Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 competence and sporulation. Genetic competence, defined as a state that permits the uptake of exogenous DNA, is widespread among both gram-positive and gram-negative bacteria. It is a genetically programmed state during which a small percentage of cells in a population can uptake DNA from the environment and integrate it into their chromosome [57]. Particu- larly, in the case of B. subtilis 168, it is thought that the greater DNA uptake efficiency of the strain is a consequence of a laboratory selection process [2]. Most proteins that form the complex responsible for mediating the binding and uptake of DNA are part of the core (ComEC, ComFA, ComGA) or are highly con- served (ComEA). The interaction of several of these competence-specific proteins in the complex has been demonstrated, as well as interactions with the highly conserved proteins RecA, SsbB, and Smf [58]. The master regulator of the process, the ComK transcrip- tion factor, binds to competence promoters to activate transcription of many genes. A feature of competence development is the stabilization of ComK by protein ComS [59]. While the gene coding for the ComK tran- scription factor is conserved in most Bacillus (absent in B. halodurans, B. clausii, and B. coahuilensis), ComS seems to be a specialization of the B. subtilis group. ComK is itself synthesized in response to the signal-transduction network, but most genes coding for the regulatory proteins that constitute this network are not conserved. Given the conservation of the transfor- mation machinery, it is of considerable interest to understand to what extent natural genetic competence can explain genetic variability by gene acquisition, at what frequency it occurs, and which signals trigger the competence state under specific environmental conditions. A defining feature of the Bacilli is the formation of a highly resistant non-reproductive structure called the spore. Within the Firmicutes, the genus Bacillus and Clostridium produce endospores. The primary function of most spores is to ensure the survival of a bacterium through periods of environmental stress. The resistance of a spore could be considered as a crucial survival fea- ture, and therefore sporulation genes would be expected to be part of the core genome. However, previous stu- dies have found, both experimentally and in silico, that there is great intra-specific [2,60] and inter-specific var- iation in sporulation genes. The variability of sporulation genes has been only superficially reported in these stu- dies and they have mainly included non-subtilis models such as B. cereus and B. anthracis. The sporulation process has been subjected to exten- sive review [51,61-64]. This morphogenetic process is triggered by conditions of starvation that result in a dis- tinct asymmetrically positioned septum that delimits the Page 10 of 17 fore-spore and is surrounded by two membrane layers. Peptidoglycan is deposited in the space between the membranes to form the cortex and additional proteins are deposited around the cortex to form the so-called spore coat of the forming endospore. Some Bacilli also have an outer membrane composed of lipid and protein called an exosporium. The spore can quickly outgrow into a vegetative bacterium upon stimulation by an environmental cue. Each of these stages has been documented and more than 200 regulatory and structural genes are known to be expressed in B. subtilis in a temporally regulated manner. Figure 4 depicts the conservation pattern of Kyoto Encyclopedia of Genes and Genomes’ (KEGG) BRITE hierarchy [65] that comprises 185 sporulation related genes. These sporulation and germination genes are arguably the best studied transition regulators. Clus- tering of the conserved/absent sporulation and compe- tence genes resulted in 4 clear groups that were arbitrarily denominated A through D. Group A, with 52 genes, contains all of the sporulation/competence core genes; group B, with 52 genes, shows great variability with an absence bias of genes in the extremophyle/aqua- tic Bacillus; Group C, with 43 genes, is conserved mainly among strains close to B. subtilis; and group D, with 35 genes, seems to represent the specialized genes of B. subtilis. Within the sporulation core (Group A), we found genes required for the temporal and spatial regulation of sporulation gene expression that depends on four sporu- lation-specific sigma factors (SigE, F, G, and K), all of which are part of the core (the apparent lack of conser- vation of sigK is due to the fact that in B. subtilis it is encoded by two separate genes which are merged upon entrance into sporulation). As shown for B. subtilis, the initiation of sporulation is dependent on the phosphory- lation of the two-component protein Spo0A, a transcrip- tion factor that controls a large number of genes. Spo0A is regulated through a phosphorylation cascade known as the phosphorelay. Sense input signals to Spo0A are given by histidine kinases, such as KinB, which are highly conserved (missing only in O. iheyensis). KbaA, the activator of KinB, is also present in the sporulation core. The number of sensor kinases that participate in this phosphorelay has been shown to differ between B. subtilis and B. cereus (5 and 9, respectively) [66]. The highly variable nature of the amino-terminal domains of the sporulation sensor kinases of the different Bacillus species has been suggested to represent differences in the signals used to initiate the developmental program. Recently, the B. anthracis kinase BA2291 was shown to be remarkably different from other sensor kinases by having a unique specificity for GTP [67]. Response regu- lator aspartate phosphatases as well as their cognate