Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40

A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem

Mucinolytic bacteria modulate host-microbiota symbiosis and dysbiosis through their ability to degrade mucin O-glycans. However, how and to what extent bacterial enzymes are involved in the breakdown process remains poorly understood. Here we focus on a glycoside hydrolase family 20 sulfoglycosidase (BbhII) from Bifidobacterium bifidum, which releases N-acetylglucosamine-6-sulfate from sulfated mucins. Glycomic analysis showed that, in addition to sulfatases, sulfoglycosidases are involved in mucin O-glycan breakdown in vivo and that the released N-acetylglucosamine-6-sulfate potentially affects gut microbial metabolism, both of which were also supported by a metagenomic data mining analysis. Enzymatic and structural analysis of BbhII reveals the architecture underlying its specificity and the presence of a GlcNAc-6S-specific carbohydrate-binding module (CBM) 32 with a distinct sugar recognition mode that B. bifidum takes advantage of to degrade mucin O-glycans. Comparative analysis of the genomes of prominent mucinolytic bacteria also highlights a CBM-dependent O-glycan breakdown strategy used by B. bifidum.

Identification and Characterization of Three Chitinases with Potential in Direct Conversion of Crystalline Chitin into N,N′-diacetylchitobiose

Chitooligosaccharides (COSs) have been widely used in agriculture, medicine, cosmetics, and foods, which are commonly prepared from chitin with chitinases. So far, while most COSs are prepared from colloidal chitin, chitinases used in preparing COSs directly from natural crystalline chitin are less reported. Here, we characterize three chitinases, which were identified from the marine bacterium Pseudoalteromonas flavipulchra DSM 14401^T, with an ability to degrade crystalline chitin into (GlcNAc)₂ (N,N’-diacetylchitobiose). Strain DSM 14401 can degrade the crystalline α-chitin in the medium to provide nutrients for growth. Genome and secretome analyses indicate that this strain secretes six chitinolytic enzymes, among which chitinases Chia4287, Chib0431, and Chib0434 have higher abundance than the others, suggesting their importance in crystalline α-chitin degradation. These three chitinases were heterologously expressed, purified, and characterized. They are all active on crystalline α-chitin, with temperature optima of 45–50 °C and pH optima of 7.0–7.5. They are all stable at 40 °C and in the pH range of 5.0–11.0. Moreover, they all have excellent salt tolerance, retaining more than 92% activity after incubation in 5 M NaCl for 10 h at 4 °C. When acting on crystalline α-chitin, the main products of the three chitinases are all (GlcNAc)₂, which suggests that chitinases Chia4287, Chib0431, and Chib0434 likely have potential in direct conversion of crystalline chitin into (GlcNAc)₂.

A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms

Phaeocystis globosa causes severe marine pollution by forming harmful algal blooms and releasing hemolytic toxins and is therefore harmful to marine ecosystems and aquaculture industries. In this study, Microbulbifer sp. YX04 exerted high algicidal activity against P. globosa by producing and secreting metabolites. The algicidal activity of the YX04 supernatant was stable after exposure to different temperatures (−80 to 100°C) and pH values (4 to 12) for 2 h, suggesting that algicidal substances could temporarily be stored under these temperature and pH value conditions. To explore the algicidal process and mechanism, morphological and structural changes, oxidative stress, photosynthesis, autophagic flux, and global gene expression were investigated. Biochemical analyses showed that the YX04 supernatant induced reactive oxygen species (ROS) overproduction, which caused lipid peroxidation and malondialdehyde (MDA) accumulation in P. globosa. Transmission electron microscopy (TEM) observation and the significant decrease in both maximum photochemical quantum yield (Fv/Fm) and relative electron transfer rate (rETR) indicated damage to thylakoid membranes and destruction of photosynthetic system function. Immunofluorescence, immunoblot, and TEM analyses indicated that cellular damage caused autophagosome formation and triggered large-scale autophagic flux in P. globosa. Transcriptome analysis revealed many P. globosa genes that were differentially expressed in response to YX04 stress, most of which were involved in photosynthesis, respiration, cytoskeleton, microtubule, and autophagosome formation and fusion processes, which may trigger autophagic cell death. In addition to P. globosa, the YX04 supernatant showed high algicidal activity against Thalassiosira pseudonana, Thalassiosira weissflogii, Skeletonema costatum, Heterosigma akashiwo, and Prorocentrum donghaiense. This study highlights multiple mechanisms underlying YX04 supernatant toxicity toward P. globosa and its potential for controlling the occurrence of harmful algal blooms.

IMPORTANCEP. globosa is one of the most notorious harmful algal bloom (HAB)-causing species, which can secrete hemolytic toxins, frequently cause serious ecological pollution, and pose a health hazard to animals and humans. Hence, screening for bacteria with high algicidal activity against P. globosa and studies on the algicidal characteristics and mechanism will contribute to providing an ecofriendly microorganism-controlling agent for preventing the occurrence of algal blooms and reducing the harm of algal blooms to the environment. Our study first reported the algicidal characteristic and mechanism of Microbulbifer sp. YX04 against P. globosa and demonstrated that P. globosa shows different response mechanisms, including movement ability, antioxidative systems, photosynthetic systems, gene expression, and cell death mode, to adapt to the adverse environment when algicidal compounds are present.

