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Genome-wide transcriptional changes induced by different carbon sources and carbon starvation in Aspergillus nidulans

ABSTRACT: Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose or arabinogalactan as well as under carbon starved conditions. We determined both carbon stress specific changes (a carbon stress vs. glucose) and culture specific changes (a culture vs. all other cultures). Many CAZyme genes showed carbon stress specific and/or culture specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan and xylan degrading enzyme genes were observed in these gene sets. Less, 81 and 107 carbon stress specific as well as 6 and 16 culture specific upregulated genes were found on lactose and in carbon starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed culture specific upregulation on glucose and they were enriched in beta-1,4-glucanase genes. Behavioral ecological background of these characteristics was evaluated to organize comprehensively our knowledge on CAZyme production, which can lead to develop new strategies to produce enzymes for plant cell wall saccharification.

ORGANISM(S): Aspergillus nidulans

PROVIDER: GSE189016 | GEO | 2022/01/26

REPOSITORIES: GEO

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Project description:This a model from the article: Feedback regulation in the lactose operon: a mathematical modeling study and comparison with experimental data. Yildirim N, Mackey MC Biophys. J. 2003 12719218 , Abstract: A mathematical model for the regulation of induction in the lac operon in Escherichia coli is presented. This model takes into account the dynamics of the permease facilitating the internalization of external lactose; internal lactose; beta-galactosidase, which is involved in the conversion of lactose to allolactose, glucose and galactose; the allolactose interactions with the lac repressor; and mRNA. The final model consists of five nonlinear differential delay equations with delays due to the transcription and translation process. We have paid particular attention to the estimation of the parameters in the model. We have tested our model against two sets of beta-galactosidase activity versus time data, as well as a set of data on beta-galactosidase activity during periodic phosphate feeding. In all three cases we find excellent agreement between the data and the model predictions. Analytical and numerical studies also indicate that for physiologically realistic values of the external lactose and the bacterial growth rate, a regime exists where there may be bistable steady-state behavior, and that this corresponds to a cusp bifurcation in the model dynamics. The model reproduces the time profile of beta-galactosidase activity as shown in Fig 3 of the paper. The delay functions for transcription (M) and translation (B and P) have been implemented by introducing intermediates ( I1, I2 and I3) in the reaction scheme which then give their respective products (I1-> M, I2 ->B and I3 ->P) after an appropriate length of time. The steady state values, attained upon simulation of model equations, for Allolactose (A), mRNA (M), beta-galactosidase (B), Lactose (L), and Permease (P) match with those predicted by the paper. The model was successfully tested on Jarnac, MathSBML and COPASI This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

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Genome-wide transcriptional changes induced by different carbon sources and carbon starvation in Aspergillus nidulans

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