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Marine Drugs Jan 2022As a low molecular weight alginate, alginate oligosaccharides (AOS) exhibit improved water solubility, better bioavailability, and comprehensive health benefits. In...
As a low molecular weight alginate, alginate oligosaccharides (AOS) exhibit improved water solubility, better bioavailability, and comprehensive health benefits. In addition, their biocompatibility, biodegradability, non-toxicity, non-immunogenicity, and gelling capability make them an excellent biomaterial with a dual curative effect when applied in a drug delivery system. In this paper, a novel alginate lyase, Algpt, was cloned and characterized from a marine bacterium, sp. LJ-23. The purified enzyme was composed of 387 amino acid residues, and had a molecular weight of 42.8 kDa. The optimal pH of Algpt was 7.0 and the optimal temperature was 45 °C. The analysis of the conserved domain and the prediction of the three-dimensional structure indicated that Algpt was a novel alginate lyase. The dominant degradation products of Algpt on alginate were AOS dimer to octamer, depending on the incubation time, which demonstrated that Algpt degraded alginate in an endolytic manner. In addition, Algpt was a salt-independent and thermo-tolerant alginate lyase. Its high stability and wide adaptability endow Algpt with great application potential for the efficient preparation of AOS with different sizes and AOS-based products.
Topics: Alginates; Animals; Aquatic Organisms; China; Cloning, Molecular; Drug Delivery Systems; Lyases; Paenibacillus
PubMed: 35049921
DOI: 10.3390/md20010066 -
Annals of Botany Sep 2021This article comments on: Thurayya Z. S. Al Hinai, Robert A. M. Vreeburg, C. Logan Mackay, Lorna Murray, Ian H. Sadler and Stephen C. Fry. Fruit softening: evidence for...
Pectate lyase action in vivo and fruit softening. A commentary on: 'Fruit softening: evidence for pectate lyase action in vivo in date (Phoenix dactylifera) and rosaceous fruit cell walls'.
This article comments on: Thurayya Z. S. Al Hinai, Robert A. M. Vreeburg, C. Logan Mackay, Lorna Murray, Ian H. Sadler and Stephen C. Fry. Fruit softening: evidence for pectate lyase action in date () and rosaceous fruit cell walls, Annals of Botany, Volume 128, Issue 5, 8 October 2021, Pages 511–526, https://doi.org/10.1093/aob/mcab072
Topics: Cell Wall; Fruit; Phoeniceae; Polysaccharide-Lyases
PubMed: 34342644
DOI: 10.1093/aob/mcab096 -
Applied and Environmental Microbiology Feb 2018Alginate is a linear polysaccharide produced mainly by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units,... (Review)
Review
Alginate is a linear polysaccharide produced mainly by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units, β-d-mannuronate (M) and its C-5 epimer α-l-guluronate (G). Alginate lyases are polysaccharide lyases (PL) that degrade alginate via a β-elimination reaction. These enzymes play an important role in marine carbon recycling and also have widespread industrial applications. So far, more than 1,774 alginate lyase sequences have been identified and are distributed into 7 PL families. In this review, the folds, conformational changes during catalysis, and catalytic mechanisms of alginate lyases are described. Thus far, structures for 15 alginate lyases have been solved and are divided into 3 fold classes: the β-jelly roll class (PL7, -14, and -18), the (α/α)n toroid class (PL5, -15, and -17), and the β-helix fold (PL6). These enzymes adopt two different mechanisms for catalysis, and three kinds of conformational changes occur during this process. Moreover, common features in the structures, conformational changes, and catalytic mechanisms are summarized, providing a comprehensive understanding on alginate lyases.
Topics: Alginates; Catalysis; Crystallography, X-Ray; Lyases; Models, Molecular; Molecular Structure; Phaeophyceae; Polysaccharide-Lyases; Polysaccharides; Protein Conformation; Substrate Specificity
PubMed: 29150496
DOI: 10.1128/AEM.02040-17 -
ACS Chemical Biology Sep 2022The three-dimensional structure of natural products is critical for their biological activities and, as such, enzymes have evolved that specifically generate active...
