Comparison of the paralogous transcription factors AraR and XlnR in Aspergillus oryzae

Abstract

The paralogous transcription factors AraR and XlnR in Aspergillus regulate genes that are involved in degradation of cellulose and hemicellulose and catabolism of pentose. AraR and XlnR target the same genes for pentose catabolism but target different genes encoding enzymes for polysaccharide degradation. To uncover the relationship between these paralogous transcription factors, we examined their contribution to regulation of the PCP genes and compared their preferred recognition sequences. Both AraR and XlnR are involved in induction of all the pentose catabolic genes in A. oryzae except larA encoding l-arabinose reductase, which was regulated by AraR but not by XlnR. DNA-binding studies revealed that the recognition sequences of AraR and XlnR also differ only slightly; AraR prefers CGGDTAAW, while XlnR prefers CGGNTAAW. All the pentose catabolic genes possess at least one recognition site to which both AraR and XlnR can bind. Cooperative binding by the factors was not observed. Instead, they competed to bind to the shared sites. XlnR bound to the recognition sites mentioned above as a monomer, but bound to the sequence TTAGSCTAA on the xylanase promoters as a dimer. Consequently, AraR and XlnR have significantly similar, but not the same, DNA-binding properties. Such a slight difference in these paralogous transcription factors may lead to complex outputs in enzyme production depending on the concentrations of coexisting inducer molecules in the natural environment.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

References

  1. Akada R, Kitagawa T, Kaneko S, Toyonaga D, Ito S, Kakihara Y, Hoshida H, Morimura S, Kondo A, Kida K (2006) PCR-mediated seamless gene deletion and marker recycling in Saccharomyces cerevisiae. Yeast 23:399–405. https://doi.org/10.1002/yea.1365

    CAS  Article  PubMed  Google Scholar 

  2. Battaglia E, Hansen SF, Leendertse A, Madrid S, Mulder H, Nikolaev I, de Vries RP (2011a) Regulation of pentose utilisation by AraR, but not XlnR, differs in Aspergillus nidulans and Aspergillus niger. Appl Microbiol Biotech 91:387–397. https://doi.org/10.1007/s00253-011-3242-2

    CAS  Article  Google Scholar 

  3. Battaglia E, Visser L, Nijssen A, van Veluw GJ, Wosten HA, de Vries RP (2011b) Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in Eurotiales. Stud Mycol 69:31–38. https://doi.org/10.3114/sim.2011.69.03

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. Battaglia E, Klaubauf S, Vallet J, Ribot C, Lebrun MH, de Vries RP (2013) Xlr1 is involved in the transcriptional control of the pentose catabolic pathway, but not hemi-cellulolytic enzymes in Magnaporthe oryzae. Fungal Genet Biol 57:76–84. https://doi.org/10.1016/j.fgb.2013.06.005

    CAS  Article  PubMed  Google Scholar 

  5. Battaglia E, Zhou M, de Vries RP (2014) The transcriptional activators AraR and XlnR from Aspergillus niger regulate expression of pentose catabolic and pentose phosphate pathway genes. Res Microbiol 165:531–540. https://doi.org/10.1016/j.resmic.2014.07.013

    CAS  Article  PubMed  Google Scholar 

  6. Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP (2017) Regulators of plant biomass degradation in ascomycetous fungi. Biotechnol Biofuels 10:152. https://doi.org/10.1186/s13068-017-0841-x

    Article  PubMed  PubMed Central  Google Scholar 

  7. de Vries RP, Visser J, de Graaff LH (1999) CreA modulates the XlnR-induced expression on xylose of Aspergillus niger genes involved in xylan degradation. Res Microbiol 150:281–285. https://doi.org/10.1016/S0923-2508(99)80053-9

    Article  PubMed  Google Scholar 

  8. de Vries RP, van de Vondervoort PJ, Hendriks L, van de Belt M, Visser J (2002) Regulation of the α-glucuronidase-encoding gene (aguA) from Aspergillus niger. Mol Gen Genom 268:96–102. https://doi.org/10.1007/s00438-002-0729-7

    CAS  Article  Google Scholar 

  9. de Groot MJ, Prathumpai W, Visser J, Ruijter GJ (2005) Metabolic control analysis of Aspergillus niger l-arabinose catabolism. Biotechnol Prog 21:1610–1616. https://doi.org/10.1021/bp050189o

    CAS  Article  PubMed  Google Scholar 

  10. de Vries RP, Benoit I, Doehlemann G, Kobayashi T, Magnuson JK, Panisko EA, Baker SE, Lebrun MH (2011) Post-genomic approaches to understanding interactions between fungi and their environment. IMA Fungus 2:81–86. https://doi.org/10.5598/imafungus.2011.02.01.11

