Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant

The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.     

Phylogenetic Relationship and Secondary Metabolite Production of Marine Fungi Producing the Cyclodepsipeptides Scopularide A and B

Strains originally affiliated to the genera Scopulariopsis and Microascus were compared regarding the scopularide production in order to investigate their ability to produce the cyclodepsipeptides and select the best suited candidate for subsequent optimisation processes. Phylogenetic calculations using available sequences of the genera Scopulariopsis and Microascus revealed that most of the sequences clustered within two closely related groups, comprising mainly Scopulariopsis/Microascus brevicaulis and Microascus sp., respectively. Interestingly, high yields of scopularide A were exhibited by three strains belonging to S./M. brevicaulis, while lower titres were observed for two strains of Microascus sp. Close phylogenetic distances within and between the two groups supported the proposed combination of both genera into one holomorph group. Short phylogenetic distances did not allow a clear affiliation at the species level on the basis of ribosomal DNA sequences, especially for Microascus sp. strains. Additionally, several sequences originating from strains assigned to Scopulariopsis exhibited a polyphyletic nature. The production pattern is in accordance with the phylogenetic position of the strains and significant production of scopularide B could only be observed for the S./M. brevicaulis strain LF580. Thus, the phylogenetic position marks the biotechnologically interesting strains and matters in optimisation strategies. In conclusion, the ability of all five strains to produce at least one of the scopularides suggests a distribution of the responsible gene cluster within the holomorph group. Setting the focus on the production of the cyclodepsipeptides, strain LF580 represents the best candidate for further strain and process optimisation.     

De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster

The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis.     

Polysaccharide-Degrading Activity in Marine and Terrestrial Strains of Mycelial Fungi

The activity of extracellular polysaccharide-degrading enzymes and glycosidases from mycelial fungi towards various carbohydrates and carbohydrate derivatives from plant and algal cell walls has been screened. Twenty-three strains of mycelial fungi isolated from the marine sediment and dung were grown by submerged cultivation on a plant-based substrate (a by-product of the grain processing industry) for previous screening for their biomass and protein productivity. Molecular identification allowed for the assignment of marine fungal strains to the following species: Sirastachys phyllophila, Ochroconis mirabilis, Pseudallescheria boydii, Pseudallescheria ellipsoidea, Beauveria felina, Scopulariopsis brevicaulis, Cladosporium sp., and Trichoderma sp. The terrestrial strains belonged to the species Thermomyces thermophilus, Thermomyces dupontii, Thermomyces lanuginosus, Fusarium avenaceum, Mycothermus thermophilum, and Thermothelomyces thermophila. Seven strains of thermophilic terrestrial fungal species T. thermophila, T. thermophilus, T. dupontii and M. thermophilus and two marine fungal strains of S. brevicaulis and Beauveria felina exhibited the highest protein yields and a wide range of polysaccharide-degrading activity when the cultures were cultivated at 22–25°C. The cellulolytic thermophilic strain M. thermophilus 55 isolated from dung demonstrated unusual specificity, most intensive increase of mycelial biomass, and high activity towards algal polysaccharides after seven days of cultivation. The specific activity of laminarinase was one order of magnitude higher than in the marine strains and amounted to 1180 U/mg, and the alginate lyase, carrageenase, polymannuronate lyase, agarase, and fucoidanase activity levels (from 208 to 500 U/mg) were also higher than in all marine strains. All active polysaccharide-degrading strains of thermophilic terrestrial and marine fungi identified in the present study are of considerable interest, as the potential of these fungi for polysaccharide degradation can be applied in the transformation of various agricultural and maricultural waste of plant origin and in the modification of carbohydrate-containing substances in structural research and biotechnology.     

