title: Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli.
abstract: Rhizobia are soil bacteria that can fix nitrogen in symbiosis with leguminous plants or exist free living in the rhizosphere. Crucial to their complex lifestyle is the ability to sense and respond to diverse environmental stimuli, requiring elaborate signaling pathways. In the majority of bacteria, the nucleotide-based second messenger cyclic diguanosine monophosphate (c-di-GMP) is involved in signal transduction. Surprisingly, little is known about the importance of c-di-GMP signaling in rhizobia. We have analyzed the genome sequences of six well-studied type species (Bradyrhizobium japonicum, Mesorhizobium loti, Rhizobium etli, Rhizobium leguminosarum, Sinorhizobium fredii, and Sinorhizobium meliloti) for proteins possibly involved in c-di-GMP signaling based on the presence of four domains: GGDEF (diguanylate cyclase), EAL and HD-GYP (phosphodiesterase), and PilZ (c-di-GMP sensor). We find that rhizobia possess a high number of these proteins. Conservation analysis suggests that c-di-GMP signaling proteins modulate species-specific pathways rather than ancient rhizobia-specific processes. Two hybrid GGDEF-EAL proteins were selected for functional analysis, R. etli RHE_PD00105 (CdgA) and RHE_PD00137 (CdgB). Expression of cdgA and cdgB is repressed by the alarmone (p)ppGpp. cdgB is significantly expressed on plant roots and free living. Mutation of cdgA, cdgB, or both does not affect plant root colonization, nitrogen fixation capacity, biofilm formation, motility, and exopolysaccharide production. However, heterologous expression of the individual GGDEF and EAL domains of each protein in Escherichia coli strongly suggests that CdgA and CdgB are bifunctional proteins, possessing both diguanylate cyclase and phosphodiesterase activities. Taken together, our results provide a platform for future studies of c-di-GMP signaling in rhizobia.
authors.affiliation: Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. Box 2460, 3001, Heverlee, Belgium.
authors.forename: Shanjun
authors.initials: S
authors.lastname: Gao
authors.forename: Samir Ben
authors.initials: SB
authors.lastname: Romdhane
authors.forename: Serge
authors.initials: S
authors.lastname: Beullens
authors.forename: Volkhard
authors.initials: V
authors.lastname: Kaever
authors.forename: Ivo
authors.initials: I
authors.lastname: Lambrichts
authors.forename: Maarten
authors.initials: M
authors.lastname: Fauvart
authors.forename: Jan
authors.initials: J
authors.lastname: Michiels
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D018441:Biofilms / Q000254:growth & development; D020369:Bradyrhizobium / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D019295:Computational Biology; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D059128:Mesorhizobium / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D009586:Nitrogen Fixation; D018517:Plant Roots / Q000382:microbiology; D011134:Polysaccharides / Q000378:metabolism; D012230:Rhizobiaceae / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D011134:Polysaccharides; C062025:bis(3',5')-cyclic diguanylic acid; D006152:Cyclic GMP