The low complexity proteins from enteric pathogenic bacteria: taxonomic parallels embedded in diversity.
The number and functions of the low complexity (LC) proteins from four enteric bacterial pathogens Escherichia coli O157, Vibrio cholerae, Helicobacter pylori and Campylobacter jejuni were compared. For this purpose the LC proteins were grouped into 3 categories for pairwise comparisons. These were COMMON, VARIANT and LC proteins with No Homologues (LCNH). Homologous LC proteins in both species in a given pairwise comparison were grouped as COMMON. LC Proteins of same function but not of low complexity in either of the species in a given pair were grouped as VARIANT. LC proteins without any homologues in either species were grouped as LCNH. Conservation patterns were inferred by comparing them under 3 functional classes CELLULAR PROCESSES (CP), TRANSPORT and MEMBRANE ASSOCIATED (TM) and CHARACTERISTIC (CH). In the COMMON category, highest similarity was found between E. coli O157 and V. cholerae on the one hand and H. pylori and C. jejuni on the other under the functional class CP. This parallels taxonomic classification in that E. coli and V. cholerae are classified under gamma subdivision of proteobacteria whereas H. pylori and C. jejuni are classified under the epsilon subdivision. The data from LCNH group, although more diffuse, was complementary the to pattern drawn from COMMON category in that the numbers of LCNH in the pair [E. coli O157, V. cholerae] and in [H. pylori, C. jejuni] were lowest. No consistent patterns were observed in the VARIANT category. These observations indicate that although low complexity segments are thought to undergo variations, species patterns do exist in a limited set of low complexity proteins that parallels taxonomic classification.
Nandi
Tannistha
T
G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India.
Kannan
Krishnamoorthy
K
Ramachandran
Srinivasan
S
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics*; D016123:Campylobacter jejuni / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics; D008969:Molecular Sequence Data; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D014734:Vibrio cholerae / Q000235:genetics
D001426:Bacterial Proteins