Chitin biomass and production in the marine environment

Supramolecular Binding with Lectins: A New Route for Non-Covalent Functionalization of Polysaccharide Matrices

The chemical functionalization of polysaccharides to obtain functional materials has been of great interest in the last decades. This traditional synthetic approach has drawbacks, such as changing the crystallinity of the material or altering its morphology or texture. These modifications are crucial when a biogenic matrix is exploited for its hierarchical structure. In this work, the use of lectins and carbohydrate-binding proteins as supramolecular linkers for polysaccharide functionalization is proposed. As proof of concept, a deproteinized squid pen, a hierarchically-organized β-chitin matrix, was functionalized using a dye (FITC) labeled lectin; the lectin used was the wheat germ agglutinin (WGA). It has been observed that the binding of this functionalized protein homogenously introduces a new property (fluorescence) into the β-chitin matrix without altering its crystallographic and hierarchical structure. The supramolecular functionalization of polysaccharides with protein/lectin molecules opens up new routes for the chemical modification of polysaccharides. This novel approach can be of interest in various scientific fields, overcoming the synthetic limits that have hitherto hindered the technological exploitation of polysaccharides-based materials.

N-Alkylated Chitin Nanocrystals as a Collector in Malachite Flotation

The majority of reagents currently used in mineral flotation processes are fossil-based and potentially harmful to the environment. Therefore, it is necessary to find environmentally-friendly alternatives to reduce the impact of mineral processing activities. Chitin nanocrystals are a renewable resource that, due to the natural presence of amino groups on its surface, represents a promising collector for various minerals of economic relevance. This study examines the one-pot functionalization of chitin nanocrystals with aldehyde structures to obtain hydrophobized colloids suitable for mineral flotation. The chemical properties of these nano-colloids were investigated by nuclear magnetic resonance spectroscopy, their colloidal behavior and structure by electrophoretic light scattering and atomic force microscopy, and their wettability through water contact angle measurements. The functionalized N-alkylated chitin nanocrystals possessed a hydrophobic character, were able to dress mineral particles and featured a performance in the flotation of malachite similar to commercial collectors, which proves the high potential of chitin nanocrystals in this field of application.

Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy

Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our understanding of the organic molecules transferred between these microbial groups. In an experimental bloom study consisting of three heterotrophic marine bacteria growing together with the diatom Thalassiosira pseudonana, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. Twenty-two diatom endometabolites were annotated, with nine increasing in internal concentration in the late stage of the bloom, eight decreasing, and five showing no variation through the bloom progression. Some metabolite changes could be linked to shifts in diatom gene expression, as well as to shifts in bacterial community composition and their expression of substrate uptake and catabolism genes. Yet an overall low match indicated that endometabolome concentration was not a good predictor of exometabolite availability, and that complex physiological and ecological interactions underlie metabolite exchange. Six diatom endometabolites accumulated to higher concentrations in the bacterial co-cultures compared to axenic cultures, suggesting a bacterial influence on rates of synthesis or release of glutamate, arginine, leucine, 2,3-dihydroxypropane-1-sulfonate, glucose, and glycerol-3-phosphate. Better understanding of phytoplankton metabolite production, release, and transfer to assembled bacterial communities is key to untangling this nearly invisible yet pivotal step in ocean carbon cycling.

Fabrication and characterization of Rhizochitosan and its incorporation with platelet concentrates to promote wound healing

Composite dressing composed of Rhizochitosan and Regenplex™ to promote wound healing were assessed. Rhizochitosan was fabricated by deacetylation of Rhizochitin, which obtained by simply depigmenting sporangium-free mycelial mattress produced from Rhizopus stolonifer F6. Physicochemical characterizations of Rhizochitosan demonstrated that it contained 13.5% chitosan with a water-absorption ability of 35-fold dry weight and exhibiting hydrogel nature after hydration. In a wound-healing study on SD rats with full-thickness injury, the composite dressing had a better healing effect than those for each individual components and control group and wound even healed as functional tissue instead of scar tissue. The underlying mechanism of the composite beneficial to wound remodeling is likely attributable to a more reduction level of matrix metalloproteinase (MMP)-9 expression in early stage and a higher MMP-2 expression level in a later stage of healing process. Conclusively, the composite dressing demonstrated to be highly beneficial to the healing of full-thickness injury wound.

