Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing.

A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall-degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.

Degradation of polyester polyurethane by a newly isolated soil bacterium, Bacillus subtilis strain MZA-75.

A polyurethane (PU) degrading bacterial strain MZA-75 was isolated from soil through enrichment technique. The bacterium was identified through 16S rRNA gene sequencing, the phylogenetic analysis indicated the strain MZA-75 belonged to genus Bacillus having maximum similarity with Bacillus subtilis strain JBE0016. The degradation of PU films by strain MZA-75 in mineral salt medium (MSM) was analyzed by scanning electron microscopy (SEM), fourier transform infra-red spectroscopy (FT-IR) and gel permeation chromatography (GPC). SEM revealed the appearance of widespread cracks on the surface. FTIR spectrum showed decrease in ester functional group. Increase in polydispersity index was observed in GPC, which indicates chain scission as a result of microbial treatment. CO2 evolution and cell growth increased when PU was used as carbon source in MSM in Sturm test. Increase in both cell associated and extracellular esterases was observed in the presence of PU indicated by p-Nitrophenyl acetate (pNPA) hydrolysis assay. Analysis of cell free supernatant by gas chromatography-mass spectrometry (GC-MS) revealed that 1,4-butanediol and adipic acid monomers were produced. Bacillus subtilis strain MZA-75 can degrade the soft segment of polyester polyurethane, unfortunately no information about the fate of hard segment could be obtained. Growth of strain MZA-75 in the presence of these metabolites indicated mineralization of ester hydrolysis products into CO2 and H2O.

Gene expression and protein synthesis of esterase from Streptococcus mutans are affected by biodegradation by-product from methacrylate resin composites and adhesives.

An esterase from S. mutans UA159, SMU_118c, was shown to hydrolyze methacrylate resin-based dental monomers. OBJECTIVE: To investigate the association of SMU_118c to the whole cellular hydrolytic activity of S. mutans toward polymerized resin composites, and to examine how the bacterium adapts its hydrolytic activity in response to environmental stresses triggered by the presence of a resin composites and adhesives biodegradation by-product (BBP). MATERIALS AND METHODS: Biofilms of S. mutans UA159 parent wild strain, SMU_118c knockout strain (ΔSMU_118c), and SMU_118c complemented strain (ΔSMU_118cC) were incubated with photo-polymerized resin composite. High performance liquid chromatography was used to quantify the amount of a universal 2,2-Bis[4-(2-hydroxy-3-methacryloxypropoxy)phenyl]propane (bisGMA)-derived BBP, bishydroxy-propoxy-phenyl-propane (bisHPPP) in the media. Fluorescence in situ hybridization (FISH) and quantitative proteomic analysis were used to measure SMU_118c gene expression and production of SMU_118c protein, respectively, from biofilms of S. mutans UA159 wild strain that were cultured with bisHPPP. RESULTS: The levels of bisHPPP released from composite were similar for ΔSMU_118c and media control, and these were significantly lower compared to the parent wild-strain UA159 and complemented strain (ΔSMU_118cC) (p < 0.05). Gene expression of SMU_118c and productions of SMU_118c protein were higher for bisHPPP incubated biofilms (p < 0.05). SIGNIFICANCE: This study suggests that SMU_118c is a dominant esterase in S. mutans and capable of catalyzing the hydrolysis of the resinous matrix of polymerized composites and adhesives. In turn, the bacterial response to BBP was to increase the expression of the esterase gene and enhance esterase production, potentially accelerating the biodegradation of the restoration, adhesive and restoration-tooth interface, ultimately contributing to premature restoration failure. STATEMENT OF SIGNIFICANCE: We recently reported (Huang et al., 2018) on the isolation and initial characterization of a specific esterase (SMU_118c) from S. mutans that show degradative activity toward the hydrolysis of dental monomers. The current study further characterize this enzyme and shows that SMU_118c is a dominant degradative esterase activity in the cariogenic bacterium S. mutans and is capable of catalyzing the hydrolysis of the resinous matrix of polymerized composites and adhesives. In turn, the bacterial response to biodegradation by-products from composites and adhesives was to increase the expression of the esterase gene and enhance esterase production, accelerating the biodegradation of the restoration, adhesive and the restoration-tooth interface, potentially contributing to the pathogenesis of recurrent caries around resin composite restorations.

In vitro measurement of antigen-specific cell-mediated immune responses using recombinant HIV-1 proteins adsorbed to latex microspheres.

