Modeling and Re-Engineering of Azotobacter vinelandii Alginate Lyase to Enhance Its Catalytic Efficiency for Accelerating Biofilm Degradation

Jang, Chul Ho; Piao, Yu Lan; Huang, Xiaoqin; Yoon, Eunju; Park, So Hee; Lee, Kyung Ho; Chen, Zhan; Cho, Hoon

doi:10.1371/journal.pone.0156197

Cited by 28 publications

(10 citation statements)

References 49 publications

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“…EPS disruption strategies (including the use of alginate lyase) have, despite advances in enzyme engineering, so far proved ineffective. 31 More recently, products derived from the marine environment have been investigated for antimicrobial/anti-biofilm activity e.g., furanones from the red algae Delisea pulchra . 32 , 33 However, none of these potential therapeutic approaches are as yet in clinical use.…”

Section: Introductionmentioning

confidence: 99%

Targeted disruption of the extracellular polymeric network of Pseudomonas aeruginosa biofilms by alginate oligosaccharides

Powell

Pritchard

Ferguson

et al. 2018

npj Biofilms Microbiomes

144

118

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Acquisition of a mucoid phenotype by Pseudomonas sp. in the lungs of cystic fibrosis (CF) patients, with subsequent over-production of extracellular polymeric substance (EPS), plays an important role in mediating the persistence of multi-drug resistant (MDR) infections. The ability of a low molecular weight (Mn = 3200 g mol−1) alginate oligomer (OligoG CF-5/20) to modify biofilm structure of mucoid Pseudomonas aeruginosa (NH57388A) was studied in vitro using scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) with Texas Red (TxRd®)-labelled OligoG and EPS histochemical staining. Structural changes in treated biofilms were quantified using COMSTAT image-analysis software of CLSM z-stack images, and nanoparticle diffusion. Interactions between the oligomers, Ca2+ and DNA were studied using molecular dynamics (MD) simulations, Fourier transform infrared spectroscopy (FTIR) and isothermal titration calorimetry (ITC). Imaging demonstrated that OligoG treatment (≥0.5%) inhibited biofilm formation, revealing a significant reduction in both biomass and biofilm height (P < 0.05). TxRd®-labelled oligomers readily diffused into established (24 h) biofilms. OligoG treatment (≥2%) induced alterations in the EPS of established biofilms; significantly reducing the structural quantities of EPS polysaccharides, and extracellular (e)DNA (P < 0.05) with a corresponding increase in nanoparticle diffusion (P < 0.05) and antibiotic efficacy against established biofilms. ITC demonstrated an absence of rapid complex formation between DNA and OligoG and confirmed the interactions of OligoG with Ca2+ evident in FTIR and MD modelling. The ability of OligoG to diffuse into biofilms, potentiate antibiotic activity, disrupt DNA-Ca2+-DNA bridges and biofilm EPS matrix highlights its potential for the treatment of biofilm-related infections.

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Section: Introductionmentioning

confidence: 99%

Targeted disruption of the extracellular polymeric network of Pseudomonas aeruginosa biofilms by alginate oligosaccharides

Powell

Pritchard

Ferguson

et al. 2018

npj Biofilms Microbiomes

144

118

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“…CMO (choline monooxygenase) can catalyze the first step of glycine betaine synthesis [ 80 ], which indicates that glycine betaine can be used as an osmoprotectant in marine Oligoflexia as well. In addition, there are many genes involved in transport or transformation of sugar as osmoprotectant, such as malK , msmX , rgpF and algI genes in Oligoflexia ( Table 2 ) [ 81 , 82 , 83 , 84 ]. In light of all these results, betaine as an osmoprotectant is commonly used among different groups of Bdellovibrionota, all having a variety of genes for fitness in the ocean.…”

Section: Resultsmentioning

confidence: 99%

Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

Zhou

Wei

et al. 2021

Microorganisms

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Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.

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“…For example, the alginate lyase A1-III, which originated from Sphingomonas sp. A1, was used as a template to model the homology of another alginate lyase AlgL (Jang et al 2016). The binding structure of the AlgL-alginate complex showed that the substrate-binding cleft and the adjacent molecular surface of the enzyme were covered with positively charged residues (e.g., K 194 , K 245 and K 319 ).…”

Section: Rational Design Of Alginate Lyasementioning

confidence: 99%

Evolving strategies for marine enzyme engineering: recent advances on the molecular modification of alginate lyase

Cao

et al. 2021

Mar Life Sci Technol

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Alginate, an acidic polysaccharide, is formed by β-d-mannuronate (M) and α-l-guluronate (G). As a type of polysaccharide lyase, alginate lyase can efficiently degrade alginate into alginate oligosaccharides, having potential applications in the food, medicine, and agriculture fields. However, the application of alginate lyase has been limited due to its low catalytic efficiency and poor temperature stability. In recent years, various structural features of alginate lyase have been determined, resulting in modification strategies that can increase the applicability of alginate lyase, making it important to summarize and discuss the current evidence. In this review, we summarized the structural features and catalytic mechanisms of alginate lyase. Molecular modification strategies, such as rational design, directed evolution, conserved domain recombination, and non-catalytic domain truncation, are also described in detail. Lastly, the application of alginate lyase is discussed. This comprehensive summary can inform future applications of alginate lyases.

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Modeling and Re-Engineering of Azotobacter vinelandii Alginate Lyase to Enhance Its Catalytic Efficiency for Accelerating Biofilm Degradation

Cited by 28 publications

References 49 publications

Targeted disruption of the extracellular polymeric network of Pseudomonas aeruginosa biofilms by alginate oligosaccharides

Targeted disruption of the extracellular polymeric network of Pseudomonas aeruginosa biofilms by alginate oligosaccharides

Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

Evolving strategies for marine enzyme engineering: recent advances on the molecular modification of alginate lyase

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