Abstract
Aspartic proteases are proteolytic enzymes widely distributed in living organisms and viruses. Although they have been extensively studied in many plant species, they are poorly described in potatoes. The present study aimed to identify and characterize S. tuberosum aspartic proteases. Gene structure, chromosome and protein domain organization, phylogeny, and subcellular predicted localization were analyzed and integrated with RNAseq data from different tissues, organs, and conditions focused on abiotic stress. Sixty-two aspartic protease genes were retrieved from the potato genome, distributed in 12 chromosomes. A high number of intronless genes and segmental and tandem duplications were detected. Phylogenetic analysis revealed eight StAP groups, named from StAPI to StAPVIII, that were differentiated into typical (StAPI), nucellin-like (StAPIIIa), and atypical aspartic proteases (StAPII, StAPIIIb to StAPVIII). RNAseq data analyses showed that gene expression was consistent with the presence of cis-acting regulatory elements on StAP promoter regions related to water deficit. The study presents the first identification and characterization of 62 aspartic protease genes and proteins on the potato genome and provides the baseline material for functional gene determinations and potato breeding programs, including gene editing mediated by CRISPR.
Highlights
Aspartic proteases (APs) (EC 3.4.23) are widely distributed among living organisms and viruses [1,2,3,4]
In silico analysis of the Arabidopsis thaliana genome revealed the presence of 51 genes that encode possible APs (AtAP), 46 of which presented different primary structure characteristics compared to the canonical forms
S. tuberosum aspartic protease (StAP) were distributed along all 12 potato chromosomes, the majority of them localized in chromosomes I, II, V, VI, VII, and VIII (Figure 3)
Summary
Aspartic proteases (APs) (EC 3.4.23) are widely distributed among living organisms and viruses [1,2,3,4]. These enzymes have been extensively studied and constitute one of the four superfamilies of proteolytic enzymes. The MEROPs database classified APs into 15 families based on their amino acid sequence similarity and grouped them into 5 different clans based on their evolutionary relationship and tertiary structure [7]. Most of the plant APs belong to the A1 family, are active at acidic pH, are inhibited by pepstatin A, and present a great structural diversity [8,9]. Based on the sequence of the active sites and the organization of domains, AtAPs are currently sorted into three groups or categories: typical, atypical, and nucellin-like [10]
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