Design and genome engineering of microbial cell factories for efficient conversion of lignocellulose to fuel.

The gradually increasing need for fossil fuels demands renewable biofuel substitutes. This has fascinated an increasing investigation to design innovative energy fuels that have comparable Physico-chemical and combustion characteristics with fossil-derived fuels. The efficient microbes for bioenergy synthesis desire the proficiency to consume a large quantity of carbon substrate, transfer various carbohydrates through efficient metabolic pathways, capability to withstand inhibitory components and other degradation compounds, and improve metabolic fluxes to synthesize target compounds. Metabolically engineered microbes could be an efficient methodology for synthesizing biofuel from cellulosic biomass by cautiously manipulating enzymes and metabolic pathways. This review offers a comprehensive perspective on the trends and advances in metabolic and genetic engineering technologies for advanced biofuel synthesis by applying various heterologous hosts. Probable technologies include enzyme engineering, heterologous expression of multiple genes, CRISPR-Cas technologies for genome editing, and cell surface display.

Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up.

The manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.

Nanobiocatalysts: Advancements and applications in enzyme technology.

Nanobiocatalysts are one of the most promising biomaterials produced by synergistically integrating advanced biotechnology and nanotechnology. These have a lot of potential to improve enzyme stability, function, efficiencyand engineering performance in bioprocessing. Functional nanostructures have been used to create nanobiocatalystsbecause of their specific physicochemical characteristics and supramolecular nature. This review covers a wide range of nanobiocatalysts including polymeric, metallic, silica and carbon nanocarriers as well as their recent developments in controlling enzyme activity. The enormous potential of nanobiocatalysts in bioprocessing in designing effective laboratory trials forapplications in various fields such as food, pharmaceuticals, biofuel, and bioremediation is also discussed extensively.

Global Sexual Fertility in the Opportunistic Pathogen Aspergillus fumigatus and Identification of New Supermater Strains.

A sexual cycle in Aspergillus fumigatus was first described in 2009 with isolates from Dublin, Ireland. However, the extent to which worldwide isolates can undergo sexual reproduction has remained unclear. In this study a global collection of 131 isolates was established with a near 1:1 ratio of mating types. All isolates were crossed to MAT1-1 or MAT1-2 Irish strains, and a subset of isolates from different continents were crossed together. Ninety seven percent of isolates were found to produce cleistothecia with at least one mating partner, showing that sexual fertility is not limited to the Irish population but is a characteristic of global A. fumigatus. However, large variation was seen in numbers of cleistothecia produced per cross, suggesting differences in the possibility for genetic exchange between strains in nature. The majority of crosses produced ascospores with >50% germination rates, but with wide variation evident. A high temperature heat shock was required to induce ascospore germination. Finally, a new set of highly fertile MAT1-1 and MAT1-2 supermater strains were identified and pyrimidine auxotrophs generated for community use. Results provide insights into the potential for the A. fumigatus sexual cycle to generate genetic variation and allow gene flow of medically important traits.

Sensitivity enhancement for mycotoxin determination by optical waveguide lightmode spectroscopy using gold nanoparticles of different size and origin.

Mycotoxins, present in a wide range of food and feed commodities, are toxic secondary metabolites produced by a number of different fungi. Certain mycotoxins do not readily degrade at high temperatures, therefore are resistant to food processing, and consequently are present in the human and animal food supply. Optical waveguide lightmode spectroscopy (OWLS) was applied for the detection of aflatoxin B1, in a competitive immunoassay format, to compare the analytical sensitivity achieved with an immunosensor design allowing signal enhancement by increasing the sensor surface through immobilization of gold nanoparticles (AuNPs) of different size and origin (obtained by chemical or biotechnological synthesis). The effects of AuNPs median size, the methods of sensitization and the biochemical parameters on immunosensor performace were examined. After optimization of the sensitized sensor surface, an immunosensing method was developed for the analysis of aflatoxin in paprika matrix and the results were compared with HPLC reference measurements.

Green synthesis of gold nanoparticles by thermophilic filamentous fungi.

