Bacillus subtilis

The accumulation, over more than half a century, of detailed knowledge of the biochemistry, genetics and physiology of Bacillus subtilis , enhanced in recent years by a number of systematic ‘omics’ studies, has resulted in the recognition of this bacterium as a highly amenable chassis for synthetic biology. This chapter describes the features of this bacterium that support this recognition. Although the genome of B. subtilis was first published more that 15 years ago, recent genomic and transcriptomic studies have helped to provide more accurate and detailed descriptions of the genome and are main distinguishing features. A key feature of B. subtilis is the ease with which its genome can be engineered, and the principles underlying approaches to engineer changes in its genome are outlined in detail. These include the generation of markerless and synthetic lethal mutations and the use of integration and autonomously replicating vectors and promoters for controlled gene expression. The impact of a recent detailed analysis of the B. subtilis transcriptome is discussed, with pointers to the relevant web and database resources. Methodologies associated with reporter genes, including gene libraries, life cell arrays and the analysis of population heterogeneity, are reviewed. Sections on the analysis of the proteome and metabolome are also included, although these are dealt with in more detail in Volume 39 of Methods in Microbiology , entitled Systems Biology of Bacteria. Finally, the use of B. subtilis as a versatile chassis is described, including the availability of parts, systems and devices, computational tools and resources.