Enhanced conversion of sucrose to isomaltulose by a mutant of Erwinia rhapontici

Mutagenesis of Erwinia rhapontici was performed to enhance the production of isomaltulose from sucrose. A mutant strain, BN 68089, was obtained through a screening process involving automated and miniaturized cultivation in Bioscreen C. This high-throughput, miniaturized screening system was optimized to identify the mutant strain, which had a conversion yield (90%) and productivity (194 g l^–1 h^–1). The BN 68089 mutant cells were immobilized in sodium alginate and when operated in a packed bed reactor gave a yield of 89% and a productivity of 144 g l^–1 h^–1 of at 30 °C, the optimal temperature. Immobilized BN 68089 cells exhibited 8% and 15% higher yield and productivity, respectively, than those of the wild-type strain.     

Internal and External Mycoflora of the American Dog Tick, Dermacentor variabilis (Acari: Ixodidae), and Its Ecological Implications

Scopulariopsis brevicaulis, the anamorph of Microascus brevicaulis (Microascaceae, Ascomycota), has been identified in the body contents of the tick Dermacentor variabilis. After topical application of the fungal inoculum, tick mortality was marked. This is the first account describing the internal mycoflora of D. variabilis with a novel technique used to recover potential biological control agents.     

FINE STRUCTURE OF ANNELLOPHORES. I. SCOPULARIOPSIS BREVICAULIS AND S. KONINGII

Fine-structure observations of annelloconidium production in filamentous Hyphomycetes are reported for the first time. The difference in conidium morphology between Scopulariopsis brevicaulis and S. koningii was quite distinct. In S. brevicaulis, verrucosities appeared early in conidium ontogeny and formed an integral part of the primary wall layer of mature conidia. In S. koningii, verrucosities were absent. In S. brevicaulis, annellations did not invariably result on conidiophore necks with the production of each conidium in the basipetal sequence, but alternatively could be left on subapical regions of subsequently formed conidia. In S. koningii, annellations were more distinct, and the position of a conidium-delimiting septum was variable. If a septum were formed at a position proximal to previous septa, a portion of the annellophore neck remained attached to the base f the seceding conidium. In both species, a spherical electron-dense body, perhaps analogous to septal pore plugs in vegetative hyphae, plugged the pore between conidia and conidiophores and remained embedded in the base of seceded conidia.     

Deviation from the usual relationships between the temperature,the growth rate,the fatty acid composition and the lipid microviscosity of four different fungi (Mucor mucedo,Aspergillus ochraceus,Scopulariopsis brevicaulis,Achlya bisexualis)

Acclimation at cold temperature of four fungi with different temperature optima for growth (Mucor mucedo, psychrotolerant; Aspergillus ochraceus and Scopulariopsis brevicaulis, strict mesophilic; and Achlya bisexualis, thermotolerant) has been investigated. The growth rate, the fatty acid unsaturation, and the lipid microviscosity (from DPH fluorescence anisotropy) of the WHOLE cells and of the CRUDE lipid extracts were measured. A significant deviation from the commonly followed line, i.e. a correlation between cold temperature acclimation, an increase in the fatty acid unsaturation and an increased lipid fluidity, was observed.     

Screening and Identification of Endomannanase-Producing Microfungi from Hypersaline Environments

A culture-dependent enrichment technique was used to isolate endo-1,4-β-mannanase–producing fungi from a hypersaline environment. Galactomannan was used as carbon source and resulted in isolation of strains of Scopulariopsis brevicaulis, S. candida, and Verticillium dahliae. The Scopulariopsis isolates were found to be more dominant and could be isolated from consecutive evaporation ponds, whereas Verticillium was only isolated from one pond. The Scopulariopsis strains exhibited only endomannanase activity, whereas Verticillium displayed broad-activity spectrum by secreting endoxylanases and cellulases in addition to endomannanases. S. candida LMK004 and LMK008 produced 7420 and 14750 nkat g⁻¹ biomass, respectively. Endomannanase production in these strains increased with an increase in NaCl concentration up to 10% (w/v), after which both growth and enzyme production was decreased. V. dahliae LMK006 grew and produced up to 5000 nkat g⁻¹ biomass endomannanase in the absence of NaCl. Increased NaCl concentration had a negative effect on this strain. S. brevicaulis LMK002 showed poor endomannanase production but a similar growth trend as the other Scopulariopsis strains. In general, the Scopulariopsis strains exhibited better halotolerance than V. dahliae and could grow in the presence of 20% NaCl on solid medium.     

