Purification and crystallization of Phd, the antitoxin of the<i>phd</i>/<i>doc</i>operon

García-Pino, Abel; Sterckx, Yann G.J.; Vandenbussche, Guy; Loris, Remy

doi:10.1107/s1744309109051550

Cited by 5 publications

(4 citation statements)

References 33 publications

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“…Our study also corroborates results of metagenomic analysis between health and periodontitis, in which higher abundance of genes related to the metabolism of carbohydrates, amino acids, energy were present in the healthy group compared with the periodontitis group 44 . In our study, the health‐associated community also showed an overabundance of antitoxin Phd, which is part of a regulatory complex that neutralizes and reverses the action of bacterial toxins 45 . As such, our results suggest that there may be a continuous compensatory regulation among community members in this environment which maintains homeostasis.…”

Section: Discussionsupporting

confidence: 89%

“…44 In our study, the health-associated community also showed an overabundance of antitoxin Phd, which is part of a regulatory complex that neutralizes and reverses the action of bacterial toxins. 45 As such, our results suggest that there may be a continuous compensatory regulation among community members in this environment which maintains homeostasis. In general, studies converge to attribute a genetic profile related to biofilm formation and primary metabolism to the healthy environment, probably due to a predominance of primary colonizers and because the maturation process requires metabolic and genetic exchanges for environmental adaptation.…”

Section: Discussionmentioning

confidence: 62%

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Predicted functional and taxonomic analysis of subgingival biofilm of Grade C periodontitis in young patients under maintenance therapy

Paz

Monteiro

Stolf

et al. 2022

Journal of Periodontology

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Background In Grade C periodontitis in young patients (PerioC‐Y), the functional roles of the subgingival community after years of periodontal treatment are still underexplored. This study evaluated the taxonomic and predicted functional content of the subgingival microbiome of PerioC‐Y patients under supportive periodontal therapy (SPT). Methods Clinical and microbiological data from subgingival biofilm were assessed from 10 PerioC‐Y patients at two time points: at baseline and after 5.7 ± 1.3 years of SPT. This was compared with 15 patients without a history of periodontitis. The V1‐V3 and V4‐V5 regions of the 16S rRNA were sequenced using the Illumina Miseq. Microbial composition was evaluated by the core microbiome, and alpha‐ and beta‐diversity. The microbiome functional content was predicted using Picrust2, and the gene differential abundance was analyzed with DESeq2. Results Clinical improvements were seen in PerioC‐Y‐SPT. Differences in β‐diversity between PerioC‐Y and health were observed (health x PerioC‐Y‐baseline, P = 0.02; health x PerioC‐Y‐SPT, P = 0.05). Moreover, although β‐diversity did not statistically change between baseline and SPT in PerioC‐Y, the microbial correlation evidenced increased Streptococcus and decreased Treponema network contributions during SPT. Based on predicted functional data, treatment induced a reduction in genes related to flagellar protein and signal transduction in PerioC‐Y. However, compared with healthy individuals, some genes remained more highly abundant in PerioC‐Y‐SPT, such as quorum sensing and efflux pump transporters. Conclusion Despite clinical improvements and a shift in taxonomic composition, the PerioC‐Y patients' periodontal treatment was not enough to reach a similar microbiome to patients without disease experience. Some functional content in this biofilm remained altered in PerioC‐Y regardless of disease control.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 62%

Predicted functional and taxonomic analysis of subgingival biofilm of Grade C periodontitis in young patients under maintenance therapy

Paz

Monteiro

Stolf

et al. 2022

Journal of Periodontology

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“…4). Although type II TA antitoxins are generally very difficult to crystallize because they contain intrinsically disordered regions, other antitoxins have also been crystallized in their unbound state ( Garcia-Pino, Sterckx et al, 2010). Using the PISA server (Krissinel & Henrick, 2007) we estimated that the AtaR dimer interface encompasses 920 Å 2 , which is of the order of the average interface area (1100 Å 2 ) of other RHH antitoxin dimers (Francuski & Saenger, 2009;Madl et al, 2006;Ruangprasert et al, 2014).…”

Section: Crystallization Of the Atar-atat-dna Complexmentioning

confidence: 99%

Crystallization and X-ray analysis of all of the players in the autoregulation of theataRTtoxin–antitoxin system

