Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi

Abstract

Subtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal kingdom. Our comparative genomic analyses of the subtilase superfamily indicated that extensive gene duplications, losses and functional diversifications have occurred in fungi, and that the four families of subtilase enzymes in fungi, including proteinase K-like, Pyrolisin, kexin and S53, have distinct evolutionary histories which may have facilitated the adaptation of fungi to a broad array of life strategies. Our study provides new insights into the evolution of the subtilase superfamily in fungi and expands our understanding of the evolution of fungi with different lifestyles.

Figure 1. CLANS clustering of 993 subtilase sequences obtained from 83 whole genome sequenced fungal species.

The name of each group is marked. Four new groups are identified in our study with new 1, new 3 and new 4 groups being the same as the classification of Muszewska et al., and new 2 group in our study corresponding to the new 6 group proposed by Muszewska et al..

Figure 2. Phylogenetic relationships of the proteinase K-like subfamily in Sordariomycetes fungi.

Phylogenetic analyses were performed using maximum likelihood (ML) methods as implemented in PHYML 3.0 with GTR+I+G model based on an alignment of 184 amino acids from 138 proteinase K-like genes from Sordariomycetes fungi and 8 outgroup genes from the four Taphrinomycotina fungi. Five clades were designated (SF1-SF5). The bootstrap support value for each clade is shown. The 10 proteinase K-like subfamily genes Pr1A, Pr1B, Pr1D to Pr1K and the duplicated genes newly identified in Metarhizium spp. are highlighted.

Figure 3. Phylogenetic relationships of the Pyrolisin subfamily.

Phylogenetic analyses were performed using maximum likelihood (ML) methods as implemented in PHYML 3.0 with GTR+I+G model based on an alignment of 282 amino acids from 136 Pyrolisin sequences. Seven clades were designated (sf1-sf7) and the bootstrap support value for each clade is shown. The Pyrolisin subfamily genes Pr1C and the duplicated genes newly identified in Metarhizium spp. are highlighted.

Figure 4. Phylogenetic relationships of the kexin subfamily.

Phylogenetic analyses were performed using maximum likelihood (ML) methods as implemented in PHYML 3.0 with TrN+I+G model based on an alignment of 465-bp amino acids from 84 kexin sequences.

Figure 5. Phylogenetic relationships of the S53 family.

Phylogenetic analyses were performed using maximum likelihood (ML) methods as implemented in PHYML 3.0 with TrN+I+G model based on an alignment of 363 amino acids from 126 S53 family sequences. Five clades were designated (S53-1 to S53-5) and the bootstrap support value for each clade is shown.