Marine-polysaccharide degrading enzymes: Status and prospects

Marine-polysaccharide degrading enzymes have recently been studied extensively. They are particularly interesting as they catalyze the cleavage of glycosidic bonds in polysaccharide macromolecules and produce oligosaccharides with low degrees of polymerization. Numerous findings have demonstrated that marine polysaccharides and their biotransformed products possess beneficial properties including antitumor, antiviral, anticoagulant, and anti-inflammatory activities, and they have great value in healthcare, cosmetics, the food industry, and agriculture. Exploitation of enzymes that can degrade marine polysaccharides is in the ascendant, and is important for high-value use of marine biomass resources. In this review, we describe research and prospects regarding the classification, biochemical properties, and catalytic mechanisms of the main types of marine-polysaccharide degrading enzymes, focusing on chitinase, chitosanase, alginate lyase, agarase, and carrageenase, and their product oligosaccharides. The state-of-the-art discussion of marine-polysaccharide degrading enzymes and their properties offers information that might enable more efficient production of marine oligosaccharides. We also highlight current problems in the field of marine-polysaccharide degrading enzymes and trends in their development. Understanding the properties, catalytic mechanisms, and modification of known enzymes will aid the identification of novel enzymes to degrade marine polysaccharides and facilitation of their use in various biotechnological processes.

Influence of the genus Bacillus bacteria on the content of H2O2 and the activity of hydrolases and their inhibitors in potato plants during Phytophthora infestans Mont. de Bary infection

The authors studied the effect of treatment with bacteria Bacillus subtilis Cohn (strains 26D) and B. thuringiensis Berliner (strain B-6066) on the hydrogen peroxide (H2O2) content, the activity of hydrolytic enzymes and their protein inhibitors in potato plants (Solanum tuberosum L.) in connection with development of resistance to the late blight pathogen - oomycete Phytophthora infestans Mont. de Bary. Studies were carried out on potato plants of the susceptible Early Rose potato cultivar that were treated with a suspension of B. subtilis and B. thuringiensis bacteria (108 cells/ml) and infected with P. infestans (107 spores/ml). A decrease in the degree of leaf damage by oomycete was revealed under the influence of the genus Bacillus bacteria, depending on the strain. The increase in potato resistance to P. infestans infection was mediated by the stimulating effect of the B. subtilis 26D and the B. thuringiensis B-6066 bacteria on the concentration of H2O2, the modulating effect on the activity of hydrolytic enzymes and the enhancement of the transcriptional activity of protease and amylase inhibitor genes in plant tissues. Differences in the degree of activation of the transcriptional activity of hydrolase inhibitor genes by the B. subtilis 26D and the B. thuringiensis B-6066 bacteria were revealed, which suggests differential ways of forming the potato resistance to P. infestans under their influence.

Widespread effect of N-acetyl-D-glucosamine assimilation on the metabolisms of amino acids, purines, and pyrimidines in Scheffersomyces stipitis

BACKGROUND

Following cellulose, chitin is the most abundant renewable resource and is composed of the monomeric amino sugar N-acetyl-D-glucosamine (GlcNAc). Although many yeasts, including Saccharomyces cerevisiae, have lost their ability to utilize GlcNAc, some yeasts are able to use GlcNAc as a carbon source. However, our understanding of the effects of GlcNAc on the intracellular metabolism of nitrogen-containing compounds in these yeast species is limited.

RESULTS

In the present study, we quantitatively investigated the metabolic responses to GlcNAc in the GlcNAc-assimilating yeast Scheffersomyces stipitis (formerly known as Pichia stipitis) using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). The comprehensive analysis of the metabolites extracted from S. stipitis cells grown in glucose, xylose, or GlcNAc revealed increased intracellular accumulation of a wide range of nitrogen-containing compounds during GlcNAc assimilation in this yeast. The levels of aromatic, branched-chain, and sulfur-containing amino acids and adenine, guanine, and cytosine nucleotides were the highest in GlcNAc-grown cells.

CONCLUSIONS

The CE-TOFMS analysis revealed a positive effect for GlcNAc on the intracellular concentration of a wide range of nitrogen-containing compounds. The metabolomic data gathered in this study will be useful for designing effective genetic engineering strategies to develop novel S. stipitis strains for the production of valuable nitrogen-containing compounds from GlcNAc.

Recent Advances and Challenges towards Sustainable Polyhydroxyalkanoate (PHA) Production

Sustainable biofuels, biomaterials, and fine chemicals production is a critical matter that research teams around the globe are focusing on nowadays. Polyhydroxyalkanoates represent one of the biomaterials of the future due to their physicochemical properties, biodegradability, and biocompatibility. Designing efficient and economic bioprocesses, combined with the respective social and environmental benefits, has brought together scientists from different backgrounds highlighting the multidisciplinary character of such a venture. In the current review, challenges and opportunities regarding polyhydroxyalkanoate production are presented and discussed, covering key steps of their overall production process by applying pure and mixed culture biotechnology, from raw bioprocess development to downstream processing.

