Assessment of biochemical methods to detect enzymatic depolymerization of polysaccharides

Dynamics of two-step reversible enzymatic reaction under fractional derivative with Mittag-Leffler Kernel

Chemical kinetics is a branch of chemistry that is founded on understanding chemical reaction rates. Chemical kinetics relates many aspects of cosmology, geology, and even in some cases of, psychology. There is a need for mathematical modelling of these chemical reactions. Therefore, the present research is based on chemical kinetics-based modelling and dynamics of enzyme processes. This research looks at the two-step substrate-enzyme reversible response. In the two step-reversible reactions, substrate combines with enzymes which is further converted into products with two steps. The model is displayed through the flow chart, which is then transformed into ODEs. The Atangana-Baleanu time-fractional operator and the Mittag-Leffler kernel are used to convert the original set of highly nonlinear coupled integer order ordinary differential equations into a fractional-order model. Additionally, it is shown that the solution to the investigated fractional model is unique, limited, and may be represented by its response velocity. A numerical scheme, also known as the Atangana-Toufik method, based on Newton polynomial interpolation technique via MATLAB software, is adopted to find the graphical results. The dynamics of reaction against different reaction rates are presented through various figures. It is observed that the forward reaction rates increase the reaction speed while backward reaction rates reduce it.

Influence of the Carbon and Nitrogen Sources on Diabolican Production by the Marine Vibrio diabolicus Strain CNCM I-1629

Recent advances in glycobiotechnology show that bacterial exopolysaccharides (EPS) presenting glycosaminoglycan (GAG)-like properties can provide a valuable source of bio-active macromolecules for industrial applications. The HE800 EPS, named diabolican, is a marine-derived anionic high-molecular-weight polysaccharide produced by Vibrio diabolicus CNCM I-1629 which displays original structural features close to those of hyaluronic acid. We investigated the impact of carbon and nitrogen substrates on both Vibrio diabolicus growth and diabolican production. Both substrates were screened by a one-factor-at-a-time method, and experimental designs were used to study the effect of glucose, mannitol, and ammonium acetate various concentrations. Results showed that the medium composition affected not only the bacterium growth and EPS yield, but also the EPS molecular weight (MW). EPS yields of 563 and 330 mg L⁻¹ were obtained in the presence of 69.3 g L⁻¹ glucose and 24.6 g L⁻¹ mannitol, respectively, both for 116.6 mM ammonium acetate. MW was the highest, with 69.3 g L⁻¹ glucose and 101.9 mM ammonium acetate (2.3 × 10⁶ g mol⁻¹). In parallel, the bacterial maximum specific growth rate was higher when both carbon and nitrogen substrate concentrations were low. This work paves the way for the optimization of marine exopolysaccharide production of great interest in the fields of human health and cosmetics.

Bacteria enhance the production of extracellular polymeric substances by the green dinoflagellate Lepidodinium chlorophorum

High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric Substances (EPS). To understand whether the EPS are produced by L. chlorophorum or its associated bacteria, or if they are a product of their interaction, batch cultures were performed under non-axenic and pseudo-axenic conditions for three strains. Maximum dinoflagellate cell abundances were observed in pseudo-axenic cultures. The non-sinking fraction of polymers (Soluble Extracellular Polymers, SEP), mainly composed of proteins and the exopolysaccharide sulphated galactan, slightly increased in pseudo-axenic cultures. The amount of Transparent Exopolymer Particles (TEP) per cell increased under non-axenic conditions. Despite the high concentrations of Particulate Organic Carbon (POC) measured, viscosity did not vary. These results suggest that the L. chlorophorum-bacteria interaction could have a detrimental consequence on the dinoflagellate, translating in a negative effect on L. chlorophorum growth, as well as EPS overproduction by the dinoflagellate, at concentrations that should not affect seawater viscosity.

