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*Genes and Gene Therapy

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Journal of Bacteriology, January 2009, p. 32-41, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01084-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes{triangledown}

Amoolya H. Singh, Tobias Doerks, Ivica Letunic, Jeroen Raes, and Peer Bork*

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany

Received 5 August 2008/ Accepted 1 October 2008

The emerging coverage of diverse habitats by metagenomic shotgun data opens new avenues of discovering functional novelty using computational tools. Here, we apply three different concepts for predicting novel functions within light-mediated microbial pathways in five diverse environments. Using phylogenetic approaches, we discovered two novel deep-branching subfamilies of photolyases (involved in light-mediated repair) distributed abundantly in high-UV environments. Using neighborhood approaches, we were able to assign seven novel functional partners in luciferase synthesis, nitrogen metabolism, and quorum sensing to BLUF domain-containing proteins (involved in light sensing). Finally, by domain analysis, for RcaE proteins (involved in chromatic adaptation), we predict 16 novel domain architectures that indicate novel functionalities in habitats with little or no light. Quantification of protein abundance in the various environments supports our findings that bacteria utilize light for sensing, repair, and adaptation far more widely than previously thought. While the discoveries illustrate the opportunities in function discovery, we also discuss the immense conceptual and practical challenges that come along with this new type of data.

* Corresponding author. Mailing address: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Phone: 49-6221-387-8526. Fax: 49-6221-387517. E-mail: bork{at}embl.de

{triangledown} Published ahead of print on 10 October 2008.

Journal of Bacteriology, January 2009, p. 32-41, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01084-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



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