Revisiting the Cellulosimicrobium cellulans yeast-lytic beta-1,3-glucanases toolbox: a review

Novel, cold-adapted D-laminaribiose- and D-glucose-releasing GH16 endo-β-1,3-glucanase from Hymenobacter siberiensis PAMC 29290, a psychrotolerant bacterium from Arctic marine sediment

Endo-β-1,3-glucanase is a glycoside hydrolase (GH) that plays an essential role in the mineralization of β-glucan polysaccharides. In this study, the novel gene encoding an extracellular, non-modular GH16 endo-β-1,3-glucanase (GluH) from Hymenobacter siberiensis PAMC 29290 isolated from Arctic marine sediment was discovered through an in silico analysis of its whole genome sequence and subsequently overexpressed in Escherichia coli BL21. The 870-bp GluH gene encoded a protein featuring a single catalytic GH16 domain that shared over 61% sequence identity with uncharacterized endo-β-1,3-glucanases from diverse Hymenobacter species, as recorded in the National Center for Biotechnology Information database. The purified recombinant endo-β-1,3-glucanase (rGluH: 31.0 kDa) demonstrated peak activity on laminarin at pH 5.5 and 40°C, maintaining over 40% of its maximum endo-β-1,3-glucanase activity even at 25°C. rGluH preferentially hydrolyzed D-laminarioligosaccharides and β-1,3-linked polysaccharides, but did not degrade D-laminaribiose or structurally unrelated substrates, confirming its specificity as a true endo-β-1,3-glucanase without ancillary GH activities. The biodegradability of various substrate polymers by the enzyme was evaluated in the following sequence: laminarin > barley β-glucan > carboxymethyl-curdlan > curdlan > pachyman. Notably, the specific activity (253.1 U mg-1) and catalytic efficiency (k cat /K m : 105.72 mg-1 s-1 mL) of rGluH for laminarin closely matched its specific activity (250.2 U mg-1) and k cat /K m value (104.88 mg-1 s-1 mL) toward barley β-glucan. However, the k cat /K m value (9.86 mg-1 s-1 mL) of rGluH for insoluble curdlan was only about 9.3% of the value for laminarin, which correlates well with the observation that rGluH displayed weak binding affinity (< 40%) to the insoluble polymer. The biocatalytic hydrolysis of D-laminarioligosaccharides with a degree of polymerization between 3 and 6 and laminarin generally resulted in the formation of D-laminaribiose as the predominant product and D-glucose as the secondary product, with a ratio of approximately 4:1. These findings suggest that highly active rGluH is an acidic, cold-adapted D-laminaribiose- and D-glucose-releasing GH16 endo-β-1,3-glucanase, which can be exploited as a valuable biocatalyst for facilitating low temperature preservation of foods.

Cellulamides: A New Family of Marine-Sourced Linear Peptides from the Underexplored Cellulosimicrobium Genus

Bioprospecting the secondary metabolism of underexplored Actinomycetota taxa is a prolific route to uncover novel chemistry. In this work, we report the isolation, structure elucidation, and bioactivity screening of cellulamides A and B (1 and 2), two novel linear peptides obtained from the culture of the macroalga-associated Cellulosimicrobium funkei CT-R177. The host of this microorganism, the Chlorophyta Codium tomentosum, was collected in the northern Portuguese coast and, in the scope of a bioprospecting study focused on its associated actinobacterial community, strain CT-R177 was isolated, taxonomically identified, and screened for the production of antimicrobial and anticancer compounds. Dereplication of a crude extract of this strain using LC-HRMS(/MS) analysis unveiled a putative novel natural product, cellulamide A (1), that was isolated following mass spectrometry-guided fractionation. An additional analog, cellulamide B (2) was obtained during the chromatographic process and chemically characterized. The chemical structures of the novel linear peptides, including their absolute configurations, were elucidated using a combination of HRMS, 1D/2D NMR spectroscopy, and Marfey's analysis. Cellulamide A (1) was subjected to a set of bioactivity screenings, but no significant biological activity was observed. The cellulamides represent the first family of natural products reported from the Actinomycetota genus Cellulosimicrobium, showcasing not only the potential of less-explored taxa but also of host-associated marine strains for novel chemistry discovery.

A First Expression, Purification and Characterization of Endo-β-1,3-Glucanase from Penicillium expansum

β-1,3-glucanase plays an important role in the biodegradation, reconstruction, and development of β-1,3-glucan. An endo-β-1,3-glucanase which was encoded by PeBgl1 was expressed, purified and characterized from Penicillium expansum for the first time. The PeBgl1 gene was amplified and transformed into the competent cells of E. coli Rosetta strain with the help of the pET-30a cloning vector. The recombinant protein PeBgl1 was expressed successfully at the induction conditions of 0.8 mmol/L IPTG at 16 °C for 16 h and then was purified by nickel ion affinity chromatography. The optimum reaction temperature of PeBgl1 was 55 °C and it had maximal activity at pH 6.0 according to the enzymatic analysis. Na2HPO4-NaH2PO4 buffer (pH 6.0) and NaCl have inhibitory and enhancing effects on the enzyme activities, respectively. SDS, TritonX-100 and some metal ions (Mg2+, Ca2+, Ba2+, Cu2+, and Zn2+) have an inhibitory effect on the enzyme activity. The results showed that PeBgl1 protein has good enzyme activity at 50-60 °C and at pH 5.0-9.0, and it is not a metal dependent enzyme, which makes it robust for storage and transportation, ultimately holding great promise in green biotechnology and biorefining.