Microbial community development on model particles in the deep sulfidic waters of the Black Sea

Microorganisms attached to particles have been shown to be different from free-living microbes and to display diverse metabolic activities. However, little is known about the ecotypes associated with particles and their substrate preference in anoxic marine waters. Here, we investigate the microbial community colonizing particles in the anoxic and sulfide-rich waters of the Black Sea. We incubated beads coated with different substrates in situ at 1000 and 2000 m depth. After 6 h, the particle-attached microbes were dominated by Gamma- and Alpha-proteobacteria, and groups related to the phyla Latescibacteria, Bacteroidetes, Planctomycetes and Firmicutes, with substantial variation across the bead types, indicating that the attaching communities were selected by the substrate. Further laboratory incubations for 7 days suggested the presence of a community of highly specialized taxa. After incubation for 35 days, the microbial composition across all beads and depths was similar and primarily composed of putative sulfur cycling microbes. In addition to the major shared microbial groups, subdominant taxa on chitin and protein-coated beads were detected pointing to specialized microbial degraders. These results highlight the role of particles as sites for attachment and biofilm formation, while the composition of organic matter defined a secondary part of the microbial community.

Crab vs. Mushroom: A Review of Crustacean and Fungal Chitin in Wound Treatment

Chitin and its derivative chitosan are popular constituents in wound-treatment technologies due to their nanoscale fibrous morphology and attractive biomedical properties that accelerate healing and reduce scarring. These abundant natural polymers found in arthropod exoskeletons and fungal cell walls affect almost every phase of the healing process, acting as hemostatic and antibacterial agents that also support cell proliferation and attachment. However, key differences exist in the structure, properties, processing, and associated polymers of fungal and arthropod chitin, affecting their respective application to wound treatment. High purity crustacean-derived chitin and chitosan have been widely investigated for wound-treatment applications, with research incorporating chemically modified chitosan derivatives and advanced nanocomposite dressings utilizing biocompatible additives, such as natural polysaccharides, mineral clays, and metal nanoparticles used to achieve excellent mechanical and biomedical properties. Conversely, fungi-derived chitin is covalently decorated with -glucan and has received less research interest despite its mass production potential, simple extraction process, variations in chitin and associated polymer content, and the established healing properties of fungal exopolysaccharides. This review investigates the proven biomedical properties of both fungal- and crustacean-derived chitin and chitosan, their healing mechanisms, and their potential to advance modern wound-treatment methods through further research and practical application.

Nanomaterials Derived from Fungal Sources-Is It the New Hype?

Greener alternatives to synthetic polymers are constantly being investigated and sought after. Chitin is a natural polysaccharide that gives structural support to crustacean shells, insect exoskeletons, and fungal cell walls. Like cellulose, chitin resides in nanosized structural elements that can be isolated as nanofibers and nanocrystals by various top-down approaches, targeted at disintegrating the native construct. Chitin has, however, been largely overshadowed by cellulose when discussing the materials aspects of the nanosized components. This Perspective presents a thorough overview of chitin-related materials research with an analytical focus on nanocomposites and nanopapers. The red line running through the text emphasizes the use of fungal chitin that represents several advantages over the more popular crustacean sources, particularly in terms of nanofiber isolation from the native matrix. In addition, many β-glucans are preserved in chitin upon its isolation from the fungal matrix, enabling new horizons for various engineering solutions.

Environmental Reservoirs of Vibrio cholerae: Challenges and Opportunities for Ocean-Color Remote Sensing

The World Health Organization has estimated the burden of the on-going pandemic of cholera at 1.3 to 4 million cases per year worldwide in 2016, and a doubling of case-fatality-rate to 1.8% in 2016 from 0.8% in 2015. The disease cholera is caused by the bacterium Vibrio cholerae that can be found in environmental reservoirs, living either in free planktonic form or in association with host organisms, non-living particulate matter or in the sediment, and participating in various biogeochemical cycles. An increasing number of epidemiological studies are using land- and water-based remote-sensing observations for monitoring, surveillance, or risk mapping of Vibrio pathogens and cholera outbreaks. Although the Vibrio pathogens cannot be sensed directly by satellite sensors, remotely-sensed data can be used to infer their presence. Here, we review the use of ocean-color remote-sensing data, in conjunction with information on the ecology of the pathogen, to map its distribution and forecast risk of disease occurrence. Finally, we assess how satellite-based information on cholera may help support the Sustainable Development Goals and targets on Health (Goal 3), Water Quality (Goal 6), Climate (Goal 13), and Life Below Water (Goal 14).

