Skip to main content
SpringerLink
Log in

Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes

  • Original Article
  • Published:
Mycorrhiza Aims and scope Submit manuscript

Abstract

Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Agerer R (2001) Exploration types of ectomycorrhizae. Mycorrhiza 11:107–114

    Article  Google Scholar 

  • Ando A, Harada A, Miura K, Tamai Y (2001) A gene encoding a hydrophobin, fvh1, is specifically expressed after the induction of fruiting in the edible mushroom Flammulina velutipes. Curr Genet 39:190–197

    Article  CAS  PubMed  Google Scholar 

  • Asgeirdottir SA, de Vries OMH, Wessels JGH (1998) Identification of three differentially expressed hydrophobins in Pleurotus ostreatus (oyster mushroom). Microbiology 144:2961–2969

    Article  Google Scholar 

  • de Groot PW, Schaap PJ, Sonnenberg ASM, Visser J, Van Griensven JLD (1996) The Agaricus bisporus hypA gene encodes a hydrophobin and specifically accumulates in peel tissue of mushroom caps during fruit body development. J Mol Biol 257:1008–1018

    Article  PubMed  Google Scholar 

  • de Vocht ML, Scholtmeijer K, van der Vegte EW, de Vries OMH, Sonveaux N, Wösten HAB, Ruysschaert JM, Hadziioannou G, Wessels JGH, Robillard GT (1998) Structural characterization of the hydrophobin SC3, as a monomer and after self-assembly at hydrophobic/hydrophilic interfaces. Biophys Journal 74:2059–2069

    Article  Google Scholar 

  • Dyer PS (2002) Hydrophobins in the lichen symbiosis. New Phytol 154(1):1–4

  • He Z, Zhang H, Gao S, Lercher MJ, Chen WH, Hu S (2016) Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res 44(W1):W236–W241. doi:10.1093/nar/gkw370

    Article  PubMed  PubMed Central  Google Scholar 

  • Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Comput Graph Stat 5(3):299–314

  • Källberg M, Margaryan G, Wang S, Ma J, Xu J (2012) RaptorX server: a resource for template-based protein structure modeling. Methods Mol Biol 1137:17–27

    Article  Google Scholar 

  • Karlsson M, Stenlid J, Olson A (2007) Two hydrophobin genes from the conifer pathogen Heterobasidion annosum are expressed in aerial hyphae. Mycologia 99:227–231

    Article  CAS  PubMed  Google Scholar 

  • Kelley L, Sternberg MJE (2009) Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc 4:363–371

    Article  CAS  PubMed  Google Scholar 

  • Kershaw MJ, Talbot NJ (1998) Hydrophobins and repellents: proteins with fundamental roles in fungal morphogenesis. Fungal Genet Biol 23(1):18–33. doi:10.1006/fgbi.1997.1022

  • Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canback B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Dore J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Hogberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm R, Perotto S, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Mycorrhizal Genomics Initiative Consortium, Tunlid A, Grigoriev IV, Hibbett DS, Martin F (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet 47:410–415

    Article  CAS  PubMed  Google Scholar 

  • Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM (2006) Proteins 64:559–574

    Article  CAS  PubMed  Google Scholar 

  • Kwan AHY, Winefield RD, Sunde M, Matthews JM, Haverkamp RG, Templeton MD, Mackay JP (2006) Structural basis for rodlet assembly in fungal hydrophobins. PNAS 103:3621–3626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lienemann M, Gandier JA, Joensuu JJ, Iwanaga A, Takatsuji Y, Haruyama T, Master E, Tenkanen M, Linder MB (2013) Structure-function relationships in hydrophobins: probing the role of charged side chains. Appl Env Microbiol 79:5533–5538

    Article  CAS  Google Scholar 

  • Linder MB, Szilvay GR, Nakari-Setälä T, Penttila ME (2005) Hydrophobins: the protein-amphiphiles of filamentous fungi. FEMS Microbiol Rev 29:877–896

    Article  CAS  PubMed  Google Scholar 

  • Lugones LG, Wosten HAB, Wessels JGH (1998) A hydrophobin (ABH3) specifically secreted by vegetatively growing hyphae of Agaricus bisporus (common white button mushroom). Microbiology 144:2345–2353

    Article  CAS  PubMed  Google Scholar 

  • Lugones LG, Wösten H a B, Birkenkamp KU, Sjollema K a, Zagers J, Wessels JGH (1999) Hydrophobins line air channels in fruiting bodies of Schizophyllum commune and Agaricus bisporus. Mycol Res 103(5):635–640. doi:10.1017/S0953756298007552

