Abstract
BackgroundCyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa.ResultsProteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins.ConclusionsComparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.
Highlights
Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality
We identified genes that encode proteins containing the GGDEF, EAL, HD-GYP and PilZ domains and other associated sensing domains in the complete or draft genome sequences of 24 M. aeruginosa strains available in GenBank
propensity for gene loss (PGL) analysis revealed most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains
Summary
Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. Cyanobacteria are able to inhabit most of Earth’s environments because they evolved mechanisms to monitor and rapidly adapt to environmental changes through a web of complex signaling networks, such as using second messengers to regulate physiology or metabolism [8]. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), which was first identified as an allosteric activator of cellulose synthase in Gluconacetobacter xylinus in 1987, plays an important role in regulating biofilm formation or dispersal in response to various environmental cues and cell–cell signals [10,11,12,13,14]. Ute Römling et al list a census of all GGDEF, EAL, and HD-GYP domains in bacterial genomes [12, 27]
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