Abstract
Hypoxia imposes a challenge upon most filamentous fungi that require oxygen for proliferation. Here, we used whole genome DNA microarrays to investigate global transcriptional changes in Aspergillus nidulans gene expression after exposure to hypoxia followed by normoxia. Aeration affected the expression of 2,864 genes (27% of the total number of genes in the fungus), of which 50% were either induced or repressed under hypoxic conditions. Up-regulated genes included those for glycolysis, ethanol production, the tricarboxylic acid (TCA) cycle, and for the γ-aminobutyrate (GABA) shunt that bypasses two steps of the TCA cycle. Ethanol and lactate production under hypoxic conditions indicated that glucose was fermented to these compounds via the glycolytic pathway. Since the GABA shunt bypasses the NADH-generating reaction of the TCA cycle catalyzed by oxoglutarate dehydrogenase, hypoxic A. nidulans cells eliminated excess NADH. Hypoxia down-regulated some genes involved in transcription initiation by RNA polymerase II, and lowered the cellular mRNA content. These functions were resumed by re-oxygenation, indicating that A. nidulans controls global transcription to adapt to a hypoxic environment. This study is the first to show that hypoxia elicits systematic transcriptional responses in A. nidulans.
Similar content being viewed by others
Abbreviations
- GABA:
-
γ-Aminobutyrate
- GDH:
-
Glutamate dehydrogenase
- OGDH:
-
2-Oxoglutarate dehydrogenase
- TCA:
-
Tricarboxylic acid
References
Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J (2008) A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci USA 105:4387–4392
Aoki H, Uda I, Tagami K, Furuya Y, Endo Y, Fujimoto K (2003) The production of a new tempeh-like fermented soybean containing a high level of gamma-aminobutyric acid by anaerobic incubation with Rhizopus. Biosci Biotechnol Biochem 67:1018–1023
Barratt RW, Johnson GB, Ogata WN (1965) Wild-type and mutant stocks of Aspergillus nidulans. Genetics 52:233–246
Bonaccorsi ED, Ferreira AJ, Chambergo FS, Ramos AS, Mantovani MC, Farah JP, Sorio CS, Gombert AK, Tonso A, El-Dorry H (2006) Transcriptional response of the obligatory aerobe Trichoderma reesei to hypoxia and transient anoxia: implications for energy production and survival in the absence of oxygen. Biochemistry 45:3912–3924
Brun I, Sentenac A, Werner M (1997) Dual role of the C34 subunit of RNA polymerase III in transcription initiation. EMBO J 16:5730–5741
Bunn HF, Poyton RO (1996) Oxygen sensing and molecular adaptation to hypoxia. Physiol Rev 76:839–885
Chun CD, Liu OW, Madhani HD (2007) A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans. PLoS Pathog 3:e22
Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, Slijper M, Heck AJ, Daran JM, de Winde JH, Westerhoff HV, Pronk JT, Bakker BM (2007) The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Natl Acad Sci USA 104:15753–15758
David PS, Poyton RO (2005) Effects of a transition from normoxia to anoxia on yeast cytochrome c oxidase and the mitochondrial respiratory chain: implications for hypoxic gene induction. Biochim Biophys Acta 1709:169–180
David H, Ozçelik IS, Hofmann G, Nielsen J (2008) Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics 9:163
Di Pierro D, Tavazzi B, Perno CF, Bartolini M, Balestra E, Caliò R, Giardina B, Lazzarino G (1997) An ion-pairing high-performance liquid chromatographic method for the direct simultaneous determination of nucleotides, deoxynucleotides, nicotinic coenzymes, oxypurines, nucleosides, and bases in perchloric acid cell extracts. Anal Biochem 231:407–412
Diano A, Peeters J, Dynesen J, Nielsen J (2009) Physiology of Aspergillus niger in oxygen-limited continuous cultures: influence of aeration, carbon source concentration and dilution rate. Biotechnol Bioeng 103:956–965
Eschenlauer JB, Kaiser MW, Gerlach VL, Brow DA (1993) Architecture of a yeast U6 RNA gene promoter. Mol Cell Biol 13:3015–3026
Flipphi M, Sun J, Robellet X, Karaffa L, Fekete E, Zeng AP, Kubiecek CP (2009) Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal Genet Biol 46:19–44
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kötter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391
Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62:465–503