Biocompatible Crosslinked Nanofibers of Poly(Vinyl Alcohol)/Carboxymethyl-Kappa-Carrageenan Produced by a Green Process

This study presents a new type of biocompatible nanofiber based on poly(vinyl alcohol) (PVA) and carboxymethyl-kappa-carrageenan (CMKC) blends, produced with no generation of hazardous waste. The nanofibers are produced by electrospinning using PVA:CMKC blends with ratios of 1:0, 1:0.25, 1:0.4, 1:0.5, and 1:0.75 (w/w PVA:CMKC) in aqueous solution, followed by thermal crosslinking. The diameter of the fibers is in the nanometer scale and below 300 nm. Fourier transform infrared spectroscopy shows the presence of the carboxyl and sulfate groups in all the fibers with CMKC. The nanofibers from water-soluble polymers are stabilized by thermal crosslinking. The incorporation of CMKC improves cytocompatibility, biodegradability, cell growth, and cell adhesion, compared to PVA nanofibers. Furthermore, the incorporation of CMKC modulates phenotype of human adipose-derived stem cells (ADSCs). PVA/CMKC nanofibers enhance ADSC response to osteogenic differentiation signals and are therefore good candidates for application in tissue engineering to support stem cells.

Deep-sea Hydrothermal Vent Bacteria as a Source of Glycosaminoglycan-Mimetic Exopolysaccharides

Bacteria have developed a unique strategy to survive in extreme environmental conditions through the synthesis of an extracellular polymeric matrix conferring upon the cells a protective microenvironment. The main structural component of this complex network constitutes high-molecular weight hydrophilic macromolecules, namely exopolysaccharides (EPS). EPS composition with the presence of particular chemical features may closely be related to the specific conditions in which bacteria evolve. Deep-sea hydrothermal vent bacteria have already been shown to produce EPS rich in hexosamines and uronic acids, frequently bearing some sulfate groups. Such a particular composition ensures interesting functional properties, including biological activities mimicking those known for glycosaminoglycans (GAG). The aim of the present study was to go further into the exploration of the deep-sea hydrothermal vent IFREMER (French Research Institute for Exploitation of the Sea) collection of bacteria to discover new strains able to excrete EPS endowed with GAG-like structural features. After the screening of our whole collection containing 692 strains, 38 bacteria have been selected for EPS production at the laboratory scale. EPS-producing strains were identified according to 16S rDNA phylogeny. Chemical characterization of the obtained EPS highlighted their high chemical diversity with the presence of atypical compositional patterns. These EPS constitute potential bioactives for a number of biomedical applications, including regenerative medicines and cancer treatment.

Bioprospecting for Exopolysaccharides from Deep-Sea Hydrothermal Vent Bacteria: Relationship between Bacterial Diversity and Chemical Diversity

Many bacteria biosynthesize structurally diverse exopolysaccharides (EPS) and excrete them into their surrounding environment. The EPS functional features have found many applications in industries such as cosmetics and pharmaceutics. In particular, some EPS produced by marine bacteria are composed of uronic acids, neutral sugars, and N-acetylhexosamines, and may also bear some functional sulfate groups. This suggests that they can share common structural features with glycosaminoglycans (GAG) like the two EPS (HE800 and GY785) originating from the deep sea. In an attempt to discover new EPS that may be promising candidates as GAG-mimetics, fifty-one marine bacterial strains originating from deep-sea hydrothermal vents were screened. The analysis of the EPS chemical structure in relation to bacterial species showed that Vibrio, Alteromonas, and Pseudoalteromonas strains were the main producers. Moreover, they produced EPS with distinct structural features, which might be useful for targeting marine bacteria that could possibly produce structurally GAG-mimetic EPS.

Purification of the exopolysaccharide produced by Alteromonas infernus: identification of endotoxins and effective process to remove them

Alteromonas infernus bacterium isolated from deep-sea hydrothermal vents can produce by fermentation a high molecular weight exopolysaccharide (EPS) called GY785. This EPS described as a new source of glycosaminoglycan-like molecule presents a great potential for pharmaceutical and biotechnological applications. However, this unusual EPS is secreted by a Gram-negative bacterium and can be therefore contaminated by endotoxins, in particular the lipopolysaccharides (LPS). Biochemical and chemical analyses of the LPS extracted from A. infernus membranes have shown the lack of the typical LPS architecture since 3-deoxy-D-manno-oct-2-ulopyranosonic acid (Kdo), glucosamine (GlcN), and phosphorylated monosaccharides were not present. Unlike for other Gram-negative bacteria, the results revealed that the outer membrane of A. infernus bacterium is most likely composed of peculiar glycolipids. Furthermore, the presence of these glycolipids was also detected in the EPS batches produced by fermentation. Different purification and chemical detoxification methods were evaluated to efficiently purify the EPS. Only the method based on a differential solubility of EPS and glycolipids in deoxycholate detergent showed the highest decrease in the endotoxin content. In contrast to the other tested methods, this new protocol can provide an effective method for obtaining endotoxin-free EPS without any important modification of its molecular weight, monosaccharide composition, and sulfate content.

