Elucidation of primary metabolic pathways in Aspergillus species: Orphaned research in characterizing orphan genes

Briefings in Functional Genomics

Volumn 13, Issue 6, 2014, Pages 451-455

  Andersen, Mikael Rørdam ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Aspergillus; Functional genomics; Metabolic networks; Primarymetabolism

Indexed keywords

ARTICLE; ASPERGILLUS; ASPERGILLUS FUMIGATUS; ASPERGILLUS NIGER; ASPERGILLUS ORYZAE; EMERICELLA NIDULANS; ENZYME ACTIVITY; ENZYME SYNTHESIS; ESCHERICHIA COLI; FUNCTIONAL GENOMICS; FUNGAL GENE; FUNGAL GENOME; FUNGAL METABOLISM; GENE FUNCTION; GENETIC ANALYSIS; NONHUMAN; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; GENETICS; GENOMICS; MEDICAL RESEARCH; METABOLISM; PROCEDURES;

ASPERGILLUS; FUNGI;

ASPERGILLUS; BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; GENES, FUNGAL; GENOME, FUNGAL; GENOMICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL;

EID: 84918534052     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elu029     Document Type: Article

References (35)

1. Tatum EL, Beadle GW. Genetic control of biochemical reactions in neurospora: an "aminobenzoicless" mutant. ProcNatl Acad SciUSA 1942;28:234-43.
2. Beadle GW, Tatum EL. Genetic control of biochemical reactions in neurospora. Proc Natl Acad Sci USA 1941;27: 499-506.
3. Papagianni M. Advances in citric acid fermentation by Aspergillus niger: biochemical aspects, membrane transport and modeling. Biotechnol Adv 2007;5:244-63.
4. Pontecorvo G, Roper JA, Hemmons LM, et al. The genetics of Aspergillus nidulans. Adv Genet 1953;5:141-238.
5. Machida M, Asai K, Sano M, et al. Genome sequencing and analysis of Aspergillus oryzae. Nature 2005;438:1157-61.
6. Nierman WC, Pain A, Anderson MJ, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2005;438:1151-6.
7. Gibbons JG, Beauvais A, Beau R, et al. Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryot Cell 2012; 11:68-78.
8. Andersen MR, Salazar MP, Schaap PJ, et al. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res 2011;21:885-97.
9. Galagan JE, Calvo SE, Cuomo C, et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 2005;438:1105-15.
10. Arnaud MB, Cerqueira GC, Inglis DO, et al. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. NucleicAcidsRes 2012; 40:D653-9.
11. Karp PD, Keseler IM, Shearer A, et al. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 2007;35:7577-90.
12. Karaffa L, Kubicek CP. Aspergillus niger citric acid accumulation: do we understand this well working black box? ApplMicrobiol Biotechnol 2003;61:189-96.
13. Sanchez JF, Somoza AD, Keller NP, Wang CCC. Advances in Aspergillus secondary metabolite research in the post-genomic era. Nat Prod Rep 2012;29:351-71.
14. Coutinho PM, Andersen MR, Kolenova K, et al. Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet Biol 2009;46:S161-9.
15. De Souza WR, de Gouvea PF, Savoldi M, et al. Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse. Biotechnol Biofuels 2011;4:40.
16. David H, Ozçelik IS, Hofmann G, Nielsen J. Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics 2008;9:163.
17. Vongsangnak W, Olsen P, Hansen K, et al. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMCGenomics 2008;9:245.
18. Andersen MR, Nielsen ML, Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 2008;4:178.
19. Mojzita D, Herold S, Metz B, et al. L-xylo-3-hexulose reductase is the missing link in the oxidoreductive pathway for D-galactose catabolism in filamentous fungi. JBiolChem 2012;287:26010-18.
20. Mojzita D, Vuoristo K, Koivistoinen OM, et al. The "true" L-xylulose reductase of filamentous fungi identified in Aspergillus niger. FEBS Lett 2010;584:3540-4.
21. Galagan JE, Calvo SE, Cuomo C, et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 2005;438:1105-15.
22. Machida M, Asai K, Sano M, et al. Genome sequencing and analysis of Aspergillus oryzae. Nature 2005;438:1157-61.
23. Pel HJ, de Winde JH, Archer DB, et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 2007;25:221-31.
24. Blin K, Medema MH, Kazempour D, et al. antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 2013;41: W204-12.
25. Cantarel BL, Coutinho PM, Rancurel C, et al. The carbohydrate- active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 2009;37: D233-8.
26. Andersen MR, Giese M, de Vries RP, Nielsen J. Mapping the polysaccharide degradation potential of Aspergillus niger. BMCGenomics 2012;13:313.
27. Andersen MR, Nielsen JB, Klitgaard A, et al. Accurate prediction of secondary metabolite gene clusters in filamentous fungi. ProcNatl Acad SciUSA 2013;110:E99-107.
28. Stelzer M, Sun J, Kamphans T, et al. An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. Integr Biol (Camb) 2011;3:1071-86.
29. Caspi R, Altman T, Billington R, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. NucleicAcidsRes 2014;42:D459-71.
30. Thiele I, Palsson B.Ø. A protocol for generating a highquality genome-scale metabolic reconstruction. Nat Protoc 2010;5:93-121.
31. Pitkänen E, Jouhten P, Hou J, et al. Comparative genomescale reconstruction of gapless metabolic networks for present and ancestral species. PLoS Comput Biol 2014;10: e1003465.
32. Sun J, Lu X, Rinas U, Zeng AP. Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biol 2007;8:R182.
33. Dreyfuss JM, Zucker JD, Hood HM, et al. Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol 2013;9:e1003126.
34. Flipphi M, Sun J, Robellet X, et al. Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal Genet Biol 2009;46: S19-44.
35. Colabardini AC, Ries LNA, Brown NA, et al. Functional characterization of a xylose transporter in Aspergillusnidulans. Biotechnol Biofuels 2014;7:46.