Synthesis and regulation of extracellular keratinase in three fungi isolated from the grounds of a gelatin factory,Jabalpur, India

Chrysosporium queenslandicum, Graphium penicilloideus andScopulariopsis brevicaulis were grown on various supplemented basal salts media to compare keratinase induction, activity and repression. All three fungi can utilize keratin as a sole source of carbon, nitrogen and sulfur. Total keratinase activity inC. queenslandicum andS. brevicaulis, was not repressed by supplementation of keratin-containing medium with glucose, ammonium or sulfate. The production of keratinase activity was not derepressible in keratin-free media. Keratin utilization commenced before the detection of significant extracellular keratinase activity which was always associated with mycelial growth.     

Customized media based on miniaturized screening improve growth rate and cell yield of methane-oxidizing bacteria of the genus Methylomonas

The growth of twelve methanotrophic strains within the genus Methylomonas, including the type strains of Methylomonas methanica and Methylomonas koyamae, was evaluated with 40 different variations of standard diluted nitrate mineral salts medium in 96-well microtiter plates. Unique profiles of growth preference were observed for each strain, showing a strong strain dependency for optimal growth conditions, especially with regards to the preferred concentration and nature of the nitrogen source. Based on the miniaturized screening results, a customized medium was designed for each strain, allowing the improvement of the growth of several strains in a batch setup, either by a reduction of the lag phase or by faster biomass accumulation. As such, the maintenance of fastidious strains could be facilitated while the growth of fast-growing Methylomonas strains could be further improved. Methylomonas sp. R-45378 displayed a 50 % increase in cell dry weight when grown in its customized medium and showed the lowest observed nitrogen and oxygen requirement of all tested strains. We demonstrate that the presented miniaturized approach for medium optimization is a simple tool allowing the quick generation of strain-specific growth preference data that can be applied downstream of an isolation campaign. This approach can also be applied as a first step in the search for strains with biotechnological potential, to facilitate cultivation of fastidious strains or to steer future isolation campaigns.     

The production of polyhydroxyalkanoate by Bacillus licheniformis using sequential mutagenesis and optimization

The purpose of this study was to enhance the production of polyhydroxyalkanoate (PHA) by sequential mutation of Bacillus licheniformis PHAs-007, using UV and N-methyl-N′-nitro-N-nitrosoguanidine (NTG). In addition, the effect of nutrient additions and environmental conditions were optimized to increase the production of PHA. Bacillus licheniformis PHAs-007 produced high amounts of PHA (64.09 ～ 68.80% of DCW) under both synthetic and renewable substrates. After mutagenesis treatment, mutant M2-12 was selected from 380 strains, based on its high biomass and PHA concentration. The mutant M2-12 gave the highest value of specific growth rate (0.09/h), biomass (22.24 g/L) and PHA content (19.55 g/L) under optimal conditions, consisting of 3% palm oil mill effluent, with no additional trace elements, at 45oC and pH 7. The mutant strain showed higher resistance to substrate concentrations, as well as pH and temperature, than the wild type. The accumulation of PHA was increased by 3.18-fold compared to the wild type, and the production of PHA by the mutant M2-12 was constantly retained over 12 times of cultivation. The mutation and optimization strategy appear to be suitable for producing high density PHA, reducing the medium cost and consequently lowering the production cost. Interestingly, the mutant strain could synthesize the novel PHA copolymers such as 3-hydroxyvalerate and 3-hydroxyhexanoate, which were not produced by the wild type.     