Alternative methods, including green synthetic approaches for the preparation of various types of nanoparticles are important to maintain sustainable development. Extracellular or intracellular extracts of fungi are perfect candidates for the synthesis of metal nanoparticles due to the scalability and cost efficiency of fungal growth even on industrial scale. There are several methods and techniques that use fungi-originated fractions for synthesis of gold nanoparticles. However, there is less knowledge about the drawbacks and limitations of these techniques. Additionally, identification of components that play key roles in the synthesis is challenging. Here we show and compare the results of three different approaches for the synthesis of gold nanoparticles using either the extracellular fraction, the autolysate of the fungi or the intracellular fraction of 29 thermophilic fungi. We observed the formation of nanoparticles with different sizes (ranging between 6 nm and 40 nm) and size distributions (with standard deviations ranging between 30% and 70%) depending on the fungi strain and experimental conditions. We found by using ultracentrifugal filtration technique that the size of reducing agents is less than 3 kDa and the size of molecules that can efficiently stabilize nanoparticles is greater than 3 kDa.

Ultrasound-assisted extraction and characterization of hydrolytic and oxidative enzymes produced by solid state fermentation.

Ligninolytic and hydrolytic enzymes were produced with six selected fungi on flax substrate by solid state fermentation (SSF). The extracellular enzyme production of the organisms in two SSF media was evaluated by measuring the soluble protein concentration and the filter paper, endoxylanase, 1,4-ß-d-glucosidase, 1,4-ß-d-endoglucanase, polygalacturonase, lignin peroxidase, manganese peroxidase and laccase activities of the clear culture solutions produced by conventional extraction from the SSF materials. The SSF material of the best enzyme producer (Trichoderma virens TUB F-498) was further investigated to enhance the enzyme recovery by low frequency ultrasound treatment. Performance of both the original and ultrasound macerated crude enzyme mixtures was evaluated in degradation of the colored lignin-containing and waxy materials of raw linen fabric. Results proved that sonication (at 40%, 60% and 80% amplitudes, for 60min) did not result in reduction in the filter paper, lignin peroxidase and laccase activities of the crude enzyme solution, but has a significant positive effect on the efficiency of enzyme extraction from the SSF material. Depending on the parameters of sonication, the enzyme activities in the extracts obtained can be increased up to 129-413% of the original activities measured in the control extracts recovered by a common magnetic stirrer. Sonication also has an effect on both the enzymatic removal of the lignin-containing color materials and hydrophobic surface layer from the raw linen.

Novel Penicillium cellulases for total hydrolysis of lignocellulosics.

The (hemi)cellulolytic systems of two novel lignocellulolytic Penicillium strains (Penicillium pulvillorum TUB F-2220 and P. cf. simplicissimum TUB F-2378) have been studied. The cultures of the Penicillium strains were characterized by high cellulase and ß-glucosidase as well moderate xylanase activities compared to the Trichoderma reesei reference strains QM 6a and RUTC30 (volumetric or per secreted protein, respectively). Comparison of the novel Penicillium and T. reesei secreted enzyme mixtures in the hydrolysis of (ligno)cellulose substrates showed that the F-2220 enzyme mixture gave higher yields in the hydrolysis of crystalline cellulose (Avicel) and similar yields in hydrolysis of pre-treated spruce and wheat straw than enzyme mixture secreted by the T. reesei reference strain. The sensitivity of the Penicillium cellulase complexes to softwood (spruce) and grass (wheat straw) lignins was lignin and temperature dependent: inhibition of cellulose hydrolysis in the presence of wheat straw lignin was minor at 35°C while at 45°C by spruce lignin a clear inhibition was observed. The two main proteins in the F-2220 (hemi)cellulase complex were partially purified and identified by peptide sequence similarity as glycosyl hydrolases (cellobiohydrolases) of families 7 and 6. Adsorption of the GH7 enzyme PpCBH1 on cellulose and lignins was studied showing that the lignin adsorption of the enzyme is temperature and pH dependent. The ppcbh1 coding sequence was obtained using PCR cloning and the translated amino acid sequence of PpCBH1 showed up to 82% amino acid sequence identity to known Penicillium cellobiohydrolases.

The Longibrachiatum Clade of Trichoderma: a revision with new species.

The Longibrachiatum Clade of Trichoderma is revised. Eight new species are described (T. aethiopicum, T. capillare, T. flagellatum, T. gillesii, T. gracile, T. pinnatum, T. saturnisporopsis, T. solani). The twenty-one species known to belong to the Longibrachiatum Clade are included in a synoptic key. Trichoderma parareesei and T. effusum are redescribed based on new collections or additional observations. Hypocrea teleomorphs are reported for T. gillesii and T. pinnatum. Previously described species are annotated.

Effect of precultural and nutritional parameters on compactin production by solid-state fermentation.

