Two-component signal transduction systems (TCSs) represent the dominant sense-response mechanisms to regulate a wide array of physiological pathways in prokaryotes. TCSs can regulate the majority of physiological processes, including bacterial growth, chemotaxis, osmoregulation, sporulation, biosynthesis of secondary metabolites, virulence of pathogens, biofilm formation, etc. In this paper, we predicted all the TCS genes and comprehensively analyzed their biological functions in the whole

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... es of 8 Xanthomonas strains. We depicted a systematic classification of these proteins, then analyzed their structures and putative biological functions by sequence alignment, multiple sequence alignment, phylogenetic tree analysis, Hidden Markov Model (HMM), secondary structure prediction etc, and finally constructed the regulatory networks in which some TCSs involved. Our research revealed the relationship between TCS genes and the pathogenicity of Xanthomonas, as well as the possible evolutionary relationship; furthermore, our results could lay the foundation for exploring new drug targets.