    Article  CAS  Google Scholar 

  • Macindoe I, Kwan AH, Ren Q, Morris VK, Yang W, Mackay JP, Sunde M (2012) Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS. Proc Natl Acad Sci U S A 109(14):E804–E811. doi:10.1073/pnas.1114052109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mackay JP, Matthews JM, Winefield RD, Mackay LG, Haverkamp LG, Templeton MD (2001) The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures. Structure 9:83–91

    Article  CAS  PubMed  Google Scholar 

  • Mankel A, Krause K, Kothe E (2002) Identification of a hydrophobin gene that is developmentally regulated in the ectomycorrhizal fungus Tricholoma terreum. Appl Environ Microbiol 68(3):1408–1413. doi:10.1128/AEM.68.3.1408-1413.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin F, Aerts A, Ahren D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buee M, Brokstein P, Canback B, Cohen D, Courty PE, Coutinho PM, Delaruelle C, Detter JC, Deveau A, DiFazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labbe J, Lin YC, Legue V, Le TF, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP, Peter M, Quesneville H, Rajashekar B, Reich M, Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat B, Kues U, Lucas S, Van de PY, Podila GK, Polle A, Pukkila PJ, Richardson PM, Rouze P, Sanders IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88–92

    Article  CAS  PubMed  Google Scholar 

  • Maurer-Stroh S, Debulpaep M, Kuemmerer N, Lopez de la Paz M, Martins IC, Reumers J, Morris KL, Copland A, Serpell L, Serrano L, Schymkowitz JW, Rousseau F (2010) Exploring the sequence determinants fo amyloid structure using position-specific scoring matrices. Nat Methods 7:237–242

    Article  CAS  PubMed  Google Scholar 

  • Mc Indoe I, Kwan AH, Ren Q, Morris VK, Yang W, Mackay JP, Sunde M (2012) Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS. PNAS 109:E804–E811

    Article  Google Scholar 

  • Mgbeahuruike AC, Kovalchuk A, Chen H, Ubhayasekera W, Asiegbu FO (2013) Evolutionary analysis of hydrophobin gene family in two wood-degrading basidiomycetes, Phlebia brevispora and Heterobasidion annosum s.l. BMC Evol Biol 13:240–256

    Article  PubMed  PubMed Central  Google Scholar 

  • Penas MM, Rust B, Larraya L, Rairez L, Pisabarro AG (2002) Differentially regulated, vegetative-mycelium-specific hydrophobins of the edible basidiomycete Pleurotus ostreatus. Appl Environ Microbiol 68:3891–3898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C (2009) A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol 9:51

    Article  PubMed  PubMed Central  Google Scholar 

  • Plett JM, Gibon J, Kohler A, Duffy K, Hoegger PJ, Velagapudi R, Han J, Kües U, Grigoriev IV, Martin F (2012) Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor. Fung Gen Biol 49:199–209

    Article  CAS  Google Scholar 

  • Raudaskoski M, Kothe E (2015) Novel findings on the role of signal exchange in arbuscular and ectomycorrhizal symbioses. Mycorrhiza 25(4):243–252. doi:10.1007/s00572-014-0607-2

    Article  CAS  PubMed  Google Scholar 

  • Ron EZ, Rosenberg E (2001) Natural roles of biosurfactants. Env Microbiol 3:229–236

    Article  CAS  Google Scholar 

  • Shah F, Rineau F, Canback B, Johansson T, Tunlid A (2013) The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus. New Phytol 200(3):875–887

  • Shah F, Nicolas C, Bentzer J, Ellström M, Smits M, Rineau F, Canbäck B, Carleer R, Lackner G, Braesel J, Hoffmeister D, Henrissat B, Hibbett DS, Martin F, Ahrén D, Johansson T, Persson P, Tunlid A (2016) Ectomycorrhizal fungi decompose humus-rich litter material using oxidative mechanisms adapted from saprotrophic ancestors. New Phytol 209:1705–1719

    Article  CAS  PubMed  Google Scholar 

  • Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 75:758–771

    Article  Google Scholar 

  • Stolzer M, Lai H, Xu M, Sathay D, Vernot B, Durand D (2012) Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28:409–415. doi:10.1093/bioinformatics/bts386

    Article  Google Scholar 

  • Tagu T, Nasse B, Martin F (1996) Cloning and characterization of hydrophobins-encoding cDNAs from the ectomycorrhizal Basidiomycete Pisolithus tinctorius. Gene 168:93–97