Effect of temperature in Chitin and Chitosan production by solid culture of Penicillium Camembertii on YPG medium

This study was devoted to polysaccharides extraction (Chitin and Chitosan) from Penicillium camembertii cell wall. A culture on solid medium was adopted under carefully selected conditions, appropriate to mycelium growth: duration 6 days, medium YPGA and pH 5. The temperature was adjusted (20 °C to 28 °C) in order to study the effect of temperature on Chitin/Chitosan production. Biomass decreased with increasing temperatures: 13 g/L at 20 °C and 11.6 g/L at 28 °C. For all tested temperatures, the yields of insoluble alkaline fractions (AIM) were almost identical (200 mg/g). The solubility of fractions in 2% acetic acid allowed obtaining two fractions: an insoluble fraction (AcIM) with 18% of maximum yield and soluble fraction (AcSM) with 1% yield. The SEM micrographs of AcIM fractions were similar to AIM fractions. These showed a compact structure different from commercial Chitin. The presence of Chitin in P. Camembertii cultured in YPGA medium was also confirmed by ATR spectroscopy.

Physics-based prediction of biopolymer degradation

In the natural environment, insoluble biomatter provides a preeminent source of carbon for bacteria. Its degradation by microbial communities thus plays a major role in the global carbon-cycle. The prediction of degradation processes and their sensitivity to changes in environmental conditions can therefore provide critical insights into globally occurring environmental adaptations. To elucidate and quantify this macro-scale phenomenon, we conduct micro-scale experiments that examine the degradation of isolated biopolymer particles and observe highly nonlinear degradation kinetics. Since conventional scaling arguments fail to explain these observations, it is inferred that the coupled influence of both the physical and biochemical processes must be considered. Hence, we develop a theoretical model that accounts for the bio-chemo-mechanically coupled kinetics of polymer degradation, by considering the production of bio-degraders and their ability to both dissociate the material from its external boundaries and to penetrate it to degrade its internal mechanical properties. This change in mechanical properties combined with the intake of solvent or moisture from the environment leads to chemo-mechanically coupled swelling of the material and, in-turn, influences the degradation kinetics. We show that the model quantitatively captures our experimental results and reveals distinct signatures of different bacteria that are independent of the specific experimental conditions (i.e. particle volume and initial concentrations). Finally, after validating our model against the experimental data we extend our predictions for degradation processes across various length and time scales that are inaccessible in a laboratory setting.

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

Understanding the principles that govern the assembly of microbial communities across earth's biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2-4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions-in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly-i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes.

Immunohistochemical Localization of Fibrinogen C Domain Containing 1 on Epithelial and Mucosal Surfaces in Human Tissues

Fibrinogen C domain containing 1 (FIBCD1) is a transmembrane receptor that binds chitin and other acetylated compounds with high affinity. FIBCD1 has previously been shown to be present in the epithelium of the gastrointestinal tract. In the present study, we performed a detailed analysis of normally structured human tissues for the expression of FIBCD1 by quantitative PCR and immunohistochemistry. We find that FIBCD1 is expressed in epithelial cells derived from all three germ layers. Endodermal-derived epithelial cells throughout the gastrointestinal tract and the respiratory system showed high expression of FIBCD1 and also mesodermal-derived cells in the genitourinary system and ectodermal-derived epidermis and sebaceous glands cells expressed FIBCD1. In some columnar epithelial cells, for example, in the salivary gland and gall bladder, the FIBCD1 expression was clearly polarized with strong apical reaction, while other columnar cells, for example, in small and large intestine and in bronchi, the staining was equally strong apically and basolaterally. In keratinocytes in skin, tongue, and oral cavity, the FIBCD1 staining was granular. This expression pattern together with the known binding properties supports that FIBCD1 plays a role in innate immunity in the skin and at mucosal surfaces.

A protocol for the simultaneous identification of chitin-containing particles and their associated bacteria

Chitin is the second most abundant polymer on Earth, playing a crucial role in the biogeochemical cycles. A core issue for studying its processing in aquatic systems is the identification and enumeration of chitin-containing particles and organisms, ideally in a manner that can be directly linked to bulk chitin quantification. The aim of this study was the development of such a technique. We successfully combined the methodology of bulk chitin determination using wheat germ agglutinin (FITC-WGA) for staining chitin-containing particles and organisms along with CARD-FISH staining of either chitin-containing eukaryotic cells or bacteria associated with them. Environmental chitin staining was successfully applied to natural water samples. Fungal hyphae, diatoms, and dinoflagellates, sestonic aggregates and chitin-containing structures derived from metazoa were observed. Also, hybridized bacteria attached to chitinaceous debris were clearly visualized. Finally, as proof of principle, cultured yeast cells were simultaneously-targeted by FITC-WGA and the EUK516 probe without exhibiting any interference between both stains. The presented approach appears as a powerful tool to evaluate the contribution of different size classes and organisms to chitin production and consumption, opening the possibility for application of single-cell approaches targeting the ecophysiology of chitin transformations in aquatic systems.

