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Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli

  • Genomics, transcriptomics, proteomics
  • Published:
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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.

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Acknowledgments

This research has been funded by the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office and was supported by grants from the Research Council of the KU Leuven (GOA/011/2008) and from the Fund for Scientific Research-Flanders (G.0412.10). S.B.R. received a fellowship from the Fund for Scientific Research-Flanders. We gratefully acknowledge the help of Claudine Vereecke, Public Collection Curator of the BCCM/LMG Bacteria Collection, Ghent, Belgium, for her part in the smooth deposition of R. etli CNPAF512 and Annette Garbe, Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, Germany, for performing c-di-GMP quantifications.

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  1. Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. Box 2460, 3001, Heverlee, Belgium

    Shanjun Gao, Samir Ben Romdhane, Serge Beullens, Maarten Fauvart & Jan Michiels

  2. Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, 30625, Hannover, Germany

    Volkhard Kaever

  3. Biomedical Research Institute, Hasselt University, 3590, Diepenbeek, Belgium

    Ivo Lambrichts

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  1. Shanjun Gao
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  2. Samir Ben Romdhane
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Correspondence to Jan Michiels.

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Maarten Fauvart and Jan Michiels contributed equally as senior authors.

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Gao, S., Romdhane, S.B., Beullens, S. et al. Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli . Appl Microbiol Biotechnol 98, 4589–4602 (2014). https://doi.org/10.1007/s00253-014-5722-7

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