Bioconversion of Iminodiacetonitrile to Iminodiacetic acid with whole cells of <Emphasis Type="Italic">Lysinibacillus boronitolerans</Emphasis> MTCC 107614 (IICT-akl252)

Biotechnological potential of nitrilases are prompting significant interest in finding the novel microbes capable of hydrolyzing nitriles. In this view, we have screened about 450 bacterial strains for nitrilase production using bioconversion of iminodiacetonitrile (IDAN) to iminodiacetic acid (IDA) through hydrolysis and obtained six nitrilase-producing isolates. Among these six isolates, IICT-akl252 was promising which was identified as Lysinibacillus boronitolerans. This is the first report on L. boronitolerans for nitrilase activity. Optimization of various medium and reaction parameters for maximizing the nitrilase production using whole cells in shake flask was carried out for L. boronitolerans IICT-akl252. Sucrose (2 %) as a carbon source attained better nitrilase yield while IDAN appeared to be the preferable inducer (0.2 %). The maximum IDA formation was achieved with 100 mM IDAN and 150 mg/ml cells at 30 °C and pH 6.5. After optimization of the culture and reaction conditions, the activity of nitrilase was increased by 2.3-fold from 27.2 to 64.5 U. The enzyme was stable up to 1 h at 50 °C. The enzyme was able to hydrolyze aliphatic, aromatic and heterocyclic nitrile substrates.     

Studies on Bacteriolytic Enzymes

About 100 soil samples were subjected to screening for microorganisms which were capable of producing lytic enzyme toward Staphylococcus aureus. A strain belonging to Streptomyces was isolated and found to produce lytic enzyme(s) noninduciblly, when grown aerobically at 37°C for 25 hr in a medium containing 7.5% soybean cake extract, 2% dextrin, 0.6% K₂HPO₄, 0.02% each of MgSO₄·7H₂O and KCl, pH 7.0. The crude enzyme preparation was active at pH values of 8.5 and 5.8 toward S. aureus, B. subtilis, L. bulgaricus and Str. faecalis but was completely inert against M. lysodeikticus, indicating the enzyme(s) to be distinguished from other bacteriolytic enzymes of Streptomyces so far reported.     

Isolation of dextran‐hydrolyzing intestinal bacteria and characterization of their dextranolytic activities

The aim of this study was to isolate dextran‐hydrolyzing bacteria from the human intestines and to identify their dextranolytic enzymes. For this, dextranase‐producing microorganisms were screened from fecal samples by using blue dextran‐containing media. Colonies producing a decolorized zone were isolated and they were grouped using RAPD‐PCR. 16S rRNA gene sequencing analysis revealed the isolates were Bacteroides (B.) thetaiotaomicron, B. ovatus, B. vulgatus, B. dorei, B. xylanisolvens, B. uniformis, and Veillonella (V.) rogosae. Thin layer chromatography analysis showed that the dextranases exhibit mainly endo‐type activity and produce various oligosaccharides including isomaltose and isomaltotriose. Zymogram analysis demonstrated that enzymes localized mainly in the cell membrane fraction and the molecular weight was 50–70 kDa. When cultured in a dextran‐containing medium, all strains isolated in this study produced short‐chain fatty acids, with butyric acid as the major compound. This is the first study to report that human intestinal B. xylanisolvens, B. dorei, and V. rogosae metabolize dextran utilizing dextranolytic enzymes. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 321–327, 2015.     

Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity

The debranching enzyme Nostoc punctiforme debranching enzyme (NPDE) from the cyanobacterium Nostoc punctiforme (PCC73102) hydrolyzes the α‐1,6 glycosidic linkages of malto‐oligosaccharides. Despite its high homology to cyclodextrin/pullulan (CD/PUL)‐hydrolyzing enzymes from glycosyl hydrolase 13 family (GH‐13), NPDE exhibits a unique catalytic preference for longer malto‐oligosaccharides (>G8), performing hydrolysis without the transgylcosylation or CD‐hydrolyzing activities of other GH‐13 enzymes. To investigate the molecular basis for the property of NPDE, we determined the structure of NPDE at 2.37‐Å resolution. NPDE lacks the typical N‐terminal domain of other CD/PUL‐hydrolyzing enzymes and forms an elongated dimer in a head‐to‐head configuration. The unique orientation of residues 25–55 in NPDE yields an extended substrate binding groove from the catalytic center to the dimeric interface. The substrate binding groove with a lengthy cavity beyond the ?1 subsite exhibits a suitable architecture for binding longer malto‐oligosaccharides (>G8). These structural results may provide a molecular basis for the substrate specificity and catalytic function of this cyanobacterial enzyme, distinguishing it from the classical neopullulanases and CD/PUL‐hydrolyzing enzymes. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Evaluation of the efficacy of chemical disinfectants for disinfection of heat‐polymerised acrylic resin

doi: 10.1111/j.1741‐2358.2010.00400.x
Evaluation of the efficacy of chemical disinfectants for disinfection of heat‐polymerised acrylic resin Objective: This study evaluated the efficacy of disinfectants on the internal aspect of heat‐polymerised acrylic resin contaminated with microbial strains. Background: Dentures absorb oral fluids and become contaminated by different microorganisms. Methods: Two hundred and fifty rectangular specimens were made of heat‐polymerised acrylic resin, and then divided into five groups corresponding to the microbial strains (Staphylococcus aureus, Pseudomonas aeruginosa, Candida albicans, S. mutans and Enterococcus faecalis). After contamination, the specimens were immersed in 1 and 2% sodium hypochlorite and 2% glutaraldehyde for periods of 5, 10 and 15 min. The specimens were placed into tubes containing different broths and incubated at 35°C and then visually analysed. Turbidity in the medium indicated microbial growth. The Fisher’s exact test was used in the analysis of the results. Results: The strain E. faecalis was the most resistant to the disinfectant solutions, and among them, glutaraldehyde was more effective than 2 and 1% hypochlorite for disinfection for 5 min; in the 10‐min period there were no differences between the disinfectants. In 15 min of immersion, 1% hypochlorite and glutaraldehyde were more effective than 2% hypochlorite. Conclusions: Disinfection for 10 min with 1% hypochlorite and glutaraldehyde is effective in disinfecting the internal aspect of heat‐polymerised acrylic resin.     

Purification and properties of fluoroacetate dehalogenase from <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis> DSM 8341

The degradation of fluoroacetate by microorganisms has been established for some time, although only a handful of dehalogenases capable of hydrolyzing the stable C–F bond have been studied. Pseudomonas fluorescens DSM 8341 was originally isolated from soil and readily degrades fluoroacetate, thus it was thought that its dehalogenase might have some desirable properties. The enzyme was purified from cell-free extracts and characterised: it is a monomer of 32,500 Da, with a pH optimum of 8 and is stable between pH 4 and 10; its activity is stimulated by some metal ions (Mg²⁺, Mn²⁺ and Fe³⁺), but inhibited by others (Hg²⁺, Ag²⁺). The enzyme is specific for fluoroacetate, and the K _m for this substrate (0.68 mM) is the lowest determined for enzymes of this type that have been investigated to date.     

Solvent Effects on Circular Dichroism of Colominic Acid

To produce acrylamide from acrylonitrile by use of a new enzyme, nitrile hydratase, a number of nitrile-utilizing microorganisms were screened for the enzyme activity by an intact cell system. An isobutyronitrile-utilizing bacterium, strain B23, showed the best productivity among 186 strains tested. The strain was identified taxonomically as Pseudomonas chlor or aphis. The culture and reaction conditions for the production were studied for the strain. Under the optimum conditions, 400 grams/liter of acrylamide was produced in 7.5 hr. The yield was nearly 100% with a trace amount of acrylic acid. The cell-free extract of the strain showed strong activity of nitrile hydratase toward acrylonitrile and extremely low activity of amidase toward acrylamide.     