Recombinant proteins representing full-length and truncated forms of the human immunodeficiency virus type 1 envelope protein gp160 were produced in E. coli and sf9 insect cells. These proteins were denatured and reduced as a function of purification. We adsorbed these proteins onto latex microspheres and used the protein-coated particles as a vehicle to present the antigen in vitro to splenic mononuclear cells from immune mice. Recombinant proteins presented on the latex particles induced antigen-specific proliferative responses that were dependent on the antigen concentration. The proliferative responses were similar to those produced against an identical protein used in soluble form and equivalent protein concentrations. Latex microspheres coated with recombinant proteins could also induce precursor cytotoxic T lymphocytes to mature to functional effector cells in vitro. The use of the latex microspheres to present recombinant proteins as antigens allowed for the use of denatured proteins in our assay that were not soluble in aqueous solutions, such as cell culture media. This system of delivering recombinant proteins in vitro should greatly facilitate the use of recombinant proteins in assays involving live cells.

The Tween 80 reaction does not correlate to triglyceride lipase production of Staphylococcus aureus.

This comparison of Tween 80 reaction with triglyceride lipase production comprises 357 Staphylococcus aureus strains from various clinical sources. Tween 80 is a water-soluble substrate, and thus estimates esterase activity. Lipase production was assayed using water-insoluble substrates (radiolabelled triglyceride emulsions). Only a minor proportion of Tween 80-positive strains had significant triglyceride lipase production (greater than 5 mU/10(9) bacteria). The discrepancy between the two methods was most pronounced in subgroups of samples with low frequency of lipase production, e.g. from isolates from superficial locations such as nasal mucosa and impetigo. Owing to its low specificity, the Tween 80 reaction therefore seems unsuitable as a marker for lipase activity in clinical isolates of Staphylococcus aureus.

Production of hydrolytic enzymes by oral isolates of Eikenella corrodens.

Eikenella corrodens isolates from periodontally healthy subjects and adult periodontitis patients were compared for their ability to produce a range of potential virulence factors. All were positive for proline aminopeptidase, thiol-dependent haemolysin and esterase activities. Low or negative activities were found against casein, phospholipid, lipid, collagen, aminophosphate, phosphate under acid or alkaline conditions, and eleven other amino acid substrates tested. In oral infections, the haemolytic activity of E. corrodens could be amplified in the reduced environment of the periodontal pocket and damage host cells. Proline aminopeptidase may act against proline residues in collagen, immunoglobulins and complement proteins.

The identification and partial characterisation of a novel inducible extracellular thermostable esterase from the archaeon Sulfolobus shibatae.

Extracellular esterases have so far only been reported in eubacteria, here we report the first identification and partial characterisation of a novel inducible extracellular esterase from the thermoacidophilic archaeon Sulfolobus shibatae. This esterase exhibits remarkable stability to both acid and heat. Esterase activity is induced by growth on a range of polyoxyethylenesorbitan (Tween) compounds as sole carbon source. Activity occurs over a wide temperature (25-99 degrees C) and pH (pH4.0-9.0) range and is optimal at 90 degrees C and pH6.0. It exhibits high thermal stability, with a half-life of 20 min at 120 degrees C, and shows a transient thermal activation of 60% at 90 degrees C. The thermal inactivation of function occurs by first order kinetics, and after 120 min incubation at 120 degrees C 50% of activity still remains. It is able to hydrolyse mono- and diglycerides, but is unable to hydrolyse the triglycerides olive oil and triolein, which is indicative of an esterase and not a lipase.

Aerobic biological treatment of synthetic municipal wastewater in membrane-coupled bioreactors.

Membrane-coupled bioreactors (MBRs) offer many benefits compared to conventional biological wastewater treatment systems; however, their performance characteristics are poorly understood. Laboratory-scale MBRs were used to study bacterial adaptations in physiology and community structure. MBRs were fed a mixture of starch, gelatin, and polyoxyethylene-sorbitan monooleate to simulate the polysaccharide, protein, and lipid components of municipal wastewater. Physiological adaptations were detected by measuring ectoenzyme activity while structural dynamics were studied by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments. As cell biomass accumulated in the MBRs, pollutant removal efficiency initially improved and then stabilized with respect to effluent concentrations of chemical oxygen demand, protein, and carbohydrate. Comparison of the MBR effluent to filtered reactor fluid indicated that a portion of the observed pollutant removal was due to filtration by the membrane rather than microbial activity. The rates of ectoenzyme-mediated polysaccharide (alpha-glucosidase) and protein (leucine aminopeptidase) hydrolysis became relatively constant once pollutant removal efficiency stabilized. However, the maximum rate of lipid hydrolysis (heptanoate esterase) concomitantly increased more than 10-fold. Similarly, alpha-glucosidase and leucine aminopeptidase ectoenzyme affinities were relatively constant, while the heptanoate esterase affinity increased more than 30-fold. Community analysis revealed that a substantial community shift occurred within the first 7 days of operation. A Flavobacterium-like bacterial population dominated the community (>50% of total band intensity) and continued to do so for the remainder of the experiment.