    Article  PubMed  PubMed Central  Google Scholar 

  11. de Souza WR, Maitan-Alfenas GP, de Gouvêa PF, Brown NA, Savoldi M, Battaglia E, Goldman MH, de Vries RP, Goldman GH (2013) The influence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in d-xylose, l-arabinose and steam-exploded sugarcane bagasse. Fungal Genet Biol 60:29–45. https://doi.org/10.1016/j.fgb.2013.07.007

    CAS  Article  PubMed  Google Scholar 

  12. Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, de Vries RP (2017) Expression-based clustering of CAZyme-encoding genes of Aspergillus niger. BMC Genom 18:900. https://doi.org/10.1186/s12864-017-4164-x

    Article  Google Scholar 

  13. Hasper AA, Visser J, de Graaff LH (2000) The Aspergillus niger transcriptional activator XlnR, which is involved in the degradation of the polysaccharides xylan and cellulose, also regulates d-xylose reductase gene expression. Mol Microbiol 36:193–200. https://doi.org/10.1046/j.1365-2958.2000.01843.x

    CAS  Article  PubMed  Google Scholar 

  14. Huberman LB, Liu J, Qin L, Glass NL (2016) Regulation of the lignocellulolytic response in filamentous fungi. Fung Biol Rev 30:101–111. https://doi.org/10.1016/j.fbr.2016.06.001

    Article  Google Scholar 

  15. Kaneda J, Sasaki K, Gomi K, Shintani T (2011) Heterologous expression of Aspergillus oryzae xylose reductase and xylitol dehydrogenase genes facilitated xylose utilization in the yeast Saccharomyces cerevisiae. Biosci Biotechnol Biochem 75:168–170. https://doi.org/10.1271/bbb.100639

    CAS  Article  PubMed  Google Scholar 

  16. Klaubauf S, Narang HM, Post H, Zhou M, Brunner K, Mach-Aigner AR, Mach RL, Heck AJ, Altelaar AF, de Vries RP (2014) Similar is not the same: differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi. Fungal Genet Biol 72:73–81. https://doi.org/10.1016/j.fgb.2014.07.007

    CAS  Article  PubMed  Google Scholar 

  17. Kowalczyk JE, Benoit I, de Vries RP (2014) Regulation of plant biomass utilization in Aspergillus. Adv Appl Microbiol 88:31–56. https://doi.org/10.1016/B978-0-12-800260-5.00002-4

    CAS  Article  PubMed  Google Scholar 

  18. Kowalczyk JE, Gruben BS, Battaglia E, Wiebenga A, Majoor E, de Vries RP (2015) Genetic interaction of Aspergillus nidulans galR, xlnR and araR in regulating d-galactose and l-arabinose release and catabolism gene expression. PloS One 10:e0143200. https://doi.org/10.1371/journal.pone.0143200

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Kunitake E, Kobayashi T (2017) Conservation and diversity of the regulators of cellulolytic enzyme genes in Ascomycete fungi. Curr Genet 63:951–958. https://doi.org/10.1007/s00294-017-0695-6

    CAS  Article  PubMed  Google Scholar 

  20. Kunitake E, Hagiwara D, Miyamoto K, Kanamaru K, Kimura M, Kobayashi T (2016) Regulation of genes encoding cellulolytic enzymes by Pal-PacC signaling in Aspergillus nidulans. Appl Microbiol Biotechnol 100:3621–3635. https://doi.org/10.1007/s00253-016-7409-8

    CAS  Article  PubMed  Google Scholar 

  21. Li N, Kunitake E, Aoyama M, Ogawa M, Kanamaru K, Kimura M, Koyama Y, Kobayashi T (2016) McmA-dependent and -independent regulatory systems governing expression of ClrB-regulated cellulase and hemicellulase genes in Aspergillus nidulans. Mol Microbiol 102:810–826. https://doi.org/10.1111/mmi.13493

    CAS  Article  PubMed  Google Scholar 

  22. Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193:265–275

    CAS  PubMed  Google Scholar 

  23. Marui J, Kitamoto N, Kato M, Kobayashi T, Tsukagoshi N (2002a) Transcriptional activator, AoXlnR, mediates cellulose-inductive expression of the xylanolytic and cellulolytic genes in Aspergillus oryzae. FEBS Lett 528:279–282. https://doi.org/10.1016/S0014-5793(02)03328-8

    CAS  Article  PubMed  Google Scholar 

  24. Marui J, Tanaka A, Mimura S, de Graaff LH, Visser J, Kitamoto N, Kato M, Kobayashi T, Tsukagoshi N (2002b) A transcriptional activator, AoXlnR, controls the expression of genes encoding xylanolytic enzymes in Aspergillus oryzae. Fungal Genet Biol 35:157–169. https://doi.org/10.1006/fgbi.2001.1321

    CAS  Article  PubMed  Google Scholar 

  25. Mojzita D, Penttilä M, Richard P (2010a) Identification of an l-arabinose reductase gene in Aspergillus niger and its role in l-arabinose catabolism. J Biol Chem 285:23622–23628. https://doi.org/10.1074/jbc.M110.113399

