Genome-Wide Analyses of Aspartic Proteases on Potato Genome (Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress

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.

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

“…For example, aspartic-type endopeptidases (cluster 6) have been associated with plant defense response mechanisms, hybrid sterility, reproductive development, abiotic and biotic stresses, chloroplast homeostasis, and lateral root development [ 48 ]. It has been shown that segmental and tandem duplications are characteristic of genes in this group in the potato genome, and the expression of approximately 21% of these genes changes under salt, osmotic, or temperature treatments [ 49 ]. Genes from the 3 rd functional cluster (replication factor A) are also shown to change expression associated with endoplasmic reticulum stress and potential involvement in genotoxic stress responses [ 50 ].…”

Phylogenetic and AlphaFold predicted structure analyses provide insights for A1 aspartic protease family classification in Arabidopsis

“…Though A1 aspartic protease family members have been identified and described by different investigators in last two decades, the gene number of A1 family ranges from 51 to 69 (Beers et al, 2004;Faro and Gal, 2005;Takahashi et al, 2008;Wang et al, 2019;Yu et al, 2021). To obtain as many A1 members as possible in Arabidopsis, the HMM profile of ASP domain (PF00026), which has been used to identify A1 family genes in rice (Chen et al, 2009), grape (Guo et al, 2013), poplar (Cao et al, 2019), wheat (Yang and Feng, 2020), moso bamboo (Wang et al, 2021) and potato (Norero et al, 2022), was used as a query to identify AP genes in the first round search. Then only 64 genes were identified (Table S1), which is obviously underestimated since reported aspartic proteases such as SAP1(AT1G03220) and SAP2(AT1G03230) cannot be not identified (Wang et al, 2019).…”

Production of a novel milk‐clotting enzyme from solid‐substrate Mucor spp. culture

“…Aspartic proteases, commonly known as acid proteases or aspartyl proteases, are classified as hydrolases (group 3) within subgroup 4, which can hydrolyze peptide bonds. They are diversely found in living organisms as well as in viruses (Norero et al., 2022). They are endopeptidases that use an activated water molecule bound to one or two aspartate residues for catalysis.…”