In the present study, production of compactin by Penicillium brevicompactum WA 2315 was studied. In the first step, various precultural parameters were studied by substituting one factor at a time. Subsequently, the effect of maltodextrin DE 18 on compactin production was studied. The optimized parameters gave maximum compactin production of 850 mug/gds as compared with 678 mug/gds before optimization. Statistical study was performed to further improve the production and develop a robust model. An improved yield of 950 mug/gds was obtained using the conditions proposed by the experimental model. The present study emphasizes the importance of precultural and nutritional parameters on the production of compactin, and further confirms the usefulness of solid-state fermentation for the production of industrially important secondary metabolites. It also confirms that complex nitrogen sources such as oil cakes can be used for the production of compactin.

Enzymatic hydrolysis of steam-pretreated lignocellulosic materials with Trichoderma atroviride enzymes produced in-house.

BACKGROUND: Improvement of the process of cellulase production and development of more efficient lignocellulose-degrading enzymes are necessary in order to reduce the cost of enzymes required in the biomass-to-bioethanol process. RESULTS: Lignocellulolytic enzyme complexes were produced by the mutant Trichoderma atroviride TUB F-1663 on three different steam-pretreated lignocellulosic substrates, namely spruce, wheat straw and sugarcane bagasse. Filter paper activities of the enzymes produced on the three materials were very similar, while beta-glucosidase and hemicellulase activities were more dependent on the nature of the substrate. Hydrolysis of the enzyme preparations investigated produced similar glucose yields. However, the enzymes produced in-house proved to degrade the xylan and the xylose oligomers less efficiently than a commercial mixture of cellulase and beta-glucosidase. Furthermore, accumulation of xylose oligomers was observed when the TUB F-1663 supernatants were applied to xylan-containing substrates, probably due to the low beta-xylosidase activity of the enzymes. The efficiency of the enzymes produced in-house was enhanced by supplementation with extra commercial beta-glucosidase and beta-xylosidase. When the hydrolytic capacities of various mixtures of a commercial cellulase and a T. atroviride supernatant produced in the lab were investigated at the same enzyme loading, the glucose yield appeared to be correlated with the beta-glucosidase activity, while the xylose yield seemed to be correlated with the beta-xylosidase level in the mixtures. CONCLUSION: Enzyme supernatants produced by the mutant T. atroviride TUB F-1663 on various pretreated lignocellulosic substrates have good filter paper activity values combined with high levels of beta-glucosidase activities, leading to cellulose conversion in the enzymatic hydrolysis that is as efficient as with a commercial cellulase mixture. On the other hand, in order to achieve good xylan conversion, the supernatants produced by the mutant have to be supplemented with additional beta-xylosidase activity.

High lovastatin production by Aspergillus terreus in solid-state fermentation on polyurethane foam: an artificial inert support.

A novel solid-state fermentation (SSF) process, using high-density polyurethane foam (PUF) as an inert support, was developed for the production of lovastatin. Results indicated that forced aeration is not conducive to metabolite production since it reduces the solid medium's moisture content. The highest level of production was achieved in closed flasks (CF), in which 7.5 mg of lovastatin was generated per gram of dry culture, equivalent to 493 mug/mg dry mycelium. However, since mycelial growth is aeration-dependent, the CF cultures presented the lowest level of growth: 15.19 mg/gdc (milligrams per gram of dry culture). It was possible to increase the biomass concentration to 24.4 mg/gdc by increasing the culture medium concentration to 2.5x and the initial moisture content of the solid medium to 85%. Results also revealed that the density of the culture support is a key parameter in determining lovastatin production; high yields were only obtained on PUF at a density of 17 or 20 kg/m(3). SSF using the latter reached a lovastatin level of 19.95 mg/gdc, with specific production of 815 mug/mg dry mycelium. A comparative study showed that lovastatin production during PUF SSF was two-fold higher than that of the better-known system of bagasse SSF. Moreover, lovastatin yields on PUF were 30 times higher than those of liquid submerged fermentation (SmF; 0.57 mg/ml) and lovastatin biomass was almost 15 times more productive.

Comparative enzymatic hydrolysis of pretreated spruce by supernatants, whole fermentation broths and washed mycelia of Trichoderma reesei and Trichoderma atroviride.

