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Nucleic Acids Research Advance Access published online on November 6, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn883
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Using shotgun sequence data to find active restriction enzyme genes

Yu Zheng, Janos Posfai, Richard D. Morgan, Tamas Vincze and Richard J. Roberts*

New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA

*To whom correspondence should be addressed. Tel: +1 978 380 7405; Fax: +1 978 380 7406; Email: roberts{at}neb.com

Received February 29, 2008. Revised October 11, 2008. Accepted October 20, 2008.

Whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a biological experiment. It determines which segments of the genome can be cloned into Escherichia coli and which cannot. By analyzing the complete set of sequences from such an experiment, it is possible to identify genes lethal to E. coli. Among this set are genes encoding restriction enzymes which, when active in E. coli, lead to cell death by cleaving the E. coli genome at the restriction enzyme recognition sites. By analyzing shotgun sequence data sets we show that this is a reliable method to detect active restriction enzyme genes in newly sequenced genomes, thereby facilitating functional annotation. Active restriction enzyme genes have been identified, and their activity demonstrated biochemically, in the sequenced genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus.


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