In silico comparative analysis of GGDEF and EAL domain signaling proteins from the Azospirillum genomes

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.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1157-0) contains supplementary material, which is available to authorized users.

Expression Patterns, Genomic Conservation and Input Into Developmental Regulation of the GGDEF/EAL/HD-GYP Domain Proteins in Streptomyces

“…Four of the genes coding for c-di-GMP turnover enzymes found in the pan genome are unique to certain species or are present in very few species. Such diversity in the c-di-GMP metabolism genes in a genus is not unusual since e.g., in the genomes of Azospirillum strains, the number of genes encoding GGDEF/EAL proteins varies between 29 and 41 ( Mata et al, 2018 ). However, the biological reasons underlying such diversification are difficult to explore but may involve adaptation to specific environmental niches.…”

Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

“…5a (left), the WebLogo alignment revealed that the RXXD and GGEEF motifs of the GGEEF domain were highly conserved in the same amino acid residues: Arg-Gln-Val-Asp (RQVD) and Gly-Gly-Glu-Glu-Phe (GGEEF), respectively. The GG[D/E]EF domain of the putative DGCs possessed the conserved amino acid residues essential for GTP binding, indicating that the DGCs may have catalytic activity [26].…”

“…Moreover, GGDEF and EAL domains can both be present in the same protein, forming "hybrid" proteins, even though they have opposing activities [23,24]. In that case, only one of the two domains is catalytically active, and the other performs a regulatory function, or a third regulatory domain is present that may disjoin the activity of the GGDEF and EAL domains [23,25,26]. Ute Römling et al list a census of all GGDEF, EAL, and HD-GYP domains in bacterial genomes [12,27].…”

Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

“…As shown inFig. 5a (left), the WebLogo alignment revealed that the RXXD and GGEEF motifs of the GGEEF domain were highly conserved in the same amino acid residues: Arg-EF domain of the putative DGCs possessed the conserved amino acid residues essential for GTP binding, indicating that the DGCs may have catalytic activity[26].Because only three genomes had partial EAL domains, the EAL domain in hybrid proteins from the M. aeruginosa NIES843 genome were chosen as paradigms to examine the crystal structure. Based on the crystal structure of the GGDEF-EAL domain of RmcA (PDB ID: 5M3C), which has a crystallographic resolution of 2.8 Å[54], the GGDEF and EAL domains in the hybrid protein of NIES843 were modeled.…”