Chitin extraction from blue crab (Portunus segnis) and shrimp (Penaeus kerathurus) shells using digestive alkaline proteases from P. segnis viscera

Since chitin is closely associated with proteins, deproteinization is a crucial step in the process of extracting chitin. Thus, this research aimed to extract chitin from Portunus segnis and Penaeus kerathurus shells by means of crude digestive alkaline proteases from the viscera of P. segnis, regarding deproteinization step, as an alternative to chemical treatment. Casein zymography revealed that five caseinolytic proteases bands exist, suggesting the presence of at least five different major proteases. The optimum pH and temperature for protease activity were pH 8.0 and 60°C, respectively, using casein as a substrate. The crude enzymes extract was highly stable at low temperatures and over a wide range of pH from 6.0 to 12.0. The crude alkaline protease extract was found to be effective in the deproteinization of blue crab and shrimp shells, to produce chitin. The best efficiency in deproteinization (84.69±0.65% for blue crab shells and 91.06±1.40% for shrimp shells) was achieved with an E/S ratio of 5U/mg of proteins after 3h incubation at 50°C. These results suggest that enzymatic deproteinization of crab and shrimp wastes by fish endogenous alkaline proteases could be a potential alternative in the chitin production process.

Multifunctional biomaterials from the sea: Assessing the effects of chitosan incorporation into collagen scaffolds on mechanical and biological functionality

Natural biomaterials such as collagen show promise in tissue engineering applications due to their inherent bioactivity. The main limitation of collagen is its low mechanical strength and somewhat unpredictable and rapid degradation rate; however, combining collagen with another material, such as chitosan, can reinforce the scaffold mechanically and may improve the rate of degradation. Additionally, the high cost and the risk of prion transmission associated with mammal-derived collagen has prompted research into alternative sources such as marine-origin collagen. In this context, the overall goal of this study was to determine if the incorporation of chitosan into collagen scaffolds could improve the mechanical and biological properties of the scaffold. In addition the study assessed if collagen, derived from salmon skin (marine), can provide an alternative to collagen derived from bovine tendon (mammal) for tissue engineering applications. Scaffold architecture and mechanical properties were assessed as well as their ability to support mesenchymal stem cell growth and differentiation. Overall, the addition of chitosan to bovine and salmon skin-derived collagen scaffolds improved the mechanical properties, increasing the compressive strength, swelling ratio and prolonged the degradation rate. Mesenchymal stem cell (MSC) attachment and proliferation was most improved on the bovine-derived collagen scaffold containing a 75:25 ratio of collagen:chitosan, and when MSC osteogenic and chondrogenic potential on the scaffold was assessed, a significant increase in calcium production (p<0.001) and sulfated glycosaminoglycan (sGAG) production (p<0.001) was observed respectively. Regardless of chitosan content, the bovine-derived collagen scaffolds out-performed the salmon skin-derived collagen scaffolds, displaying a larger pore size and higher percentage porosity, more regular architecture, higher compressive modulus, a greater capacity for water uptake and allowed for more MSC proliferation and differentiation. This versatile scaffold incorporating the marine biomaterial chitosan show great potential as appropriate platforms for promoting orthopaedic tissue repair while the use of salmon skin-derived collagen may be more suitable in the repair of soft tissues such as skin.

STATEMENT OF SIGNIFICANCE

Collagen is commonly used in tissue engineering due to its biocompatibility; however, it has low mechanical strength and an unpredictable degradation rate. In addition, high cost and risk of prion transmission associated with mammalian-derived collagen has prompted research into alternative collagen sources, namely, marine-derived collagen. In this study, scaffolds made from salmon-skin collagen were compared to the more commonly used bovine-derived collagen with a focus on orthopaedic applications. To improve the mechanical properties of these scaffolds, another marine biomaterial, chitosan, was added to produce scaffolds with increased mechanical stability. The collagen-chitosan composites were also shown to support mesenchymal stem cell differentiation towards both bone and cartilage tissue. This multi-functional scaffold therefore has potential in both bone and cartilage regeneration applications.

Probing the Catalytic Mechanism of Vibrio harveyi GH20 β-N-Acetylglucosaminidase by Chemical Rescue

BACKGROUND

Vibrio harveyi GH20 β-N-acetylglucosaminidase (VhGlcNAcase) is a chitinolytic enzyme responsible for the successive degradation of chitin fragments to GlcNAc monomers, activating the onset of the chitin catabolic cascade in marine Vibrios.