The first bacterial β-1,6-endoglucanase from Saccharophagus degradans 2-40T for the hydrolysis of pustulan and laminarin

β-1,6-glucan is a polysaccharide found in brown macroalgae and fungal cell walls. In this study, a β-1,6-endoglucanase gene from Saccharophagus degradans 2-40T, gly30B, was cloned and overexpressed in Escherichia coli. Gly30B, which belongs to the glycoside hydrolase family 30 (GH30), was found to possess β-1,6-endoglucanase activity by hydrolyzing β-1,6-glycosidic linkages of pustulan (β-1,6-glucan derived from fungal cell walls) and laminarin (β-1,3-glucan with β-1,6-branchings, derived from brown macroalgae) to produce gentiobiose and glucose as the final products. The optimal pH and temperature for Gly30B activity were found to be pH 7.0 and 40 °C, respectively. The kinetic constants of Gly30B, V max, K M, and k cat were determined to be 153.8 U/mg protein, 24.2 g/L, and 135.6 s-1 for pustulan and 32.8 U/mg protein, 100.8 g/L, and 28.9 s-1 for laminarin, respectively. To our knowledge, Gly30B is the first β-1,6-endoglucanase characterized from bacteria. Gly30B can be used to hydrolyze β-1,6-glucans of brown algae or fungal cell walls for producing gentiobiose as a high-value sugar and glucose as a fermentable sugar.

Marine Microbiological Enzymes: Studies with Multiple Strategies and Prospects

Marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. Both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. In this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (AHL) lactonase, which is an important but largely unexplored enzyme. We also detail the status and catalytic mechanism of the main types of polysaccharide-degrading enzymes that broadly exist among marine microorganisms but have been poorly explored. In order to facilitate understanding, the regulatory and synthetic biology strategies of terrestrial microorganisms are also mentioned in comparison. We anticipate that this review will provide an outline of multiple strategies for promising marine microbial enzymes and open new avenues for the exploration, engineering and application of various enzymes.

A laboratory case study of efficient polyhydoxyalkonates production by Bacillus cereus, a contaminant in Saccharophagus degradans ATCC 43961 in minimal sea salt media

A contaminating bacterium growing along with the stock culture of Saccharophagus degradans ATCC 43961 (Sde 2-40) on marine agar plate was isolated and investigated for its ability to produce polyhydoxyalkonates (PHA). Preliminary screening by Sudan black B and Nile blue A staining indicated positive characteristic of the isolate to produce PHA. The isolate was able to grow and produce PHA in minimal sea salt medium broth. PHA quantification studies with gas chromatographic analyses of the dry cells derived from culture broths revealed accumulation of PHA in bacterial cells. PHA production started after 20 h and increased with cell growth and attained maximum values of 61 % of dry cell weight at 70 h of cultivation. After 70 h, a slight decrease in the level of PHA content was observed. The nature/type of PHA was found to be poly(3-hydroxybutyraye) by Fourier transform-infrared spectroscopy. Microbiological and 16S rRNA gene sequencing analyses suggested that the PHA producing bacterial isolate belongs to Bacillus genera and shows 100 % nucleotide sequence similarity with Bacillus cereus species in GenBank. This study is a first report for ability of Bacillus species to grow in marine sea salt media and produce PHA. The media used for the polymer production was novel in the context of the genus Bacillus and the production of PHA was three-fold higher than Sde 2-40 using same growth medium. This study shows that the contaminant bacteria once properly investigated can be used for advantageous characteristic of metabolites production in place of original cultures.

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.

Bacterial chitin utilisation at extremely haloalkaline conditions

Chitin is produced in large amounts in hypersaline habitats with neutral pH due to the high biomass production of brine shrimp Artemia. Recently, a high abundance of Artemia was also noticed in hypersaline soda lakes in the Kulunda Steppe (Altai, Russia), which prompted us to survey the possibility of microbial chitin utilization at extremely haloalkaline conditions in soda brines. Most active chitin utilisation-supporting microbial growth was found at anaerobic conditions at pH 10 and up to 3.5 M total Na(+). At aerobic conditions, the degradation of chitin was slower, mostly incomplete and active at <2 M total Na(+), although very slow partial degradation was possible up to 4 M Na(+). Anaerobic enrichments at pH 10 yielded two different groups of obligately haloalkaliphilic fermentative anaerobes, exclusively specialized to utilise insoluble chitin as the only growth substrate. One group was represented by a single strain growing at moderate salinity, and another comprised multiple isolates growing up to 3.5 M Na(+). These groups represent two novel bacterial phyla not closely related to any other cultured bacteria. Aerobic enrichments from the lake sediments were dominated by several obligately haloalkaliphilic members of the genus Marinimicrobium in the Gammaproteobacteria. They were less specialised than the anaerobes and grew with chitin and its monomer and oligomers at a pH of 10 up to 2.5 M Na(+). Furthermore, several strains of haloalkaliphilic Gram-positive chitinolytics belonging to bacilli and actinobacteria were isolated from soda lake sediments and surrounding soda soils. In general, the results indicate the presence of an active and diverse haloalkaliphilic chitinolytic microbial community in hypersaline soda habitats.