Changes in macrophage function and morphology due to biomedical polyurethane surfaces undergoing biodegradation.

Monocytes are recruited to the material surface of an implanted biomedical device recognizing it as a foreign body. Differentiation into macrophages subsequently occurs followed by fusion to form foreign body giant cells (FBGCs). Consequently, implants can become degraded, cause chronic inflammation or become isolated by fibrous encapsulation. In this study, a relationship between material surface chemistry and the FBGC response was demonstrated by seeding mature monocyte-derived macrophages (MDMs) on polycarbonate-based polyurethanes that differed in their chemical structures (synthesized with poly(1,6-hexyl 1,2-ethyl carbonate) diol, and either (14)C-hexane diisocyanate and butanediol (BD) (referred to as HDI) or 4,4'-methylene bisphenyl diisocyanate and (14)C-BD (referred to as MDI)) and material degradation assessed. At 48 h of cell-material interaction, the FBGC attached to HDI were more multinucleated (73%) compared to MDI or the polystyrene (PS) control (21 and 36%, respectively). There was a fivefold increase in the synthesis and secretion of a protein with an approximate molecular weight of 48 kDa and a pI of 6.1 (determined by two-dimensional gel electrophoresis) only from cells seeded on HDI. Immunoprecipitation confirmed that MSE and CE were synthesized and secreted de novo. Immunoblotting also showed an increase in secreted monocyte-specific esterase (MSE) and cholesterol esterase (CE) from cells seeded on HDI relative to PS and MDI. Significantly more radiolabel ((14)C) release and esterase activity were elicited by MDMs on HDI than MDI (P < 0.05). The material that was more degradable (HDI), elicited greater protein synthesis and esterase secretion as well as more multinucleated MDMs than MDI, suggesting that the material surface chemistry modulates the function of MDM at the site of an inflammatory response to an implanted device.

Lipase and esterase formation by psychrophilic and mesophilic Acinetobacter species.

Acinetobacter O16, a psychrophilic species, produced extracellular lipase (measured by hydrolysis of olive oil, tributyrin, or beta-naphthyl laurate) when grown on a complex medium (peptone plus yeast extract). Most lipase was produced during the logarithmic phase of growth. Very little cell-bound lipase was formed. These cells also produced an esterase (measured by the hydrolysis of beta-naphthyl acetate). At first, all esterase was cell bound; significant amounts appeared in the external medium late in growth. Breaking the cells did not increase cell-bound lipase activity. After breaking of the cells, most of the cell-bound lipase and esterase activity was solubilized, even after very high speed centrifugation. No appreciable amounts of these enzymes were released by osmotic shock. Lipase formation was greatly affected by nutrient conditions. Lowering either the yeast extract of the peptone content of the normal complex medium lowered or abolished lipase formation. Esterase activity was lowered to a lesser extent. Cells growing in synthetic amino acid plus vitamin medium or in acid-hydrolyzed casein produced substantial amounts of esterase but no cell-free or cell-bound lipase. However, if sodium taurocholate was added to these media, lipase was produced. Greatest production occurred if a mixture of di- and poly-peptides was also present. Taurocholate also stimulated lipase production in the normal complex medium. Adding Tween 80 or ethanol to the normal complex medium inhibited lipase production. Sodium acetate, oleic acid, olive oil, or Tween 20 added to synthetic media did not affect lipase production. The psychrophile grew more quickly at 30 degrees C than at 15 or 20 degrees C but produced more lipase at the lower temperatures. Esterase production was about the same at 20 and 30 degrees C. A mesophilic Acinetobacter species produced the same amount of lipase and esterase at 20 and 30 degrees C. The best production of lipase by the psychrophile occurred in standing cultures.