Purification and characterization of extracellular poly(beta-D-1,4-mannuronide) lyase from Dendryphiella salina IFO 32139

Specificities and Synergistic Actions of Novel PL8 and PL7 Alginate Lyases from the Marine Fungus Paradendryphiella salina

Alginate is an anionic polysaccharide abundantly present in the cell walls of brown macroalgae. The enzymatic depolymerization is performed solely by alginate lyases (EC 4.2.2.x), categorized as polysaccharide lyases (PLs) belonging to 12 different PL families. Until now, the vast majority of the alginate lyases have been found in bacteria. We report here the first extensive characterization of four alginate lyases from a marine fungus, the ascomycete Paradendryphiella salina, a known saprophyte of seaweeds. We have identified four polysaccharide lyase encoding genes bioinformatically in P. salina, one PL8 (PsMan8A), and three PL7 alginate lyases (PsAlg7A, -B, and -C). PsMan8A was demonstrated to exert exo-action on polymannuronic acid, and no action on alginate, indicating that this enzyme is most likely an exo-acting polymannuronic acid specific lyase. This enzyme is the first alginate lyase assigned to PL8 and polymannuronic acid thus represents a new substrate specificity in this family. The PL7 lyases (PsAlg7A, -B, and -C) were found to be endo-acting alginate lyases with different activity optima, substrate affinities, and product profiles. PsAlg7A and PsMan8A showed a clear synergistic action for the complete depolymerization of polyM at pH 5. PsAlg7A depolymerized polyM to mainly DP5 and DP3 oligomers and PsMan8A to dimers and monosaccharides. PsAlg7B and PsAlg7C showed substrate affinities towards both polyM and polyG at pH 8, depolymerizing both substrates to DP9-DP2 oligomers. The findings elucidate how P. salina accomplishes alginate depolymerization and provide insight into an efficient synergistic cooperation that may provide a new foundation for enzyme selection for alginate degradation in seaweed bioprocessing.

Proteomic enzyme analysis of the marine fungus Paradendryphiella salina reveals alginate lyase as a minimal adaptation strategy for brown algae degradation

We set out to investigate the genetic adaptations of the marine fungus Paradendryphiella salina CBS112865 for degradation of brown macroalgae. We performed whole genome and transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina grown on three species of brown algae and under carbon limitation. Genome comparison with closely related terrestrial fungi revealed that P. salina had a similar but reduced CAZyme profile relative to the terrestrial fungi except for the presence of three putative alginate lyases from Polysaccharide Lyase (PL) family 7 and a putative PL8 with similarity to ascomycete chondroitin AC lyases. Phylogenetic and homology analyses place the PL7 sequences amongst mannuronic acid specific PL7 proteins from marine bacteria. Recombinant expression, purification and characterization of one of the PL7 genes confirmed the specificity. Proteomic analysis of the P. salina secretome when growing on brown algae, revealed the PL7 and PL8 enzymes abundantly secreted together with enzymes necessary for degradation of laminarin, cellulose, lipids and peptides. Our findings indicate that the basic CAZyme repertoire of saprobic and plant pathogenic ascomycetes, with the addition of PL7 alginate lyases, provide P. salina with sufficient enzymatic capabilities to degrade several types of brown algae polysaccharides.

Characterization of alginase and elicitor-active oligosaccharides from Gracilibacillus A7 in alleviating salt stress for Brassica campestris L

Alginase was purified from Gracilibacillus A7 and evaluated for its ability to produce elicitor-active oligosaccharides. The optimum conditions for the alginase reaction are as follows: temperature, 40 °C; pH, 8.0; alginate content, 0.3-0.7%; and the presence of Na(+) and Mg(2+) metal ions. The degree of polymerization (DP) decreased as the reaction time of the alginase progressed, achieving values of 5.4 and 3.3 after 240 and 300 min, respectively. The relative root length (RRL) of the Brassica campestris L. increased with the addition of oligosaccharides with reduced DP values. The oligosaccharides with lower DP values are effective in reducing the effect of salt stress on the activity of the superoxide dismutase (SOD) and guaiacol peroxidase (POD), and oligosaccharides with moderate DP values can reduce the increase in lipid peroxidation activities (as malondialdehyde content) induced by salt stress. These results suggest that oligosaccharides may act as osmoprotective agents during the plant germination process.

