Insights into the GTP‐dependent allosteric control of c‐di‐GMP hydrolysis from the crystal structure of PA0575 protein from <i>Pseudomonas aeruginosa</i>

Mantoni, Federico; Paiardini, Alessandro; Brunotti, Paolo; D’Angelo, Cecilia; Cervoni, Laura; Paone, Alessio; Cappellacci, Loredana; Petrelli, Riccardo; Ricciutelli, Massimo; Leoni, Livia; Rampioni, Giordano; Arcovito, Alessandro; Rinaldo, Serena; Cutruzzolà, Francesca; Giardina, G.

doi:10.1111/febs.14634

Cited by 33 publications

(47 citation statements)

References 61 publications

(149 reference statements)

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“…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. Compared with 5M3C, the GGDEF-EAL domains in the hybrid proteins showed sequence conservation of 35.9-37.8% (Additional file 1, Table S9).…”

Section: Structural Features Of Ggdef Domain Eal Domain and Hd-gyp mentioning

confidence: 99%

“…In this platform, templates are ranked based on the expected quality of the resulting models, and estimated by Global Model Quality Estimate and Quaternary Structure Quality Estimate [88,89]. The crystal structures of a DGC (WspR) from P. aeruginosa [52], the GG[D/E]EF-EAL hybrid domain protein RmcA from P. aeruginosa [54], the HD-GYP domain containing protein PA4781 from P. aeruginosa [56], and the PilZ domain-containing protein BcsA from R. sphaeroides were selected as templates for the structural analyses [31]. QMEAN scoring functions were used to estimate alternative models and screen for models whose scores strongly matched highresolution structures that were then used to create the corresponding model [90].…”

Section: Proteins Structural Analysesmentioning

confidence: 99%

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

Chen

et al. 2020

BMC Genomics

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Background: 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. 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. Results: Proteins 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. Conclusions: Comparative 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.

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Section: Structural Features Of Ggdef Domain Eal Domain and Hd-gyp mentioning

confidence: 99%

Section: Proteins Structural Analysesmentioning

confidence: 99%

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

Chen

et al. 2020

BMC Genomics

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“…aeruginosa [52], the GG[D/E]EF-EAL hybrid domain protein RmcA from P. aeruginosa [54], the HD-GYP domain containing protein PA4781 from P. aeruginosa [57], and the PilZ domain-containing protein…”

Section: Proteins Structural Analysesmentioning

confidence: 99%

“…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.…”

mentioning

confidence: 99%

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

Chen

et al. 2020

Preprint

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Background : 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. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimericguanosine 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 .Results: Proteins 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. Conclusions: Comparative 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.3 Background Cyanobacteria, which are phototrophic bacteria that survive in ecologically diverse habitats, have received growing attention because they have been forming toxic blooms in eutrophic water bodies worldwide for decades [1][2]. Dense blooms are considered seriously harmful to aquatic ecosystems because of their deleterious effects on water quality, such as increased turbidity, smothering submerged aquatic vegetation, and producing taste and odor compounds [3][4]. Moreover, some cyanobacteria species can synthesize toxic secondary metabolites, such as hepatotoxin microcystins that can inhibit eukaryotic protein phosphatases; thus, they threaten the functional of water bodies for drinking, bathing, and fishing, and they also ultimately pose potential risks to animal and hum...

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“…In P. aeruginosa PAO1, twelve genes code for proteins with PAS domains linked to DGC domains, nine of which additionally contain PDE domains 5 , namely pa0285, pa0290, pa0338, pa0575 9 , pa0847, pa0861 ( rbdA 10 ), pa1181 ( yegE ), pa2072 , pa4601 ( morA 11–13 ), pa4959 ( fimX 14 ), pa5017 ( dipA 15 ), and pa5442 . The recurrence of proteins with similar architecture, and which play a role in biofilm regulation, poses two key questions: Firstly, if DGCs and PDEs regulate the transition between sessility and the planktonic state, how do the specific protein sensory domains then control mechanisms of motility?…”

Section: Introductionmentioning

confidence: 99%

Differential impact on motility and biofilm dispersal of closely related phosphodiesterases in Pseudomonas aeruginosa

Cai¹,

Hutchin

Craddock

et al. 2019

Preprint

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AbstractBacteria typically occur either as free-swimming planktonic cells or within a sessile, biofilm mode of growth. In Pseudomonas aeruginosa, the transition between these lifestyles is known to be modulated by the intracellular secondary messenger cyclic dimeric-GMP (c-di-GMP). We are interested in the control of distinct biofilm-relevant phenotypes in P. aeruginosa through the modulation of intracellular c-di-GMP. Here, we characterise motility and associated biofilm formation and dispersal in two pairs of related multi-domain proteins with putative c-di-GMP turnover domains, selected to contain additional PAS (Per-Arnt-Sim) homology domains known for their ability to process environmental stimuli. The enzymes PA0861 (RbdA) and PA2072 have distinct functions despite their similar domain structures. The ΔrbdA deletion mutant showed significantly increased biofilm formation while biofilm formation was impaired in ΔPA2072. Using a GFP transcriptional reporter fused to the cyclic di-GMP-responsive cdrA promoter, we show correlation between biofilm phenotype and c-di-GMP levels. Both proteins are shown to play a role in nitric oxide (NO) induced biofilm dispersal. We further studied pseudo-enzymes of similar architecture. PA5017 (DipA) is an inactive cyclase, and PA4959 (FimX) is described here as an inactive cyclase/phosphodiesterase. Loss of swimming and twitching motilities, respectively, is observed in deletion variants, which correlated with NO-induced biofilm dispersal phenotypes, as ΔdipA dispersed less well while ΔfimX dispersed better than wild type. The study highlights how Pseudomonas differentiates c-di-GMP output – in this case motility – using structurally very similar proteins and underlines a significant role for pseudo-enzymes in motility regulation and associated biofilm dispersal.ImportanceBacterial biofilms exert pervasive economic and societal impact across a range of environmental, engineered and clinical contexts. The secondary messenger cyclic guanosine di-phosphate, c-di-GMP, is known to control the ability of many bacteria to form biofilms. The opportunistic human pathogen Pseudomonas aeruginosa PAO1 has 38 putative enzymes that can regulate c-di-GMP turnover, and these proteins modulate various cellular functions and influence bacterial lifestyle. The specific protein sensory domains and mechanisms of motility that lead to biofilm dispersal remain to be fully understood. Here we studied multi-domain proteins with the PAS (Per-Arnt-Sim) homology domains, these being classic sensors to environmental stimuli. Our study demonstrates the significant roles for the pseudo-enzymes PA4959 (FimX) and PA5017 (DipA) in regulation of biofilm phenotype and motility. Further, enzymes with highly homologous structures, such as PA0861 (RbdA) and PA2072, have almost orthogonal function in biofilm and motility control.

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Insights into the GTP‐dependent allosteric control of c‐di‐GMP hydrolysis from the crystal structure of PA0575 protein from Pseudomonas aeruginosa

Cited by 33 publications

References 61 publications

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

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

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

Differential impact on motility and biofilm dispersal of closely related phosphodiesterases in Pseudomonas aeruginosa

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