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. Mojzita D, Vuoristo K, Koivistoinen OM, Penttilä M, Richard P (2010b) The ‘true’ l-xylulose reductase of filamentous fungi identified in Aspergillus niger. FEBS Lett 584:3540–3544. https://doi.org/10.1016/j.febslet.2010.06.037

    CAS  Article  PubMed  Google Scholar 

  27. Noguchi Y, Sano M, Kanamaru K, Ko T, Takeuchi M, Kato M, Kobayashi T (2009) Genes regulated by AoXlnR, the xylanolytic and cellulolytic transcriptional regulator, in Aspergillus oryzae. Appl Microbiol Biotechnol 85:141–154. https://doi.org/10.1007/s00253-009-2236-9

    CAS  Article  PubMed  Google Scholar 

  28. Noguchi Y, Tanaka H, Kanamaru K, Kato M, Kobayashi T (2011) Xylose triggers reversible phosphorylation of XlnR, the fungal transcriptional activator of xylanolytic and cellulolytic genes in Aspergillus oryzae. Biosci Biotechnol Biochem 75:953–959. https://doi.org/10.1271/bbb.100923

    CAS  Article  PubMed  Google Scholar 

  29. Ogawa M, Tokuoka M, Jin FJ, Takahashi T, Koyama Y (2010) Genetic analysis of conidiation regulatory pathways in koji-mold Aspergillus oryzae. Fungal Genet Biol 47:10–18. https://doi.org/10.1016/j.fgb.2009.10.004

    CAS  Article  PubMed  Google Scholar 

  30. Suzuki T, Tran LH, Yogo M, Idota O, Kitamoto N, Kawai K, Takamizawa K (2005) Cloning and expression of NAD+-dependent l-arabinitol 4-dehydrogenase gene (ladA) of Aspergillus oryzae. J Biosci Bioeng 100:472–474. https://doi.org/10.1263/jbb.100.472

    CAS  Article  PubMed  Google Scholar 

  31. Takahashi T, Masuda T, Koyama Y (2006a) Enhanced gene targeting frequency in ku70 and ku80 disruption mutants of Aspergillus sojae and Aspergillus oryzae. Mol Genet Genom 275:460–470. https://doi.org/10.1007/s00438-006-0104-1

    CAS  Article  Google Scholar 

  32. Takahashi T, Masuda T, Koyama Y (2006b) Identification and analysis of Ku70 and Ku80 homologs in the koji molds Aspergillus sojae and Aspergillus oryzae. Biosci Biotechnol Biochem 70:135–143. https://doi.org/10.1271/bbb.70.135

    CAS  Article  PubMed  Google Scholar 

  33. Tani S, Kawaguchi T, Kobayashi T (2014) Complex regulation of hydrolytic enzyme genes for cellulosic biomass degradation in filamentous fungi. Appl Microbiol Biotechnol 98:4829–4837. https://doi.org/10.1007/s00253-014-5707-6

    CAS  Article  PubMed  Google Scholar 

  34. Todd RB, Andrianopoulos A (1997) Evolution of a fungal regulatory gene family: the Zn(II)2Cys6 binuclear cluster DNA binding motif. Fungal Genet Biol 21:388–405. https://doi.org/10.1006/fgbi.1997.0993

    CAS  Article  PubMed  Google Scholar 

  35. Tran LH, Kitamoto N, Kawai K, Takamizawa K, Suzuki T (2004) Cloning and expression of a NAD+-dependent xylitol dehydrogenase gene (xdhA) of Aspergillus oryzae. J Biosci Bioeng 97:419–422. https://doi.org/10.1016/S1389-1723(04)70229-7

    CAS  Article  PubMed  Google Scholar 

  36. van Peij NN, Gielkens MM, de Vries RP, Visser J, de Graaff LH (1998a) The transcriptional activator XlnR regulates both xylanolytic and endoglucanase gene expression in Aspergillus niger. Appl Environ Microbiol 64:3615–3619

    PubMed  PubMed Central  Google Scholar 

  37. van Peij NN, Visser J, de Graaff LH (1998b) Isolation and analysis of xlnR, encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger. Mol Microbiol 27:131–142. https://doi.org/10.1046/j.1365-2958.1998.00666.x

    Article  PubMed  Google Scholar 

Download references

Funding

This work was partially supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry and by the Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries, and Food Industry.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Tetsuo Kobayashi.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Communicated by M. Kupiec.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 2555 KB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ishikawa, K., Kunitake, E., Kawase, T. et al. Comparison of the paralogous transcription factors AraR and XlnR in Aspergillus oryzae. Curr Genet 64, 1245–1260 (2018). https://doi.org/10.1007/s00294-018-0837-5

Download citation

Keywords

  • Aspergillus oryzae
  • Pentose catabolism
  • AraR
  • XlnR