Analysis of Aspergillus nidulans metabolism at the genome-scale

<p>Abstract</p> <p>Background</p> <p><it>Aspergillus nidulans </it>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, <it>A. nidulans </it>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 <it>Aspergillus </it>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.</p> <p>Results</p> <p>In this work, we have manually assigned functions to 472 orphan genes in the metabolism of <it>A. nidulans</it>, by using a pathway-driven approach and by employing comparative genomics tools based on sequence similarity. The central metabolism of <it>A. nidulans</it>, as well as biosynthetic pathways of relevant secondary metabolites, was reconstructed based on detailed metabolic reconstructions available for <it>A. niger </it>and <it>Saccharomyces cerevisiae</it>, and information on the genetics, biochemistry and physiology of <it>A. nidulans</it>. Thereby, it was possible to identify metabolic functions without a gene associated, and to look for candidate ORFs in the genome of <it>A. nidulans </it>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 <it>A. nidulans</it>.</p> <p>Conclusion</p> <p>We demonstrate how pathway modeling of <it>A. nidulans </it>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.</p

Taxonomic comments on the treatment of the Zygaenidae (Lepidoptera) in volume 3 of Moths of Europe, Zygaenids, Pyralids 1 and Brachodids (2012)

Critical taxonomic comments are provided on the section dealing with the Zygaenidae in volume 3 of Moths of Europe (Leraut 2012). A number of newly described nominal taxa in that work are here synonymised as are nominal subgenera and subspecies that were reinstated as valid. At the subgeneric level these are Hesychia Hübner, [1819] (syn. rev.), Coelestis Burgeff, 1926 (syn. rev.) and Santolinophaga Burgeff, 1926 (syn. rev.), all synonyms of the monophyletic subgenus Mesembrynus Hübner, [1819], and Coelestina Holik, 1953 (syn. rev.), Epizygaena Jordan, 1907 (syn. rev.) and Lictoria Burgeff, 1926 (syn. rev.), all synonyms of the paraphyletic subgenus Agrumenia Hübner, [1819]. At the subspecific level Adscita geryon parisiensis Leraut, 2012 (syn. n.) and A. geryon aeris (Verity, 1946) (syn. rev.) are synonyms of A. geryon geryon (Hübner, [1813]). Zygaena exulans altaretensis Le Charles, 1942 (syn. rev.) and Z. exulans bourgognei Le Charles, 1942 (syn. rev.) are synonyms of Z. exulans exulans (Hohenwarth, 1792). Zygaena trifolii vindilisensis Leraut, 2012 (syn. n.) is a synonym of Z. trifolii subsyracusia Verity, 1925. Zygaena carniolica besseensis Leraut, 2012 (syn. n.) and Z. carniolica rogervillensis Leraut, 2012 (syn. n.) are synonyms of Z. carniolica modesta Burgeff, 1914. Zygaena hilaris nigriventris Leraut, 2012 (syn. n.) is a synonym of Z. hilaris chrysophaea Le Charles, [1934]. Zygaena rhadamanthus boixolsis Aistleitner, 1990 (syn. n.) is a synonym of Z. rhadamanthus rhadamanthus Esper, [1789], Z. rhadamanthus cleui Dujardin, 1956 (syn. rev.) is a synonym of Z. rhadamanthus grisea Oberthür, 1909, and Z. rhadamanthus aragonia Tremewan, 1961 (stat. rev.), Z. rhadamanthus azurea Burgeff, 1914 (stat. rev.) and Z. rhadamanthus aurargentea Mazel, 1979 (stat. rev.) are reinstated as valid subspecies

CO2 exchange of a temperate fen during the conversion from moderately rewetting to flooding

Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Biogeosciences 118 (2013): 940–950, doi:10.1002/jgrg.20069.Year-round flooding provides a common land management practice to reestablish the natural carbon dioxide (CO2) sink function of drained peatlands. Here we present eddy covariance measurements of net CO2 exchange from a temperate fen during three consecutive growing seasons (May–October) that span a period of conversion from moderately rewetting to flooding. When we started our measurements in 2009, the hydrological conditions were representative for the preceding 20 years with a mean growing season water level (MWGL) of 0 cm but considerably lower water levels in summer. Flooding began in 2010 with an MWGL of 36 cm above the surface. The fen was a net CO2 sink throughout all growing seasons (2009: −333.3 ± 12.3, 2010: −294.1 ± 8.4, 2011: −352.4 ± 5.1 g C m−2), but magnitudes of canopy photosynthesis (CP) and ecosystem respiration (Reco) differed distinctively. Rates of CP and Reco were high before flooding, dropped by 46% and 61%, respectively, in 2010, but increased again during the beginning of growing season 2011 until the water level started to rise further due to strong rainfalls during June and July. We assume that flooding decreases not only the CO2 release due to inhibited Reco under anaerobic conditions but also CO2 sequestration rates are constricted due to decreased CP. We conclude that rewetting might act as a disturbance for a plant community that has adapted to drier conditions after decades of drainage. However, if the recent species are still abundant, a rise in CP and autotrophic Reco can be expected after plants have developed plastic response strategies to wetter conditions.F.K. was supported by a scholarship of the Federal State of Mecklenburg-Western Pomerania and by the German Research Foundation (DFG). The German Academic Exchange Service (DAAD) funded the collaboration with I.F.2013-12-2

Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans

BACKGROUND: Aspergillus nidulans (the asexual form of Emericella nidulans) is a model organism for aspergilli, which are an important group of filamentous fungi that encompasses human and plant pathogens as well as industrial cell factories. Aspergilli have a highly diversified metabolism and, because of their medical, agricultural and biotechnological importance, it would be valuable to have an understanding of how their metabolism is regulated. We therefore conducted a genome-wide transcription analysis of A. nidulans grown on three different carbon sources (glucose, glycerol, and ethanol) with the objective of identifying global regulatory structures. Furthermore, we reconstructed the complete metabolic network of this organism, which resulted in linking 666 genes to metabolic functions, as well as assigning metabolic roles to 472 genes that were previously uncharacterized. RESULTS: Through combination of the reconstructed metabolic network and the transcription data, we identified subnetwork structures that pointed to coordinated regulation of genes that are involved in many different parts of the metabolism. Thus, for a shift from glucose to ethanol, we identified coordinated regulation of the complete pathway for oxidation of ethanol, as well as upregulation of gluconeogenesis and downregulation of glycolysis and the pentose phosphate pathway. Furthermore, on change in carbon source from glucose to ethanol, the cells shift from using the pentose phosphate pathway as the major source of NADPH (nicotinamide adenine dinucleotide phosphatase, reduced form) for biosynthesis to use of the malic enzyme. CONCLUSION: Our analysis indicates that some of the genes are regulated by common transcription factors, making it possible to establish new putative links between known transcription factors and genes through clustering