    Article  CAS  PubMed  Google Scholar 

  • Tagu D, Kottke I, Martin FM (1998) Hydrophobins in ectomycorrhizal symbiosis: hypothesis. Symbiosis 25:5–18

    CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599 (Publication PDF at http://www.kumarlab.net/publications)

    Article  CAS  PubMed  Google Scholar 

  • Tartaglia G, Vendruscolo M (2008) The Zyggregator method for predicting protein aggregation propensities. Chem Soc Rev 37:1395–1401

    Article  CAS  PubMed  Google Scholar 

  • Tasaki Y, Ohata K, Hara T, Joh T (2004) Three genes specifically expressed during phosphate deficiency in Pholiota nameko strain N2 encode hydrophobins. Curr Genet 45:19–27

    Article  CAS  PubMed  Google Scholar 

  • Trembley ML, Ringli C, Honegger R (2007) Differential expression of hydrophobins DGH1 , DGH2 and DGH3 and immunolocalization of DGHI in strata of the lichenized basidiocarp of Dictyonema glabratum. New Phytol 154(1):185–195

  • Wessels JGH (2000) Hydrophobins, unique fungal proteins. Mycologist 14:153–159

    Article  Google Scholar 

  • Wessels JGH, de Vries OMH, Ásgeirsdóttir SA, Schuren FHJ (1991) Hydrophobin genes involved in formaiton of aerial hyphae and fruit bodies in Schizophyllum. Plant Cell 3:793–799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Whiteford JR, Spanu PD (2002) Hydrophobins and the interactions between fungi and plants. Mol Plant Patho 3:391–400

    Article  CAS  Google Scholar 

  • Wösten HAB, de Vocht ML (2000) Hydrophobins, the fungal coat unravelled. Biochim Biophys Acta 1469:79–86

    Article  PubMed  Google Scholar 

  • Wösten HA, Schuren FH, Wessels JG (1994) Interfacial self-assembly of a hydrophobin into an amphipathic protein membrane mediates fungal attachment to hydrophobic surfaces. EMBO J 13(24):5848–5854

  • Wosten HA, Bohlmann R, Eckerskorn C, Lottspeich F, Bolker M, Kahmann R (1996) A novel class of small amphipathic peptides affect aerial hyphal growth and surface hydrophobicity in Ustilago maydis. EMBO J 15(16):4274–4281 Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8861956\nhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC452153/pdf/emboj00016-0196.pdf

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wösten HAB, van Wetter MA, Lugones LG, van der Mei HC, Busscher HJ, Wessels JGH (1999) How a fungus escapes the water to grow into the air. Curr Biol 9:85–89

    Article  PubMed  Google Scholar 

  • Xu D, Zhang Y (2013) Ab initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep 3:1895

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are thankful to the Mycorrhizal Genomics Initiative for providing access to genomic and transcriptomic data. Hafida Lmalem and Francois Rineau are grateful to the BOF (Special Research Fund) from Hasselt University for financing their research. The authors also thank Tom Artois, Anders Tunlid and Michiel Op De Beeck for useful comments on the manuscript.

Author information

Authors and Affiliations

  1. Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium

    F. Rineau, H. Lmalem, L. Coninx, J. Ruytinx, H. Nguyen, J. Vangronsveld & J. V. Colpaert

  2. Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62, Lund, SE, Sweden

    D. Ahren & T. Johansson

  3. Department of food and environmental sciences, University of Helsinki, Helsinki, Finland

    F. Shah

  4. US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, USA

    I. Grigoriev & A. Kuo

  5. Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), Institut National de la Recherche Agronomique (INRA), UMR 1136, Champenoux, France

    A. Kohler, E. Morin & F. Martin

  6. Laboratory of Excellence ARBRE, University of Lorraine, UMR 1136, Champenoux, France

    A. Kohler, E. Morin & F. Martin

Authors
  1. F. Rineau
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. H. Lmalem
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. D. Ahren
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. F. Shah
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. T. Johansson
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. L. Coninx
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. J. Ruytinx
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. H. Nguyen
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. I. Grigoriev
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. A. Kuo
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. A. Kohler
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. E. Morin
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. J. Vangronsveld
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. F. Martin
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. J. V. Colpaert
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to F. Rineau.

Electronic supplementary material

ESM 1

(DOCX 748 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Rineau, F., Lmalem, H., Ahren, D. et al. Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes. Mycorrhiza 27, 383–396 (2017). https://doi.org/10.1007/s00572-016-0758-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00572-016-0758-4

Keywords

Search

Navigation