In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc

Abstract

Ramonda serbica Panc. is an ancient resurrection plant able to survive a long desiccation period and recover metabolic functions upon watering. The accumulation of protective late embryogenesis abundant proteins (LEAPs) is a desiccation tolerance hallmark. To propose their role in R. serbica desiccation tolerance, we structurally characterised LEAPs and evaluated LEA gene expression levels in hydrated and desiccated leaves. By integrating de novo transcriptomics and homologues LEAP domains, 318 R. serbica LEAPs were identified and classified according to their conserved motifs and phylogeny. The in silico analysis revealed that hydrophilic LEA4 proteins exhibited an exceptionally high tendency to form amphipathic α-helices. The most abundant, atypical LEA2 group contained more hydrophobic proteins predicted to fold into the defined globular domains. Within the desiccation-upregulated LEA genes, the majority encoded highly disordered DEH1, LEA1, LEA4.2, and LEA4.3 proteins, while the greatest portion of downregulated genes encoded LEA2.3 and LEA2.5 proteins. While dehydrins might chelate metals and bind DNA under water deficit, other intrinsically disordered LEAPs might participate in forming intracellular proteinaceous condensates or adopt amphipathic α-helical conformation, enabling them to stabilise desiccation-sensitive proteins and membranes. This comprehensive LEAPs structural characterisation is essential to understanding their function and regulation during desiccation aiming at crop drought tolerance improvement.

Identification and expression analysis of LEA gene family members in pepper (Capsicum annuum L.)

“…The LEA_2 subfamily contained the most genes, accounting for 41% of the CaLEA family. This proportion is similar to that observed in most of the species studied thus far [25,26,30,54,55]. LEA_6 is the smallest subfamily with only one member, but LEA_6 subfamily is absent in a few species, such as tomato, tea plants, and Ramonda serbica Panc.…”

“…LEA_6 is the smallest subfamily with only one member, but LEA_6 subfamily is absent in a few species, such as tomato, tea plants, and Ramonda serbica Panc. [13,30,36]. The number of CaLEA genes is roughly equal to that of other Solanaceae species such as tobacco [55] and potato [26], and the distribution of the number of subfamily genes is also similar.…”

“…The hydrophobic strip present on the class A α‐helices is positioned in a way that it can interact with the hydrophobic fatty acid tails of the outer plasma membrane, inner mitochondrial membrane, or peroxisomal membrane. Additionally, the positive strip on these α‐helices can form electrostatic interactions with the negatively charged phosphate groups of phospholipids, further contributing to the support and stability of the membranes [30,60]. According to a previous study, genetic evolution was the reason for the low number of introns.…”

“…Because of their amino acid composition, LEA proteins are disordered along their sequence [58]. For example, a group of desiccation-upregulated LEA proteins in R. serbica Panc., particularly LEA_1, LEA_3, DHN proteins, showed the highest propensity for disorder, while members of LEA_2 family showed the lowest disorder propensity [30]. The structural flexibility of LEA proteins is responsible for their interactions with other macromolecules (e.g., membrane proteins), thereby protecting them from stress factors [59].…”

“…Additionally, the downregulation of LEA_4 subgroup genes results in sensitivity to water deficit in Arabidopsis, which may be related to the maintenance of cellular function by LEA proteins during water deficit [5,7]. Furthermore, studies have indicated that LEA proteins perform vital functions under stress, acting as free radical scavengers under dry conditions [29,30], preventing the inactivation of a variety of enzymes, such as lactate dehydrogenase, during water deficit [31,32], and protecting proteins and membranes from adverse structural changes caused by dehydration [33].…”