Enhanced production of l‐lactic acid by Lactobacillus thermophilus SRZ50 mutant generated by high‐linear energy transfer heavy ion mutagenesis

The aim of this study was to improve l ‐lactic acid production of Lactobacillus thermophilus SRZ50. For this purpose, high efficient heavy‐ion mutagenesis technique was performed using SRZ50 as the original strain. To enhance the screening efficiency for high yield l ‐lactic acid producers, a scale‐down from shake flask to microtiter plate was developed. The results showed that 24‐well U‐bottom MTPs could well alternate shake flasks for L. thermophilus cultivation as a scale‐down tool due to its a very good comparability to the shake flasks. Based on this microtiter plate screening method, two high l ‐lactic acid productivity mutants, A59 and A69, were successfully screened out, which presented, respectively, 15.8 and 16.2% higher productivities than that of the original strain. Based on fed‐batch fermentation, the A69 mutant can accumulate 114.2 g/L l ‐lactic acid at 96 h. Hence, the proposed traditional microbial breeding method with efficient high‐throughput screening assay was proved to be an appropriate strategy to obtain lactic acid‐overproducing strain.     

Keratinolytic activity of purified alkaline keratinase produced by Scopulariopsis brevicaulis (Sacc.) and its amino acids profile

Sodium dodecyl sulfate–polyacrlyamide gel electrophoresis (SDS–PAGE) was used to assess the purity and molecular weight of the previously purified alkaline keratinase enzyme of Scopulariopsis brevicaulis. The enzyme was homogenous, as seen by a single band of protein, and had an apparent molecular weight of 28.5 kDa. Amino acid profile of the purified keratinase revealed that it was composed of 14 different amino acids with high proportions of glutamic acid (20.86%), alanine (14.52%), glycine (14.21%), leucine (8.59%) and serine (7.81%). The enzyme contained moderate amounts of valine (6.01%), threonine (5.58%) and phenyl alanine (5.22%). The purified enzyme of S. brevicaulis exerted a potent keratinolytic activity and was capable to hydrolyze different keratinaceous materials with highest activity on chicken feathers followed by human nails and human hair.     

A new Penicillium echinulatum strain with faster cellulase secretion obtained using hydrogen peroxide mutagenesis and screening with 2-deoxyglucose

Aims: The aim of this study is to improve cellulase production and secretion by Penicillium echinulatum using mutagenesis and selection in association with microfermentation and microanalysis methods. Methods and Results: A new genetic variant was isolated from strain 9A02S1 and named S1M29. It was obtained by mutagenesis with H₂O₂ and two screening steps, which involved selection in Petri dishes using the medium supplemented with 2‐deoxyglucose and microfermentations in submerged culture. The mutant showed higher cellulase productivity than 9A02S1 based on the Filter Paper Activity assay and endoglucanase; the peak activities for these enzymes were reached significantly faster than for the parent strain. Conclusions: The mutant obtained after mutagenesis and selection could produce and secrete cellulase faster than the parent strain. Significance and Impact of the Study: Mutagenesis followed by selection is a useful tool for rapidly generating new cellulase‐producing phenotypes in fungi. Faster production and higher titers of cellulases in mutant strains contribute to reduce the production costs for enzymatic complexes that hydrolyse lignocellulose residues and form fermented syrups, thus contributing to the economic production of bioethanol.     

Production of 1-kestose by Scopulariopsis brevicaulis

A 1-kestose-producing fungus, strain N-01, was isolated and identified as Scopulariopsis brevicaulis. The optimal conditions for 1-kestose production by strain N-01 were studied and the following conditions were established: the strain was cultivated in a 500-ml conical flask containing 25 ml of medium composed (per liter) of 150 g sucrose, 15 g yeast extract, 0.6 g urea, 1 g K₂HPO₄, and 0.3 g MgSO₄·7H₂O (pH 7.0) at 30°C for 72 h. When the strain was cultivated in a 2.5-l jar fermentor, 95 g of 1-kestose was produced with a theoretical yield of 85%. From this culture broth 1-kestose was crystallized and then recrystallized, giving purities of 98.0 and 99.8% with yields of 71.0 and 78.0%, respectively. In particular, the first crystals in the recrystallization gave over 99.9% purity. By using these crystals, the general properties of 1-kestose were determined; most of these properties coincided with the data in the literature, though the melting point range was narrower. Finally a scheme for the large-scale purification of 1-kestose is proposed.     