A Rapid and Efficient Method for the Extraction of Histone Proteins

Current protocols used to extract and purify histones are notoriously tedious, especially when using yeast cells. Here, we describe the use of a simple filter-aided sample preparation approach enabling histone extraction from yeast and mammalian cells using acidified ethanol, which not only improves extraction but also inactivates histone-modifying enzymes. We show that our improved method prevents N-terminal clipping of H3, an artifact frequently observed in yeast cells using standard histone extraction protocols. Our method is scalable and provides efficient recovery of histones when extracts are prepared from as few as two million yeast cells. We further demonstrate the application of this approach for the analysis of histone modifications in fungal clinical isolates available in a limited quantity. Compared with standard protocols, our method enables the study of histones and their modifications in a faster, simpler, and more robust manner.

Isolation, Screening, and Degradation Characteristics of a Quinclorac-Degrading Bacterium, Strain D, and Its Potential for Bioremediation of Rice Fields Polluted by Quinclorac

Quinclorac (QNC) is a persistent, highly selective, hormonal herbicide of low toxicity. QNC accumulates in soil and affects the growth and development of crops planted subsequent to its application. In this study, we isolated and screened a QNC-degrading bacterial strain, strain D, from rice paddy soil. Morphological analysis, physiological and biochemical tests, and 16S rRNA gene sequencing led us to identify strain D as a Cellulosimicrobium cellulans strain. We investigated the characteristics of strain D in relation to QNC degradation. Under optimal culture conditions, the QNC degradation rate was 45.9% after 21 days of culture. QNC degradation by strain D in the field was modeled and quantified by a pot experiment. The results show that strain D promotes rice growth and degrades QNC. This research has identified a new bacterial species that degrades QNC, providing a foundation for further research into QNC remediation. IMPORTANCE QNC-degrading bacteria have been isolated from different environments, but there are no reports of Cellulosimicrobium cellulans strains that degrade QNC. In this study, a previously unidentified bacterial strain that degrades QNC, strain D, was screened from paddy soil. The characteristics of strain D that relate to QNC degradation were investigated in detail. The results showed that strain D effectively degraded QNC. Two degradation products of QNC formed by strain D that have not been reported previously, i.e., 3-pyridylacetic acid (m/z 138.0548) and 3-ethylpyridine (m/z 108.0805), were identified using high-performance liquid chromatography-quadrupole time of flight mass spectrometry. Strain D has the capacity to degrade QNC in a QNC-polluted paddy.

Novel Anti-Fungal d-Laminaripentaose-Releasing Endo-β-1,3-glucanase with a RICIN-like Domain from Cellulosimicrobium funkei HY-13

Endo-β-1,3-glucanase plays an essential role in the deconstruction of β-1,3-d-glucan polysaccharides through hydrolysis. The gene (1650-bp) encoding a novel, bi-modular glycoside hydrolase family 64 (GH64) endo-β-1,3-glucanase (GluY) with a ricin-type β-trefoil lectin domain (RICIN)-like domain from Cellulosimicrobium funkei HY-13 was identified and biocatalytically characterized. The recombinant enzyme (rGluY: 57.5 kDa) displayed the highest degradation activity for laminarin at pH 4.5 and 40 °C, while the polysaccharide was maximally decomposed by its C-terminal truncated mutant enzyme (rGluYΔRICIN: 42.0 kDa) at pH 5.5 and 45 °C. The specific activity (26.0 U/mg) of rGluY for laminarin was 2.6-fold higher than that (9.8 U/mg) of rGluYΔRICIN for the same polysaccharide. Moreover, deleting the C-terminal RICIN domain in the intact enzyme caused a significant decrease (>60%) of its ability to degrade β-1,3-d-glucans such as pachyman and curdlan. Biocatalytic degradation of β-1,3-d-glucans by inverting rGluY yielded predominantly d-laminaripentaose. rGluY exhibited stronger growth inhibition against Candida albicans in a dose-dependent manner than rGluYΔRICIN. The degree of growth inhibition of C. albicans by rGluY (approximately 1.8 μM) was approximately 80% of the fungal growth. The superior anti-fungal activity of rGluY suggests that it can potentially be exploited as a supplementary agent in the food and pharmaceutical industries.

Analysis and application of a suite of recombinant endo-β(1,3)-D-glucanases for studying fungal cell walls

Background

The fungal cell wall is an essential and robust external structure that protects the cell from the environment. It is mainly composed of polysaccharides with different functions, some of which are necessary for cell integrity. Thus, the process of fractionation and analysis of cell wall polysaccharides is useful for studying the function and relevance of each polysaccharide, as well as for developing a variety of practical and commercial applications. This method can be used to study the mechanisms that regulate cell morphogenesis and integrity, giving rise to information that could be applied in the design of new antifungal drugs. Nonetheless, for this method to be reliable, the availability of trustworthy commercial recombinant cell wall degrading enzymes with non-contaminating activities is vital.

