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Science 326 (5957): 1200-1201

Copyright © 2009 by the American Association for the Advancement of Science

Systems Biology

Excavating the Functional Landscape of Bacterial Cells

Howard Ochman, and Rahul Raghavan

There is a poster that charts the metabolic pathways of the model bacterium Escherichia coli, and our laboratory uses it as a reference to convert each new bacterial genome sequence into an atlas of encoded functions. This is a particularly satisfying endeavor and has been best applied to those host-dependent bacteria whose highly reduced genomes contain a subset of the genes in E. coli: If a particular gene or pathway is eroded or absent, it is assumed that the bacterium is deficient in that activity and no longer has a need for the trait in its current circumstances. However, this linear mapping of genes to function rarely considers how a cell actually accomplishes the processes it has retained. Genes are viewed simply as performing a specified function despite the many internal and external factors that might affect their implementation. Three papers in this issue—by Güell et al. on page 1268 (1), Yus et al. on page 1263 (2), and Kühner et al. on page 1235 (3)—report features of transcriptional control and protein organization that are much more subtle and intricate than were previously considered possible in bacteria, and in many ways, appear similar to mechanisms in eukaryotes.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85718, USA.

E-mail: hochman{at}

Mapping Condition-Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae.
M. C. Jewett, C. T. Workman, I. Nookaew, F. A. Pizarro, E. Agosin, L. I. Hellgren, and J. Nielsen (2013)
g3 3, 1979-1995
   Abstract »    Full Text »    PDF »
Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria.
Y. D. Kelkar and H. Ochman (2013)
Genetics 193, 303-307
   Abstract »    Full Text »    PDF »

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