A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress

Abstract

The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. However, due to a lack of information regarding the HMA gene family in the Cucurbitaceae family, a comprehensive genome-wide analysis of the HMA family was performed in ten Cucurbitaceae species: Citrullus amarus, Citrullus colocynthis, Citrullus lanatus, Citrullus mucosospermus, Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita moschata, Cucurbita pepo, and Legenaria siceraria. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across species. The phylogenetic and structural analysis confirmed that the Cucurbitaceae HMA protein family could be further classified into two major clades: Zn/Co/Cd/Pb and Cu/Ag. The GO-annotation-based subcellular localization analysis predicted that all HMA gene family members were localized on membranes. Moreover, the analysis of conserved motifs and gene structure (intron/exon) revealed the functional divergence between clades. The interspecies microsynteny analysis demonstrated that maximum orthologous genes were found between species of the Citrullus genera. Finally, nine candidate HMA genes were selected, and their expression analysis was carried out via qRT-PCR in root, leaf, flower, and fruit tissues of C. pepo under arsenic stress. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. Overall, this study provides insights into the functional analysis of the HMA gene family in Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions.

From genes to ecosystems: Decoding plant tolerance mechanisms to arsenic stress

“…However, its specific function in the presence of As has not yet been fully elucidated [ 67 ]. The expression patterns of the Heavy Metal ATPase (HMA) family have been analyzed in Cucurbita pepo under As (V) stress [ 114 ]. The Cu/Ag clade members showed a positive modulation, especially CpHMA6, which exhibited high up-regulation in root and shoot tissues.…”

HarbouringStarships: The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi

“…Among these cluster-accessory genes, several were frequently present, specifically two genes with no functional description available and a basic region leucine zipper (bZIP), potentially playing a similar role to the bZIP transcription factor ARR1/YAP8, which is both required for the transcription of ARR2 and ARR3 in S. cerevisiae (Wysocki et al, 2004) and activated by arsenite binding (Navarro et al, 2022). Additionally, two other cluster-accessory genes were found close to the cluster in several different Starship-related regions; TRX1, a thioredoxin both inhibited by arsenic and shown to confer resistance (Jovanovic et al, 2021;Lu et al, 2007;Park, 2020) and a heavy metal associated p-type ATPase, similar to pcaA, shown to confer resistance to cadmium and lead in Hephaestus, possibly involved in arsenic/arsenite transport (Antonucci et al, 2017;Flores-Iga et al, 2023;H. Yan et al, 2019).…”