The Diversification of Evolutionarily Conserved MAPK Cascades Correlates with the Evolution of Fungal Species and Development of Lifestyles

Abstract

The fungal kingdom displays an extraordinary diversity of lifestyles, developmental processes, and ecological niches. The MAPK (mitogen-activated protein kinase) cascade consists of interlinked MAPKKK, MAPKK, and MAPK, and collectively such cascades play pivotal roles in cellular regulation in fungi. However, the mechanism by which evolutionarily conserved MAPK cascades regulate diverse output responses in fungi remains unknown. Here we identified the full complement of MAPK cascade components from 231 fungal species encompassing 9 fungal phyla. Using the largest data set to date, we found that MAPK family members could have two ancestors, while MAPKK and MAPKKK family members could have only one ancestor. The current MAPK, MAPKK, and MAPKKK subfamilies resulted from duplications and subsequent subfunctionalization during the emergence of the fungal kingdom. However, the gene structure diversification and gene expansion and loss have resulted in significant diversity in fungal MAPK cascades, correlating with the evolution of fungal species and lifestyles. In particular, a distinct evolutionary trajectory of MAPK cascades was identified in single-celled fungi in the Saccharomycetes. All MAPK, MAPKK, and MAPKKK subfamilies expanded in the Saccharomycetes; genes encoding MAPK cascade components have a similar exon-intron structure in this class that differs from those in other fungi.

Keywords: MAPK cascades; evolutionary diversity; fungi; gene duplication; gene family evolution; gene loss.

Fig. 1.—

Flow chart of the identification of MAPK cascade components from 231 fungal species.

Fig. 2.—

Phylogenetic analysis of MAPK family members (A), MAPKK family members (B), and MAPKKK family members (C). The trees were constructed with the protein sequence of the kinase domain PF00069 of MAPK cascade components. Numbers at nodes represent Bayesian posterior probabilities (left) and bootstrap values of ML (right), respectively.

Fig. 3.—

Distribution of MAPK cascades and their components in the fungal kingdom. (A) Pie diagram showing the number of fungal species with a complete (green), incomplete (brown), and null (gray) complement of MAPK cascade components. The percentage shows the proportion of the total of 231 fungal species. Complete complement: Presence of all four MAPK, three MAPKK, and three MAPKKK subfamilies; incomplete complement: Lack of at least one of the four MAPK, three MAPKK, and three MAPKKK subfamilies; null complement: No MAPK cascade components. (B) Bar diagram showing the presence of the MAPK cascade components in the 231 fungal species. The number of fungal species with only one member within each of the MAPK, MAPKK, and MAPKKK subfamilies is shown in blue, multiple in red, and none in gray. The upper left pie shows the number of fungal species with a complete set (green), incomplete set (brown), and none (gray) of the four MAPK subfamilies, and the upper middle and right pie shows the presence of three MAPKK and three MAPKKK subfamilies, respectively. (C) Bar diagram showing the number of fungal species with complete (blue), incomplete (brown), and no (gray) Fus3/Kss1-MAPK, Hog1-MAPK, and Slt2/Smk1-MAPK cascades. Pie diagram showing the percentage of the 231 fungal species with all 3 complete cascades (green), and that lack at least one cascade (brown), and without cascade (gray). (D) The distribution of the ten subfamilies of MAPK cascades (middle) and three MAPK cascades (right) in the nine fungal phyla. The left tree was the modified fungal life tree described in the Result section. For the distribution of MAPK cascade components (middle), the portions of the colored pie diagram show the percentage of the total number of species (purple) in a taxon with multiple members (orange), one member (blue), and no members (gray) within a subfamily. For the three MAPK cascades (right), the portions of the colored pie diagram show the percentage of the total number of species in a taxon with a complete MAPK cascade (blue), incomplete MAPK cascade (brown), and no MAPK cascade (gray).

Fig. 4.—

Pairwise estimation of the Ka/Ks values of the MAPK cascade components in the fungal kingdom. (A) Pairwise estimates of Ka/Ks values within members of each of the 4 MAPK, 3 MAPKK, and 3 MAPKKK subfamilies from the 231 fungal species. (B) The mean Ka/Ks values of the four MAPK, three MAPKK, and thee MAPKKK subfamilies across the fungal kingdom, two dikarya fungal phyla, and six major classes.

Fig. 5.—

Diversification of the amino acid sequences of TXY motifs in the activation loops among members from each of the four MAPK subfamilies. Middle table: The number of members from an MAPK subfamily had a specific TXY motif named at the top of the table. Right panel: Logos showing the sequence conservation of the TXY motifs in the four MAPK subfamilies. The inserted logo shows the sequence conservation of the TXY motifs in Slt2/Smk1-MAPK subfamily members from the Saccharomycetes fungi. Left panel: Phylogenetic tree of the four MAPK subfamilies (simplified from fig. 2A). The digits in parentheses are the number of members in an MAPK subfamily.

Fig. 6.—

The mean number of exons in each of the four MAPK, three MAPKK, and three MAPKKK subfamilies at the phylum level (A) and class level within the Ascomycota (B).

Fig. 7.—

Diversification of the gene structure of MAPK cascade CDSs. (A) The number of exons in all MAPK cascade components. In each subfamily, the 231 fungal species were organized according to their lineage status shown in the legend. For example, a red dot shows the number of exons in a gene from a Saccharomycetes fungus. (B) Stacked bar charts show the gene structure diversity among members of a subfamily. The digit within a bar shows the number of fungal species that demonstrate a difference (blue) or no difference (red) in gene structure among multiple subfamily members. (C) The diversity in gene structure among members within the Fus3/Kss1 or Slt2/Smk1-MAPK subfamily from Saccharomycete fungi (upper panel) and non-Saccharomycete fungi (down panel). The digits within the pie denote the number of fungal species with a difference (blue) or no difference (red) in gene structure among members of the Fus3/Kss1 or Slt2/Smk1-MAPK subfamily.