Cloning and sequencing of alginate lyase genes from deep-sea strains of Vibrio and Agarivorans and characterization of a new Vibrio enzyme

Four alginate lyase genes were cloned and sequenced from the genomic DNAs of deep-sea bacteria, namely members of Vibrio and Agarivorans. Three of them were from Vibrio sp. JAM-A9m, which encoded alginate lyases, A9mT, A9mC, and A9mL. A9mT was composed of 286 amino acids and 57% homologous to AlxM of Photobacterium sp. A9mC (221 amino acids) and A9mL (522 amino acids) had the highest degree of similarity to two individual alginate lyases of Vibrio splendidus with 74% and 84% identity, respectively. The other gene for alginate lyase, A1mU, was shotgun cloned from Agarivorans sp. JAM-A1m. A1mU (286 amino acids) showed the highest homology to AlyVOA of Vibrio sp. with 76% identity. All alginate lyases belong to polysaccharide lyase family 7, although, they do not show significant similarity to one another with 14% to 58% identity. Among the above lyases, the recombinant A9mT was purified to homogeneity and characterized. The molecular mass of A9mT was around 28 kDa. The enzyme was remarkably salt activated and showed the highest thermal stability in the presence of NaCl. A9mT favorably degraded mannuronate polymer in alginate. We discussed substrate specificities of family 7 alginate lyases based on their conserved amino acid sequences.

Polysaccharide Lyases: Recent Developments as Biotechnological Tools

Polysaccharide lyases, which are polysaccharide cleavage enzymes, act mainly on anionic polysaccharides. Produced by prokaryote and eukaryote organisms, these enzymes degrade (1,4) glycosidic bond by a beta elimination mechanism and have unsaturated oligosaccharides as major products. New polysaccharides are cleaved only by their specific polysaccharide lyases. From anionic polysaccharides controlled degradations, various biotechnological applications were investigated. This review catalogues the degradation of bacterial, plant and animal polysaccharides (neutral and anionic) by this family of carbohydrate acting enzymes.

Purification and properties of a glucuronan lyase from Sinorhizobium meliloti M5N1CS (NCIMB 40472)

A glucuronan lyase extracted from Sinorhizobium meliloti strain M5N1CS was purified to homogeneity by anion-exchange chromatography. The purified enzyme corresponds to a monomer with a molecular mass of 20 kDa and a pI of 4.9. A specific activity was found only for polyglucuronates leading to the production of 4,5-unsaturated oligoglucuronates. The enzyme activity was optimal at pH 6.5 and 50 degrees C. Zn(2+), Cu(2+), and Hg(2+) (1 mM) inhibited the enzyme activity. No homology of the enzyme N-terminal amino acid sequence was found with any of the previously published protein sequences. This enzyme purified from S. meliloti strain M5N1CS corresponding to a new lyase was classified as an endopolyglucuronate lyase.

ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications

Alginate lyases, characterized as either mannuronate (EC 4.2.2.3) or guluronate lyases (EC 4.2.2.11), catalyze the degradation of alginate, a complex copolymer of alpha-L-guluronate and its C5 epimer beta-D-mannuronate. Lyases have been isolated from a wide range of organisms, including algae, marine invertebrates, and marine and terrestrial microorganisms. This review catalogs the major characteristics of these lyases, the methods for analyzing these enzymes, as well as their biological roles. Analysis of primary sequence data identifies some markedly conserved motifs that should help elucidate functional domains. Information about the three-dimensional structure of a mannuronate lyase from Sphingomonas sp., combined with various mutagenesis studies, has identified residues that are important for catalytic activity in several lyases. Characterization of alginate lyases will enhance and expand the use of these enzymes to engineer novel alginate polymers for applications in various industrial, agricultural, and medical fields. In this review, we explore both past and present applications of this important enzyme and discuss its future prospects.

Cloning and sequence analysis of a gene (aly PG) encoding poly(α-l-guluronate)lyase from Corynebacterium sp. strain ALY-1

The aly PG gene, coding for a poly alpha-l-guluronate lyase (PG lyase) of Corynebacterium strain ALY-1, was cloned and sequenced. The gene consists of 768 bp encoding a signal peptide of 32 amino acids and a mature protein of 224 amino acids. Two disulfide bond cross-linkages were found to be formed between Cys-4 and Cys-51 and between Cys-200 and Cys-206 in the native PG lyase molecule. The deduced amino acid sequence of the Corynebacterium sp. aly PG gene exhibited 29% homology toward that of the Klebsiella pneumoniae, subsp. aerogenes aly A gene, with two conserved regions (the amino acid sequences from Y-102 to M-110 and from Y-221 to Q-229).

Enzymatic and genetic bases on assimilation, depolymerization, and transport of heteropolysaccharides in bacteria

When microorganisms utilize macromolecules for their growth, they commonly produce extracellular depolymerization enzymes and then incorporate the depolymerized low-molecular-weight products. Assimilation of heteropolysaccharides (gellan and xanthan) by Bacillus sp. GL1 depends on this generally accepted mechanism. On the other hand, Sphingomonas sp. A1 represents an unexplored specific and interesting system for macromolecule assimilation. In the presence of heteropolysaccharide (alginate), the bacterium forms a mouthlike pit on its cell surface and directly incorporates the macromolecule using a novel ATP-binding cassette transporter (ABC transporter). In this review, we discuss enzymatic and genetic bases on the depolymerization and assimilation routes of heteropolysaccharides in bacteria, with particular emphasis on the novel incorporation system for macromolecules, characteristic post-translational modification processes of polysaccharide lyases and on the mouthlike pit structure on the bacterial cell surface.