Abstract
BackgroundThe cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile life-styles in bacteria. Cellular c-di-GMP levels in bacteria are regulated by the opposite enzymatic activities of diguanylate cyclases and phosphodiesterases, which are proteins that have GGDEF and EAL domains, respectively. Azospirillum is a genus of plant-growth-promoting bacteria, and members of this genus have beneficial effects in many agronomically and ecologically essential plants. These bacteria also inhabit aquatic ecosystems, and have been isolated from humus-reducing habitats. Bioinformatic and structural approaches were used to identify genes predicted to encode GG[D/E]EF, EAL and GG[D/E]EF-EAL domain proteins from nine genome sequences.ResultsThe analyzed sequences revealed that the genomes of A. humicireducens SgZ-5T, A. lipoferum 4B, Azospirillum sp. B510, A. thiophilum BV-ST, A. halopraeferens DSM3675, A. oryzae A2P, and A. brasilense Sp7, Sp245 and Az39 encode for 29 to 41 of these predicted proteins. Notably, only 15 proteins were conserved in all nine genomes: eight GGDEF, three EAL and four GGDEF-EAL hybrid domain proteins, all of which corresponded to core genes in the genomes. The predicted proteins exhibited variable lengths, architectures and sensor domains. In addition, the predicted cellular localizations showed that some of the proteins to contain transmembrane domains, suggesting that these proteins are anchored to the membrane. Therefore, as reported in other soil bacteria, the Azospirillum genomes encode a large number of proteins that are likely involved in c-di-GMP metabolism. In addition, the data obtained here strongly suggest host specificity and environment specific adaptation.ConclusionsBacteria of the Azospirillum genus cope with diverse environmental conditions to survive in soil and aquatic habitats and, in certain cases, to colonize and benefit their host plant. Gaining information on the structures of proteins involved in c-di-GMP metabolism in Azospirillum appears to be an important step in determining the c-di-GMP signaling pathways, involved in the transition of a motile cell towards a biofilm life-style, as an example of microbial genome plasticity under diverse in situ environments.
Highlights
The cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile life-styles in bacteria
We advanced our understanding of c-di-GMP signaling in the most important species of Azospirillum, e.g., those that are used as inoculants to promote plant growth or in soil bioremediation, by studying how many domain architectures and tridimensional structures were contained in the predicted proteins of genes encoding DCGs, PDEs and diguanylate cyclases (DGCs)-PDEs; these genes are widespread and are found in other environmental and soil bacteria
Approximately 29 to 41 genes encoding these modular signaling proteins were identified in the Azospirillum genomes, establishing that the distribution of this genes in Azospirillum is comparable to that in other bacteria from soil or marine environmental bacteria, such as Sinorhizobium meliloti [82], other species of Rhizobium [83], Pseudomonas putida [62], Shewanella oneidensis [63, 84], and Burkholderia lata SK875 [85], which reportedly encode a considerable number of proteins predicted to be involved in c-di-GMP metabolism
Summary
The cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile life-styles in bacteria. Azospirillum is a genus of plant-growth-promoting bacteria, and members of this genus have beneficial effects in many agronomically and ecologically essential plants. These bacteria inhabit aquatic ecosystems, and have been isolated from humusreducing habitats. Bioinformatic and structural approaches were used to identify genes predicted to encode GG[D/E]EF, EAL and GG[D/E]EF-EAL domain proteins from nine genome sequences. Bacteria are able to sense and respond to ecologically distinct abiotic and biotic conditions [15] These systems are necessary of these bacteria to adapt to changing environmental conditions and to enable survival in highly competitive habitats, such as the plant rhizosphere, soil or aquatic environments. Several chemotaxis and aerotaxis operons have been identified in A. brasilense [6, 16, 17], and different mutant strains are defective in biofilm formation and root surface colonization [18, 19]
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