The three-dimensional structure of natural products is critical for their biological activities and, as such, enzymes have evolved that specifically generate active stereoisomers. Lanthipeptides are post-translationally modified peptidic natural products that contain macrocyclic thioethers featuring lanthionine (Lan) and/or methyllanthionine (MeLan) residues with defined stereochemistry. In this report, we compare two class I lanthipeptide biosynthetic gene clusters (BGCs), and , that represent two families of lanthipeptide gene clusters found in Actinobacteria. The precursor peptides and BGCs are quite similar with genes encoding a dehydratase, cyclase, and methyltransferase (MT). We illustrate that the precursor peptide CoiA1 is converted by these enzymes into a polymacrocyclic product, mCoiA1, that contains an analogous ring pattern to the previously characterized post-translationally modified OlvA peptide (mOlvA). However, a clear distinction between the two BGCs is an additional Thr-glutamyl lyase (GL) domain that is fused to the MT, CoiS, which results in divergence of the product stereochemistry for the BGC. Two out of three MeLan rings of mCoiA1 contain different stereochemistry than the corresponding residues in mOlvA, with the most notable difference being a rare d--l-MeLan residue, the formation of which is guided by CoiS. This study illustrates how nature utilizes a distinct GL to control natural product stereochemistry in lanthipeptide biosynthesis.
Topics: Biological Products; Hydro-Lyases; Lyases; Methyltransferases; Peptides; Sulfides
PubMed: 36001880
DOI: 10.1021/acschembio.2c00492 -
Applied and Environmental Microbiology May 2021Ulvan is an important marine polysaccharide. Bacterial ulvan lyases play important roles in ulvan degradation and marine carbon cycling. Until now, only a small number...
Ulvan is an important marine polysaccharide. Bacterial ulvan lyases play important roles in ulvan degradation and marine carbon cycling. Until now, only a small number of ulvan lyases have been characterized. Here, a new ulvan lyase, Uly1, belonging to polysaccharide lyase family 24 (PL24) from the marine bacterium Catenovulum maritimum, is characterized. The optimal temperature and pH for Uly1 to degrade ulvan are 40°C and pH 9.0, respectively. Uly1 degrades ulvan polysaccharides in the endolytic manner, mainly producing ΔRha3S, consisting of an unsaturated 4-deoxy-l--hex-4-enopyranosiduronic acid and a 3-O-sulfated α-l-rhamnose. The structure of Uly1 was resolved at a 2.10-Å resolution. Uly1 adopts a seven-bladed β-propeller architecture. Structural and site-directed mutagenesis analyses indicate that four highly conserved residues, H128, H149, Y223, and R239, are essential for catalysis. H128 functions as both the catalytic acid and base, H149 and R239 function as the neutralizers, and Y223 plays a supporting role in catalysis. Structural comparison and sequence alignment suggest that Uly1 and many other PL24 enzymes may directly bind the substrate near the catalytic residues for catalysis, different from the PL24 ulvan lyase LOR_107, which adopts a two-stage substrate binding process. This study provides new insights into ulvan lyases and ulvan degradation. Ulvan is a major cell wall component of green algae of the genus Many marine heterotrophic bacteria can produce extracellular ulvan lyases to degrade ulvan for a carbon nutrient. In addition, ulvan has a range of physiological bioactivities based on its specific chemical structure. Ulvan lyase thus plays an important role in marine carbon cycling and has great potential in biotechnological applications. However, only a small number of ulvan lyases have been characterized over the past 10 years. Here, based on biochemical and structural analyses, a new ulvan lyase of polysaccharide lyase family 24 is characterized, and its substrate recognition and catalytic mechanisms are revealed. Moreover, a new substrate binding process adopted by PL24 ulvan lyases is proposed. This study offers a better understanding of bacterial ulvan lyases and is helpful for studying the application potentials of ulvan lyases.
Topics: Alteromonadaceae; Amino Acid Sequence; Catalysis; Phylogeny; Polysaccharide-Lyases; Polysaccharides; Substrate Specificity
PubMed: 33771786
DOI: 10.1128/AEM.00412-21 -
Applied and Environmental Microbiology Feb 2021Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. Herein, we describe a...
Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. Herein, we describe a thermostable alginate lyase that belongs to polysaccharide lyase family 17 (PL17) and was derived from an Arctic Mid-Ocean Ridge (AMOR) metagenomics data set. This enzyme, AMOR_PL17A, is a thermostable exolytic oligoalginate lyase (EC 4.2.2.26), which can degrade alginate, poly-β-d-mannuronate, and poly-α-l-guluronate within a broad range of pHs, temperatures, and salinity conditions. Site-directed mutagenesis showed that tyrosine Y251, previously suggested to act as a catalytic acid, indeed is essential for catalysis, whereas mutation of tyrosine Y446, previously proposed to act as a catalytic base, did not affect enzyme activity. The observed reaction products are protonated and deprotonated forms of the 4,5-unsaturated uronic acid monomer, Δ, two hydrates of DEH (4-deoxy-l--5-hexulosuronate), which are formed after ring opening, and, finally, two epimers of a 5-member hemiketal called 4-deoxy-d--hexulofuranosidonate (DHF), formed through intramolecular cyclization of hydrated DEH. The detection and nuclear magnetic resonance (NMR) assignment of these hemiketals refine our current understanding of alginate degradation. The potential markets for seaweed-derived products and seaweed processing technologies are growing, yet commercial enzyme cocktails for complete conversion of seaweed to fermentable sugars are not available. Such an enzyme cocktail would require the catalytic properties of a variety of different enzymes, where fucoidanases, laminarinases, and cellulases together with endo- and exo-acting alginate lyases would be the key enzymes. Here, we present an exo-acting alginate lyase that efficiently produces monomeric sugars from alginate. Since it is only the second characterized exo-acting alginate lyase capable of degrading alginate at a high industrially relevant temperature (≥60°C), this enzyme may be of great biotechnological and industrial interest. In addition, in-depth NMR-based structural elucidation revealed previously undescribed rearrangement products of the unsaturated monomeric sugars generated from exo-acting lyases. The insight provided by the NMR assignment of these products facilitates future assessment of product formation by alginate lyases.
Topics: Alginates; DNA, Plant; Metagenomics; Picea; Plant Proteins; Polysaccharide-Lyases; Temperature
PubMed: 33397696
DOI: 10.1128/AEM.02399-20 -
International Journal of Molecular... Dec 2022Alkaline pectate lyases have biotechnological applications in plant fiber processing, such as ramie degumming. Previously, we characterized an alkaline pectate lyase...
Alkaline pectate lyases have biotechnological applications in plant fiber processing, such as ramie degumming. Previously, we characterized an alkaline pectate lyase from S10, named BacPelA, which showed potential for enzymatic ramie degumming because of its high cleavage activity toward methylated pectins in alkaline conditions. However, BacPelA displayed poor thermo-alkaline stability. Here, we report the 1.78 Å resolution crystal structure of BacPelA in apo form. The enzyme has the characteristic right-handed β-helix fold of members of the polysaccharide lyase 1 family and shows overall structural similarity to them, but it displays some differences in the details of the secondary structure and Ca-binding site. On the basis of the structure, 10 sites located in flexible regions and showing high B-factor and positive Δ values were selected for mutation, aiming to improve the thermo-alkaline stability of the enzyme. Following site-directed saturation mutagenesis and screening, mutants A238C, R150G, and R216H showed an increase in the value at pH 10.0 of 3.0 °C, 6.5 °C, and 7.0 °C, respectively, compared with the wild-type enzyme, interestingly accompanied by a 24.5%, 46.6%, and 61.9% increase in activity. The combined mutant R150G/R216H/A238C showed an 8.5 °C increase in the value at pH 10.0, and an 86.1% increase in the specific activity at 60 °C, with approximately doubled catalytic efficiency, compared with the wild-type enzyme. Moreover, this mutant retained 86.2% activity after incubation in ramie degumming conditions (4 h, 60 °C, pH 10.0), compared with only 3.4% for wild-type BacPelA. The combined mutant increased the weight loss of ramie fibers in degumming by 30.2% compared with wild-type BacPelA. This work provides a thermo-alkaline stable, highly active pectate lyase with great potential for application in the textile industry, and also illustrates an effective strategy for rational design and improvement of pectate lyases.