METHODS

Two invariant acidic pairs (Asp303-Asp304 and Asp437-Glu438) of VhGlcNAcase were mutated using a site-directed mutagenesis strategy. The effects of these mutations were examined and the catalytic roles of these active-site residues were elucidated using a chemical rescue approach. Enhancement of the enzymic activity of the VhGlcNAcase mutants was evaluated by a colorimetric assay using pNP-GlcNAc as substrate.

RESULTS

Substitution of Asp303, Asp304, Asp437 or Glu438 with Ala/Asn/Gln produced a dramatic loss of the GlcNAcase activity. However, the activity of the inactive D437A mutant was recovered in the presence of sodium formate. Our kinetic data suggest that formate ion plays a nucleophilic role by mimicking the β-COO-side chain of Asp437, thereby stabilizing the reaction intermediate during both the glycosylation and the deglycosylation steps.

CONCLUSIONS

Chemical rescue of the inactive D437A mutant of VhGlcNAcase by an added nucleophile helped to identify Asp437 as the catalytic nucleophile/base, and hence its acidic partner Glu438 as the catalytic proton donor/acceptor.

GENERAL SIGNIFICANCE

Identification of the catalytic nucleophile of VhGlcNAcases supports the proposal of a substrate-assisted mechanism of GH20 GlcNAcases, requiring the catalytic pair Asp437-Glu438 for catalysis. The results suggest the mechanistic basis of the participation of β-N-acetylglucosaminidase in the chitin catabolic pathway of marine Vibrios.

Chitinolytic Streptomyces vinaceusdrappus S5MW2 isolated from Chilika lake, India enhances plant growth and biocontrol efficacy through chitin supplementation against Rhizoctonia solani

A chitinolytic actinomycete Streptomyces vinaceusdrappus S5MW2 was isolated from water sample of Chilika lake, India and identified using 16S rRNA gene sequencing. It showed in vitro antifungal activity against the sclerotia producing pathogen Rhizoctonia solani in a dual culture assay and by chitinase enzyme production in a chitin supplemented minimal broth. Moreover, isolate S5MW2 was further characterized for biocontrol (BC) and plant growth promoting features in a greenhouse experiment with or without colloidal chitin (CC). Results of greenhouse experiment showed that CC supplementation with S5MW2 showed a significant growth of tomato plants and superior disease reduction as compared to untreated control and without CC treated plants. Moreover, higher accumulation of chitinase also recovered in the CC supplemented plants. Significant effect of CC also concurred with the Analysis of Variance of greenhouse parameters. These results show that the a marine antagonist S5MW2 has BC efficiency against R. solani and chitinase enzyme played important role in plant resistance.

Keeping track of the growing number of biological functions of chitin and its interaction partners in biomedical research

Chitin is a vital polysaccharide component of protective structures in many eukaryotic organisms but seems absent in vertebrates. Chitin or chitin oligomers are therefore prime candidates for non-self-molecules, which are recognized and degraded by the vertebrate immune system. Despite the absence of polymeric chitin in vertebrates, chitinases and chitinase-like proteins (CLPs) are well conserved in vertebrate species. In many studies, these proteins have been found to be involved in immune regulation and in mediating the degradation of chitinous external protective structures of invading pathogens. Several important aspects of chitin immunostimulation have recently been uncovered, advancing our understanding of the complex regulatory mechanisms that chitin mediates. Likewise, the last few years have seen large advances in our understanding of the mechanisms and molecular interactions of chitinases and CLPs in relation to immune response regulation. It is becoming increasingly clear that their function in this context is not exclusive to chitin producing pathogens, but includes bacterial infections and cancer signaling as well. Here we provide an overview of the immune signaling properties of chitin and other closely related biomolecules. We also review the latest literature on chitinases and CLPs of the GH18 family. Finally, we examine the existing literature on zebrafish chitinases, and propose the use of zebrafish as a versatile model to complement the existing murine models. This could especially be of benefit to the exploration of the function of chitinases in infectious diseases using high-throughput approaches and pharmaceutical interventions.

An Immune Effector System in the Protochordate Gut Sheds Light on Fundamental Aspects of Vertebrate Immunity

A variety of germline and somatic immune mechanisms have evolved in vertebrate and invertebrate species to detect a wide array of pathogenic invaders. The gut is a particularly significant site in terms of distinguishing pathogens from potentially beneficial microbes. Ciona intestinalis, a filter-feeding marine protochordate that is ancestral to the vertebrate form, possesses variable region-containing chitin-binding proteins (VCBPs), a family of innate immune receptors, which recognize bacteria through an immunoglobulin-type variable region. The manner in which VCBPs mediate immune recognition appears to be related to the development and bacterial colonization of the gut, and it is likely that these molecules are critical elements in achieving overall immune and physiological homeostasis.

