Issue 4, 2010
From the journal:

Molecular BioSystems

Interplay of heritage and habitat in the distribution of bacterial signal transduction systems†‡

Michael Y. Galperin,*a   Roger Higdonbc  and  Eugene Kolkerbcd  

* Corresponding authors

a National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
E-mail: galperin@ncbi.nlm.nih.gov
Fax: +1 301 435 7793
Tel: +1 301 435 5910

b Bioinformatics & High-throughput Analysis Laboratory, Seattle Children’s Research Institute, 1900 9th Ave., Seattle, Washington 98101, USA

c Predictive Analytics, Seattle Children’s Hospital, 4800 Sand Point Way NE, Seattle, Washington 98105, USA

d Biomedical and Health Informatics Division, Medical Education and Biomedical Health Department, School of Medicine, University of Washington, Seattle, Washington 98105, USA

Abstract

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.

Graphical abstract: Interplay of heritage and habitat in the distribution of bacterial signal transduction systems

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Article information

DOI
https://doi.org/10.1039/B908047C
Article type
Paper
Submitted
22 Apr 2009
Accepted
22 Dec 2009
First published
09 Feb 2010

Mol. BioSyst., 2010,6, 721-728

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Interplay of heritage and habitat in the distribution of bacterial signal transduction systems

M. Y. Galperin, R. Higdon and E. Kolker, Mol. BioSyst., 2010, 6, 721 DOI: 10.1039/B908047C

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