Hawkins AR, Gurr SJ, Montague P, Kinghorn JR (1989) Nucleotide sequence and regulation of expression of the Aspergillus nidulans gdhA gene encoding NADP dependent glutamate dehydrogenase. Mol Gen Genet 218:105–111
Herrero J, Valencia A, Dopazo J (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17:126–136
Hynes MJ, Szewczyk E, Murray SL, Suzuki Y, Davis MA, Sealy-Lewis HM (2007) Transcriptional control of gluconeogenesis in Aspergillus nidulans. Genetics 176:139–150
James P, Whelen S, Hall BD (1991) The RET1 gene of yeast encodes the second-largest subunit of RNA polymerase III. Structural analysis of the wild-type and ret1–1 mutant alleles. J Biol Chem 266:5616–5624
Kelly JM, Drysdale MR, Sealy-Lewis HM, Jones IG, Lockington RA (1990) Alcohol dehydrogenase III in Aspergillus nidulans is anaerobically induced and post-transcriptionally regulated. Mol Gen Genet 222:323–328
Kwast KE, Lai LC, Menda N, James DT 3rd, Aref S, Burke PV (2002) Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response. J Bacteriol 184:250–265
Lehrach H, Diamond D, Wozney JM, Boedtker H (1977) RNA molecular weight determinations by gel electrophoresis under denaturing conditions, a critical reexamination. Biochemistry 16:4743–4751
Mann C, Buhler JM, Treich I, Sentenac A (1987) RPC40, a unique gene for a subunit shared between yeast RNA polymerases A and C. Cell 48:627–637
Panagiotou G, Villas-Bôas SG, Christakopoulos P, Nielsen J, Olsson L (2005a) Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J Biotechnol 115:425–434
Panagiotou G, Christakopoulos P, Olsson L (2005b) The influence of different cultivation conditions on the metabolome of Fusarium oxysporum. J Biotechnol 118:304–315
Setiadi ER, Doedt T, Cottier F, Noffz C, Ernst JF (2006) Transcriptional response of Candida albicans to hypoxia: linkage of oxygen sensing and Efg1p-regulatory networks. J Mol Biol 361:399–411
Shimizu S, Eguchi Y, Kamiike W, Waguri S, Uchiyama Y, Matsuda H, Tsujimoto Y (1996) Retardation of chemical hypoxia-induced necrotic cell death by Bcl-2 and ICE inhibitors: possible involvement of common mediators in apoptotic and necrotic signal transductions. Oncogene 12:2045–2050
Shimizu M, Fujii T, Masuo S, Fujita K, Takaya N (2009) Proteomic analysis of Aspergillus nidulans cultured under hypoxic conditions. Proteomic 9:7–19
Shimizu M, Fujii T, Masuo S, Takaya N (2010) Mechanism of de novo branched-chain amino acid synthesis as an alternative electron sink in hypoxic Aspergillus nidulans cells. Appl Environ Microbiol 76:1507–1515
Takasaki K, Shoun H, Yamaguchi M, Takeo K, Nakamura A, Hoshino T, Takaya N (2004) Fungal ammonia fermentation-A novel metabolic mechanism that couples the dissimilatory and assimilatory pathways of both nitrate and ethanol. J Biol Chem 279:12414–12420
van der Werf MJ, Pieterse B, van Luijk N, Schuren F, der Vat B, Overkamp K, Jellema RH (2006) Multivariate analysis of microarray data by principal component discriminant analysis: prioritizing relevant transcripts linked to the degradation of different carbohydrates in Pseudomonas putida S12. Microbiology 152:257–272
Zhou Z, Takaya N, Sakairi MA, Shoun H (2001) Oxygen requirement for denitrification by the fungus Fusarium oxysporum. Arch Microbiol 175:19–25
Zhou Z, Takaya N, Nakamura A, Yamaguchi M, Takeo K, Shoun H (2002) Ammonia fermentation, a novel anoxic metabolism of nitrate by fungi. J Biol Chem 277:1892–1896
Zitomer RS, Lowry CV (1992) Regulation of gene expression by oxygen in Saccharomyces cerevisiae. Microbiol Rev 56:1–11
Acknowledgments
We thank Norma Foster for critical reading of the manuscript. This study was partly supported by the Bio-oriented Technology Research Advancement Institution, and a Grant-in-Aid for Scientific Research from Ministry of Education, Science, Culture and Sports of Japan.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by J. Perez-Martin.
S. Masuo and Y. Terabayashi equally contributed to this study.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Masuo, S., Terabayashi, Y., Shimizu, M. et al. Global gene expression analysis of Aspergillus nidulans reveals metabolic shift and transcription suppression under hypoxia. Mol Genet Genomics 284, 415–424 (2010). https://doi.org/10.1007/s00438-010-0576-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00438-010-0576-x