011387:Prokaryotic Cells / Q000737:chemistry*; D020543:Proteome / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins; D001426:Bacterial Proteins; D020543:Proteome