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.

Carbohydrase systems of Saccharophagus degradans degrading marine complex polysaccharides

Saccharophagus degradans 2-40 is a γ-subgroup proteobacterium capable of using many of the complex polysaccharides found in the marine environment for growth. To utilize these complex polysaccharides, this bacterium produces a plethora of carbohydrases dedicated to the processing of a carbohydrate class. Aiding in the identification of the contributing genes and enzymes is the known genome sequence for this bacterium. This review catalogs the genes and enzymes of the S. degradans genome that are likely to function in the systems for the utilization of agar, alginate, α- and β-glucans, chitin, mannans, pectins, and xylans and discusses the cell biology and genetics of each system as it functions to transfer carbon back to the bacterium.

Discovery and characterization of cadherin domains in Saccharophagus degradans 2-40

Saccharophagus degradans strain 2-40 is a prominent member of newly discovered group of marine and estuarine bacteria that recycle complex polysaccharides. The S. degradans 2-40 genome codes for 15 extraordinary long polypeptides, ranging from 274 to 1,600 kDa. Five of these contain at least 52 cadherin (CA) and cadherin-like (CADG) domains, the types of which were reported to bind calcium ions and mediate protein/protein interactions in metazoan systems. In order to evaluate adhesive features of these domains, recombinant CA doublet domains (two neighboring domains) from CabC (Sde_3323) and recombinant CADG doublet domains from CabD (Sde_0798) were examined qualitatively and quantitatively for homophilic and heterophilic interactions. In addition, CA and CADG doublet domains were tested for adhesion to the surface of S. degradans 2-40. Results showed obvious homophilic and heterophilic, calcium ion-dependent interactions between CA and CADG doublet domains. Likewise, CA and CADG doublet domains adhered to the S. degradans 2-40 surface of cells that were grown on xylan from birch wood or pectin, respectively, as a sole carbon source. This research shows for the first time that bacterial cadherin homophilic and heterophilic interactions may be similar in their nature to cadherin domains from metazoan lineages. We hypothesize that S. degradans 2-40 cadherin and cadherin-like multiple domains contribute to protein-protein interactions that may mediate cell-cell contact in the marine environment.

The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms)

Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2–40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.

Characterization of antifungal chitinase from marine Streptomyces sp. DA11 associated with South China Sea sponge Craniella australiensis

The gene cloning, purification, properties, kinetics, and antifungal activity of chitinase from marine Streptomyces sp. DA11 associated with South China sponge Craniella australiensis were investigated. Alignment analysis of the amino acid sequence deduced from the cloned conserved 451 bp DNA sequence shows the chitinase belongs to ChiC type with 80% similarity to chitinase C precursor from Streptomyces peucetius. Through purification by 80% ammonium sulfate, affinity binding to chitin and diethylaminoethyl-cellulose anion-exchange chromatography, 6.15-fold total purification with a specific activity of 2.95 Umg(-1) was achieved. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed a molecular weight of approximately 34 kDa and antifungal activities were observed against Aspergillus niger and Candida albicans. The optimal pH, temperature, and salinity for chitinase activity were 8.0, 50 degrees C, and 45 g per thousand psu, respectively, which may contribute to special application of this marine microbe-derived chitinase compared with terrestrial chitinases. The chitinase activity was increased by Mn(2+), Cu(2+), and Mg(2+), while strongly inhibited by Fe(2+) and Ba(2+). Meanwhile, SDS, ethyleneglycoltetraacetic acid, urea, and ethylenediaminetetraacetic acid were found to have significantly inhibitory effect on chitinase activity. With colloidal chitin as substrates instead of powder chitin, higher V (max) (0.82 mg product/min.mg protein) and lower K (m) (0.019 mg/ml) values were achieved. The sponge's microbial symbiont with chitinase activity may contribute to chitin degradation and antifungal defense. To our knowledge, it was the first time to study sponge-associated microbial chitinase.

Effect of linker and spacer on the design of a fibronectin-mimetic peptide evaluated via cell studies and AFM adhesion forces