Topics: Boehmeria; Polysaccharide-Lyases; Pectins; Biotechnology; Hydrogen-Ion Concentration
PubMed: 36613981
DOI: 10.3390/ijms24010538 -
International Journal of Molecular... Mar 2023Sphingosine-1-phosphate lyase (SPL) is a pyridoxal 5'-phosphate-dependent enzyme involved in the irreversible degradation of sphingosine-1-phosphate (S1P)-a bioactive... (Review)
Review
Sphingosine-1-phosphate lyase (SPL) is a pyridoxal 5'-phosphate-dependent enzyme involved in the irreversible degradation of sphingosine-1-phosphate (S1P)-a bioactive sphingolipid that modulates a broad range of biological processes (cell proliferation, migration, differentiation and survival; mitochondrial functioning; and gene expression). Although SPL activity leads to a decrease in the available pool of S1P in the cell, at the same time, hexadecenal and phosphoethanolamine, compounds with potential biological activity, are generated. The increased expression and/or activity of SPL, and hence the imbalance between S1P and the end products of its cleavage, were demonstrated in several pathological states. On the other hand, loss-of-function mutations in the SPL encoding gene are a cause of severe developmental impairments. Recently, special attention has been paid to neurodegenerative diseases as the most common pathologies of the nervous system. This review summarizes the current findings concerning the role of SPL in the nervous system with an emphasis on neurodegeneration. Moreover, it briefly discusses pharmacological compounds directed to inhibit its activity.
Topics: Sphingosine; Sphingolipids; Aldehyde-Lyases; Lysophospholipids
PubMed: 37047151
DOI: 10.3390/ijms24076180 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Dec 2022-coumaric acid is one of the aromatic compounds that are widely used in food, cosmetics and medicine due to its properties of antibacterium, antioxidation and...
-coumaric acid is one of the aromatic compounds that are widely used in food, cosmetics and medicine due to its properties of antibacterium, antioxidation and cardiovascular disease prevention. Tyrosine ammonia-lyase (TAL) catalyzes the deamination of tyrosine to -coumaric acid. However, the lack of highly active and specific tyrosine ammonia lyase limits cost-effective microbial production of -coumaric acid. In order to improve biosynthesis efficiency of -coumaric acid, two tyrosine ammonia-lyases, namely Fc-TAL2 derived from and Fs-TAL derived from , were selected and characterized. The optimum temperature (55 ℃) and pH (9.5) for Fs-TAL and Fc-TAL2 are the same. Under optimal conditions, the specific enzyme activity of Fs-TAL and Fc-TAL2 were 82.47 U/mg and 13.27 U/mg, respectively. Structural simulation and alignment analysis showed that the orientation of the phenolic hydroxyl group of the conserved Y50 residue on the inner lid loop and its distance to the substrate were the main reasons accounting for the higher activity of Fs-TAL than that of Fc-TAL2. The higher activity and specificity of Fs-TAL were further confirmed via whole-cell catalysis using recombinant , which could convert 10 g/L tyrosine into 6.2 g/L -coumaric acid with a yield of 67.9%. This study provides alternative tyrosine ammonia-lyases and may facilitate the microbial production of -coumaric acid and its derivatives.
Topics: Ammonia-Lyases; Coumaric Acids; Escherichia coli; Tyrosine
PubMed: 36593193
DOI: 10.13345/j.cjb.220182 -
Journal of Integrative Neuroscience Jun 2022Chondroitin sulfate proteoglycans (CSPGs) present a formidable barrier to regrowing axons following spinal cord injury. CSPGs are secreted in response to injury and... (Review)
Review
Chondroitin sulfate proteoglycans (CSPGs) present a formidable barrier to regrowing axons following spinal cord injury. CSPGs are secreted in response to injury and their glycosaminoglycan (GAG) side chains present steric hindrance preventing the growth of axons through the lesion site. The enzyme chondroitinase has been proven effective at reducing the CSPG GAG chains, however, there are issues with direct administration of the enzyme specifically due to its limited timeframe of activity. In this perspective article, we discuss the evolution of chondroitinase-based therapy in spinal cord injury as well as up-to-date advances on this critical therapeutic. We describe the success and the limitations around use of the bacterial enzyme namely issues around thermostability. We then discuss current efforts to improve delivery of chondroitinase with a push towards gene therapy, namely through the use of lentiviral and adeno-associated viral vectors, including the temporal modulation of its expression and activity. As a chondroitinase therapy for spinal cord injury inches nearer to the clinic, the drive towards an optimised delivery platform is currently underway.
Topics: Axons; Chondroitin ABC Lyase; Chondroitin Sulfate Proteoglycans; Chondroitinases and Chondroitin Lyases; Humans; Nerve Regeneration; Spinal Cord; Spinal Cord Injuries; Spinal Cord Regeneration
PubMed: 35864769
DOI: 10.31083/j.jin2104118