Downloaded from www.microbiologyresearch.org by IP: 54.157.140.51 On: Fri, 11 Mar 2016 02:59:37 Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis Christoph R. Lammers, 1 3 Lope A. Flo ´ rez, 1 3 Arne G. Schmeisky, 1 Sebastian F. Roppel, 1 Ulrike Ma ¨ der, 2 Leendert Hamoen 3 and Jo ¨ rg Stu ¨ lke 1 Correspondence Jo ¨rg Stu ¨ lke jstuelk@gwdg.de 1 Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Go ¨ ttingen, Germany 2 Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-Universita ¨t Greifswald, Germany 3 Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK Received 23 October 2009 Revised 30 November 2009 Accepted 1 December 2009 Bacillus subtilis is the model organism for a large group of Gram-positive bacteria, the Firmicutes. Several online databases have been established over time to manage its genetic and metabolic information, but they differ greatly in their rate of update and their focus on B. subtilis. Therefore, a European systems biology consortium called for an integrated solution that empowers its users to enrich online content. To meet this goal we created SubtiWiki and SubtiPathways, two complementary online tools for gene and pathway information on B. subtilis 168. SubtiWiki (http://subtiwiki.uni-goettingen.de/) is a scientific wiki for all genes of B. subtilis and their protein or RNA products. Each gene page contains a summary of the most important information; sections on the gene, its product and expression; sections concerning biological materials and laboratories; and a list of references. SubtiWiki has been seeded with key content and can be extended by any researcher after a simple registration, thus keeping it always up to date. As a complement, SubtiPathways (http://subtipathways.uni-goettingen.de/) is an online tool for navigation of the metabolism of B. subtilis and its regulation. Each SubtiPathways diagram presents a metabolic pathway with its participating enzymes, together with the regulatory mechanisms that act on their expression and activity, in an intuitive interface that is based on Google Maps. Together, SubtiWiki and SubtiPathways provide an integrated view of the processes that make up B. subtilis and its components, making it the most comprehensive web resource for B. subtilis researchers. INTRODUCTION Bacillus subtilis serves as the model for a large group of Gram-positive bacteria with a low G+C content in their genomic DNA: the Firmicutes. This group includes important pathogens such as Staphylococcus aureus, Listeria monocytogenes, Bacillus anthracis and Clostridium botulinum. The lactic acid bacteria, which are widely used in the dairy industry, important enzyme producers such as Bacillus licheniformis, and the insect pathogen Bacillus thuringiensis, which is used for crop protection, are also all members of the Firmicutes phylum. Finally, the mollicutes, such as Mycoplasma genitalium, are a phylogenetic branch of the Firmicutes that experienced substantial evolution leading to the smallest genomes that allow host-independ- ent life. The genome sequence of B. subtilis was first determined as a joint European and Japanese effort (Kunst et al., 1997). With the availability of the genome information and detailed experimental data on metabolic pathways and their players, the metabolism of B. subtilis is today quite well understood. There are models of the metabolic and regulatory pathways of B. subtilis available in the literature (Goelzer et al., 2008; Henry et al., 2009; Oh et al., 2007). Nonetheless, even today, more than 10 years after the publication of the original genome sequence, about 30 % of the genes of B. subtilis have no defined functions. However, sporadic pieces of information have become available for many of the unknown genes. This information is mainly derived from genome-level analysis such as proteomic and transcriptomic studies as well as from global interaction screenings. This information may provide clues to the function of a certain gene (e.g. if the gene is expressed 3These authors contributed equally to this work. Microbiology (2010), 156, 849–859 DOI 10.1099/mic.0.035790-0 035790 G 2010 SGM Printed in Great Britain 849