A bacterial endo-β-1,4-glucuronan lyase, CUL-I from Brevundimonas sp. SH203, belonging to a novel polysaccharide lyase family

Aim: Enterococcus faecalis is a leading nosocomial pathogen in biofilm-associated polymicrobial infections. The study aims to understand pathogenicity and biofilm determinants of the pathogen by genome analysis. Methodology: Genome sequencing of a strong biofilm forming clinical isolate Enterococcus faecalis SK460 devoid of Fsr quorum-signaling system, was performed and comparative genomics was carried out among a set of pathogenic biofilm formers and nonpathogenic weak biofilm formers. Results: Analysis revealed a pool of virulence and adhesion related factors associated with pathogenicity. Absence of CRISPR-Cas system facilitated acquisition of pheromone responsive plasmid, pathogenicity island and phages. Comprehensive analysis identified a subset of accessory genes encoding polysaccharide lyase, sugar phosphotransferase system, phage proteins and transcriptional regulators exclusively in pathogenic biofilm formers. Conclusion: The study identified a set of genes specific to pathogenic biofilm formers and these can act as targets which in turn help to develop future treatment endeavors against enterococcal infections.

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Screening of a Novel Polysaccharide Lyase Family 10 Pectate Lyase from Paenibacillus polymyxa KF-1: Cloning, Expression and Characterization

Molecules ◽

10.3390/molecules23112774 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2774 ◽

Cited By ~ 6

Author(s):

Yan Zhao ◽

Ye Yuan ◽

Xinyu Zhang ◽

Yumei Li ◽

Qiang Li ◽

...

Keyword(s):

Textile Industry ◽

Pectate Lyase ◽

Paenibacillus Polymyxa ◽

Polygalacturonic Acid ◽

Optimal Conditions ◽

Citrus Pectin ◽

Plant Fiber ◽

Polysaccharide Lyase ◽

Glycosidic Bonds ◽

Fiber Processing

Pectate lyase (EC 4.2.2.2) catalyzes the cleavage of α-1,4-glycosidic bonds of pectin polymers, and it has potential uses in the textile industry. In this study, a novel pectate lyase belonging to polysaccharide lyase family 10 was screened from the secreted enzyme extract of Paenibacillus polymyxa KF-1 and identified by liquid chromatography-MS/MS. The gene was cloned from P. polymyxa KF-1 genomic DNA and expressed in Escherichia coli. The recombinant enzyme PpPel10a had a predicted Mr of 45.2 kDa and pI of 9.41. Using polygalacturonic acid (PGA) as substrate, the optimal conditions for PpPel10a reaction were determined to be 50 °C and pH 9.0, respectively. The Km, vmax and kcat values of PpPel10a with PGA as substrate were 0.12 g/L, 289 μmol/min/mg, and 202.3 s−1, respectively. Recombinant PpPel10a degraded citrus pectin, producing unsaturated mono- and oligogalacturonic acids. PpPel10a reduced the viscosity of PGA, and weight loss of ramie (Boehmeria nivea) fibers was observed after treatment with the enzyme alone (22.5%) or the enzyme in combination with alkali (26.3%). This enzyme has potential for use in plant fiber processing.

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Cloning, Expression, and Characterization of a New Glycosaminoglycan Lyase from Microbacterium sp. H14

Marine Drugs ◽

10.3390/md17120681 ◽

2019 ◽

Vol 17 (12) ◽

pp. 681

Author(s):

Junhao Sun ◽

Xu Han ◽

Guanrui Song ◽

Qianhong Gong ◽

Wengong Yu

Keyword(s):

Enzyme Activity ◽

Metal Ions ◽

Animal Experiments ◽

Basic Research ◽

Facilitated Diffusion ◽

Divalent Metal Ions ◽

Polysaccharide Lyase ◽

Functional Studies ◽

Dose Dependent

Glycosaminoglycan (GAG) lyase is an effective tool for the structural and functional studies of glycosaminoglycans and preparation of functional oligosaccharides. A new GAG lyase from Microbacterium sp. H14 was cloned, expressed, purified, and characterized, with a molecular weight of approximately 85.9 kDa. The deduced lyase HCLaseM belonged to the polysaccharide lyase (PL) family 8. Based on the phylogenetic tree, HCLaseM could not be classified into the existing three subfamilies of this family. HCLaseM showed almost the same enzyme activity towards hyaluronan (HA), chondroitin sulfate A (CS-A), CS-B, CS-C, and CS-D, which was different from reported GAG lyases. HCLaseM exhibited the highest activities to both HA and CS-A at its optimal temperature (35 °C) and pH (pH 7.0). HCLaseM was stable in the range of pH 5.0–8.0 and temperature below 30 °C. The enzyme activity was independent of divalent metal ions and was not obviously affected by most metal ions. HCLaseM is an endo-type enzyme yielding unsaturated disaccharides as the end products. The facilitated diffusion effect of HCLaseM is dose-dependent in animal experiments. These properties make it a candidate for further basic research and application.

