A novel bacterial <scp>l</scp>‐arginine sensor controlling c‐di‐GMP levels in <i>Pseudomonas aeruginosa</i>

Paiardini, Alessandro; Mantoni, Federico; Giardina, G.; Paone, Alessio; Janson, Giacomo; Leoni, Livia; Rampioni, Giordano; Cutruzzolà, Francesca; Rinaldo, Serena

doi:10.1002/prot.25587

Cited by 34 publications

(39 citation statements)

References 58 publications

(144 reference statements)

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“…Conservation of the signature sequences on both domains suggested that the DUAL construct could display both the DGC and the PDE catalytic activities. In agreement with our preliminary evidence on P. aeruginosa PAO1-DPA0575 mutant showing cdi-GMP accumulation in the presence of L-Arginine as carbon source [10], we found that: (a) the DUAL protein is able to hydrolyse c-di-GMP into pGpG in vitro ( Fig. 1B); (b) as expected, the PDE activity is a property of the EAL domain, as it is conserved in the EAL-1 and EAL-2 constructs (Fig.…”

Section: Resultssupporting

confidence: 93%

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

et al. 2018

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Bis-(3'-5')-cyclic diguanylic acid (c-di-GMP) belongs to the class of cyclic dinucleotides, key carriers of cellular information in prokaryotic and eukaryotic signal transduction pathways. In bacteria, the intracellular levels of c-di-GMP and their complex physiological outputs are dynamically regulated by environmental and internal stimuli, which control the antagonistic activities of diguanylate cyclases (DGCs) and c-di-GMP specific phosphodiesterases (PDEs). Allostery is one of the major modulators of the c-di-GMP-dependent response. Both the c-di-GMP molecule and the proteins interacting with this second messenger are characterized by an extraordinary structural plasticity, which has to be taken into account when defining and possibly predicting c-di-GMP-related processes. Here, we report a structure-function relationship study on the catalytic portion of the PA0575 protein from Pseudomonas aeruginosa, bearing both putative DGC and PDE domains. The kinetic and structural studies indicate that the GGDEF-EAL portion is a GTP-dependent PDE. Moreover, the crystal structure confirms the high degree of conformational flexibility of this module. We combined structural analysis and protein engineering studies to propose the possible molecular mechanism guiding the nucleotide-dependent allosteric control of catalysis; we propose that the role exerted by GTP via the GGDEF domain is to allow the two EAL domains to form a dimer, the species competent to enter PDE catalysis.

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Section: Resultssupporting

confidence: 93%

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

et al. 2018

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“…In P. aeruginosa PAO1, SadC and RoeA, two of the most important DGCs implicated in biofilm formation, are necessary for the l -arginine response 8 . In addition, a multidomain transmembrane protein with PDE activity encoded by locus PA0575 (RmcA) binds l -arginine in its N-terminal domain, and a mutant in this gene shows increased c-di-GMP levels in response to the amino acid 30 . Homologs of SadC or RoeA are missing in P. putida KT2440, but a homolog of RmcA can be found (PP_0386).…”

Section: Discussionmentioning

confidence: 99%

Arginine as an environmental and metabolic cue for cyclic diguanylate signalling and biofilm formation in Pseudomonas putida

Barrientos‐Moreno

Molina‐Henares

Ramos-González

et al. 2020

Sci Rep

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Cyclic diguanylate (c-di-GMP) is a broadly conserved intracellular second messenger that influences different bacterial processes, including virulence, stress tolerance or social behaviours and biofilm development. Although in most cases the environmental cue that initiates the signal transduction cascade leading to changes in cellular c-di-GMP levels remains unknown, certain l - and d -amino acids have been described to modulate c-di-GMP turnover in some bacteria. In this work, we have analysed the influence of l -amino acids on c-di-GMP levels in the plant-beneficial bacterium Pseudomonas putida KT2440, identifying l -arginine as the main one causing a significant increase in c-di-GMP. Both exogenous (environmental) and endogenous (biosynthetic) l -arginine influence biofilm formation by P. putida through changes in c-di-GMP content and altered expression of structural elements of the biofilm extracellular matrix. The contribution of periplasmic binding proteins forming part of amino acid transport systems to the response to environmental l -arginine was also studied. Contrary to what has been described in other bacteria, in P. putida these proteins seem not to be directly responsible for signal transduction. Rather, their contribution to global l -arginine pools appears to determine changes in c-di-GMP turnover. We propose that arginine plays a connecting role between cellular metabolism and c-di-GMP signalling in P. putida .

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“…We recently characterized the catalytic moiety of RmcA from the P. aeruginosa strain PAO1, a transmembrane GGDEF-EAL containing phosphodiesterase able to recognize L-Arginine in the periplasmic space [ 26 ] and to degrade c-di-GMP [ 5 ]. We demonstrated that the GGDEF domain binds GTP and allosterically controls the phosphodiesterase activity by allowing the EAL domain to bind to c-di-GMP and dimerize [ 5 ].…”

Section: Resultsmentioning

confidence: 99%

Studying GGDEF Domain in the Act: Minimize Conformational Frustration to Prevent Artefacts

Mantoni

Rossi

Paiardini

et al. 2021

Life

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GGDEF-containing proteins respond to different environmental cues to finely modulate cyclic diguanylate (c-di-GMP) levels in time and space, making the allosteric control a distinctive trait of the corresponding proteins. The diguanylate cyclase mechanism is emblematic of this control: two GGDEF domains, each binding one GTP molecule, must dimerize to enter catalysis and yield c-di-GMP. The need for dimerization makes the GGDEF domain an ideal conformational switch in multidomain proteins. A re-evaluation of the kinetic profile of previously characterized GGDEF domains indicated that they are also able to convert GTP to GMP: this unexpected reactivity occurs when conformational issues hamper the cyclase activity. These results create new questions regarding the characterization and engineering of these proteins for in solution or structural studies.

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A novel bacterial l‐arginine sensor controlling c‐di‐GMP levels in Pseudomonas aeruginosa

Cited by 34 publications

References 58 publications

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

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

Arginine as an environmental and metabolic cue for cyclic diguanylate signalling and biofilm formation in Pseudomonas putida

Studying GGDEF Domain in the Act: Minimize Conformational Frustration to Prevent Artefacts

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