The design of a fibronectin-mimetic peptide that specifically binds to the alpha 5beta 1 integrin has been widely studied because of this integrin's participation in many physiological and pathological processes. A promising design for such a peptide includes both the primary binding site RGD and the synergy site PHSRN connected by a linker and extended off of a surface by a spacer. Our original hypothesis was that the degree of hydrophobicity/hydrophilicity between the two sequences (RGD and PHSRN) in fibronectin is an important parameter in designing a fibronectin-mimetic peptide (Mardilovich, A.; Kokkoli, E. Biomacromolecules 2004, 5, 950-957). A peptide-amphiphile, PR_b, that was previously designed in our laboratory employed a hydrophobic tail connected to the N terminus of a peptide headgroup that was composed of a spacer, the synergy site sequence, a linker mimicking both the distance and hydrophobicity/hydrophilicity present in the native protein fibronectin (thus presenting an overall "neutral" linker), and finally the primary binding sequence. Even though our previous work (Mardilovich, A.; Craig, J. A.; McCammon, M. Q.; Garg, A.; Kokkoli, E. Langmuir 2006, 22, 3259-3264) demonstrated that PR_b is a promising sequence compared to fibronectin, this is the first study that tests our hypothesis by comparing PR_b to other peptides with hydrophobic or hydrophilic linkers. Furthermore, different peptide-amphiphiles were designed that could be used to study the effect of building blocks systematically, such as the peptide headgroup linker length and hydrophobicity/hydrophilicity as well as the headgroup spacer length on integrin adhesion. Circular dichroism spectroscopy was first employed, and the collected spectra demonstrated that only one peptide-amphiphile exhibited a secondary structure. Their surface topography was evaluated by taking atomic force microscopy (AFM) images of Langmuir-Blodgett peptide-amphiphile membranes supported on mica. Their adhesion was first evaluated with AFM force measurements between the different sequences and an AFM tip functionalized with purified integrins. The amphiphiles were further characterized via 1-12 h cell studies that examined human umbilical vein endothelial cell adhesion and extracellular matrix fibronectin production. The AFM studies were in good agreement with the cell studies. Overall, the adhesion studies validated our hypothesis and demonstrated for the first time that a "neutral" linker, which more closely mimics the cell adhesion domain of fibronectin, supports higher levels of adhesion compared to other peptide designs with a hydrophobic or hydrophilic linker or even fibronectin. Neutral linker lengths that were within the distance found between PHSRN and RGD in fibronectin performed equally well. However, the 10 amino acid neutral linker gave slightly better cell adhesion than did the control fibronectin at all times. Also, a short spacer was shown to give higher adhesion than other sequences with no spacer or a longer spacer, suggesting that a short spacer is necessary to extend the sequence further away from the interface. In conclusion, this work outlines a logical approach that can be applied for the rational design of any protein-mimetic peptide with two binding sites.

Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331

Through a combinatorial approach of plasposon mutagenesis, genome mining, and heterologous expression, we identified genes contributing to the chitinolytic phenotype of bacterium Collimonas fungivorans Ter331. One of five mutants with abolished ability to hydrolyze colloidal chitin carried its plasposon in the chiI gene coding for an extracellular endochitinase. Two mutants were affected in the promoter of chiP-II coding for an outer-membrane transporter of chitooligosaccharides. The remaining two mutations were linked to chitobiose/N-acetylglucosamine uptake. Thus, our model for the Collimonas chitinolytic system assumes a positive feedback regulation of chitinase activity by chitin degradation products. A second chitinase gene, chiII, coded for an exochitinase that preferentially released chitobiose from chitin analogs. Genes hexI and hexII showed coding resemblance to N-acetylglucosaminidases, and the activity of purified HexI protein towards chitin analogs suggested its role in converting chitobiose to N-acetylglucosamine. The hexI gene clustered with chiI, chiII, and chiP-II in one locus, while chitobiose/N-acetylglucosamine uptake genes colocalized in another. Both loci contained genes for conversion of N-acetylglucosamine to fructose-6-phosphate, confirming that C. fungivorans Ter331 features a complete chitin pathway. No link could be established between chitinolysis and antifungal activity of C. fungivorans Ter331, suggesting that the bacterium's reported antagonism towards fungi relies on other mechanisms.

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T

The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.

A segment of the global marine carbon cycle that has been poorly characterized is the mineralization of complex polysaccharides to carbon dioxide, a greenhouse gas. It also remained a mystery whether prokaryotes mineralize plant/algal cell walls and woody material in the oceans via carbohydrase systems and, if so, which organisms are involved. We have analyzed the complete genome sequence of the marine bacterium Saccharophagus degradans to better ascertain the potential role of prokaryotes in marine carbon transformation. We discovered that S. degradans, which is related to a number of other newly discovered marine strains, has an unprecedented quantity and diversity of carbohydrases, including the first characterized marine cellulose system. In fact, extensive analysis of the S. degradans genome sequence and functional followup experiments identified an extensive collection of complete enzyme systems that degrade more than 10 complex polysaccharides. These include agar, alginate, and chitin, altogether representing an extraordinary range of catabolic capability. Genomic analyses further demonstrated that the carbohydrases are unusually modular; sequence comparisons revealed that many of the functional modules were acquired by lateral transfer. These results suggest that the prokaryotic contribution to marine carbon fluxes is substantial and cannot be ignored in predictions of climate change.

Screening of genes involved in chitinase production in Aeromonas caviae CB101 via transposon mutagenesis

AIMS

To find genes involved in chitinase production in chitinolytic bacterium Aeromonas caviae CB101.

METHODS AND RESULTS

By transposome mutagenesis, a high-quality mutant library containing around 20,000 insertion mutants was constructed in A. caviae CB101. Mutants with higher, lower and delayed chitinase-producing abilities were identified and analysed further. Genomic sequences flanking the insertion sites of these mutants were amplified by thermal asymmetric interlaced-PCR, cloned and sequenced. The mutated genes involved in chitinase production and/or secretion in CB101 include (i) nagA and nagB gene homologues that are related to the metabolism of the chitin digestion product GlcNAc; (ii) ftsX and exeL gene homologues that are related to transport or secretion systems; (iii) varA and rpoH gene homologues that are related to transcriptional regulator sequences; (iv) other genes with unknown functions.

