Molecular Systems Biology 7 Article number: 528 doi:10.1038/msb.2011.58
Published online: 30 August 2011
Citation: Molecular Systems Biology 7:528
The essential genome of a bacterium
Beat Christen1,a, Eduardo Abeliuk1,2,a, John M Collier3, Virginia S Kalogeraki1, Ben Passarelli3,4, John A Coller3, Michael J Fero1, Harley H McAdams1 & Lucy Shapiro1
Department of Developmental Biology, Stanford University, Stanford, CA, USA
Department of Electrical Engineering, Stanford University, Stanford, CA, USA
Functional Genomics Facility, Stanford University, Stanford, CA, USA
Stem Cell Institute Genome Center, Stanford University, Stanford, CA, USA
Correspondence to: Lucy Shapiro1 Department of Developmental Biology, Stanford University, B300 Beckman Center, Stanford, CA 94305, USA. Tel.: +1 650 725 7678; Fax: +1 650 725 7739; Email: shapiro@stanford.edu
Received 1 June 2011; Accepted 13 July 2011; Published online 30 August 2011
aThese authors contributed equally to this work
Abstract
Caulobacter crescentus is a model organism for the integrated circuitry that runs a bacterial cell cycle. Full discovery of its essential genome, including non-coding, regulatory and coding elements, is a prerequisite for understanding the complete regulatory network of a bacterial cell. Using hyper-saturated transposon mutagenesis coupled with high-throughput sequencing, we determined the essential Caulobacter genome at 8 bp resolution, including 1012 essential genome features: 480 ORFs, 402 regulatory sequences and 130 non-coding elements, including 90 intergenic segments of unknown function. The essential transcriptional circuitry for growth on rich media includes 10 transcription factors, 2 RNA polymerase sigma factors and 1 anti-sigma factor. We identified all essential promoter elements for the cell cycle-regulated genes. The essential elements are preferentially positioned near the origin and terminus of the chromosome. The high-resolution strategy used here is applicable to high-throughput, full genome essentiality studies and large-scale genetic perturbation experiments in a broad class of bacterial species.
Keywords: functional genomics; next-generation sequencing; systems biology; transposon mutagenesis
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