Results

Here we examined the efficiency and reproducibility of 12 recombinant endo-β(1,3)-d-glucanases for specifically degrading the cell wall β(1,3)-d-glucan by using a fast and reliable protocol of fractionation and analysis of the fission yeast cell wall. This protocol combines enzymatic and chemical degradation to fractionate the cell wall into the four main polymers: galactomannoproteins, α-glucan, β(1,3)-d-glucan and β(1,6)-d-glucan. We found that the GH16 endo-β(1,3)-d-glucanase PfLam16A from Pyrococcus furiosus was able to completely and reproducibly degrade β(1,3)-d-glucan without causing the release of other polymers. The cell wall degradation caused by PfLam16A was similar to that of Quantazyme, a recombinant endo-β(1,3)-d-glucanase no longer commercially available. Moreover, other recombinant β(1,3)-d-glucanases caused either incomplete or excessive degradation, suggesting deficient access to the substrate or release of other polysaccharides.

Conclusions

The discovery of a reliable and efficient recombinant endo-β(1,3)-d-glucanase, capable of replacing the previously mentioned enzyme, will be useful for carrying out studies requiring the digestion of the fungal cell wall β(1,3)-d-glucan. This new commercial endo-β(1,3)-d-glucanase will allow the study of the cell wall composition under different conditions, along the cell cycle, in response to environmental changes or in cell wall mutants. Furthermore, this enzyme will also be greatly valuable for other practical and commercial applications such as genome research, chromosomes extraction, cell transformation, protoplast formation, cell fusion, cell disruption, industrial processes and studies of new antifungals that specifically target cell wall synthesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01616-0.

Cellulosimicrobium fucosivorans sp. nov., isolated from San Elijo Lagoon, contains a fucose metabolic pathway linked to carotenoid production

Cellulosimicrobium strain SE3^T was isolated from the San Elijo coastal lagoon near San Diego. A whole genome-based phylogenetic comparison shows great heterogeneity within the Cellulosimicrobium genus. Based on average nucleotide identity, whole genome-based comparison, and the presence of a unique L-fucose metabolic pathway, strain SE3^T was shown to belong to a novel species within the genus, together with five other strains. The name Cellulosimicrobium fucosivorans sp. nov. is proposed, with strain SE3^T as the type strain. The strain encodes a unique alpha-L-fucosidase and the L-fucose metabolic pathway is homologous to the one recently described in Campylobacter jejuni. C. fucosivorans is able to grow on L-fucose, and interestingly, the biosynthesis of the yellow carotenoid is dependent on the presence of L-fucose in the media. The ability to metabolize fucose and the linked production of carotenoids are expected to provide C. fucosivorans with a competitive advantage in the sunny coastal lagoon area.

Enhancement of β-Glucan Biological Activity Using a Modified Acid-Base Extraction Method from Saccharomyces cerevisiae

Beta glucan (β-glucan) has promising bioactive properties. Consequently, the use of β-glucan as a food additive is favored with the dual-purpose potential of increasing the fiber content of food products and enhancing their health properties. Our aim was to evaluate the biological activity of β-glucan (antimicrobial, antitoxic, immunostimulatory, and anticancer) extracted from Saccharomyces cerevisiae using a modified acid-base extraction method. The results demonstrated that a modified acid-base extraction method gives a higher biological efficacy of β-glucan than in the water extraction method. Using 0.5 mg dry weight of acid-base extracted β-glucan (AB extracted) not only succeeded in removing 100% of aflatoxins, but also had a promising antimicrobial activity against multidrug-resistant bacteria, fungi, and yeast, with minimum inhibitory concentrations (MIC) of 0.39 and 0.19 mg/mL in the case of resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, respectively. In addition, AB extract exhibited a positive immunomodulatory effect, mediated through the high induction of TNFα, IL-6, IFN-γ, and IL-2. Moreover, AB extract showed a greater anticancer effect against A549, MDA-MB-232, and HepG-2 cells compared to WI-38 cells, at high concentrations. By studying the cell death mechanism using flow-cytometry, AB extract was shown to induce apoptotic cell death at higher concentrations, as in the case of MDA-MB-231 and HePG-2 cells. In conclusion, the use of a modified AB for β-glucan from Saccharomyces cerevisiae exerted a promising antimicrobial, immunomodulatory efficacy, and anti-cancer potential. Future research should focus on evaluating β-glucan in various biological systems and elucidating the underlying mechanism of action.

A case report of the differential diagnosis of Cellulosimicrobium cellulans-infected endocarditis combined with intracranial infection by conventional blood culture and second-generation sequencing

Background

Cellulosimicrobium cellulans is a gram-positive filamentous bacterium found primarily in soil and sewage that rarely causes human infection, especially in previously healthy adults, but when it does, it often indicates a poor prognosis.

Case presentation

We report a case of endocarditis and intracranial infection caused by C. cellulans in a 52-year-old woman with normal immune function and no implants in vivo. The patient started with a febrile headache that progressed to impaired consciousness after 20 days, and she finally died after treatment with vancomycin combined with rifampicin. C. cellulans was isolated from her blood cultures for 3 consecutive days after her admission; however, there was only evidence of C. cellulans sequences for two samples in the second-generation sequencing data generated from her peripheral blood, which were ignored by the technicians. No C. cellulans bands were detected in her cerebrospinal fluid by second-generation sequencing.

Conclusions

Second-generation sequencing seems to have limitations for certain specific strains of bacteria.