CONCLUSIONS

Transposome mutagenesis is an efficient method to identify genes involved in the chitinase production in CB101. Chitinase production in CB101 is a complex system, and genes with various functions were identified in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

Understanding regulation of chitinase production in CB101 would make molecular engineering of the bacterium for higher enzyme production possible.

Chitohexose induce the yeast proliferation of Candida albicans

Candida albicans generally grows in the hyphae form in RPMI1640 medium. Chitohexose (COS-6) induced the yeast form of C. albicans dose-dependently under this condition. When COS-6 was exposed to C. albicans, yeast proliferation was observed 6 h after starting the incubation. When we observed the growth form of C. albicans cultured with COS-6, yeast proliferation was observed at log-phase. These results showed that COS-6 was useful for the yeast form inducer of C. albicans.

Identification of a novel endochitinase from a marine bacterium Vibrio proteolyticus strain No. 442

Chitin binding proteins prepared from Vibrio proteolyticus were purified and the N-terminal amino-acid sequence of a protein from a 110-kDa band on SDS-PAGE was found to be 85-90% identical to the 22nd-41st residues of the N-termini of chitinase A precursor proteins from other vibrios. We cloned the corresponding gene, which encodes a putative protein of 850 amino acids containing a 26-residue signal sequence. The chitinase precursor from V. proteolyticus was 78-80% identical to those from Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio carchariae. However, the proteolytic cleavage site for C-terminal processing between R597 and K598 in the chitinase precursor of other vibrios was not observed in the amino acid sequence of V. proteolyticus, which instead had the sequence R600 and A601. Subsequently, full-length and truncated chitinases were generated in Escherichia coli. The specific activity of full-length chitinase expressed in E. coli was 17- and 20-folds higher for colloidal and alpha-chitins (insoluble substrate), respectively, than that of the C-terminal truncated enzyme. However, both recombinants showed similar hydrolysis patterns of hexa-N-acetyl-chitohexaose (soluble substrate), producing di-N-acetyl-chitobiose as major product on TLC analysis. We showed that the C-terminus of the V. proteolyticus chitinase A was important for expression of high specific activity against insoluble chitins.

Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes

Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically and physiologically distinct groups of bacteria that share the ability to produce botulinum neurotoxin, the most poisonous toxin known to man, and the causative agent of botulism, a severe disease of humans and animals. We report here the complete genome sequence of a representative of Group I (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19 predicted genes, respectively. Consistent with the proteolytic phenotype of this strain, the genome harbors a large number of genes encoding secreted proteases and enzymes involved in uptake and metabolism of amino acids. The genome also reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a significant lack of recently acquired DNA, indicating a stable genomic content, in strong contrast to the fluid genome of Clostridium difficile, which can form longer-term relationships with its host. Overall, the genome indicates that C. botulinum is adapted to a saprophytic lifestyle both in soil and aquatic environments. This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues.

Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis

We used a comparative genomics approach implemented in the SEED annotation environment to reconstruct the chitin and GlcNAc utilization subsystem and regulatory network in most proteobacteria, including 11 species of Shewanella with completely sequenced genomes. Comparative analysis of candidate regulatory sites allowed us to characterize three different GlcNAc-specific regulons, NagC, NagR, and NagQ, in various proteobacteria and to tentatively assign a number of novel genes with specific functional roles, in particular new GlcNAc-related transport systems, to this subsystem. Genes SO3506 and SO3507, originally annotated as hypothetical in Shewanella oneidensis MR-1, were suggested to encode novel variants of GlcN-6-P deaminase and GlcNAc kinase, respectively. Reconstitution of the GlcNAc catabolic pathway in vitro using these purified recombinant proteins and GlcNAc-6-P deacetylase (SO3505) validated the entire pathway. Kinetic characterization of GlcN-6-P deaminase demonstrated that it is the subject of allosteric activation by GlcNAc-6-P. Consistent with genomic data, all tested Shewanella strains except S. frigidimarina, which lacked representative genes for the GlcNAc metabolism, were capable of utilizing GlcNAc as the sole source of carbon and energy. This study expands the range of carbon substrates utilized by Shewanella spp., unambiguously identifies several genes involved in chitin metabolism, and describes a novel variant of the classical three-step biochemical conversion of GlcNAc to fructose 6-phosphate first described in Escherichia coli.

Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40

Saccharophagus degradans 2-40 (formerly Microbulbifer degradans 2-40) is a marine gamma-subgroup proteobacterium capable of degrading many complex polysaccharides, such as agar. While several agarolytic systems have been characterized biochemically, the genetics of agarolytic systems have been only partially determined. By use of genomic, proteomic, and genetic approaches, the components of the S. degradans 2-40 agarolytic system were identified. Five agarases were identified in the S. degradans 2-40 genome. Aga50A and Aga50D include GH50 domains. Aga86C and Aga86E contain GH86 domains, whereas Aga16B carries a GH16 domain. Novel family 6 carbohydrate binding modules (CBM6) were identified in Aga16B and Aga86E. Aga86C has an amino-terminal acylation site, suggesting that it is surface associated. Aga16B, Aga86C, and Aga86E were detected by mass spectrometry in agarolytic fractions obtained from culture filtrates of agar-grown cells. Deletion analysis revealed that aga50A and aga86E were essential for the metabolism of agarose. Aga16B was shown to endolytically degrade agarose to release neoagarotetraose, similarly to a beta-agarase I, whereas Aga86E was demonstrated to exolytically degrade agarose to form neoagarobiose. The agarolytic system of S. degradans 2-40 is thus predicted to be composed of a secreted endo-acting GH16-dependent depolymerase, a surface-associated GH50-dependent depolymerase, an exo-acting GH86-dependent agarase, and an alpha-neoagarobiose hydrolase to release galactose from agarose.

Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T

Saccharophagus degradans strain 2-40 is a representative of an emerging group of marine complex polysaccharide (CP)-degrading bacteria. It is unique in its metabolic versatility, being able to degrade at least 10 distinct CPs from diverse algal, plant and invertebrate sources. The S. degradans genome has been sequenced to completion, and more than 180 open reading frames have been identified that encode carbohydrases. Over half of these are likely to act on plant cell wall polymers. In fact, there appears to be a full array of enzymes that degrade and metabolize plant cell walls. Genomic and proteomic analyses reveal 13 cellulose depolymerases complemented by seven accessory enzymes, including two cellodextrinases, three cellobiases, a cellodextrin phosphorylase, and a cellobiose phosphorylase. Most of these enzymes exhibit modular architecture, and some contain novel combinations of catalytic and/or substrate binding modules. This is exemplified by endoglucanase Cel5A, which has three internal family 6 carbohydrate binding modules (CBM6) and two catalytic modules from family five of glycosyl hydrolases (GH5) and by Cel6A, a nonreducing-end cellobiohydrolase from family GH6 with tandem CBM2s. This is the first report of a complete and functional cellulase system in a marine bacterium with a sequenced genome.

Unique posttranslational modifications of chitin-binding lectins of Entamoeba invadens cyst walls

Entamoeba histolytica, which causes amebic dysentery and liver abscesses, is spread via chitin-walled cysts. The most abundant protein in the cyst wall of Entamoeba invadens, a model for amebic encystation, is a lectin called EiJacob1. EiJacob1 has five tandemly arrayed, six-Cys chitin-binding domains separated by low-complexity Ser- and Thr-rich spacers. E. histolytica also has numerous predicted Jessie lectins and chitinases, which contain a single, N-terminal eight-Cys chitin-binding domain. We hypothesized that E. invadens cyst walls are composed entirely of proteins with six-Cys or eight-Cys chitin-binding domains and that some of these proteins contain sugars. E. invadens genomic sequences predicted seven Jacob lectins, five Jessie lectins, and three chitinases. Reverse transcription-PCR analysis showed that mRNAs encoding Jacobs, Jessies, and chitinases are increased during E. invadens encystation, while mass spectrometry showed that the cyst wall is composed of an approximately 30:70 mix of Jacob lectins (cross-linking proteins) and Jessie and chitinase lectins (possible enzymes). Three Jacob lectins were cleaved prior to Lys at conserved sites (e.g., TPSVDK) in the Ser- and Thr-rich spacers between chitin-binding domains. A model peptide was cleaved at the same site by papain and E. invadens Cys proteases, suggesting that the latter cleave Jacob lectins in vivo. Some Jacob lectins had O-phosphodiester-linked carbohydrates, which were one to seven hexoses long and had deoxysugars at reducing ends. We concluded that the major protein components of the E. invadens cyst wall all contain chitin-binding domains (chitinases, Jessie lectins, and Jacob lectins) and that the Jacob lectins are differentially modified by site-specific Cys proteases and O-phosphodiester-linked glycans.

CHDL: A cadherin-like domain in Proteobacteria and Cyanobacteria

We identified a cadherin-like domain (CHDL) using computational analysis. The CHDL domain is mostly distributed in Proteobacteria and Cyanobacteria, although it is also found in some eukaryotic proteins. Prediction of three-dimensional protein folding indicated that the CHDL domain has an immunoglobulin beta-sandwich fold and belongs to the cadherin superfamily. The CHDL domain does not have LDRE and DxNDN motifs, which are conserved in the cadherin domain, but has three other motifs: PxAxxD, DxDxD and YT-V/I-S/T-D, which might contribute to forming a calcium-binding site. The identification of this cadherin-like domain indicates that the cadherin superfamily may exhibit wider sequence and structural diversity than previously appreciated. Domain architecture analysis revealed that the CHDL domain is also associated with other adhesion domains as well as enzyme domains. Based on computational analysis and previous experimental data, we predict that the CHDL domain has calcium-binding and also carbohydrate-binding activity.

