Phenotypic–genotypic analysis of GGDEF/EAL/HD‐GYP domain‐encoding genes in <i>Pseudomonas putida</i>

Nie, Hailing; Xiao, Yujie; He, Jinzhi; Liu, Huizhong; Nie, Liang; Chen, Wenli; Huang, Qiaoyun

doi:10.1111/1758-2229.12808

Cited by 15 publications

(25 citation statements)

References 52 publications

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“…We then transformed the plasmids into the wild-type strain, bifA mutant (Δ bifA ), fleQ mutant (Δ fleQ ), and fleQ - bifA double mutant (Δ fleQ Δ bifA ) and further tested their GFP fluorescence intensity. Our previous study has shown that deletion of BifA (a phosphodiesterase with c-di-GMP degradation activity) causes increased c-di-GMP levels in P. putida ( 23 ). The results showed that GFP fluorescence intensity of the Δ bifA mutant containing the lapE - gfp fusion reporter was much higher than that of the wild type, whereas the fluorescence intensity of the Δ bifA mutant containing the cyaA - gfp fusion reporter was lower than that of the wild type ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Identification of c-di-GMP/FleQ-Regulated New Target Genes, Including cyaA , Encoding Adenylate Cyclase, in Pseudomonas putida

et al. 2021

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The bacterial second messenger cyclic diguanylate (c-di-GMP) modulates plankton-to-biofilm lifestyle transition of Pseudomonas species through its transcriptional regulatory effector FleQ. FleQ regulates transcription of biofilm- and flagellum-related genes in response to c-di-GMP. Through transcriptomic analysis and FleQ-DNA binding assay, this study identified five new target genes of c-di-GMP/FleQ in P. putida, including PP_0681, PP_0788, PP_4519 (lapE), PP_5222 (cyaA), and PP_5586. Except lapE encoding an outer membrane pore protein and cyaA encoding an adenylate cyclase, the functions of the other three genes encoding hypothetical proteins remain unknown. FleQ and c-di-GMP coordinately inhibit transcription of PP_0788 and cyaA and promote transcription of PP_0681, lapE, and PP_5586. Both in vitro and in vivo assays show that FleQ binds directly to promoters of the five genes. Further analyses confirm that LapE plays a central role of in the secretion of adhesin LapA and that c-di-GMP/FleQ increases lapE transcription, thereby promoting adhesin secretion and biofilm formation. The adenylate cyclase CyaA is responsible for synthesis of another second messenger, cyclic AMP (cAMP). FleQ and c-di-GMP coordinate to decrease the content of cAMP, suggesting that c-di-GMP and FleQ coregulate cAMP by modulating cyaA expression. Overall, this study adds five new members to the c-di-GMP/FleQ-regulated gene family and reveals the role of c-di-GMP/FleQ in LapA secretion and cAMP synthesis regulation in P. putida. IMPORTANCE c-di-GMP/FleQ promotes the plankton-to-biofilm lifestyle transition at the transcriptional level via FleQ in Pseudomonas species. Identification of new target genes directly regulated by c-di-GMP/FleQ helps to broaden the knowledge of c-di-GMP/FleQ-mediated transcriptional regulation. Regulation of lapE by c-di-GMP/FleQ guarantees highly efficient LapA secretion and biofilm formation. The mechanism of negative correlation between c-di-GMP and cAMP in both P. putida and P. aeruginosa remains unknown. Our result concerning transcriptional inhibition of cyaA by c-di-GMP/FleQ reveals the mechanism underlying the decrease of cAMP content by c-di-GMP in P. putida.

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Section: Resultsmentioning

confidence: 99%

Identification of c-di-GMP/FleQ-Regulated New Target Genes, Including cyaA , Encoding Adenylate Cyclase, in Pseudomonas putida