Chitinolytic proteins secreted by Cellulosimicrobium sp. NTK2

Cellulosimicrobium sp. NTK2 (NTK2 strain) was isolated as a chitinolytic bacterium from mature compost derived from chitinous waste. The growth of the NTK2 strain was enhanced by supplementation of the culture medium with 2% crystalline chitin. Approximately 70% of the supplemented crystalline chitin was degraded during cultivation. Whole genome analysis of the NTK2 strain identified eight chitinases and two chitin-binding proteins. The NTK2 strain secreted two bacterial extracellular solute-binding proteins, three family 18 glycosyl hydrolases and one lytic polysaccharide monooxygenase specifically in the presence of crystalline chitin. A chitinolytic enzyme with a molecular mass of 29 kDa on SDS-PAGE under native conditions was also secreted. This chitinolytic enzyme exhibited the largest band upon zymography but could not be identified. In an attempt to identify all the chitinases secreted by the NTK2 strain, we expressed recombinant versions of the proteins exhibiting chitinolytic activity in Escherichia coli. Our results suggest that the 29 kDa protein belonging to family 19 glycosyl hydrolase was expressed specifically in the presence of 2% crystalline chitin.

Key extracellular enzymes triggered high-efficiency composting associated with bacterial community succession

A consortium of key bacterial taxa plays critical roles in the composting process. In order to elucidate the identity and mechanisms by which specific bacterial species drive high-efficiency composting, the succession of key bacterial consortia and extracellular enzymes produced during the composting process were monitored in composting piles with varying initial C/N ratios. Results showed that C/N ratios of 25 and 35 enhanced composting efficiency through elevated temperatures, higher germination indices, enhanced cellulose and hemicellulose degradation, and higher cellulase and dehydrogenase activities. The activities of cellulase and β-glucosidase, cellulase and protease, and cellulase and β-glucosidase exhibited significant relationships with bacterial community composition within the mesophilic, thermophilic, and mature phases, respectively. Putative key taxa, linked to a higher composting efficiency, such as Nonomuraea, Desemzia, Cellulosimicrobium, Virgibacillus, Clostridium, and Achromobacter, exhibited significantly positive relationships with extracellular enzyme activities, suggesting a significant contribution to these taxa to the development of composting maturity.

Effects of Different Carbon Sources on Enzyme Production and Ultrastructure of Cellulosimicrobium cellulans

The secretomes of the strain Cellulosimicrobium cellulans F16 grown on different carbon sources were analyzed by zymography, and the subcellular surface structures were extensively studied by electron microscope. The exo-cellulase and xylanase systems were sparse when cells were grown on soluble oligosaccharides, but were significantly increased when grown on complex and water-insoluble polysaccharides, such as Avicel, corn cob, and birchwood xylan. The cellulosome-like protuberant structures were clearly observed on the cell surfaces of strain F16 grown on cellulose, with diameters of 15-20 nm. Fibrous structures that connected the adjacent cells can be seen under microscope. Moreover, protuberances that adsorbed the cell to cellulose were also observed. As the adhesion of Cellulosimicrobium cellulans cells onto cellulose surfaces occurs via thick bacterial curdlan-type exopolysaccharides (EPS), such surface layer is potentially important in the digestion of insoluble substrates such as cellulose or hemicellulose, and the previously reported xylanosomes are part of such complex glycocalyx layer on the surface of the bacterial cell.

The Interior Surfaces of Wooden Barrels Are an Additional Microbial Inoculation Source for Lambic Beer Production

Traditional lambic beer production takes place through wort inoculation with environmental air and fermentation and maturation in wooden barrels. These wooden casks or foeders are possible additional inoculation sources of microorganisms for lambic worts. To date, however, these lambic barrels have been examined only with culture-dependent techniques, thereby missing a portion of the microorganisms present. Moreover, the effects of the cleaning procedures (involving high-pressure water and/or fumigation) and the barrel type on the microbial community structures of the interior surfaces of wooden lambic barrels were unclear. The culture-dependent plating and culture-independent amplicon sequencing of swab samples obtained from the interior surfaces of different wooden casks and foeders used for traditional lambic beer production in Belgium revealed that the microbial compositions of these surfaces differed statistically throughout the barrel-cleaning procedures applied. At the end of the cleaning procedures, amplicon sequencing still detected fermentation- and maturation-related microorganisms, although only a few colonies were still detectable using culture-dependent methods. It is possible that some of the surviving microorganisms were missed due to the presence of many of these cells in a viable but not culturable state and/or engrained deeper in the wood. These surviving microorganisms could act as an additional inoculation source, besides brewery air and brewery equipment, thereby helping to establish a stable microbial community in the wort to diminish batch-to-batch variations in fermentation profiles. Furthermore, the microbial compositions of the interior barrel surfaces differed statistically based on the barrel type, possibly reflecting different characteristics of the lambic barrels in terms of age, wood thickness, and wood porosity.IMPORTANCE Although the coolship step is generally regarded as the main contributor to the spontaneous inoculation by environmental air of fresh worts for lambic beer production, it is known that microorganisms often associate with specific surfaces present in a brewery. However, knowledge about the association of microorganisms with the interior surfaces of wooden lambic barrels is limited. To clarify the role of casks and foeders as additional microbial inoculation sources, it was important to determine the influence of the barrel characteristics and the cleaning procedures on the microbial communities of the interior barrel surfaces. Moreover, this helped to elucidate the complex spontaneous lambic beer fermentation and maturation process. It will allow further optimization of the lambic beer production process, as well as the wooden-barrel-cleaning procedures applied.

Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species

The present study combined high-throughput culture-dependent plating and culture-independent amplicon sequencing with a metabolite target analysis to systematically dissect the identity, evolution, and role of the microorganisms, substrates, and metabolites during the four-phase fermentation and maturation process of lambic beer production. This led to the following new insights. The changing physicochemical parameters and substrate and metabolite compositions of the fermenting wort and maturing lambic beer provoked several transitions between microbial species and explained the four-step production process. Manual wort acidification with lactic acid shortened the enterobacterial phase and thus kept biogenic amine formation by enterobacteria present during the early stages of fermentation at a minimum. Growth advantages during the alcoholic fermentation phase caused a transition from the prevalence by Hanseniaspora uvarum and Kazachstania species to that by Saccharomyces cerevisiae and later on Saccharomyces kudriavzevii, due to changing environmental parameters. During the acidification phase, Pediococcus damnosus was prevalent and performed a malolactic fermentation. Acetobacter pasteurianus produced acetic acid and acetoin. Upon maturation, Dekkera species appeared, together with P. damnosus and Pichia membranifaciens, thereby contributing to acetic acid production, depending on the oxygen availability. Moreover, the Dekkera species consumed the acetoin produced by the acetic acid bacteria for redox balancing. The breakdown of maltooligosaccharides seemed to be independent of the occurrence of Dekkera species and started already early in the fermentation process.

Isolation of β-1,3-Glucanase-Producing Microorganisms from Poria cocos Cultivation Soil via Molecular Biology

β-1,3-Glucanase is considered as a useful enzymatic tool for β-1,3-glucan degradation to produce (1→3)-linked β-glucan oligosaccharides with pharmacological activity properties. To validly isolate β-1,3-glucanase-producing microorganisms, the soil of Wolfiporia extensa, considered an environment rich in β-1,3-glucan-degrading microorganisms, was subjected to high throughput sequencing. The results demonstrated that the genera Streptomyces (1.90%) and Arthrobacter (0.78%) belonging to the order Actinomycetales (8.64%) in the phylum Actinobacteria (18.64%) were observed in soil for P. cocos cultivation (FTL₁). Actinomycetes were considered as the candidates for isolation of glucan-degrading microorganisms. Out of 58 isolates, only 11 exhibited β-1,3-glucan-degrading activity. The isolate SYBCQL belonging to the genus Kitasatospora with β-1,3-glucan-degrading activity was found and reported for the first time and the isolate SYBC17 displayed the highest yield (1.02 U/mg) among the isolates. To check the β-1,3-glucanase contribution to β-1,3-glucan-degrading activity, two genes, 17-W and 17-Q, encoding β-1,3-glucanase in SYBC17 and one gene QLK1 in SYBCQL were cloned and expressed for verification at the molecular level. Our findings collectively showed that the isolates able to secrete β-1,3-glucanase could be obtained with the assistance of high-throughput sequencing and genes expression analysis. These methods provided technical support for isolating β-1,3-glucanase-producing microorganisms.

Species of family Promicromonosporaceae and family Cellulomonadeceae that produce cellulosome-like multiprotein complexes

OBJECTIVES

To screen the phylogenetically-nearest members of Cellulosimicrobium cellulans for the production of cellulosome-like multienzyme complexes and extracellular β-xylosidase activity against 7-xylosyltaxanes and to get corresponding molecular insights.

RESULTS

Cellulosimicrobium (family Promicromonosporaceae) and all genera of the family Cellulomonadeceaec produced both cellulosome-like multienzyme complexes and extracellular β-xylosidase activity, while the other genera of the family Promicromonosporaceae did not. Multiple sequence alignments further indicated that hypothetic protein M768_06655 might be a possible key subunit.

CONCLUSION

This is the first report that many actinobacteria species can produce cellulosome-like multienzyme complexes. The production of cellulosome-like complexes and the extracellular β-xylosidase activity against 7-xylosyltaxanes might be used to differentiate the genus Cellulosimicrobium from other genera of the family Promicromonosporaceae.

Tryptophan introduction can change β-glucan binding ability of the carbohydrate-binding module of endo-1,3-β-glucanase

Endo-1,3-β-glucanase from Cellulosimicrobium cellulans DK-1 has a carbohydrate-binding module (CBM-DK) at the C-terminal side of a catalytic domain. Out of the imperfect tandem α-, β-, and γ-repeats in CBM-DK, the α-repeat primarily contributes to β-glucan binding. This unique feature is derived from Trp273 in α-repeat, whose corresponding residues in β- and γ-repeats are Asp314 and Gly358, respectively. In this study, we generated Trp-switched mutants, W273A/D314W, D270A/W273A/D314W, W273A/G358W, and D270A/W273A/G358W, and analyzed their binding abilities toward laminarioligosaccharides and laminarin. While the binding affinities of D270A/W273A and W273A mutants were either lost or much lower than that of the wild-type, those of Trp-switched mutants recovered, indicating that a Trp introduction in β- or γ-repeat can substitute the α-repeat by primarily contributing to β-glucan binding. Thus, we have successfully engineered a CBM-DK that binds to laminarin by a mechanism different from that of the wild-type, but with similar affinity.