Identification of a tomatinase in the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382

The insertion site of a transposon mutant of Clavibacter michiganensis subsp. michiganensis NCPPB382 was cloned and found to be located in the gene tomA encoding a member of the glycosyl hydrolase family 10. The intact gene was obtained from a cosmid library of C. michiganensis subsp. michiganensis. The deduced protein TomA (543 amino acids, 58 kDa) contains a predicted signal peptide and two domains, the N-terminal catalytic domain and a C-terminal fibronectin III-like domain. The closest well-characterized relatives of TomA were tomatinases from fungi involved in the detoxification of the tomato saponin alpha-tomatine which acts as a growth inhibitor. Growth inhibition of C. michiganensis subsp. michiganensis by alpha-tomatine was stronger in the tomA mutants than in the wild type. Tomatinase activity assayed by deglycosylation of alpha-tomatine to tomatidine was demonstrated in concentrated culture supernatants of C. michiganensis subsp. michiganensis. No activity was found with the tomA mutants. However, neither the transposon mutant nor a second mutant constructed by gene disruption was affected in virulence on the tomato cv. Moneymaker.

Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides

Gammaproteobacteria belonging and related to the genus Microbulbifer are an emerging group of complex carbohydrate-degrading marine bacteria. Previously, all of the representatives were placed within Microbulbifer or were unclassified. Recently, a new genus, Teredinibacter, represented by a single species, Teredinibacter turnerae, was formed to include an endosymbiotic branch of these organisms. In this study, based on 16S rRNA gene sequence similarity and phenotypic analyses, a new genus, Saccharophagus, is proposed to accommodate the most versatile marine carbohydrate degrader yet identified, Saccharophagus degradans gen. nov., sp. nov. 2-40T (=ATCC 43961T=DSM 17024T). S. degradans strain 2-40T can degrade 10 tested complex polysaccharides: agar, alginate, chitin, cellulose, fucoidan, laminarin, pectin, pullulan, starch and xylan. S. degradans 2-40T shares 90·5 % 16S rRNA gene sequence similarity with the type strain of the Microbulbifer type species, Microbulbifer hydrolyticus IRE-31T, and 91·5 % with T. turnerae T7902T, and can be further distinguished from members of these two genera by 16S rRNA gene cluster analysis, the ability to utilize 10 different complex polysaccharides as sole carbon sources, a significantly lower G+C content and differences in fatty acid content. The three genera of complex polysaccharide-degrading, marine bacteria now encompass 20 strains from diverse marine niches.

Structural and functional diversity of lectin repertoires in invertebrates, protochordates and ectothermic vertebrates

During the past few years, substantial progress has been accomplished in the elucidation of the structural diversity of the lectin repertoires of invertebrates, protochordates and ectothermic vertebrates, providing particularly valuable information on those groups that constitute the invertebrate/vertebrate 'boundary'. Although representatives of lectin families typical of mammals, such as C-type lectins, galectins and pentraxins, have been described in these taxa, the detailed study of selected model species has yielded either novel variants of the structures described for the mammalian lectin representatives or novel lectin families with unique sequence motifs, multidomain arrangements and a new structural fold. Along with the high structural diversity of the lectin repertoires in these taxa, a wide spectrum of biological roles is starting to emerge, underscoring the value of invertebrate and lower vertebrate models for gaining insight into structural, functional and evolutionary aspects of lectins.

Density functional study of infinite polyserine chains

Two different helical conformations (alpha and 3-10 helices) of polyserine are studied using density functional theory. The infinite system characterized by exact translational-rotational symmetry is examined in vacuum using the BLYP exchange-correlation functional. Geometry analysis in terms of hydrogen bond strength and total energies of the different conformers are presented. The structural changes due to the presence of the serine side chain are identified comparing the polyserine and polyglycine chains. The rotational energy curves of the side chain are presented for both investigated helices. Band structures of polyserine and polyglycine conformers are also compared.

Cloning, expression, and characterization of a highly thermostable family 18 chitinase from Rhodothermus marinus

A family 18 chitinase gene chiA from the thermophile Rhodothermus marinus was cloned and expressed in Escherichia coli. The gene consisted of an open reading frame of 1,131 nucleotides encoding a protein of 377 amino acids with a calculated molecular weight of 42,341 Da. The deduced ChiA was a non-modular enzyme with one unique glycoside hydrolase family 18 catalytic domain. The catalytic domain exhibited 43% amino acid identity with Bacillus circulans chitinase C. Due to poor expression of ChiA, a signal peptide-lacking mutant, chiADeltasp, was designed and used subsequently. The optimal temperature and pH for chitinase activity of both ChiA and ChiADeltasp were 70 degrees C and 4.5-5, respectively. The enzyme maintained 100% activity after 16 h incubation at 70 degrees C, with half-lives of 3 h at 90 degrees C and 45 min at 95 degrees C. Results of activity measurements with chromogenic substrates, thin-layer chromatography, and viscosity measurements demonstrated that the chitinase is an endoacting enzyme releasing chitobiose as a major end product, although it acted as an exochitobiohydrolase with chitin oligomers shorter than five residues. The enzyme was fully inhibited by 5 mM HgCl2, but excess ethylenediamine tetraacetic acid relieved completely the inhibition. The enzyme hydrolyzed 73% deacetylated chitosan, offering an attractive alternative for enzymatic production of chitooligosaccharides at high temperature and low pH. Our results show that the R. marinus chitinase is the most thermostable family 18 chitinase isolated from Bacteria so far.