Purification and characterization of an exo-type β-N-acetylglucosaminidase from Pseudomonas fluorescens JK-0412

Aims: To purify and characterize an exo‐acting chitinolytic enzyme produced from a Gram‐negative bacterium Pseudomonas fluorescens JK‐0412. Methods and Results: A chitinolytic bacterial strain that showed confluent growth on a minimal medium containing powder chitin as the sole carbon source was isolated and identified based on a 16S ribosomal DNA sequence analysis and named Ps. fluorescens JK‐0412. From the culture filtrates of this strain, a chito‐oligosaccharides‐degrading enzyme was purified to apparent homogeneity with a molecular mass of 50 kDa on SDS–PAGE gels. The kinetics, optimum pH and temperature, and substrate specificity of the purified enzyme (named as NagA) were determined. Conclusions: An extracellular chitinolytic enzyme was purified from the Ps. fluorescens JK‐0412 and shown to be an exo‐type β‐N‐acetylglucosaminidase yielding GlcNAc as the final product from the natural chito‐oligosaccharides, (GlcNAc)_n, n = 2–5. Significance and Impact of the Study: As NagA is secreted extracellularly in the presence of colloidal chitin, Ps. fluorescens JK‐0412 can be recognized as a potent producer for industry‐level and cost‐effective production of chitinolytic enzyme. This enzyme appears to have potential applications as an efficient tool for the degradation of chitinous materials and industry‐level production of GlcNAc. To the best of our knowledge, this is the first report on an exo‐type chitinolytic enzyme of Pseudomonas species.     

A high-throughput screening strategy for nitrile-hydrolyzing enzymes based on ferric hydroxamate spectrophotometry

Nitrile-hydrolyzing enzymes (nitrilase or nitrile hydratase/amidase) have been widely used in the pharmaceutical industry for the production of carboxylic acids and their derivatives, and it is important to build a method for screening for nitrile-hydrolyzing enzymes. In this paper, a simple, rapid, and high-throughput screening method based on the ferric hydroxamate spectrophotometry has been proposed. To validate the accuracy of this screening strategy, the nitrilases from Rhodococcus erythropolis CGMCC 1.2362 and Alcaligenes sp. ECU0401 were used for evaluating the method. As a result, the accuracy for assaying aliphatic and aromatic carboxylic acids was as high as the HPLC-based method. Therefore, the method may be potentially used in the selection of microorganisms or engineered proteins with nitrile-hydrolyzing enzymes.     

Development of a chemically defined medium for the production of enterolysin A from Enterococcus faecalis B9510

Aim

This study aimed to develop a simplified chemically defined medium that could sustain the growth and bacteriocin (enterolysin A) production by Enterococcus faecalis B9510.

Methods and Results

The nutritional requirements of E. faecalis B9510 in a chemically defined medium were determined by single omission experiments. It was observed that eight amino acids (arginine, glycine, histidine, isoleucine, leucine, methionine, tryptophan and valine), three B vitamins (nicotinic acid, Ca‐pantothenic acid and pyridoxal) and magnesium sulphate were essential for growth. Based on this information, a Simplified Defined Medium (SDM) was formed consisting of 26 components. Comparison of SDM with M‐17 showed that growth and bacteriocin production in SDM was similar to that in M‐17. The bacteriocin from SDM was then purified by ultrafiltration. The retentate of ultrafiltration step was analysed by SDS‐PAGE and the results showed a single active band in the gel, which was excised and analysed by mass spectrometry, which indicated that the active band was enterolysin A, a cell wall degrading bacteriocin.

Conclusions

A simplified defined medium can be formulated for the growth and bacteriocin production by Enterococcus faecalis, whose efficiency is comparable with that of a complex commercial medium.

Significance and Impact of the Study

The development of such a medium can be useful for bacteriocin production and subsequent purification in a simplified manner and, therefore, helpful in the identification of novel bacteriocins.     