Structure Prediction of a Novel Exo-β-1,3-Glucanase: Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12

We report a detailed structural analysis of the psychrophilic exo-β-1,3-glucanase (GaExg55) from Glaciozyma antarctica PI12. This study elucidates the structural basis of exo-1,3-β-1,3-glucanase from this psychrophilic yeast. The structural prediction of GaExg55 remains a challenge because of its low sequence identity (37 %). A 3D model was constructed for GaExg55. Threading approach was employed to determine a suitable template and generate optimal target-template alignment for establishing the model using MODELLER9v15. The primary sequence analysis of GaExg55 with other mesophilic exo-1,3-β-glucanases indicated that an increased flexibility conferred to the enzyme by a set of amino acids substitutions in the surface and loop regions of GaExg55, thereby facilitating its structure to cold adaptation. A comparison of GaExg55 with other mesophilic exo-β-1,3-glucanases proposed that the catalytic activity and structural flexibility at cold environment were attained through a reduced amount of hydrogen bonds and salt bridges, as well as an increased exposure of the hydrophobic side chains to the solvent. A molecular dynamics simulation was also performed using GROMACS software to evaluate the stability of the GaExg55 structure at varying low temperatures. The simulation result confirmed the above findings for cold adaptation of the psychrophilic GaExg55. Furthermore, the structural analysis of GaExg55 with large catalytic cleft and wide active site pocket confirmed the high activity of GaExg55 to hydrolyze polysaccharide substrates.

Structural and binding properties of laminarin revealed by analytical ultracentrifugation and calorimetric analyses

One of the β-1,3-glucans, laminarin, has been widely used as a substrate for enzymes including endo-1,3-β-glucanase. To obtain quantitative information about the molecular interaction between laminarin and endo-1,3-β-glucanase, the structural properties of laminarin should be determined. The results from pioneering work using analytical ultracentrifugation for carbohydrate analysis showed that laminarin from Laminaria digitata predominantly exists as a single-chain species with approximately 5% of triple-helical species. Differential scanning calorimetry experiments did not show a peak assignable to the transition from triple-helix to single-chain, supporting the notion that a large proportion of laminarin is the single-chain species. The interaction of laminarin with an inactive variant of endo-1,3-β-glucanase from Cellulosimicrobium cellulans, E119A, was quantitatively analyzed using isothermal titration calorimetry. The binding was enthalpically driven and the binding affinity was approximately 10(6) M(-1). The results from binding stoichiometric analysis indicated that on average, E119A binds to laminarin in a 2:1 ratio. This seems to be reasonable, because laminarin mainly exists as a monomer, the apparent molecular mass of laminarin is 3.6 kDa, and E119A would have substrate-binding subsites corresponding to 6 glucose units. The analytical ultracentrifugation experiments could detect different complex species of laminarin and endo-1,3-β-glucanase.

Functional and structural properties of a novel cellulosome-like multienzyme complex: efficient glycoside hydrolysis of water-insoluble 7-xylosyl-10-deacetylpaclitaxel

Cellulosome is a kind of multienzyme complex that displays high activity, selectivity, and stability. Here, we report a novel, non-cellulolytic, cellulosome-like multienzyme complex that produced by the Cellulosimicrobium cellulans wild-type strain F16 isolated from soil microflora. This multienzyme complex, with excellent catalytic efficiency of kcat 13.2 s(-1) to remove the C-7 xylosyl group from 7-xylosyl-10-deacetylpaclitaxel (10-DAXP), has an outstanding tolerance against organic solvents and an excellent general stability, with the long half-life of 214 hours. This cellulosome-like multienzyme complex has a novel structure distinct from the well-documented ones. The key catalytic subunit responsible for the β-xylosidase activity against 10-DAXP is identified to be a novel protein, indicating a new glycoside hydrolase (GH) family. The pioneering work described here offers a novel nanoscale biocatalyst for the production of biofuels and chemicals from renewable plant-based natural resources.

Bioflocculant production from untreated corn stover using Cellulosimicrobium cellulans L804 isolate and its application to harvesting microalgae

BACKGROUND

Microalgae are widely studied for biofuel production. Nevertheless, harvesting step of biomass is still a critical challenge. Bioflocculants have been applied in numerous applications including the low-cost harvest of microalgae. A major bottleneck for commercial application of bioflocculant is its high production cost. Lignocellulosic substrates are abundantly available. Hence, the hydrolyzates of rice stover and corn stover have been used as carbon source to produce the bioflocculant in previous studies. However, the hydrolyzates of biomass required the neutralization of pH before the downstream fermentation processes, and the toxic by-products produced during hydrolysis process inhibited the microbial activities in the subsequent fermentation processes and contaminated the bioflocculant product. Therefore, strains that can secrete plant cell-wall-degrading enzymes and simultaneously produce bioflocculants through directly degrading the lignocellulosic biomasses are of academic and practical interests.

RESULTS

A lignocellulose-degrading strain Cellulosimicrobium cellulans L804 was isolated in this study, which can produce the bioflocculant MBF-L804 using untreated biomasses, such as corn stover, corn cob, potato residues, and peanut shell. The effects of culture conditions including initial pH, carbon source, and nitrogen source on MBF-L804 production were analyzed. The results showed that over 80 % flocculating activity was achieved when the corn stover, corn cob, potato residues, and peanut shell were used as carbon sources and 4.75 g/L of MBF-L804 was achieved under the optimized condition: 20 g/L dry corn stover as carbon source, 3 g/L yeast extract as nitrogen source, pH 8.2. The bioflocculant MBF-L804 contained 68.6 % polysaccharides and 28.0 % proteins. The Gel permeation chromatography analysis indicated that the approximate molecular weight (MW) of MBF-L804 was 229 kDa. The feasibility of harvesting microalgae Chlamydomonas reinhardtii and Chlorella minutissima using MBF-L804 was evaluated. The highest flocculating efficiencies for C. reinhardtii and C. minutissima were 99.04 and 93.83 %, respectively.

