A vast collection of microbial genes that are toxic to bacteria

  1. Rotem Sorek1,6
  1. 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel;
  2. 2Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA;
  3. 3DOE Joint Genome Institute, Walnut Creek, California 94598, USA;
  4. 4Genome Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    1. 5 These authors contributed equally to this work.

    Abstract

    In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes, we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes, our assays revealed novel toxins and restriction enzymes, and new classes of small, non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short, toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator DnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.

    Footnotes

    • 6 Corresponding author.

      E-mail rotem.sorek{at}weizmann.ac.il.

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.133850.111.

    • Received October 25, 2011.
    • Accepted January 25, 2012.
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