Flavobacterium johnsoniae chitinase ChiA is required for chitin utilization and is secreted by the type IX secretion system

Flavobacterium johnsoniae, a member of phylum Bacteriodetes, is a gliding bacterium that digests insoluble chitin and many other polysaccharides. A novel protein secretion system, the type IX secretion system (T9SS), is required for gliding motility and for chitin utilization. Five potential chitinases were identified by genome analysis. Fjoh_4555 (ChiA), a 168.9-kDa protein with two glycoside hydrolase family 18 (GH18) domains, was targeted for analysis. Disruption of chiA by insertional mutagenesis resulted in cells that failed to digest chitin, and complementation with wild-type chiA on a plasmid restored chitin utilization. Antiserum raised against recombinant ChiA was used to detect the protein and to characterize its secretion by F. johnsoniae. ChiA was secreted in soluble form by wild-type cells but remained cell associated in strains carrying mutations in any of the T9SS genes, gldK, gldL, gldM, gldNO, sprA, sprE, and sprT. Western blot and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses suggested that ChiA was proteolytically processed into two GH18 domain-containing proteins. Proteins secreted by T9SSs typically have conserved carboxy-terminal domains (CTDs) belonging to the TIGRFAM families TIGR04131 and TIGR04183. ChiA does not exhibit strong similarity to these sequences and instead has a novel CTD. Deletion of this CTD resulted in accumulation of ChiA inside cells. Fusion of the ChiA CTD to recombinant mCherry resulted in secretion of mCherry into the medium. The results indicate that ChiA is a soluble extracellular chitinase required for chitin utilization and that it relies on a novel CTD for secretion by the F. johnsoniae T9SS.

Chitosan for gene delivery and orthopedic tissue engineering applications

Gene therapy involves the introduction of foreign genetic material into cells in order exert a therapeutic effect. The application of gene therapy to the field of orthopaedic tissue engineering is extremely promising as the controlled release of therapeutic proteins such as bone morphogenetic proteins have been shown to stimulate bone repair. However, there are a number of drawbacks associated with viral and synthetic non-viral gene delivery approaches. One natural polymer which has generated interest as a gene delivery vector is chitosan. Chitosan is biodegradable, biocompatible and non-toxic. Much of the appeal of chitosan is due to the presence of primary amine groups in its repeating units which become protonated in acidic conditions. This property makes it a promising candidate for non-viral gene delivery. Chitosan-based vectors have been shown to transfect a number of cell types including human embryonic kidney cells (HEK293) and human cervical cancer cells (HeLa). Aside from its use in gene delivery, chitosan possesses a range of properties that show promise in tissue engineering applications; it is biodegradable, biocompatible, has anti-bacterial activity, and, its cationic nature allows for electrostatic interaction with glycosaminoglycans and other proteoglycans. It can be used to make nano- and microparticles, sponges, gels, membranes and porous scaffolds. Chitosan has also been shown to enhance mineral deposition during osteogenic differentiation of MSCs in vitro. The purpose of this review is to critically discuss the use of chitosan as a gene delivery vector with emphasis on its application in orthopedic tissue engineering.

Molecular uptake of chitooligosaccharides through chitoporin from the marine bacterium Vibrio harveyi

BACKGROUND

Chitin is the most abundant biopolymer in marine ecosystems. However, there is no accumulation of chitin in the ocean-floor sediments, since marine bacteria Vibrios are mainly responsible for a rapid turnover of chitin biomaterials. The catabolic pathway of chitin by Vibrios is a multi-step process that involves chitin attachment and degradation, followed by chitooligosaccharide uptake across the bacterial membranes, and catabolism of the transport products to fructose-6-phosphate, acetate and NH(3).

PRINCIPAL FINDINGS

This study reports the isolation of the gene corresponding to an outer membrane chitoporin from the genome of Vibrio harveyi. This porin, expressed in E. coli, (so called VhChiP) was found to be a SDS-resistant, heat-sensitive trimer. Immunoblotting using anti-ChiP polyclonal antibody confirmed the expression of the recombinant ChiP, as well as endogenous expression of the native protein in the V. harveyi cells. The specific function of VhChiP was investigated using planar lipid membrane reconstitution technique. VhChiP nicely inserted into artificial membranes and formed stable, trimeric channels with average single conductance of 1.8±0.13 nS. Single channel recordings at microsecond-time resolution resolved translocation of chitooligosaccharides, with the greatest rate being observed for chitohexaose. Liposome swelling assays showed no permeation of other oligosaccharides, including maltose, sucrose, maltopentaose, maltohexaose and raffinose, indicating that VhChiP is a highly-specific channel for chitooligosaccharides.