CONCLUSIONS

This study shows for the first time that C. cellulans L804 can directly convert corn stover, corn cob, potato residues and peanut shell into the bioflocculants, which can be used to effectively harvest microalgae.

Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring

Microbial mats situated at the Manikaran hot springs (>95°C) are characterized by their high arsenic content (140 ppb), qualifying as a stressed niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding sequences, with an average % G+C of 74.4%.

Nitrate assimilation contributes to Ralstonia solanacearum root attachment, stem colonization, and virulence

Ralstonia solanacearum, an economically important plant pathogen, must attach, grow, and produce virulence factors to colonize plant xylem vessels and cause disease. Little is known about the bacterial metabolism that drives these processes. Nitrate is present in both tomato xylem fluid and agricultural soils, and the bacterium's gene expression profile suggests that it assimilates nitrate during pathogenesis. A nasA mutant, which lacks the gene encoding the catalytic subunit of R. solanacearum's sole assimilatory nitrate reductase, did not grow on nitrate as a sole nitrogen source. This nasA mutant exhibited reduced virulence and delayed stem colonization after soil soak inoculation of tomato plants. The nasA virulence defect was more severe following a period of soil survival between hosts. Unexpectedly, once bacteria reached xylem tissue, nitrate assimilation was dispensable for growth, virulence, and competitive fitness. However, nasA-dependent nitrate assimilation was required for normal production of extracellular polysaccharide (EPS), a major virulence factor. Quantitative analyses revealed that EPS production was significantly influenced by nitrate assimilation when nitrate was not required for growth. The plant colonization delay of the nasA mutant was externally complemented by coinoculation with wild-type bacteria but not by coinoculation with an EPS-deficient epsB mutant. The nasA mutant and epsB mutant did not attach to tomato roots as well as wild-type strain UW551. However, adding either wild-type cells or cell-free EPS improved the root attachment of these mutants. These data collectively suggest that nitrate assimilation promotes R. solanacearum virulence by enhancing root attachment, the initial stage of infection, possibly by modulating EPS production.

Identification of an elongation factor 1Bγ protein with glutathione transferase activity in both yeast and mycelial morphologies from human pathogenic Blastoschizomyces capitatus

Blastoschizomyces capitatus is an uncommon, opportunistic pathogenic fungus, which causes invasive and disseminated infections. This microorganism is normally present in both environmental and normal human flora. Within a host, B. capitatus is able to grow in both unicellular yeast and multicellular filamentous growth forms. In this study, we obtained in vitro morphological conversion of B. capitatus from yeast-to-mycelial phase to investigate the presence and expression of glutathione transferase (GST) enzymes in both cell forms. A protein with GST activity using the model substrate 1-chloro-2,4-dinitrobenzene was detected in both morphologies and identified by tandem mass spectrometry as a eukaryotic elongation factor 1Bγ (eEF1Bγ) protein, a member of the GST superfamily. No significant difference in GST-specific activity and kinetic constants were observed between mycelial and yeast forms, indicating that eEF1Bγ protein did not show differential expression between the two phases.

Glucanase induces filamentation of the fungal pathogen Candida albicans

Candida albicans is the most common human fungal pathogen. Many organisms, including C. albicans, secrete glucanases under different environmental conditions. Here, we report a novel role for beta-1, 3- glucanase in inducing Candida albicans to form filaments at 22°C and enhancing filamentation at 37°C in nutrient-rich medium. Quorum sensing, the efg1-signaling and cek1 MAP kinase pathways are involved in this process. Our data suggest that the natural antifungal agent beta–glucanase may support morphologic transformation of Candida albicans at a wide range of ambient temperatures.

Mycolytic enzymes produced by Streptomyces violaceusniger and their role in antagonism towards wood-rotting fungi

Extracellular mycolytic enzymes produced under submerged fermentation by the fungal antagonist Streptomyces violaceusniger MTCC 3959 were characterized. This streptomycete produced higher amounts of extracellular chitinase and protease during late exponential phase, whereas β-1,3-glucanase production was at peak in mid-stationary phase. Cell-free culture filtrate (CCF) exhibited a broad range of antifungal activity against both white rot and brown rot fungi. The inhibitory activity was completely lost after treatment with proteinase K and heat, indicating that extracellular antifungal metabolites are heat labile and proteinaceous in nature. Optimum pH and temperature for enzyme activity were: 9.0 and 60 °C for chitinase; 6.0 and 60 °C for β-1,3-glucanase; and 9.0 and 70 °C for protease. Mycolytic enzymes were moderately thermostable, and had a wide pH stability range extending from pH 5.0 to 10.0. The zymogram analysis of CCF revealed five chitinase isoenzymes with an apparent molecular weight of 20.8, 33.3, 45.6, 67.4, and 114.8 kDa, one β-1,3-glucanase appeared as a single band of ∼131.8 kDa and four protease isoenzymes with approximate molecular weights of 22.8, 62.52, 74.64, and 120.5 kDa. S. violaceusniger MTCC 3959 produced mycolytic enzymes that can be effectively used for suppression of phytopathogenic basidiomycetes. It has the potential to be an effective biofungicide.

