Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis

  • Margarita Salazar
  • Wanwipa Vongsangnak
  • Gianni Panagiotou
  • Mikael R. Andersen
  • Jens Nielsen
Original Paper

Abstract

Glycerol is catabolized by a wide range of microorganisms including Aspergillus species. To identify the transcriptional regulation of glycerol metabolism in Aspergillus, we analyzed data from triplicate batch fermentations of three different Aspergilli (Aspergillus nidulans, Aspergillus oryzae and Aspergillus niger) with glucose and glycerol as carbon sources. Protein comparisons and cross-analysis with gene expression data of all three species resulted in the identification of 88 genes having a conserved response across the three Aspergilli. A promoter analysis of the up-regulated genes led to the identification of a conserved binding site for a putative regulator to be 5′-TGCGGGGA-3′, a binding site that is similar to the binding site for Adr1 in yeast and humans. We show that this Adr1 consensus binding sequence was over-represented on promoter regions of several genes in A. nidulans, A. oryzae and A. niger. Our transcriptome analysis indicated that genes involved in ethanol, glycerol, fatty acid, amino acids and formate utilization are putatively regulated by Adr1 in Aspergilli as in Saccharomyces cerevisiae and this transcription factor therefore is likely to be cross-species conserved among Saccharomyces and distant Ascomycetes. Transcriptome data were further used to evaluate the high osmolarity glycerol pathway. All the components of this pathway present in yeast have orthologues in the three Aspergilli studied and its gene expression response suggested that this pathway functions as in S. cerevisiae. Our study clearly demonstrates that cross-species evolutionary comparisons among filamentous fungi, using comparative genomics and transcriptomics, are a powerful tool for uncovering regulatory systems.

Keywords

Aspergillus species Glycerol metabolism Transcriptional regulation 

Supplementary material

438_2009_486_MOESM1_ESM.pdf (3.5 mb)
A. nidulans differentially expressed genes mapped to metabolic map of A. oryzae resulting from glucose versus glycerol t-test analysis (PDF 3.54 MB)
438_2009_486_MOESM2_ESM.pdf (3.5 mb)
A. oryzae differentially expressed genes mapped to metabolic map of A. oryzae resulting from glucose versus glycerol t-test analysis (PDF 3.54 MB)
438_2009_486_MOESM3_ESM.pdf (3.5 mb)
A. niger differentially expressed genes mapped to metabolic map of A. oryzae resulting from glucose versus glycerol t-test analysis (PDF 3.54 MB)
438_2009_486_MOESM4_ESM.pdf (90 kb)
Significant genes differentially expressed and mapped to the metabolic maps of A. niger and A. oryzae. Selected pathways included: central carbon metabolism, TCA cycle, C2 and C3 carbon metabolism and fatty acid metabolism. Complete metabolic maps of A. nidulans, A. oryzae and A. niger, using A. oryzae as a template are included in Supplementary Figs 1, 2 and 3, respectively. The abbreviation of metabolites is described as follows. C2 metabolism: ETH, ethanol; AC, acetate, ACAL, acetaldehyde; ACCOA, acetyl-CoA. C3 metabolism: GL, glycerol; GLYAL, D-glyceraldehyde; GLYN, glycerone; GL3P, sn-glycerol 3-phosphate; T3P2, glycerone phosphate. Pyruvate metabolism: F6P, Beta-D-fructose 6-phosphate; FDP, Beta-D-fructose 1,6-bisphosphate; T3P1, D-glyceraldehyde 3-phosphate; 13PDG, 1,3-Bisphospho-D-glycerate; 3PG, 3-Phospho-D-glycerate 2PG, 2-Phospho-D-glycerate; PEP, phosphoenolpyruvate; PYR, pyruvate; MTHGXL, methylglyoxal; RGT, glutathione; LACAL, D-lactaldehyde; LAC, D-lactate; LGT, (R)-S-lactoylglutathione; LLAC, L-lactate. TCA cycle: OA, oxaloacetate; CIT, citrate; ACO, Cis-aconitate; ICIT, isocitrate AKG, 2-oxoglutarate; SUCCOA, succinyl coenzyme A; SUCC, succinate; FUM, fumarate; MAL, (S)-malate; GABAL, 4-aminobutyraldehyde; GABA, 4-aminobutanoate; GLU, L-glutamate; SUCCSAL, succinate semialdehyde. Fatty acid catabolism: C120COA, dodecanoyl-Coenzyme A; C120CAR, dodecanoyl-carnitine; C12DCOA, dodecanoyl-dehydro-Coenzyme A; C12HCOA, dodecanoyl-Hydroxy-Coenzyme A; C12OCOA, dodecanoyl-oxo-Coenzyme A; C140COA, myristoyl-Coenzyme A; C140CAR, myristoyl-carnitine; C14DCOA, myristoyl-dehydro-Coenzyme A; C14HCOA, myristoyl-Hydroxy-Coenzyme A; C14OCOA, myristoyl-oxo-Coenzyme A; C160COA, hexadecanoyl-Coenzyme A; C160CAR, hexadecanoyl-carnitine; C16DCOA, hexadecanoyl-dehydro-Coenzyme A; C16HCOA, hexadecanoyl-Hydroxy-Coenzyme A; C160COA, hexadecanoyl-Coenzyme A; C180COA, stearoyl-Coenzyme A; C180CAR, octadecanoyl-carnitine; C18DCOA, stearoyl-dehydro-Coenzyme A; C18HCOA, stearoyl-Hydroxy-Coenzyme A; C180COA, Stearoyl-oxo-Coenzyme A. Extracellular metabolites are designated by subscript ‘e’; mitochondrial metabolites by subscript ‘m’ (PDF 90.2 KB)
438_2009_486_MOESM5_ESM.pdf (204 kb)
Supplementary Table 1. (PDF 204 KB)
438_2009_486_MOESM6_ESM.xls (50 kb)
Supplementary Table 2. (XLS 50 KB)
438_2009_486_MOESM7_ESM.xls (457 kb)
Supplementary Table 3. (XLS 457 KB)
438_2009_486_MOESM8_ESM.xls (44 kb)
Supplementary Table 4. (XLS 43.5 KB)
438_2009_486_MOESM9_ESM.pdf (25 kb)
Supplementary Table 5. (PDF 24.6 KB)
438_2009_486_MOESM10_ESM.xls (34 kb)
Supplementary Table 6. (XLS 34.0 KB)
438_2009_486_MOESM11_ESM.xls (274 kb)
Supplementary Table 7. (XLS 274 KB)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Margarita Salazar
    • 1
  • Wanwipa Vongsangnak
    • 1
  • Gianni Panagiotou
    • 2
  • Mikael R. Andersen
    • 2
  • Jens Nielsen
    • 1
  1. 1.Department of Chemical and Biological EngineeringChalmers University of TechnologyGöteborgSweden
  2. 2.Department of Systems Biology, Center for Microbial BiotechnologyTechnical University of DenmarkKongens LyngbyDenmark

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