Relationship between energy substrate utilization and specific growth rate in Aspergillus nidulans

Analysis of Aspergillus nidulans metabolism at the genome-scale

Background

Aspergillus nidulans is a member of a diverse group of filamentous fungi, sharing many of the properties of its close relatives with significance in the fields of medicine, agriculture and industry. Furthermore, A. nidulans has been a classical model organism for studies of development biology and gene regulation, and thus it has become one of the best-characterized filamentous fungi. It was the first Aspergillus species to have its genome sequenced, and automated gene prediction tools predicted 9,451 open reading frames (ORFs) in the genome, of which less than 10% were assigned a function.

Results

In this work, we have manually assigned functions to 472 orphan genes in the metabolism of A. nidulans, by using a pathway-driven approach and by employing comparative genomics tools based on sequence similarity. The central metabolism of A. nidulans, as well as biosynthetic pathways of relevant secondary metabolites, was reconstructed based on detailed metabolic reconstructions available for A. niger and Saccharomyces cerevisiae, and information on the genetics, biochemistry and physiology of A. nidulans. Thereby, it was possible to identify metabolic functions without a gene associated, and to look for candidate ORFs in the genome of A. nidulans by comparing its sequence to sequences of well-characterized genes in other species encoding the function of interest. A classification system, based on defined criteria, was developed for evaluating and selecting the ORFs among the candidates, in an objective and systematic manner. The functional assignments served as a basis to develop a mathematical model, linking 666 genes (both previously and newly annotated) to metabolic roles. The model was used to simulate metabolic behavior and additionally to integrate, analyze and interpret large-scale gene expression data concerning a study on glucose repression, thereby providing a means of upgrading the information content of experimental data and getting further insight into this phenomenon in A. nidulans.

Conclusion

We demonstrate how pathway modeling of A. nidulans can be used as an approach to improve the functional annotation of the genome of this organism. Furthermore we show how the metabolic model establishes functional links between genes, enabling the upgrade of the information content of transcriptome data.

Modelling the growth of filamentous fungi

Despite the considerable industrial importance of filamentous fungi there have been very few attempts to model the complex growth process of these microorganisms. With a new generation of high performance, computerized bioreactors and new analytical techniques it is possible to obtain the necessary experimental data for setting up reliable structured models describing the growth process of filamentous fungi. It is therefore interesting to review the mathematical models described previously in the literature and the experimental data on which these models are built. Only structured models are considered due to the complex metabolism of filamentous fungi and to the natural cellular structuring of the biomass, i.e. the biomass can be divided into different cell types. In order to set up good structured models it is strictly necessary to have a detailed knowledge of the mechanisms underlying the growth process. This involves both biochemical insight and understanding of the interactions between different macromolecules and cytological organelles.

Fungal morphology and metabolite production in submerged mycelial processes

The use of fungi for the production of commercial products is ancient, but it has increased rapidly over the last 50 years. Fungi are morphologically complex organisms, differing in structure at different times in their life cycle, differing in form between surface and submerged growth, differing also with the nature of the growth medium and physical environment. Many genes and physiological mechanisms are involved in the process of morphogenesis. In submerged culture, a large number of factors contribute to the development of any particular morphological form. Factors affecting morphology include the type and concentration of carbon substrate, levels of nitrogen and phosphate, trace minerals, dissolved oxygen and carbon dioxide, pH and temperature. Physical factors affecting morphology include fermenter geometry, agitation systems, rheology and the culture modes, whether batch, fed-batch or continuous. In many cases, particular morphological forms achieve maximum performance. It is a very difficult task to deduce unequivocal general relationships between process variables, product formation and fungal morphology since too many parameters influence these interrelationships and the role of many of them is still not fully understood. The use of automatic image analysis systems during the last decade proved an invaluable tool for characterizing complex mycelial morphologies, physiological states and relationships between morphology and productivity. Quantified morphological information can be used to build morphologically structured models of predictive value. The mathematical modeling of the growth and process performance has led to improved design and operation of mycelial fermentations and has improved the ability of scientists to translate laboratory observations into commercial practice. However, it is still necessary to develop improved and new experimental techniques for understanding phenomena such as the mechanisms of mycelial fragmentation and non-destructive measurement of concentration profiles in mycelial aggregates. This would allow the establishment of a process control on a physiological basis. This review is focused on the factors influencing the fungal morphology and metabolite production in submerged culture.

Antisense silencing of the creA gene in Aspergillus nidulans

Antisense expression of a portion of the gene encoding the major carbon catabolite repressor CREA in Aspergillus nidulans resulted in a substantial increase in the levels of glucose-repressible enzymes, both endogenous and heterologous, in the presence of glucose. The derepression effect was approximately one-half of that achieved in a null creA mutant. Unlike results for that mutant, however, growth parameters and colony morphology in the antisense transformants were not affected.

Phenotypic changes in the chemistry of Aspergillus nidulans: influence of culture conditions on mycelial composition

A quantitative study was made of macromolecular (nucleic acids, protein), carbohydrate and mineral (magnesium, potassium and phosphorus) components of Aspergillus nidulans in glucose limited chemostat cultures, under varying conditions of dilution rate, temperature, pH and NaCl concentration. The overall mineral content showed greatest variation in response to changes in culture salinity, which also affected the mycelial carbohydrate content. Concomitant and opposite changes in the content of cations and carbohydrates under conditions of increasing salinity may be interpreted in terms of mycelial osmoregulation. Slight variations in DNA content but gross fluctuations in the level of RNA were noted under the different cultural conditions examined. Co-ordinate changes in RNA and Mg2+ contents were evident only under certain conditions: dilution rate from 0.05--0.07 h-1 or temperature from 22--30 degrees C. The constant molar stoichiometry between RNA and Mg2+ characteristic of unicellular microorganisms was not a feature of fungal growth. The protein content was most affected by shifts of temperature and reached minimal values at 25 and 50 degrees C. The growth environment had a marked influence on the protein synthesising activity of RNA, which increased eightfold as the dilution rate was increased from 0.02--0.175 h-1, doubled within the temperature range 20--30 degrees C and fell by 50% between 40 and 50 degrees C. These observations are discussed in the context of the constant ribosomal efficiency in protein synthesis hypothesis.