Cellulase and beta-glucosidase production on steam pretreated spruce (SPS) with Trichoderma reesei Rut C30, Trichoderma atroviride TUB F-1505 and TUB F-1663 was investigated. The enzymes were compared in term of activity, temperature optima and hydrolytic capacity. The T. atroviride cellulases proved to have lower temperature optima for filter paper activity (FPA) assay (50 degrees C) and for hydrolysis of SPS (40 degrees C) than the Rut C30 enzymes (60 degrees C for FPA and 50 degrees C for hydrolysis). Due to high levels of extracellular beta-glucosidases, the T. atroviride enzyme supernatants hydrolyzed the washed SPS to glucose more efficiently than the enzymes produced by T. reesei. On the other hand, when the whole fermentation broths were used instead of the supernatants, thus the mycelium bound enzymes were also present, the hydrolytic capacity of T. reesei Rut C30 was enhanced by approximately 200%, while an improvement of only 15% was observed in case of the T. atroviride isolates.

Application of DNA bar codes for screening of industrially important fungi: the haplotype of Trichoderma harzianum sensu stricto indicates superior chitinase formation.

Selection of suitable strains for biotechnological purposes is frequently a random process supported by high-throughput methods. Using chitinase production by Hypocrea lixii/Trichoderma harzianum as a model, we tested whether fungal strains with superior enzyme formation may be diagnosed by DNA bar codes. We analyzed sequences of two phylogenetic marker loci, internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA-encoding gene cluster and the large intron of the elongation factor 1-alpha gene, tef1, from 50 isolates of H. lixii/T. harzianum, which were also tested to determine their ability to produce chitinases in solid-state fermentation (SSF). Statistically supported superior chitinase production was obtained for strains carrying one of the observed ITS1 and ITS2 and tef1 alleles corresponding to an allele of T. harzianum type strain CBS 226.95. A tef1-based DNA bar code tool, TrichoCHIT, for rapid identification of these strains was developed. The geographic origin of the strains was irrelevant for chitinase production. The improved chitinase production by strains containing this haplotype was not due to better growth on N-acetyl-beta-D-glucosamine or glucosamine. Isoenzyme electrophoresis showed that neither the isoenzyme profile of N-acetyl-beta-glucosaminidases or the endochitinases nor the intensity of staining of individual chitinase bands correlated with total chitinase in the culture filtrate. The superior chitinase producers did not exhibit similarly increased cellulase formation. Biolog Phenotype MicroArray analysis identified lack of N-acetyl-beta-D-mannosamine utilization as a specific trait of strains with the chitinase-overproducing haplotype. This observation was used to develop a plate screening assay for rapid microbiological identification of the strains. The data illustrate that desired industrial properties may be an attribute of certain populations within a species, and screening procedures should thus include a balanced mixture of all genotypes of a given species.

Fungal biosynthesis of endochitinase and chitobiase in solid state fermentation and their application for the production of N-acetyl-D-glucosamine from colloidal chitin.

The present study was directed to the production of N-acetyl-D-glucosamine using endochitinase and chitobiase from fungal cultures in solid culturing. Fifteen fungal strains were evaluated for endochitinase and chitobiase production under solid-state fermentation using agro-industrial residues, of which Penicillium aculeatum NRRL 2129 showed maximum endochitinase activity whereas Trichoderma harzianum TUBF 927 showed maximum chitobiase activity. Eleven substrates, alone and in combination with chitin, were evaluated for the enzyme production. Optimization of physico-chemical parameters such as incubation period and initial moisture content, and nutritional parameters such as chitin source, inorganic and organic nitrogen sources, were carried out. Optimization resulted in more than 3-fold increase in endochitinase production (from 3.5 to 12.53 U/g dry weight of substrate) and about 1.5-fold increase in chitobiase production (from 1.6 to 2.25 U/g dry weight of substrate). Studies on the degradation of colloidal chitin to N-acetyl-D-glucosamine showed improved efficiency when endochitinase and chitobiase were used in combination.

Rice bran as a substrate for proteolytic enzyme production

Rice bran was used as the substrate for screening nine strains of Rhizopus sp. for neutral protease production by solid-state fermentation. The best producer, Rhizopus microsporus NRRL 3671, was used for optimizing the process parameters for enzyme production. Fermentation carried out with 44.44 percent initial moisture content at a temperature of 30 C for 72 h was found to be the optimum for enzyme secretion by the fermenting organism. While most of the carbon supplements favored enzyme production, addition of casein resulted in a marginal increase in protease yield. Fermentation was then carried out under optimized conditions to obtain the crude extract of the enzyme, which was partially purified by precipitation and dialysis. A 3-fold increase in the enzyme purity was achieved in this manner. The enzyme was found to be a metalloprotease, being activated by Mn2+, with maximal activity at a temperature of 60 C and pH 7.0.