Studies on the production of enantioselective nitrilase in a stirred tank bioreactor by Pseudomonas putida MTCC 5110

Nitrilases constitute an important class of hydrolases, having numerous industrial applications. The present work aims to address the production of nitrile hydrolyzing enzymes from Pseudomonas putida MTCC 5110 in a 6l bioreactor. Effect of various physico-chemical conditions and process parameters like pH, temperature, aeration and agitation rates and inducer concentration was studied. Further, the enzyme activity was enhanced by adopting the inducer feeding strategy. Various biochemical engineering parameters pertaining to the cultivation of P. putida in different physico-chemical conditions were reported. Finally, segregation of growth phase from the enzyme production phase allowed significant reduction in total fermentation time.     

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms

Synthetic extreme environments like carwash effluent tanks and drains are potential sources of biotechnologically important microorganisms and molecules which have, however, remained unexplored. Using culture‐ and molecular‐based methods, a total of 17 bacterial isolates belonging to the genera Shewanella, Proteus, Paenibacillus, Enterobacter and Citrobacter, Aeromonas, Pseudomonas and Pantoea were identified. Hydrocarbon utilization and enzyme production screening assays showed that Aeromonas sp. CAC11, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 and Citrobacter sp. PCW7 were able to degrade benzanthracene, naphthalene and diesel oil, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 could produce cellulase enzyme, while Proteus sp. BPS2, Pseudomonas sp. SAS8 and Proteus sp. CAL3 could produce lipase. GC‐MS analysis of bacterial secondary metabolites resulted in identification of 107 different compounds produced by Proteus sp. BPS2, Paenibacillus sp. CAC12, Pseudomonas sp. SAS8, Proteus sp. CAL3 and Paenibacillus sp. CAC13. Most of the compounds identified by both GC‐MS and LC‐MS have previously been determined to have antibacterial, antifungal and/or anticancer properties. Further, microbial metabolites which have previously been known to be produced only by plants or microorganisms found in natural extreme environments were also identified in this study. This research has revealed the immense bioresource potential of microorganisms inhabiting synthetic extreme environments.     

Gut flora of Galleria mellonella suppressing ingested bacteria.

Streptococcus faecalis, the only bacterium occurring almost invariably at high populations in guts of Galleria mellonella larvae, suppresses bacteria ingested with food by producing bacteriocin, an antibioticlike substance having a narrow range of bactericidal activity, and by releasing a lysozymelike enzyme, especially in the presence of proteolytic enzymes. The insect intestinal fluid apparently increases the activity of S. faecalis lytic enzyme. Unlike other organisms tested, S. faecalis has shown a strong bactericidal action against various species of unrelated bacteria. Microscopical examination of the sensitive organisms used as indicators has revealed changes resembling formation of protoplasts, gradually leading to destruction of bacterial cells. The insect guts could not be infected, even when the larvae had ingested a high dose of Pseudomonas aeruginosa, Proteus mirabilis, or Bacillus thuringiensis. The mechanism by which S. faecalis could suppress the ingested bacteria is suggested.     

Genetic alteration of UDP‐rhamnose metabolism in Botrytis cinerea leads to the accumulation of UDP‐KDG that adversely affects development and pathogenicity

Botrytis cinerea is a model plant‐pathogenic fungus that causes grey mould and rot diseases in a wide range of agriculturally important crops. A previous study has identified two enzymes and corresponding genes (bcdh, bcer) that are involved in the biochemical transformation of uridine diphosphate (UDP)‐glucose, the major fungal wall nucleotide sugar precursor, to UDP‐rhamnose. We report here that deletion of bcdh, the first biosynthetic gene in the metabolic pathway, or of bcer, the second gene in the pathway, abolishes the production of rhamnose‐containing glycans in these mutant strains. Deletion of bcdh or double deletion of both bcdh and bcer has no apparent effect on fungal development or pathogenicity. Interestingly, deletion of the bcer gene alone adversely affects fungal development, giving rise to altered hyphal growth and morphology, as well as reduced sporulation, sclerotia production and virulence. Treatments with wall stressors suggest the alteration of cell wall integrity. Analysis of nucleotide sugars reveals the accumulation of the UDP‐rhamnose pathway intermediate UDP‐4‐keto‐6‐deoxy‐glucose (UDP‐KDG) in hyphae of the Δbcer strain. UDP‐KDG could not be detected in hyphae of the wild‐type strain, indicating fast conversion to UDP‐rhamnose by the BcEr enzyme. The correlation between high UDP‐KDG and modified cell wall and developmental defects raises the possibility that high levels of UDP‐KDG result in deleterious effects on cell wall composition, and hence on virulence. This is the first report demonstrating that the accumulation of a minor nucleotide sugar intermediate has such a profound and adverse effect on a fungus. The ability to identify molecules that inhibit Er (also known as NRS/ER) enzymes or mimic UDP‐KDG may lead to the development of new antifungal drugs.     

