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.
Highlights
To survive, fungi depend on their ability to harvest nutrients from living or dead organic materials
Most members of the subtilase superfamily are inhibited by general serine peptidase inhibitors such as diisopropyl fluorophosphate (DFP) and phenylmethane sulfonylfluoride(PMSF), but kexin is resistant to PMSF and requires high concentrations of DFP, which initially led to its misidentification as a cysteine peptidase[18]
We identified the near-complete repertories of subtilase genes from 83 fungal species with different life-styles
Summary
Based on the phylogeny of the fungal kingdom which constructed by James et al.[23] and Spatafora et al.[24], we selected representatives of the whole genome sequenced fungi that are distributed among all the main fungal lineages, including the main phyla of Ascomycota, Basidiomycota, Mucormycotina and the very ancestral Microsporidia for this study. To find putative homologs of subtilases in the 83 fungal genome sequences employed in this study, the HMM profile Peptidase_S8 (PF00082; http://pfam.xfam.org/family/PF00082#curationBlock), which includes both S8 and S53 domains, was downloaded and used as a query in the search for homologous proteins using the program HMMSEARCH from the HMMER package (http://hmmer.wustl.edu/). MUSCLE v3.7 was used to generate protein alignment with default settings[26]. The aligned amino acid sequences of each gene family/subfamily were performed using two different tree construction methods: Neighbor-joining (NJ) analysis and Maximum likelihood (ML) analysis. In the ML analysis, the reliability of the tree topology was evaluated using bootstrap support with 100 repeats[34]
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