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The first structure of pectate lyase belonging to polysaccharide lyase family 3

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444901014482 ◽

2001 ◽

Vol 57 (12) ◽

pp. 1786-1792 ◽

Cited By ~ 31

Author(s):

Masatake Akita ◽

Atsuo Suzuki ◽

Tohru Kobayashi ◽

Susumu Ito ◽

Takashi Yamane

Keyword(s):

Pectate Lyase ◽

Polysaccharide Lyase

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Probing the Dependence of pH on Sugar Binding and Protein Structure in a Polysaccharide Lyase

Biophysical Journal ◽

10.1016/j.bpj.2014.11.327 ◽

2015 ◽

Vol 108 (2) ◽

pp. 54a

Author(s):

Sook Wong ◽

Jeffery B. Klauda

Keyword(s):

Protein Structure ◽

Polysaccharide Lyase ◽

Sugar Binding

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The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29

Journal of Biological Chemistry ◽

10.1074/jbc.ra118.004510 ◽

2018 ◽

Vol 293 (46) ◽

pp. 17906-17916 ◽

Cited By ~ 8

Author(s):

Didier Ndeh ◽

Jose Munoz Munoz ◽

Alan Cartmell ◽

David Bulmer ◽

Corinne Wills ◽

...

Keyword(s):

Dermatan Sulfate ◽

Microbial Interactions ◽

Bacteroides Thetaiotaomicron ◽

Human Gut ◽

Polysaccharide Lyase ◽

Founding Member ◽

Degrading Enzymes ◽

Biochemical Assays ◽

Gut Microbe ◽

Inducible Genes

Glycosaminoglycans (GAGs) and GAG-degrading enzymes have wide-ranging applications in the medical and biotechnological industries. The former are also an important nutrient source for select species of the human gut microbiota (HGM), a key player in host–microbial interactions. How GAGs are metabolized by the HGM is therefore of interest and has been extensively investigated in the model human gut microbe Bacteroides thetaiotaomicron. The presence of as-yet uncharacterized GAG-inducible genes in its genome and of related species, however, is testament to our incomplete understanding of this process. Nevertheless, it presents a potential opportunity for the discovery of additional GAG-degrading enzymes. Here, we investigated a gene of unknown function (BT_3328) from the chondroitin sulfate (CS) utilization locus of B. thetaiotaomicron. NMR and UV spectroscopic assays revealed that it encodes a novel polysaccharide lyase (PL), hereafter referred to as BtCDH, reflecting its source (B. thetaiotaomicron (Bt)) and its ability to degrade the GAGs CS, dermatan sulfate (DS), and hyaluronic acid (HA). When incubated with HA, BtCDH generated a series of unsaturated HA sugars, including Δ4,5UA-GlcNAc, Δ4,5UA-GlcNAc-GlcA-GlcNac, Δ4,5UA-[GlcNAc-GlcA]2-GlcNac, and Δ4,5UA-[GlcNAc-GlcA]3-GlcNac, as end products and hence was classed as endo-acting. A combination of genetic and biochemical assays revealed that BtCDH localizes to the cell surface of B. thetaiotaomicron where it enables extracellular GAG degradation. BtCDH homologs were also detected in several other HGM species, and we therefore propose that it represents the founding member of a new polysaccharide lyase family (PL29). The current discovery also contributes new insights into CS metabolism by the HGM.

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Biochemical Characterization and Elucidation of Action Pattern of a Novel Polysaccharide Lyase 6 Family Alginate Lyase from Marine Bacterium Flammeovirga sp. NJ-04

Marine Drugs ◽

10.3390/md17060323 ◽

2019 ◽

Vol 17 (6) ◽

pp. 323 ◽

Cited By ~ 7

Author(s):

Qian Li ◽

Fu Hu ◽

Benwei Zhu ◽

Yun Sun ◽

Zhong Yao

Keyword(s):

Biochemical Characterization ◽

Alginate Lyase ◽

Ionization Mass ◽

Action Pattern ◽

Polysaccharide Lyase ◽

Glycosidic Bonds ◽

Alginate Oligosaccharides ◽

Degradation Pattern ◽

Alginate Lyases ◽

Layer Chromatography

Alginate lyases have been widely used to prepare alginate oligosaccharides in food, agricultural, and medical industries. Therefore, discovering and characterizing novel alginate lyases with excellent properties has drawn increasing attention. Herein, a novel alginate lyase FsAlyPL6 of Polysaccharide Lyase (PL) 6 family is identified and biochemically characterized from Flammeovirga sp. NJ-04. It shows highest activity at 45 °C and could retain 50% of activity after being incubated at 45 °C for 1 h. The Thin-Layer Chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analysis indicates that FsAlyPL6 endolytically degrades alginate polysaccharide into oligosaccharides ranging from monosaccharides to pentasaccharides. In addition, the action pattern of the enzyme is also elucidated and the result suggests that FsAlyPL6 could recognize tetrasaccharide as the minimal substrate and cleave the glycosidic bonds between the subsites of −1 and +3. The research provides extended insights into the substrate recognition and degradation pattern of PL6 alginate lyases, which may further expand the application of alginate lyases.

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