A bioinformatics and experimental analysis of proteins of two-component systems in Myxococcus xanthus

Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str., 35043 Marburg, Germany

^* To whom correspondence should be addressed. Email: sogaard{at}mpi-marburg.mpg.de.

	Abstract

Proteins of two-component systems (TCS) have essential functions in the sensing of external and self-generated signals in bacteria as well as in the generation of appropriate output responses. Accordingly, in Myxococcus xanthus TCS are important for normal motility and fruiting body formation and sporulation. Here, we analyzed the M. xanthus genome for the presence and genetic organization of genes encoding TCS. 272 TCS genes were identified, 251 of which are not part of che gene clusters. We report that the TCS genes are unusually organized with 55% being orphan and 16% in complex gene clusters whereas only 29% display the standard paired gene organization. Hybrid histidine protein kinases and histidine protein kinases predicted to be localized to the cytoplasm are overrepresented among proteins encoded by orphan genes or in complex gene clusters. Similarly, response regulators without output domains are overrepresented among proteins encoded by orphan genes or in complex gene clusters. The most frequently occurring output domains in response regulators are involved in DNA binding and cyclic-di-GMP metabolism. Our analyzes suggest that TCS encoded by orphan genes and complex gene clusters are functionally distinct from TCS encoded by paired genes and that the connectivity of the pathways made up of TCS encoded by orphan genes and complex gene clusters is different from that of pathways involving TCS encoded by paired genes. Experimentally, we observed that orphan TCS genes are overrepresented among genes that display altered transcription during fruiting body formation. The systematic analysis of the 25 orphan genes encoding histidine protein kinases that are transcriptionally up-regulated during development showed that two such genes are likely essential for viability and identified seven histidine protein kinases including four not previously characterized that have important function in fruiting body formation or spore germination.