Fig 1.
DSF family signals and the organization of rpf gene clusters that direct signal synthesis and perception.
(A) RpfF, an enzyme of the crotonase superfamily, is involved in synthesis of DSF in all bacteria. Two core pathways of DSF perception have been described: (1) the RpfCG two-component system first identified in xanthomonads and (2) RpfR, a protein with PAS, GGDEF, and EAL domains, first identified in Burkholderia species. In Xanthomonas campestris, the genes encoding RpfC and RpfG are organized in an operon that is convergently transcribed to rpfF (top). This operon also contains rpfH, a gene encoding a protein similar to the input domain of RpfC but of no known function. The rpfF gene is found in an operon with rpfB, which encodes a fatty acyl CoA ligase but also has its own promoter. This organization of rpf genes occurs in all xanthomonads with the variations that rpfH is not widely conserved and rpfB can be located in a different genomic location, as is seen in Xylella fastidiosa. In Burkholderia species, rpfF is convergently transcribed with rpfR, which encodes the sensor protein. In Pseudomonas aeruginosa, the dspI gene that encodes an RpfF homolog is located in a cluster of genes encoding enzymes implicated in fatty acid metabolism. The identity of the sensor for the signal is not known. (B) The DSF family of signals comprises cis-2-unsaturated fatty acids of different chain lengths and branching. The paradigm cis-11-methyl–dodecenoic acid designated DSF, was first described in Xanthomonas campestris. Different signals were then described in Burkholderia cenocepacia (BDSF), Pseudomonas aeruginosa (cis-2-decenoic acid), Xylella fastidiosa (cis-2-tetradecenoic acid) and Xanthomonas oryzae (cis,cis-11 methyldodeca-2,5-dienoic acid). It is now established that each of these bacteria produces multiple DSF family signals, although each genus seems to be most responsive to the major signal that it produces. DSF family signals can be involved in bi-directional interspecies signaling. However unidirectional signaling is evident; Pseudomonas aeruginosa responds to DSF and BDSF produced by xanthomonads, but these latter organisms do not respond to cis-2-decenoic acid, the P. aeruginosa signal.
Fig 2.
The roles of RpfF and RpfB in DSF signaling.
RpfF encodes an enzyme from the crotonase family that possesses both desaturase and thioesterase activities and uses fatty acyl ACP substrates derived from fatty acid biosynthesis as substrates. DSF family signals are generated from 3-hydroxy-fatty acyl ACPs by consecutive or coordinated desaturase and thioesterase action. In addition, the thioesterase activity of RpfF generates a range of free hydroxylated and non-hydroxylated fatty acids. DSF family signals leave the cell by as-yet-unknown efflux mechanisms (indicated by the question mark). Free fatty acids whose synthesis depends upon RpfF can also be found in the culture supernatant. The role of RpfB is in mobilization of these free fatty acids. Uptake, which may involve FadL, is followed by conversion to fatty acyl CoA derivatives that can be used in phospholipid biosynthesis or for degradation. This figure is a modified version of that published by Bi and colleagues [15].
Fig 3.
Signal transduction mechanisms for DSF family signals in different bacteria.
(A) Xanthomonas campestris. DSF perception involves the complex histidine kinase RpfC. Binding of DSF to the sensory input domain, which comprises five transmembrane helices, leads to autophosphorylation, phosphorelay via the receiver and histidine phosphotranfer domains, and phosphotransfer to the receiver domain of the response regulator RpfG. RpfG has an HD-GYP domain, which is a cyclic di-GMP phosphodiesterase; phosphorylation activates RpfG for cyclic di-GMP degradation. A second sensing system for DSF involves the soluble histidine kinase RpfS, which binds DSF through the N-terminal PAS_4 domain. RpfS influences the expression of a sub-set of DSF-regulated genes, in particular those involved in the epiphytic growth phase. This action is likely exerted through the response regulator XC_2578. The RpfGC system is “core,” being found in all xanthomonads, including Xylella fastidiosa, whereas RpfS is “accessory” and is not fully conserved. In Xylella, DSF signal transduction also involves RpfF (see text for details). (B) Burkholderia cenocepacia. BDSF perception involves the soluble PAS-GGDEF-EAL domain protein RpfR. Binding of BDSF to the N-terminal PAS domain activates RpfR for cyclic di-GMP degradation by the cyclic di-GMP phosphodiesterase EAL domain. A second sensing system for BDSF involves the histidine kinase BCAM0227, which differs from RpfC in having two transmembrane helices and a large periplasmic domain. Signal transduction from BCAM0227 involves autophosphorylation upon BDSF binding, phosphorelay, and phosphotransfer to the DNA-binding regulator BCAM0228. The RpfFR system is “core,” being found in widely in Burkholderia and other genera, whereas BCAM0227 is “accessory” and is only found in strains of B. cenocepacia. (C) Interspecies signaling in Pseudomonas aeruginosa. BDSF or DSF perception involves the membrane-associated histidine kinase PA1396, which resembles RpfC but does not have an HPt domain. Signal transduction from PA1396 involves autophosphorylation upon BDSF binding, phosphorelay, and phosphotransfer via an orphan HPt domain protein to the DNA-binding regulator PA1397. This system influences the expression of genes involved in polymyxin resistance and stress tolerance.
Table 1.
Virulence-related and other factors that are regulated by DSF family signals in diverse pathogens.
Fig 4.
Signals of the DSF family in interspecies and inter-kingdom signaling.
DSF family signals produced by Stenotrophomonas maltophilia (principally DSF) and Burkholderia cenocepacia (principally BDSF) influence the behavior of Pseudomonas aeruginosa and the yeast–hyphal transition in Candida albicans. The P. aeruginosa signal cis-2-decenoic acid prevents biofilm by Candida albicans and growth and biofilm formation by Staphylococcus aureus. The effects of DSF and BDSF on Pseudomonas aeruginosa are exerted via the sensor kinase PA1396, which does not respond to cis-2-decenoic. The production of DSF and BDSF may allow interspecies communication between Stenotrophomonas maltophilia and Burkholderia cenocepacia. Other signal molecules are also involved in interaction between some of these organisms, but are not indicated here for clarity. For example, 3-oxo-dodecanoyl-homoserine lactone produced by P. aeruginosa can influence C. albicans and B. cenocepacia.