CONCLUSION/SIGNIFICANCE

We provide the first evidence that chitoporin from V. harveyi is a chitooligosaccharide specific channel. The results obtained from this study help to establish the fundamental role of VhChiP in the chitin catabolic cascade as the molecular gateway that Vibrios employ for chitooligosaccharide uptake for energy production.

Application of marine microbial enzymes in the food and pharmaceutical industries

Over billions of years, the ocean is regarded as the origin of life on Earth, and the ocean includes the largest habitats hosting the most life forms. Competition among microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to the evolution. The evolution prompts the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. Therefore, marine microbial enzymes can offer novel biocatalysts with extraordinary properties. This review deals with the research and development work done on the occurrence and bioprocessing of marine microbial enzymes.

Bacterial chitin hydrolysis in two lakes with contrasting trophic statuses

Chitin, which is a biopolymer of the amino sugar glucosamine (GlcN), is highly abundant in aquatic ecosystems, and its degradation is assigned a key role in the recycling of carbon and nitrogen. In order to study the significance of chitin decomposition in two temperate freshwater lakes with contrasting trophic and redox conditions, we measured the turnover rate of the chitin analog methylumbelliferyl-N,N'-diacetylchitobioside (MUF-DC) and the presence of chitinase (chiA) genes in zooplankton, water, and sediment samples. In contrast to the eutrophic and partially anoxic lake, chiA gene fragments were detectable throughout the oligotrophic water column and chiA copy numbers per ml of water were up to 15 times higher than in the eutrophic waters. For both lakes, the highest chiA abundance was found in the euphotic zone--the main habitat of zooplankton, but also the site of production of easily degradable algal chitin. The bulk of chitinase activity was measured in zooplankton samples and the sediments, where recalcitrant chitin is deposited. Both, chiA abundance and chitinase activity correlated well with organic carbon, nitrogen, and concentrations of particulate GlcN. Our findings show that chitin, although its overall contribution to the total organic carbon is small (~0.01 to 0.1%), constitutes an important microbial growth substrate in these temperate freshwater lakes, particularly where other easily degradable carbon sources are scarce.

The importance of chitin in the marine environment

Chitin is the most abundant renewable polymer in the oceans and is an important source of carbon and nitrogen for marine organisms. The process of chitin degradation is a key step in the cycling of nutrients in the oceans and chitinolytic bacteria play a significant role in this process. These bacteria are autochthonous to both marine and freshwater ecosystems and produce chitinases that degrade chitin, an insoluble polysaccharide, to a biologically useful form. In this brief review, a description of the structure of chitin and diversity of chitinolytic bacteria in the oceans is provided, in the context of the significance of chitin degradation for marine life.

A Biopolymer Chitosan and Its Derivatives as Promising Antimicrobial Agents against Plant Pathogens and Their Applications in Crop Protection

Recently, much attention has been paid to chitosan as a potential polysaccharide resource. Although several efforts have been reported to prepare functional derivatives of chitosan by chemical modifications, few attained their antimicrobial activity against plant pathogens. The present paper aims to present an overview of the antimicrobial effects, mechanisms, and applications of a biopolymer chitosan and its derivatives in crop protection. In addition, this paper takes a closer look at the physiochemical properties and chemical modifications of chitosan molecule. The recent growth in this field and the latest research papers published will be introduced and discussed.

Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

Background

The world's oceans are home to a diverse array of microbial life whose metabolic activity helps to drive the earth's biogeochemical cycles. Metagenomic analysis has revolutionized our access to these communities, providing a system-scale perspective of microbial community interactions. However, while metagenome sequencing can provide useful estimates of the relative change in abundance of specific genes and taxa between environments or over time, this does not investigate the relative changes in the production or consumption of different metabolites.

Results

We propose a methodology, Predicted Relative Metabolic Turnover (PRMT) that defines and enables exploration of metabolite-space inferred from the metagenome. Our analysis of metagenomic data from a time-series study in the Western English Channel demonstrated considerable correlations between predicted relative metabolic turnover and seasonal changes in abundance of measured environmental parameters as well as with observed seasonal changes in bacterial population structure.