β-1,3-glucan modifying enzymes in Aspergillus fumigatus

In Aspergillus fumigatus like in other filamentous ascomycetes, β-1,3-glucan constitutes a prominent cell wall component being responsible for rigidity of the cell wall structure. In filamentous fungi, softening of the cell wall is absolutely required during conidial germination and hyphal branching. Because of the central structure of β-1,3-glucans, it is expected that β-1,3-glucanases play a major role in cell wall softening. Based on in silico and experimental data, this review gives an overview of β-1,3-glucan modifying enzymes in A. fumigatus genome and their putative role during morphogenesis.

Critical roles of Asp270 and Trp273 in the α-repeat of the carbohydrate-binding module of endo-1,3-β-glucanase for laminarin-binding avidity

A carbohydrate-binding module from family 13 (CBM13), appended to the catalytic domain of endo-1,3-β-glucanase from Cellulosimicrobium cellulans, was overexpressed in E. coli, and its interactions with β-glucans, laminarin and laminarioligosaccharides, were analyzed using surface plasmon resonance biosensor and isothermal titration calorimetry. The association constants for laminarin and laminarioligosaccharides were determined to be approximately 10(6) M(-1) and 10(4) M(-1), respectively, indicating that 2 or 3 binding sites in the α-, β-, and γ-repeats of CBM13 are involved in laminarin binding in a cooperative manner. The binding avidity is approximately 2-orders higher than the monovalent binding affinity. Mutational analysis of the conserved Asp residues in the respective repeats showed that the α-repeat primarily contributes to β-glucan binding. A Trp residue is predicted to be exposed to the solvent only in the α-repeat and would contribute to β-glucan binding. The α-repeat bound β-glucan with an affinity of approximately 10(4) M(-1), and the other repeats additionally bound laminarin, resulting in the increased binding avidity. This binding is unique compared to the recognition mode of another CBM13 from Streptomyces lividans xylanase.

Study of antimycotic activity of lyticase

Laboratory studies of lyticase (enzymatic drug) as an antimycotic agent were carried out. The enzyme reduced optical density of Candida albicans test culture, inhibited adhesion of yeast-like fungi on vaginal epitheliocytes, stimulated the formation of germinative tubes, and made Candida albicans more available for phagocytosis.

Tetrapisispora phaffii killer toxin is a highly specific beta-glucanase that disrupts the integrity of the yeast cell wall

Background

Killer yeasts have been used to combat contaminating wild yeasts in food, to control pathogenic fungi in plants, and in the medical field, to develop novel antimycotics for the treatment of human and animal fungal infections. Among these killer yeasts, Tetrapisispora phaffii (formerly known as Kluyveromyces phaffii) secretes a glycoprotein known as Kpkt that is lethal to spoilage yeasts under winemaking conditions. In the present study, the mode of action of Kpkt, and the specific damage produced by this toxin on sensitive yeasts is investigated.

Results

The use of castanospermine, a β-glucanase inhibitor, demonstrated that β-glucanase activity is essential for the Kpkt killer activity in vivo. Accordingly, Kpkt has no killer activity on either sensitive yeast spheroplasts or whole sensitive cells in the presence of isosmothic medium (0.8 molar sorbitol). Kpkt induces ultrastructural modifications in the cell wall of sensitive strains, as shown by confocal microscopy, laser-scanning electron microscopy, and atomic force microscopy. The Kpkt killer action is mediated by the glucidic portion of the toxin. This, in turn, appears to be involved both in the stronger cytocidal activity and in the selectivity for the sensitive strain shown by Kpkt compared to laminarinase.

Conclusion

Collectively, these data indicate that the mode of action of Kpkt is directed towards the disruption of cell-wall integrity, and that this is mediated by a highly specific β-glucanase activity. In this, Kpkt differs from other microbial β-glucanases that do not show killer activities.

Bacteria and yeast cell disruption using lytic enzymes

Enzymatic methods provide a convenient alternative for overcoming technical disadvantages of mechanical disruption. Protocols for protein extraction from bacteria and Saccharomyces cerevisiae using lytic enzymes are presented in this chapter. Adaptation of the yeast protocol to a microtiter plate format makes this protocol amenable for proteomic applications and high-throughput screening of libraries expressing genetic variants in yeast. This methodology can also be applied to bacteria.

Enzymatic lysis of microbial cells

Cell wall lytic enzymes are valuable tools for the biotechnologist, with many applications in medicine, the food industry, and agriculture, and for recovering of intracellular products from yeast or bacteria. The diversity of potential applications has conducted to the development of lytic enzyme systems with specific characteristics, suitable for satisfying the requirements of each particular application. Since the first time the lytic enzyme of excellence, lysozyme, was discovered, many investigations have contributed to the understanding of the action mechanisms and other basic aspects of these interesting enzymes. Today, recombinant production and protein engineering have improved and expanded the area of potential applications. In this review, some of the recent advances in specific enzyme systems for bacteria and yeast cells rupture and other applications are examined. Emphasis is focused in biotechnological aspects of these enzymes.