et al. 2021

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“…Another emerging theme is that the integration of positive or negative feedback loops is probably common for c-di-GMP signalling systems, presumably for rapid signal amplification and noise attenuation. The mechanisms discussed in this minireview are likely to be operational in many pseudomonads, considering that the orthologs of flgZ, mapZ and fimW and many genes implicated in c-di-GMP signalling, flagellum/pili-dependent motility, and surface adhesion are found in all the sequenced pseudomonads (Choy et al, 2004;Feil et al, 2005;Duque et al, 2013;Nogales et al, 2015;Wang et al, 2019;Nie et al, 2020). It is nonetheless important to note that adaptive evolution has generated phenotypic and genotypic diversity among the pseudomonads (Silby et al, 2011;Redondo-Nietoet al, 2012;Chandler et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Early studies of Escherichia coli and other model organisms suggested that cellular c-di-GMP concentrations influence flagellum-dependent motility, as evidenced by the motility defects caused by the deletion of dgc and pde genes (Simm et al, 2004;Christen et al, 2007). Studies on P. aeruginosa and Pseudomonas putida confirmed the role of c-di-GMP in the regulation of flagellumdependent motility and established functional links between several c-di-GMP signalling proteins and flagellar biosynthesis or function (Caiazza et al, 2007;Kuchma et al, 2007;Merritt et al, 2007;Aragon et al, 2015;Nie et al, 2020). Today, it is firmly established that c-di-GMP-mediated flagellar gene expression is a major mechanism used by pseudomonads to downregulate flagellar activity for long-term adaptation (Wolfe and Visick, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…The second messenger c-di-GMP has emerged as a key player in the regulation of flagellum-dependent motility and the motile-to-sessile transition in recent years (Romling et al, 2013;Jenal et al, 2017). Revealed largely by the studies on the model organism P. aeruginosa (Table 1), pseudomonads possess highly complex c-di-GMP signalling networks composed of a large number of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) for controlling cellular c-di-GMP concentrations, and c-di-GMP-binding effectors/receptors for eliciting cellular responses (Kulasakara et al, 2006;Nie et al, 2020). Early studies of Escherichia coli and other model organisms suggested that cellular c-di-GMP concentrations influence flagellum-dependent motility, as evidenced by the motility defects caused by the deletion of dgc and pde genes (Simm et al, 2004;Christen et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Taming the flagellar motor of pseudomonads with a nucleotide messenger

Chandra

Liang

2020

Environmental Microbiology

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Summary Pseudomonads rely on the flagellar motor to rotate a polar flagellum for swimming and swarming, and to sense surfaces for initiating the motile‐to‐sessile transition to adopt a surface‐dwelling lifestyle. Deciphering the function and regulation of the flagellar motor is of paramount importance for understanding the behaviours of environmental and pathogenic pseudomonads. Recent studies disclosed the preeminent role played by the messenger c‐di‐GMP in controlling the real‐time performance of the flagellar motor in pseudomonads. The studies revealed that c‐di‐GMP controls the dynamic exchange of flagellar stator units to regulate motor torque/speed and modulates the frequency of flagellar motor switching via the chemosensory signalling pathways. Apart from being a rotary motor, the flagellar motor is emerging as a mechanosensor that transduces surface‐induced mechanical signals into an increase of cellular c‐di‐GMP concentration to initiate the cellular programs required for long‐term colonization. Collectively, the studies generate long‐awaited mechanistic insights into how c‐di‐GMP regulates bacterial motility and the motile‐to‐sessile transition. The new findings also raise the fundamental questions of how cellular c‐di‐GMP concentrations are dynamically coupled to flagellar output and the proton‐motive force, and how c‐di‐GMP signalling is coordinated spatiotemporally to fine‐tune flagellar response and the behaviour of pseudomonads in solutions and on surfaces.

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“…However, the identification of proteins that function as receptors/effectors for the c-di-GMP system has proven to be more complex. It is known that c-di-GMP can bind to various classes of proteins that differ in structure and amino acid sequences [ 16 , 17 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase

Balabanova

Shkryl

Slepchenko

et al. 2020

IJMS

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The biofilm-producing strains of P. aeruginosa colonize various surfaces, including food products and industry equipment that can cause serious human and animal health problems. The biofilms enable microorganisms to evolve the resistance to antibiotics and disinfectants. Analysis of the P. aeruginosa strain (serotype O6, sequence type 2502), isolated from an environment of meat processing (PAEM) during a ready-to-cook product storage (−20 °C), showed both the mosaic similarity and differences between free-living and clinical strains by their coding DNA sequences. Therefore, a cold shock protein (CspA) has been suggested for consideration of the evolution probability of the cold-adapted P. aeruginosa strains. In addition, the study of the action of cold-active enzymes from marine bacteria against the food-derived pathogen could contribute to the methods for controlling P. aeruginosa biofilms. The genes responsible for bacterial biofilm regulation are predominantly controlled by quorum sensing, and they directly or indirectly participate in the synthesis of extracellular polysaccharides, which are the main element of the intercellular matrix. The levels of expression for 14 biofilm-associated genes of the food-derived P. aeruginosa strain PAEM in the presence of different concentrations of the glycoside hydrolase of family 36, α-galactosidase α-PsGal, from the marine bacterium Pseudoalteromonas sp. KMM 701 were determined. The real-time PCR data clustered these genes into five groups according to the pattern of positive or negative regulation of their expression in response to the action of α-galactosidase. The results revealed a dose-dependent mechanism of the enzymatic effect on the PAEM biofilm synthesis and dispersal genes.

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Phenotypic–genotypic analysis of GGDEF/EAL/HD‐GYP domain‐encoding genes in Pseudomonas putida

Cited by 15 publications

References 52 publications

Identification of c-di-GMP/FleQ-Regulated New Target Genes, Including cyaA , Encoding Adenylate Cyclase, in Pseudomonas putida

Identification of c-di-GMP/FleQ-Regulated New Target Genes, Including cyaA , Encoding Adenylate Cyclase, in Pseudomonas putida

Taming the flagellar motor of pseudomonads with a nucleotide messenger

Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase

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