Conclusions

The PRMT method was successfully applied to metagenomic data to explore the Western English Channel microbial metabalome to generate specific, biologically testable hypotheses. Generated hypotheses linked organic phosphate utilization to Gammaproteobactaria, Plantcomycetes, and Betaproteobacteria, chitin degradation to Actinomycetes, and potential small molecule biosynthesis pathways for Lentisphaerae, Chlamydiae, and Crenarchaeota. The PRMT method can be applied as a general tool for the analysis of additional metagenomic or transcriptomic datasets.

Research and application of marine microbial enzymes: status and prospects

Over billions of years, the ocean has been regarded as the origin of life on Earth. The ocean includes the largest range of habitats, hosting the most life-forms. Competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. The evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. Therefore, marine microbial enzymes can offer novel biocatalysts with extraordinary properties. This review deals with the research and development work investigating the occurrence and bioprocessing of marine microbial enzymes.

Biocatalytic carboxylation

Dwindling petroleum feedstocks and increased CO(2)-concentrations in the atmosphere currently open the concept of using CO(2) as raw material for the synthesis of well-defined organic compounds. In parallel to recent advances in the chemical CO(2)-fixation, enzymatic (biocatalytic) carboxylation is currently being investigated at an increased pace. On the one hand, this critical review provides a concise overview on highly specific biosynthetic pathways for CO(2)-fixation and, on the other hand, a summary of biodegradation (detoxification) processes involving enzymes which possess relaxed substrate specificities, which allow their application for the regioselective carboxylation of organic substrates to furnish the corresponding carboxylic acids (145 references).

Chitin in diatoms and its association with the cell wall

Chitin is a globally abundant polymer widely distributed throughout eukaryotes that has been well characterized in only a few lineages. Diatoms are members of the eukaryotic lineage of stramenopiles. Of the hundreds of diatom genera, two produce long fibers of chitin that extrude through their cell walls of silica. We identify and describe here genes encoding putative chitin synthases in a variety of additional diatom genera, indicating that the ability to produce chitin is more widespread and likely plays a more central role in diatom biology than previously considered. Diatom chitin synthases fall into four phylogenetic clades. Protein domain predictions and differential gene expression patterns provide evidence that chitin synthases have multiple functions within a diatom cell. Thalassiosira pseudonana possesses six genes encoding three types of chitin synthases. Transcript abundance of the gene encoding one of these chitin synthase types increases when cells resume division after short-term silicic acid starvation and during short-term limitation by silicic acid or iron, two nutrient conditions connected in the environment and known to affect the cell wall. During long-term silicic acid starvation transcript abundance of this gene and one additional chitin synthase gene increased at the same time a chitin-binding lectin localized to the girdle band region of the cell wall. Together, these results suggest that the ability to produce chitin is more widespread in diatoms than previously thought and that a subset of the chitin produced by diatoms is associated with the cell wall.

Cell-specific beta-N-acetylglucosaminidase activity in cultures and field populations of eukaryotic marine phytoplankton

It is widely appreciated that eukaryotic marine phytoplankton can hydrolyze a variety of compounds within the dissolved organic matter (DOM) pool in marine environments. Herein, cultures and field populations of marine phytoplankton were assayed for beta-N-acetylglucosaminidase activity, a terminal enzyme of chitin degradation. A traditional bulk assay, which can assess hydrolytic rate, but is not cell-specific, was complemented with a cell-specific assay that images the activity associated with single cells using an enzyme labeled fluorescence (ELF) substrate. beta-N-acetylglucosaminidase activity was widespread across various taxa of marine phytoplankton, and activity was observed both under controlled culture conditions and in field populations. The number of cells with enzyme activity varied with the nutritional physiology of the test species in three of the 17 cultures tested. In these three cases the number of cells with activity in the low nutrient medium was higher than in nutrient replete medium. Taken together, these data suggest that a broad group of marine phytoplankton may be a relevant part of chitin-like DOM degradation and should be incorporated into conceptual models of chitin cycling in marine systems.

Native, industrial and fossil chitins

Countless living organisms continuously synthesize and degrade chitin enzymatically, for nutritional, morphogenetic and defensive or aggressive purposes. Chemically modified chitins are important in the light of their biochemical significance in medicine and crop protection; their environmentally friendly behaviour permits industrial exploitation of the huge chitinous biomasses generated by fishing activities and biotechnology. Chitin is promptly metabolized in sediments, and fossil chitin is not frequently encountered.

Homology modeling of glycosyl hydrolase family 18 enzymes and proteins

Using state-of-the-art homology modeling methods, three-dimensional coordinates for three family 18 glycosyl hydrolases were determined. The structures for Gp39, Brp39, and chitotriosidase were computer determined using the X-ray coordinates from SmChiA. The results of the modeling efforts are assessed, and comparison of the modeled structures to other known family 18 members is made.