Jurėnas

Melderen

García-Pino

2018

Acta Crystallogr F Struct Biol Commun

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The ataRT operon from enteropathogenic Escherichia coli encodes a toxin-antitoxin (TA) module with a recently discovered novel toxin activity. This new type II TA module targets translation initiation for cell-growth arrest. Virtually nothing is known regarding the molecular mechanisms of neutralization, toxin catalytic action or translation autoregulation. Here, the production, biochemical analysis and crystallization of the intrinsically disordered antitoxin AtaR, the toxin AtaT, the AtaR-AtaT complex and the complex of AtaR-AtaT with a double-stranded DNA fragment of the operator region of the promoter are reported. Because they contain large regions that are intrinsically disordered, TA antitoxins are notoriously difficult to crystallize. AtaR forms a homodimer in solution and crystallizes in space group P622, with unit-cell parameters a = b = 56.3, c = 160.8 Å. The crystals are likely to contain an AtaR monomer in the asymmetric unit and diffracted to 3.8 Å resolution. The Y144F catalytic mutant of AtaT (AtaT) bound to the cofactor acetyl coenzyme A (AcCoA) and the C-terminal neutralization domain of AtaR (AtaR) were also crystallized. The crystals of the AtaT-AcCoA complex diffracted to 2.5 Å resolution and the crystals of AtaR diffracted to 2.2 Å resolution. Analysis of these structures should reveal the full scope of the neutralization of the toxin AtaT by AtaR. The crystals belonged to space groups P622 and P321, with unit-cell parameters a = b = 58.1, c = 216.7 Å and a = b = 87.6, c = 125.5 Å, respectively. The AtaR-AtaT-DNA complex contains a 22 bp DNA duplex that was optimized to obtain high-resolution data based on the sequence of two inverted repeats detected in the operator region. It crystallizes in space group C222, with unit-cell parameters a = 75.6, b = 87.9, c = 190.5 Å. These crystals diffracted to 3.5 Å resolution.

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“…Similarly, using a metagenomic survey, a higher abundance of genes related to the metabolism of carbohydrates, amino acids, energy were described in health compared to periodontitis (Wang et al, 2013). In our study, healthy-associated community also presented an overabundance of antitoxin Phd, which is part of a regulatory complex that neutralizes and reverses the action of bacterial toxins (Garcia-Pino et al, 2010), suggesting that in this environment, there may be a continuous compensatory regulation among members of the community which guarantees homeostasis. In general, studies converge to attribute a genetic profile related to biofilm formation and primary metabolism to the healthy environment, probably due to a predominance of primary colonizers, and because the process of maturation requires metabolic and genetic exchanges for environmental adaptation (Kolenbrander et al, 2010;Marsh, 2006).…”

Section: Discussionmentioning

confidence: 63%

Perfil taxonômico e funcional do biofilme subgengival de pacientes com periodontite agressiva generalizada em terapia de manutenção

Enri de Sousa Paz

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Aims:The aim was to evaluate the taxonomic and predicted functional content of the subgingival microbiome of generalized aggressive periodontitis (GAgP) patients in supportive periodontal therapy.Methods: Clinical and microbiological data were assessed from GAgP patients at baseline and after supportive periodontal therapy (SPT) (5.7±1.3 years) and periodontally healthy controls. Taxonomic and predicted functional analyses of subgingival biofilm were performed from 16S rRNA gene sequencing data.Results: GAgP patients under SPT presented overall clinical improvements. ß-diversity was different between GAgP and Health, both at baseline and after SPT. Moreover, although diversity did not statistically change between baseline and after SPT in GAgP, a change in core microbiome was observed. Based on predicted functional data, the treatment induced a reduction in some gene's abundance. However, some KEGGS persisted in higher abundance in microbial community regardless periodontal therapy and SPT. Conclusion:The periodontal treatment in GAgP patients promoted changes in taxonomic composition and some genes abundance; however, there was a persistence of subgingival biofilm genes in patients with GAgP.

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Purification and crystallization of Phd, the antitoxin of thephd/docoperon

Cited by 5 publications

References 33 publications

Predicted functional and taxonomic analysis of subgingival biofilm of Grade C periodontitis in young patients under maintenance therapy

Predicted functional and taxonomic analysis of subgingival biofilm of Grade C periodontitis in young patients under maintenance therapy

Crystallization and X-ray analysis of all of the players in the autoregulation of theataRTtoxin–antitoxin system

Perfil taxonômico e funcional do biofilme subgengival de pacientes com periodontite agressiva generalizada em terapia de manutenção

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