Production of monosaccharides and bio-active compounds derived from marine polysaccharides using subcritical water hydrolysis

Polysaccharides are the major components of brown seaweed, accounting for approximately 40-65% of the total mass. The majority of the brown seaweed polysaccharides consists of alginate (40% of dry matter), a linear hetero-polysaccharides commonly developed in fields. However, depolymerisation of alginate is required to recover high-value compounds. In this report, depolymerisation was performed using subcritical water hydrolysis (SWH) at 180-260°C, with a ratio of material to water of 1:25 (w/v) and 1% formic acid as a catalyst. Sugar recovery was higher at low temperatures in the presence of catalyst. The antioxidant properties of Saccharina japonica showed the best activity at 180°C in the presence of a catalyst. The mass spectra produced using MALDI-TOF showed that polysaccharides and oligosaccharides were produced during hydrothermal treatment. Hydrolysis treatment at 180°C in the presence of a catalyst may be useful for modifying the structure of S. japonica and purified alginate.

Medium-throughput profiling method for screening polysaccharide-degrading enzymes in complex bacterial extracts

Polysaccharides are the most abundant and the most diverse renewable materials found on earth. Due to the stereochemical variability of carbohydrates, polysaccharide-degrading enzymes - i.e. glycoside hydrolases and polysaccharide lyases - are essential tools for resolving the structure of these complex macromolecules. The exponential increase of genomic and metagenomic data contrasts sharply with the low number of proteins that have ascribed functions. To help fill this gap, we designed and implemented a medium-throughput profiling method to screen for polysaccharide-degrading enzymes in crude bacterial extracts. Our strategy was based on a series of filtrations, which are absolutely necessary to eliminate any reducing sugars not directly generated by enzyme degradation. In contrast with other protocols already available in the literature, our method can be applied to any panel of polysaccharides having known and unknown structures because no chemical modifications are required. We applied this approach to screen for enzymes that occur in Pseudoalteromonas carrageenovora grown in two culture conditions.

Performance evaluation on a wide set of matrix-assisted laser desorption ionization matrices for the detection of oligosaccharides in a high-throughput mass spectrometric screening of carbohydrate depolymerizing enzymes

Compared to other analytical methods, matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) presents several unique advantages for the structural characterization of degradation products of carbohydrates. Our final goal is to implement this technique as a high-throughput platform, with the aim of exploring natural bio-diversity to discover new carbohydrate depolymerizing enzymes. In this approach, a variety of carbohydrates will be used as enzymes substrates and MALDI-MS will be employed to monitor the oligosaccharides produced. One drawback of MALDI, however, is that the choice of the matrix is largely dependent on the chemical properties of the analyte. In this context, our objective in the present work was to find the smallest set of MALDI matrices able to detect chemically heterogeneous oligosaccharides. This was done through the performance evaluation of more than 40 MALDI matrices preparations. Homogeneity of analyte-matrix deposits was considered as a critical feature, especially since the final objective is to fully automate the analyses. Evaluation of the matrices was done by means of a rigorous statistical approach. Amongst all tested compounds, our work proposes the use of the DHB/DMA ionic matrix as the most generic matrix, for rapid detection of a variety of polysaccharides including neutral, anionic, methylated, sulfated, and acetylated compounds. The selected matrices were then used to screen crude bacterial incubation media for the detection of enzymatic degradation products.

Antiviral activities of sulfated polysaccharides isolated from Sphaerococcus coronopifolius (Rhodophytha, Gigartinales) and Boergeseniella thuyoides (Rhodophyta, Ceramiales)

