Evolutionary analysis of hydrophobin gene family in two wood-degrading basidiomycetes, Phlebia brevispora and Heterobasidion annosum s.l.

Abstract

BackgroundHydrophobins are small secreted cysteine-rich proteins that play diverse roles during different phases of fungal life cycle. In basidiomycetes, hydrophobin-encoding genes often form large multigene families with up to 40 members. The evolutionary forces driving hydrophobin gene expansion and diversification in basidiomycetes are poorly understood. The functional roles of individual genes within such gene families also remain unclear. The relationship between the hydrophobin gene number, the genome size and the lifestyle of respective fungal species has not yet been thoroughly investigated. Here, we present results of our survey of hydrophobin gene families in two species of wood-degrading basidiomycetes, Phlebia brevispora and Heterobasidion annosum s.l. We have also investigated the regulatory pattern of hydrophobin-encoding genes from H. annosum s.s. during saprotrophic growth on pine wood as well as on culture filtrate from Phlebiopsis gigantea using micro-arrays. These data are supplemented by results of the protein structure modeling for a representative set of hydrophobins.ResultsWe have identified hydrophobin genes from the genomes of two wood-degrading species of basidiomycetes, Heterobasidion irregulare, representing one of the microspecies within the aggregate H. annosum s.l., and Phlebia brevispora. Although a high number of hydrophobin-encoding genes were observed in H. irregulare (16 copies), a remarkable expansion of these genes was recorded in P. brevispora (26 copies). A significant expansion of hydrophobin-encoding genes in other analyzed basidiomycetes was also documented (1–40 copies), whereas contraction through gene loss was observed among the analyzed ascomycetes (1–11 copies). Our phylogenetic analysis confirmed the important role of gene duplication events in the evolution of hydrophobins in basidiomycetes. Increased number of hydrophobin-encoding genes appears to have been linked to the species’ ecological strategy, with the non-pathogenic fungi having increased numbers of hydrophobins compared with their pathogenic counterparts. However, there was no significant relationship between the number of hydrophobin-encoding genes and genome size. Furthermore, our results revealed significant differences in the expression levels of the 16 H. annosum s.s. hydrophobin-encoding genes which suggest possible differences in their regulatory patterns.ConclusionsA considerable expansion of the hydrophobin-encoding genes in basidiomycetes has been observed. The distribution and number of hydrophobin-encoding genes in the analyzed species may be connected to their ecological preferences. Results of our analysis also have shown that H. annosum s.l. hydrophobin-encoding genes may be under positive selection. Our gene expression analysis revealed differential expression of H. annosum s.s. hydrophobin genes under different growth conditions, indicating their possible functional diversification.

Characterization of a Basidiomycota hydrophobin reveals the structural basis for a high-similarity Class I subdivision

“…In contrast, class I hydrophobins reside in all four quadrants of the plot displaying, as expected, comparatively high sequence variability7. In PC2, however, there is a distinct separation of Ascomycota and Basidiomycota Class I sequences, with an intermediate region containing sequences originating from both phyla consistent with previous phylogenies171834. The mixed-region of Class I contains all previously structurally characterized Class I hydrophobins and has little sequence or loop length conservation, an observation consistent with the current description of the Class I group of hydrophobins in the literature11.…”

“…While putative Class II hydrophobins are still readily identified by sequence analysis, it remains difficult to reach a single consensus as to a Class I signature, leading to the proposition for further subdivision of the class141516. Considering phylogenetic analyses of sequences from a wide range of fungi, bootstrap values support a separation of Class I ascomycota and basidiomycota sequences but are too low to confidently support further subdivisions1718. It is also important to note that while the number of predicted sequences increases, both the forces driving hydrophobin gene evolution and the roles of individual genes remain largely unclear18.…”

“…Considering phylogenetic analyses of sequences from a wide range of fungi, bootstrap values support a separation of Class I ascomycota and basidiomycota sequences but are too low to confidently support further subdivisions1718. It is also important to note that while the number of predicted sequences increases, both the forces driving hydrophobin gene evolution and the roles of individual genes remain largely unclear18.…”

Transcriptomic Responses of Phanerochaete chrysosporium to Oak Acetonic Extracts: Focus on a New Glutathione Transferase

“…Indeed, it is predicted to be secreted, the sequence is less than 300 amino acids, and it contains many cysteines. Such proteins have been studied recently in Phlebia brevispora and Heterobasidion annosum (29). The authors focused their analysis on hydrophobins.…”

Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens

“…In H. annosum s.s, a conifer pathogen with a similar life history to Ps , 16 hydrophobin-encoding genes with different regulatory patterns were observed. Several were highly up-regulated during saprotrophic growth on bark, sapwood and/or heartwood of Scots pine, suggesting that this pathogen employs different hydrophobins during growth on diverse wood components [25]. A separate study found that two H. annosum hydrophobin genes are up-regulated in aerial hyphae but are down-regulated during early infection of pine seedling roots [26].…”