05). Analyses were extended beyond S. aurantiaca, to include Sorangium cellulosum, Haliangium ochraceum and Anaeromyxobacter dehalogenans

2CP-C (Fudou et al., 2002; Schneiker CB-839 order et al., 2007; Thomas et al., 2008), for which whole-genome sequences are available. Identification of the orthologues of M. xanthus genes in S. cellulosum, A. dehalogenans and H. ochraceum was substantially more difficult than that for S. aurantiaca. Most of the regulatory genes considered in this analysis (24 of 39, see Table S1) encode components of two-component system (TCS) signalling pathways. As such, they are mostly multidomain proteins with large numbers of paralogues in myxobacterial genomes (Whitworth & Cock, 2008a, b). Assigning orthologues of TCS genes is notoriously difficult (Galperin, 2010), and this can be seen in previous studies on myxobacterial TCS genomics (Whitworth & Cock, 2008b), where the number of orthologues identified declined drastically with taxonomic distance. With increasing taxonomic distance, greater numbers of gene duplications/deletion and domain architecture alterations are observed (Whitworth & Cock, 2008b), which also complicates the assignment of orthologues. In attempts to identify orthologues in S. cellulosum, A. dehalogenans and H.

ochraceum, the original requirement that best hits be bidirectional (Materials and methods) Cobimetinib datasheet was relaxed, as this condition returned <10 genes per genome. Instead, the best blast hit was taken, with an e-value cut-off of 1 ×e−10. This allowed the identification of 34 putative orthologues of M. xanthus genes in AZD9291 in vitro A. dehalogenans and H. ochraceum, and 32 in S. cellulosum. A lack of colocalization of putative orthologues found at the same locus/operon in M. xanthus (act, red, che3 and sas) diminished our confidence that this approach identified true orthologues. Nevertheless, we assessed the genomic location and degree of conservation for the putative orthologues as described in Materials and methods for S. aurantiaca. Intracellular and intercellular genes of S. cellulosum were similarly distributed with respect to the chromosomal origin

as M. xanthus genes (mean distance 1333 and 2420 CDS, respectively), but no apparent difference in the location was observed for the intra-/intercellular genes of H. ochraceum or A. dehalogenans. In all three genomes, intercellular genes were more variable than intracellular genes (although not as pronounced as in M. xanthus), with differences in the mean identity of 6.8%, 2.3% and 2.7% for H. ochraceum, A. dehalogenans and S. cellulosum, respectively. In many organisms, accessory/variable genes are found colocalized in a genome (Bentley et al., 2002; Choudhary et al., 2007; Millard et al., 2009), but the mechanistic bases of these phenomena are unclear. In M. xanthus, intracellular genes are generally located closer to the origin than intercellular signalling genes.