Water-soluble sulfated polysaccharides isolated from two red algae Sphaerococcus coronopifolius (Gigartinales, Sphaerococcaceae) and Boergeseniella thuyoides (Ceramiales, Rhodomelaceae) collected on the coast of Morocco inhibited in vitro replication of the Human Immunodeficiency Virus (HIV) at 12.5 μg/mL. In addition, polysaccharides were capable of inhibiting the in vitro replication of Herpes simplex virus type 1 (HSV-1) on Vero cells values of EC₅₀ of 4.1 and 17.2 μg/mL, respectively. The adsorption step of HSV-1 to the host cell seems to be the specific target for polysaccharide action. While for HIV-1, these results suggest a direct inhibitory effect on HIV-1 replication by controlling the appearance of the new generations of virus and potential virucidal effect. The polysaccharides from S. coronopifolius (PSC) and B. thuyoides (PBT) were composed of galactose, 3,6-anhydrogalactose, uronics acids, sulfate in ratios of 33.1, 11.0, 7.7 and 24.0% (w/w) and 25.4, 16.0, 3.2, 7.6% (w/w), respectively.

Agarose and polyacrylamide gel electrophoresis methods for molecular mass analysis of 5- to 500-kDa hyaluronan

Agarose and polyacrylamide gel electrophoresis systems for the molecular mass-dependent separation of hyaluronan (HA) in the size range of approximately 5-500 kDa were investigated. For agarose-based systems, the suitability of different agarose types, agarose concentrations, and buffer systems was determined. Using chemoenzymatically synthesized HA standards of low polydispersity, the molecular mass range was determined for each gel composition over which the relationship between HA mobility and logarithm of the molecular mass was linear. Excellent linear calibration was obtained for HA molecular mass as low as approximately 9 kDa in agarose gels. For higher resolution separation, and for extension to molecular masses as low as approximately 5 kDa, gradient polyacrylamide gels were superior. Densitometric scanning of stained gels allowed analysis of the range of molecular masses present in a sample as well as calculation of weight-average and number-average values. The methods were validated for polydisperse HA samples with viscosity-average molecular masses of 112, 59, 37, and 22 kDa at sample loads of 0.5 μg (for polyacrylamide) to 2.5 μg (for agarose). Use of the methods for electrophoretic mobility shift assays was demonstrated for binding of the HA-binding region of aggrecan (recombinant human aggrecan G1-IGD-G2 domains) to a 150-kDa HA standard.

An in vitro study of two GAG-like marine polysaccharides incorporated into injectable hydrogels for bone and cartilage tissue engineering

Natural polysaccharides are attractive compounds with which to build scaffolds for bone and cartilage tissue engineering. Here we tested two non-standard ones, HE800 and GY785, for the two-dimensional (2-D) and three-dimensional (3-D) culture of osteoblasts (MC3T3-E1) and chondrocytes (C28/I2). These two glycosaminoglycan-like marine exopolysaccharides were incorporated into an injectable silylated hydroxypropylmethylcellulose-based hydrogel (Si-HPMC) that has already shown its suitability for bone and cartilage tissue engineering. Results showed that, similarly to hyaluronic acid (HA) (the control), HE800 and GY785 significantly improved the mechanical properties of the Si-HPMC hydrogel and induced the attachment of MC3T3-E1 and C28/I2 cells when these were cultured on top of the scaffolds. Si-HPMC hydrogel containing 0.67% HE800 exhibited the highest compressive modulus (11kPa) and allowed the best cell dispersion, especially of MC3T3-E1 cells. However, these cells did not survive when cultured in 3-D within hydrogels containing HE800, in contrast to C28/I2 cells. The latter proliferated in the microenvironment or concentrically depending on the nature of the hydrogel. Among all the constructs tested the Si-HPMC hydrogels containing 0.34% HE800 or 0.67% GY785 or 0.67% HA presented the most interesting features for cartilage tissue engineering applications, since they offered the highest compressive modulus (9.5-11kPa) while supporting the proliferation of chondrocytes.

A new method to screen polysaccharide cleavage enzymes

The activity of polysaccharide cleavage enzymes has usually been evaluated by qualitative plate screening methods and quantitative colorimetric or chromatographic assays. The recent development of protein engineering has shown the limits of these techniques when applied to high throughput screening. Here we propose a microplate method to measure the activity of polysaccharide cleavage enzymes through small variations in viscosity. Polysaccharide solutions are co-incubated with magnetic particles in enzyme buffers. The cleavage action of polymer-degrading enzymes increases the mobility of the particles in a magnetic field, even at low levels of enzyme activities. This reproducible, sensitive technique was used to evaluate enzymatic specificity towards substrates. BioFilm indices (BFI) determined by associated software were used to follow enzyme kinetics and measure the usual variables.