For the catabolism of D-glucuronate, different pathways are used by different life forms. The pathways in bacteria and animals are established, however, a fungal pathway has not been described. In this communication, we describe an enzyme that is essential for D-glucuronate catabolism in the filamentous fungus Aspergillus niger. The enzyme has an NADH dependent 2-keto-L-gulonate reductase activity forming L-idonate. The deletion of the corresponding gene, the gluC, results in a phenotype of no growth on D-glucuronate. The open reading frame of the A. niger 2-keto-L-gulonate reductase was expressed as an active protein in the yeast Saccharomyces cerevisiae. A histidine tagged protein was purified and it was demonstrated that the enzyme converts 2-keto-L-gulonate to L-idonate and, in the reverse direction, L-idonate to 2-keto-L-gulonate using the NAD(H) as cofactors. Such an L-idonate forming 2-keto-L-gulonate dehydrogenase has not been described previously. In addition, the finding indicates that the catabolic D-glucuronate pathway in A. niger differs fundamentally from the other known D-glucuronate pathways.

BackgroundPectin-rich wastes, such as citrus pulp and sugar beet pulp, are produced in considerable amounts by the juice and sugar industry and could be used as raw materials for biorefineries. One possible process in such biorefineries is the hydrolysis of these wastes and the subsequent production of ethanol. However, the ethanol-producing organism of choice, Saccharomyces cerevisiae, is not able to catabolize d-galacturonic acid, which represents a considerable amount of the sugars in the hydrolysate, namely, 18 % (w/w) from citrus pulp and 16 % (w/w) sugar beet pulp.ResultsIn the current work, we describe the construction of a strain of S. cerevisiae in which the five genes of the fungal reductive pathway for d-galacturonic acid catabolism were integrated into the yeast chromosomes: gaaA, gaaC and gaaD from Aspergillus niger and lgd1 from Trichoderma reesei, and the recently described d-galacturonic acid transporter protein, gat1, from Neurospora crassa. This strain metabolized d-galacturonic acid in a medium containing d-fructose as co-substrate.ConclusionThis work is the first demonstration of the expression of a functional heterologous pathway for d-galacturonic acid catabolism in Saccharomyces cerevisiae. It is a preliminary step for engineering a yeast strain for the fermentation of pectin-rich substrates to ethanol.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-016-0544-1) contains supplementary material, which is available to authorized users.

Current models that describe the extension of fungal hyphae and development of a mycelium either do not describe the role of vesicles in hyphal extension or do not correctly describe the experimentally observed profile for distribution of vesicles along the hypha. The present work uses the n-tanks-in-series approach to develop a model for hyphal extension that describes the intracellular transport of nutrient to a sub-apical zone where vesicles are formed and then transported to the tip, where tip extension occurs. The model was calibrated using experimental data from the literature for the extension of reproductive aerial hyphae of three different fungi, and was able to describe different profiles involving acceleration and deceleration of the extension rate. A sensitivity analysis showed that the supply of nutrient to the sub-apical vesicle-producing zone is a key factor influencing the rate of extension of the hypha. Although this model was used to describe the extension of a single reproductive aerial hypha, the use of the n-tanks-in-series approach to representing the hypha means that the model has the flexibility to be extended to describe the growth of other types of hyphae and the branching of hyphae to form a complete mycelium.

petroleum is an important energy source. Due to its intensive exploration, accidents resulting in oil spills on soil are frequent, which creates consequences to ecosystems and human health. Rhizodegradation is an efficient technique that promotes the decontamination of polluted environments through the selection and use of rhizosphere microorganisms from phytoremediation plants. the aim of this study was to isolate, identify and characterize bacteria capable of degrading petroleum from the rhizosphere of Panicum aquaticum poir., a plant that grows in petroleum contaminated soils. three bacteria were isolated and characterized at the morphological (Gram staining), molecular (16S rRNA gene sequence analysis) and biochemical level. These bacteria were identified as new strains of Bacillus thurigiensis, Bacillus pumilus and Rhodococcus hoagii, which have been reported as potential bioremediators in the literature. All three bacteria were able to use petroleum hydrocarbons as the sole carbon source during in vitro degradation assays. Gas chromatography analysis of these assays indicated reductions of petroleum hydrocarbons between 23% and 96% within 48 h. Among the isolated bacteria, Rhodococcus hoagii presented the highest efficiency of petroleum consumption, reaching 87% of degradation after only 24 h of cultivation, which corresponds to a higher and faster degradation than previously reported, confirming the potential use of Rhodococcus hoagii for petroleum biodegradation. Petroleum has a complex composition formed predominantly by aliphatic and aromatic hydrocarbons, and lower concentrations of asphaltenes, resins and metals. In turn, petroleum composition varies according to the geographical localization and physical, chemical and biological conditions of the environment where it is formed 1. Many compounds present in petroleum are toxic, mutagenic or carcinogenic 2. The effects of naphthalene in humans, for example, include skin irritation, red blood cells breakdown and nephrotoxicity 2,3. Petroleum spills into the environment result from the high volume of petroleum used as raw material for energy and chemicals production as well as the accidents during operating processes, transportation, refining, storage and consumption 4,5. In contact with the environment, petroleum undergoes changes in its original characteristics, due to the interaction between physical and biological factors 6,7. The persistence of petroleum hydrocarbons in the environment is a result of their slow biodegradation and can compromise quality of water resources and the soil and may be accumulated in food, such as vegetables, muscles and fish 2,8. Environment-friendly approaches have been proposed to remediate petroleum-contaminated environments. According to Pandey et al. 9 and Paul et al. 10 , bioremediation is widely used in environmental decontamination due to its relatively lower costs and higher efficiency when compared to chemical and physical remediation techniques. Bioremediation is based on the metabolization of pollutants through ...