[Maintenance metabolism in glucose-limited chemostat cultures of Streptomyces hygroscopicus]

Investigations with the mycelium forming bacterium Streptomyces hygroscopicus IMET JA 6599 in glucose-limited chemostat cultures gave a maintenance coefficient of m = 0.031 h-1. This low maintenance coefficient corresponds to those of moulds (RIGHELATO et al. 1968, CARTER et al. 1971). With a simple model structured in active and inactive biomass (x1 and x2) it was tried to explain the low maintenance coefficient of S. hygroscopicus in relation to nonfilamentous growing microorganisms. The model contains the transition rate k, which describes the transition of active biomass in inactive one and the decay rate beta, which considers the decay of hyphae. The model was used to study the influence of beta on the maintenance coefficient and it was shown that maintenance metabolism can be simulated by the parameter beta alone.

Evaluation of yield and maintenance coefficients, expressed in carbon units, for Pseudomonas fluorescens and P. aeruginosa

The maximum cell yield (YMc - g biomass carbon per gram substrate carbon) and the rate of maintenance metabolism (mc - g substrate carbon/g biomass carbon per hour) have been determined for substrate limited continuous cultures of Pseudomonas fluorescens and P. aeruginosa. The metabolism of the organic substrates was monitored by measuring the COD-removal1) rates at different dilution rates. The advantages of expressing yield and maintenance coefficients in carbon units is discussed.

Growth kinetics and cellulase biosynthesis in the continuous culture of Trichoderma viride

Continuous culture studies have been carried out growing Trichoderma viride QM 9123 in a 10 liter stirred fermentor on a medium containing commercial glucose as the carbon source. Experiments were carried out at 30 degrees C and at three controlled pH values of 2.5, 3.0, and 4.0 over a range of dilution rates from 0.01 to 0.11 hr-1. Steady-state values of cell, glucose, and cellulase concentration oxygen tension, and outlet gas oxygen partial pressure were recorded. Values of maximum specific growth rate, endogenous metabolism coefficient, Michaelis-Menten coefficient, yield and maintenance coefficient for glucose were derived and correlated the effect of the hydrogen ion concentration. Specific oxygen uptake rates were correlated with specific growth rates and absorption coefficients were shown to be a function of dilution rate independent of pH. Some data on cellulase biosynthesis were examined and correlated in terms of a maturation time model.

Growth, glucose metabolism and melanin formation in biotin-deficient Aspergillus nidulans

Biotin deficiency resulted in an increased growth rate of Aspergillus nidulans. The activities of hexokinase and aldolase were not much changed during the growth cycle, but activities of glucose-6-phosphate dehydrogenase and NADP-linked glutamate dehydrogenase increased significantly during the exponential phase. This change was remarkable during biotin deficiency. In contrast to the higher growth rate and respiration rate during biotin deficiency the activities of NAD(P)H oxidoreductases were low. An inverse relationship between the activity of tyrosinase and melanin content was observed. A role of the DOPA-DOPA-quinone system in maintaining culture growth is suggested.

[Aspergillus insulicola Sp. Nov]

A strain of Aspergillus sp. is described and proposed as a new species under the name "Aspergillus insulicola sp. nov." Montemayor & Santiago, 1973. This strain was isolated from soil samples taken in "Aves Island" during a scientific expedition.--Aves Island, situated at 15 degrees, 40 feet, 42 inches N and 63 degrees, 36 feet, 47 inches W, about 665 Km of the coast of Venezuela, has very special ecological conditions. Due to its smallness: 550 m long and 40 to 120 m across and to its low profile only 3 m over sea level, it is swept by the sea during the periodical storms and hurricanes in the area. It has thus a very interesting fauna and flora. We took a series of soil samples to study its mycological flora. Forty samples were inoculated by dilution method. In this first paper a species is described and proposed as a new species because of its macroscopic and microscopic characteristics, as well as by its biological properties, under the name "Aspergillus insulicola sp. nov.". In its study we have tried to follow as closely as possible the methods recommended by Kennet B. Raper & Dorothy Fenell, world authorities on the genera Aspergillus and Penicillium. The strain is being kept in USB under the number T1, and has been sent to ATCC & CBSC to be incorporated in their collections.

Growth of Bacteroides fragilis in continuous culture and in batch cultures at controlled pH

Bacteroides fragilis NCTC 9343 has been grown in continuous cultures with glucose as growth-limiting factor. At pH 7.0 and at a dilution rate of 0.07 per h, glucose limited growth in concentrations up to 0.6%. Maximal cell yield and productivity were obtained with 0.87% glucose in the inflowing medium. A pH of 7.0 was optimal for growth. With 0.6% glucose in the fresh medium and at pH 7.0, cell yield and productivity were highest at a dilution rate of 0.07 per h and 0.11 per h, respectively. At dilution rates higher than 0.07 per h, glucose was no longer growth limiting, and at dilution rates above 0.11 per h, another compound seemed to have replaced glucose also as energy source. When grown in batch cultures at pH 7.0, the best yields of B. fragilis was achieved with 0.6% glucose in the fresh medium. The highest specific growth rate (mum) determined from viable counts was 0.45, corresponding to a mean generation time of 92 min.