Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.
Comparative analysis of the complete genome sequences from a variety of poorly studied organisms aims at predicting ecological and behavioral properties of these organisms and helping in characterizing their habitats. This task requires finding appropriate descriptors that could be correlated with the core traits of each system and would allow meaningful comparisons. Using the relatively simple bacterial models, first attempts have been made to introduce suitable metrics to describe the complexity of organism's signaling machinery, which included introducing the "bacterial IQ" score. Here, we use an updated census of prokaryotic signal transduction systems to improve this parameter and evaluate its consistency within selected bacterial phyla. We also introduce a more elaborate descriptor, a set of profiles of relative abundance of members of each family of signal transduction proteins encoded in each genome. We show that these family profiles are well conserved within each genus and are often consistent within families of bacteria. Thus, they reflect evolutionary relationships between organisms as well as individual adaptations of each organism to its specific ecological niche.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA. galperin@ncbi.nlm.nih.gov
Michael Y
MY
Galperin
Roger
R
Higdon
Eugene
E
Kolker
D000222:Adaptation, Physiological; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D017753:Ecosystem; D016680:Genome, Bacterial; D008954:Models, Biological; D010802:Phylogeny; D015398:Signal Transduction / Q000235:genetics* / Q000502:physiology*; D049490:Systems Biology
D001426:Bacterial Proteins