Bioprospection and selection of bacteria isolated from environments contaminated with petrochemical residues for application in bioremediation

The use of microorganisms with hydrocarbon degrading capability and biosurfactant producers have emerged as an alternative for sustainable treatment of environmental passives. In this study 45 bacteria were isolated from samples contaminated with petrochemical residues, from which 21 were obtained from Landfarming soil contaminated with oily sludge, 11 were obtained from petrochemical industry effluents and 13 were originated directly from oily sludge. The metabolization capability of different carbon sources, growth capacity and tolerance, biosurfactant production and enzymes detection were determined. A preliminary selection carried out through the analysis of capability for degrading hydrocarbons showed that 22% of the isolates were able to degrade all carbon sources employed. On the other hand, in 36% of the isolates, the degradation of the oily sludge started within 18–48 h. Those isolates were considered as the most efficient ones. Twenty isolates, identified based on partial sequencing of the 16S rRNA gene, were pre-selected. These isolates showed ability for growing in a medium containing 1% of oily sludge as the sole carbon source, tolerance in a medium containing up to 30% of oily sludge, ability for biosurfactant production, and expression of enzymes involved in degradation of aliphatic and aromatic compounds. Five bacteria, identified as Stenotrophomonas acidaminiphila BB5, Bacillus megaterium BB6, Bacillus cibi, Pseudomonas aeruginosa, and Bacillus cereus BS20 were shown to be promising for use as inoculum in bioremediation processes (bioaugmentation) of areas contaminated with petrochemical residues since they can use oily sludge as the sole carbon source and produce biosurfactants.     

A constitutive expression system for high‐throughput screening

To reduce the amount of consumables and number of pipetting steps in high‐throughput screening, a constitutive expression system was developed that comprises four different promoters of varying strength. The system was validated by the expression of different sucrose phosphorylase enzymes from Leuconostoc mesenteroides, Lactobacillus acidophilus and Bifidobacterium adolescentis in 96‐deep‐ and low‐well plates at three temperatures. Drastically improved soluble expression in mini‐cultures was observed for the enzymes from L. mesenteroides strains by reducing the promoter strength from strong to intermediate and by expressing the proteins at lower temperatures. In contrast, the enzymes from B. adolescentis and L. acidophilus were expressed most efficiently with a strong promoter. The constitutive expression of sucrose phosphorylases in low‐well plates resulted in a level of activity that is equal or even better than what was achieved by inducible expression. Therefore, our plasmid set with varying constitutive promoters will be an indispensable tool to optimize enzyme expression for high‐throughput screening.     

Use of lignocellulose biomass for endoxylanase production by Streptomyces termitum