Species-Specific Secondary Metabolite Production in Marine Actinomycetes of the Genus Salinispora

Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.     

The Optimal Mutagen Dosage to Induce Point-Mutations in Synechocystis sp. PCC6803 and Its Application to Promote Temperature Tolerance

Random mutagenesis is a useful tool to genetically modify organisms for various purposes, such as adaptation to cultivation conditions, the induction of tolerances, or increased yield of valuable substances. This is especially attractive for systems where it is not obvious which genes require modifications. Random mutagenesis has been extensively used to modify crop plants, but even with the renewed interest in microalgae and cyanobacteria for biofuel applications, there is relatively limited current research available on the application of random mutagenesis for these organisms, especially for cyanobacteria. In the presented work we characterized the lethality and rate of non-lethal point mutations for ultraviolet radiation and methyl methanesulphonate on the model cyanobacteria Synechocystis sp. PCC6803. Based on these results an optimal dosage of 10–50 J/m² for UV and either 0.1 or 1 v% for MMS was determined. A Synechocystis wildtype culture was then mutagenized and selected for increased temperature tolerance in vivo. During the second round of mutagenesis the viability of the culture was monitored on a cell by cell level from the treatment of the cells up to the growth at an increased temperature. After four distinct rounds of treatment (two with each mutagen) the temperature tolerance of the strain was effectively raised by about 2°C. Coupled with an appropriate in vivo screening, the described methods should be applicable to induce a variety of desirable characteristics in various strains. Coupling random mutagenesis with high-throughput screening methods would additionally allow to select for important characteristics for biofuel production, which do not yield a higher fitness and can not be selected for in vivo, such as fatty acid concentration. In a combined approach with full genome sequencing random mutagenesis could be used to determine suitable target-genes for more focused methods.     

Inulinase overproduction by a mutant of the marine yeast Pichia guilliermondii using surface response methodology and inulin hydrolysis

In this study, in order to isolate inulinase overproducers from the marine yeast Pichia guilliermondii, its cells were treated by using UV light and LiCl. The mutant M-30 with enhanced inulinase production was obtained and was found to be stable after cultivation for 20 generations. Response surface methodology (RSM) was used to optimize the medium compositions and cultivation conditions for inulinase production by the mutant M-30 in liquid fermentation. Inulin, yeast extract, NaCl, temperature, pH for maximum inulinase production by the mutant M-30 were found to be 20.0 g/l, 5.0 g/l, 20.0 g/l, 28 °C and 6.5, respectively. Under the optimized conditions, 127.7 U/ml of inulinase activity was reached in the liquid culture of the mutant M-30 whereas the predicted maximum inulinase activity of 129.8 U/ml was derived from RSM regression. Under the same conditions, its parent strain only produced 48.1 U/ml of inulinase activity. This is the highest inulinase activity produced by the yeast strains reported so far. We also found that inulin could be actively converted into monosaccharides by the crude inulinase.     

The possibilities of changing the production of exocellular polysaccharides of a mutantMycobacterium strain

By second-step mutagenesis and treatment with N-methyl-N’-nitro-N-nitrosoguanidine a mutant strain ofMycobacterium sp. V-649 producing a glucan extracellular polymer and another new streptomycin-resistant mutant were prepared. This mutant strain formed more than 100% first-rate (1.0–1.2%) exocellular polysaccharide. Treatment with 1% dimethyl sulfoxide during submerged cultivation of the mutant strain did not increase the production of the extracellular polysaccharide.