title: Clusters of proteins in archaeal and bacterial proteomes using compositional analysis.
abstract: In silico proteomics complements computational genomics in characterizing genome evolution. Here we examine cluster patterns in archaeal and bacterial proteomes using compositional properties of protein sequences in contrast to the traditionally used sequence alignment procedures. Application of standard Principal Component Analysis to the multi-dimensional data identified cluster patterns. Two types of cluster patterns exist in bacterial proteomes. Proteomes of type I have one major cluster with few isolated points in space revealing an underlying largely homogeneous compositional structure. In type II proteomes two clusters of protein distribution were discernible. The two clusters differ in size and were separated from each other although the boundary was somewhat fuzzy. Proteins falling in the major cluster were labeled as 'typical' and proteins of the minor cluster were called 'atypical'. The atypical proteins were mapped to Cluster of Orthologous Groups. Species distribution in COGs maps with respect to atypical proteins illuminated the biological relationships of extreme diversity among the archaeal members and of diversity among bacteria in relation to their niche. Amino acids that were over-represented in the atypical proteins had higher biosynthetic cost compared to 'typical' ribosomal proteins. However, archaea and bacteria economize by preferring the less costly amino acid to others closely related in chemical structure. Further, over-representation of serine in atypical proteins of archaeal members suggests re-examining these proteomes for the presence of Serine/Threonine phosphatases and kinases in Archaea. Our computational procedure can serve as a useful addition to the existing tools for carrying out in silico proteomics.
authors.affiliation: G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India. tannistha_cbt@yahoo.com
authors.forename: Tannistha
authors.initials: T
authors.lastname: Nandi
authors.forename: Samir K
authors.initials: SK
authors.lastname: Brahmachari
authors.forename: Krishnamoorthy
authors.initials: K
authors.lastname: Kannan
authors.forename: Srinivasan
authors.initials: S
authors.lastname: Ramachandran
mesh_terms: D019843:Archaeal Proteins / Q000145:classification*; D001426:Bacterial Proteins / Q000145:classification*; D019295:Computational Biology / Q000379:methods*; D020543:Proteome / Q000145:classification*; D040901:Proteomics / Q000379:methods*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D020543:Proteome