Farelo de arroz foi utilizado como substrato para seleção de nove linhagens de Rhizopus sp. com vistas a produção de protease neutra. A linhagem que apresentou maior produtividade da enzima foi Rhizopus microsporus NRRL 3671, sendo utilizada na otimização dos parâmetros do processos e produção da enzima. As condições otimizadas para produção da enzima foram 44 por cento de umidade inicial, temperatura de 30°C e 72h de fermentação.A suplementação do farelo de arroz com uma fonte de carbono favoreceu a produção da enzima, porém a adição de caseína resultou em um aumento marginal do rendimento em protease. Condições otimizadas foram utilizadas para obtenção do extrato cru da enzima que foi parcialmente purificado por precipitação e diálise. A enzima purificada teve sua atividade incrementada 3 vezes. A enzima foi classificada como metalo-protease, sendo ativada pelo Mn2+ , sendo que sua atividade máxima foi obtida a temperatura de 60°C e a pH 7.0.

Low genetic variation and no detectable population structure in aspergillus fumigatus compared to closely related Neosartorya species.

Aspergillus fumigatus is an anamorphic euascomycete mold with a ubiquitous presence worldwide. Despite intensive work to understand its success as a pathogen infecting immunosuppressed patients, the population dynamics and recent evolutionary history of A. fumigatus remain understudied. We examined patterns of genetic variation at three intergenic loci for 70 natural isolates from Europe, North America, South America, Asia, Africa, and Australia. The same loci were used to analyze within-population genetic variation for 33 isolates obtained from five geographic locations. Neither data set detected evidence of population differentiation or found any association between the genetic and geographic distances among these isolates. No evidence for genetic differentiation within the two A. fumigatus mating types was detected. The genetic diversity of A. fumigatus, contrasted with that of its close teleomorphic relatives, Neosartorya fischeri and Neosartorya spinosa, is remarkably low.

Comparison of phytase production on wheat bran and oilcakes in solid-state fermentation by Mucor racemosus.

Comparisons were made for phytase production using wheat bran (WB) and oilcakes as substrates in solid-state fermentation (SSF) by Mucor racemosus NRRL 1994. WB was also used as mixed substrate with oil cakes. Sesame oil cake (SOC) served as the best carbon source for phytase synthesis by the fungal strain as it gave the highest enzyme titres (30.6 U/gds). Groundnut oil cake (GOC) also produced a reasonably good quantity of enzyme (24.3 U/gds). Enzyme production on WB was surprisingly much less (almost 3.5 times less in comparison to SOC). Mixing WB with SOC (1:1 ratio) resulted in better phytase activity (32.2 U/gds). Optimization of various process parameters such as incubation time, initial moisture content and inoculum concentration was carried out using the single variable mode optimization technique. Under optimized conditions, the production of phytase reached 44.5 U/gds, which was almost 1.5-fold higher than the highest yield obtained with any individual substrate used in this study and was more than 4-fold higher than that obtained from WB.

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea.

One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of the rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus-specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on . TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods.

Microbial synthesis of chitinase in solid cultures and its potential as a biocontrol agent against phytopathogenic fungus Colletotrichum gloeosporioides.

Antifungal activity of chitinase can be effectively utilized in biologic pest control strategies. Because solid-state cultivation has been termed a cost-effective means for fungal growth and metabolite production, chitinase production by Trichoderma harzianum was studied using wheat bran-based solid medium containing 1% colloidal chitin. Chitinase synthesis was found to be growth associated because maximum enzyme (5.4 U/g of dry substrate) and biomass production occurred at 72 h. Substrate moisture had a critical impact on chitinase production; five grams of medium having an initial moisture content of 68.4% when incubated for 72 h increased the enzyme yield to 9.3 U/g of dry substrate. Optimization of colloidal chitin concentration showed that improvements in chitinase yield and maximum activity were attained with a 2% (w/w) concentration. Supplementation of additional nitrogen sources also influenced enzyme production, and the best yield was obtained with yeast extract. The effect of crude chitinase on hyphal morphology of the phytopathogenic fungus Colletotrichum gloeosporioides was swelling as well as lysis of hyphal wall, depending on the age of the mycelium. Studies of pH and thermal stability showed that crude culture filtrate was active over pH 4.0-6.0 and retained about 48.2% activity after 40 min of incubation at 40 degrees C.