Actinobacteria isolates from Brazilian Cerrado soil were evaluated for their ability to produce enzymes of the cellulolytic and xylanolytic complex using lignocellulose residual biomass. Preliminary semiquantitative tests, made in Petri plates containing carboxymethylcellulose and beechwood xylan, indicated 11 potential species producing enzymes, all belonging to the genus Streptomyces. The species were subsequently grown in pure substrates in submerged fermentation and analyzed for the production of enzymes endoglucanase, β-glucosidase, endoxylanase, and β-xylosidase. The best results were obtained for endoxylanase enzyme production with Streptomyces termitum(UFLA CES 93). The strain was grown on lignocellulose biomass (bagasse, straw sugarcane, and cocoa pod husk) that was used in natura or acid pretreated. The medium containing sugarcane bagasse in natura favored the production of the endoxylanase that was subsequently optimized through an experimental model. The highest enzyme production 0.387?U?mL^?1, (25.8 times higher), compared to the lowest value obtained in one of the trials, was observed when combining 2.75% sugar cane bagasse and 1.0?g?L^?1 of yeast extract to the alkaline medium (pH 9.7). This is the first study using S. termitum as a producer of endoxylanase.     

Crystallization of Membrane-bound Alcohol Dehydrogenase of Acetic Acid Bacteria

We sought optimum culture conditions for the production by Pseudomonas chlororaphis B23 of nitrile hydratase activity. Addition of ferric and ferrous ions and the use of methacrylamide as an inducer greatly enhanced nitrile hydratase formation. When P. chlororaphis B23 was cultivated for 26 hr at 25°C in a medium consisting of 1 g of sucrose, 0.5 g of methacrylamide, 0.2 g of l-cysteine, 0.2 g of l-glutamate (Na), 0.2g of l-proline, 50 mg of KH₂PO₄, 50 mg of K₂HPO₄, 50 mg of MgSO₄·7H₂0, and 1 mg of FeSO₄·7H₂0 per 100 ml of tap water with the pH controlled at pH 7.5 to 7.8, the enzyme activity in the culture broth was 900-times that previously reported.     

The opportunistic pathogen Enterococcus faecalis resists phagosome acidification and autophagy to promote intracellular survival in macrophages

While many strains of Enterococcus faecalis have been reported to be capable of surviving within macrophages for extended periods, the exact mechanisms involved are largely unknown. In this study, we found that after phagocytosis by macrophages, enterococci‐containing vacuoles resist acidification, and E. faecalis is resistant to low pH. Ultrastructural examination of the enterococci‐containing vacuole by transmission electron microscopy revealed a single membrane envelope, with no evidence of the classical double‐membraned autophagosomes. Western blot analysis further confirmed that E. faecalis could trigger inhibition of the production of LC3‐II during infection. By employing cells transfected with RFP‐LC3 plasmid and infected with GFP‐labelled E. faecalis, we also observed that E. faecalis was not delivered into autophagosomes during macrophage infection. While these observations indicated no role for autophagy in elimination of intracellular E. faecalis, enhanced production of reactive oxygen species and nitric oxide were keys to this process. Stimulation of autophagy suppressed the intracellular survival of E. faecalis in macrophages in vitro and decreased the burden of E. faecalis in vivo. In summary, the results from this study offer new insights into the interaction of E. faecalis with host cells and may provide a new approach to treatment of enterococcal infections.     

Screening of microorganisms having high fumarase activity and their immobilization with carrageenan

Summary To develop an efficient method for continuous production of L-malic acid from fumaric acid using immobilized microbial cells, screening of microorganisms having high fumarase activity was carried out and cultural conditions of selected microorganisms were investigated. As a result of screening microorganisms belonging to the genera Brevibacterium, Proteus, Pseudomonas, and Sarcina were found to produce fumarase in high levels. Among these microorganisms Brevibacterium ammoniagenes, B. flavum, Proteus vulgaris, and Pseudomonas fluorescens were further selected for their high fumarase levels in the cultivation on several media. These 4 microorganisms were entrapped into a k-carrageenan gel lattice, and the resultant immobilized B. flavum showed the highest fumarase activity and operational stability.Cultural conditions for the fumarase formation and the operational stability of fumarase activity of immobilized B. flavum are detailed. Productivity for L-malic acid using immobilized B. flavum with k-carrageenan was 2.3 fold of that using immobilized B. ammoniagenes with polyacrylamide.Presented at the Annual Meeting of the Agricultural Chemical Society of Japan, Nagoya, April 3, 1978