Transcriptome Profiling and Functional Validation of RING-Type E3 Ligases in Halophyte Sesuvium verrucosum under Salinity Stress

Abstract

Owing to their sessile nature, plants have developed a tapestry of molecular and physiological mechanisms to overcome diverse environmental challenges, including abiotic stresses. Adaptive radiation in certain lineages, such as Aizoaceae, enable their success in colonizing arid regions and is driven by evolutionary selection. Sesuvium verrucosum (commonly known as Western sea-purslane) is a highly salt-tolerant succulent halophyte belonging to the Aizoaceae family; thus, it provides us with the model-platform for studying plant adaptation to salt stress. Various transcriptional and translational mechanisms are employed by plants to cope with salt stress. One of the systems, namely, ubiquitin-mediated post-translational modification, plays a vital role in plant tolerance to abiotic stress and other biological process. E3 ligase plays a central role in target recognition and protein specificity in ubiquitin-mediated protein degradation. Here, we characterize E3 ligases in Sesuvium verrucosum from transcriptome analysis of roots in response to salinity stress. Our de novo transcriptome assembly results in 131,454 transcripts, and the completeness of transcriptome was confirmed by BUSCO analysis (99.3% of predicted plant-specific ortholog genes). Positive selection analysis shows 101 gene families under selection; these families are enriched for abiotic stress (e.g., osmotic and salt) responses and proteasomal ubiquitin-dependent protein catabolic processes. In total, 433 E3 ligase transcripts were identified in S. verrucosum; among these transcripts, single RING-type classes were more abundant compared to multi-subunit RING-type E3 ligases. Additionally, we compared the number of single RING-finger E3 ligases with ten different plant species, which confirmed the abundance of single RING-type E3 ligases in different plant species. In addition, differential expression analysis showed significant changes in 13 single RING-type E3 ligases (p-value < 0.05) under salinity stress. Furthermore, the functions of the selected E3 ligases genes (12 genes) were confirmed by yeast assay. Among them, nine genes conferred salt tolerance in transgenic yeast. This functional assay supports the possible involvement of these E3 ligase in salinity stress. Our results lay a foundation for translational research in glycophytes to develop stress tolerant crops.

A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms

“…Ubiquitination is key to proteosome-mediated degradation and is performed chiefly by the E3 ubiquitin ligase family, which are important in land plants also for photomorphogenesis [140]. RING (really interesting new gene) E3 ligases contribute to growth, development, and stress response via also mediating protein-protein interactions [141][142][143][144]. We trace a number of RING finger and related proteins to terrestrialization (S9 Fig) that include, but are not limited to, DAL1 and DAL2 (for Drosophila DIAP1 like 1 and 2), KEG (Keep on going), and NIP1 and NIP2.…”

A molecular atlas of plastid and mitochondrial evolution from algae to angiosperms

“…photomorphogenesis [130]. RING (Really interesting new gene) E3 ligases contribute to growth, development and stress response via also mediating protein-protein interactions [131][132][133][134]. We trace a number of RING finger (and related) proteins to terrestrialization (Fig.…”

“…Ubiquitination is key to proteosome-mediated degradation and is performed chiefly by the E3 ubiquitin ligase family, which are important in land plants also for photomorphogenesis [142]. RING (Really interesting new gene) E3 ligases contribute to growth, development and stress response via also mediating protein-protein interactions [143][144][145][146]. We trace a number of RING finger and related proteins to terrestrialization (Fig.…”

Identification of Halophilic and Halotolerant Bacteria from the Root Soil of the Halophyte Sesuvium verrucosum Raf

“…Sesuvium verrucosum Raf. is a perennial halophytic plant of the Aizoaceae family that has a high resistance to salinity [ 7 ] and can even modify chemical characteristics of the soil such as pH and electrical conductivity to withstand saline stress [ 8 ]. Its tolerance is attributed to different mechanisms such as biochemical, morphological and structural changes [ 9 ]; however, its adaptive capacity is also attributable to the association it forms with soil bacteria that have the ability to improve plant growth [ 10 , 11 ].…”