Comparison of Amino Acids Physico-Chemical Properties and Usage of Late Embryogenesis Abundant Proteins, Hydrophilins and WHy Domain

Abstract

Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response) was found in LEAP class 8 (according to our previous classification). Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins) and to Heat Shock Proteins 12 (HSP12). Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance.

Characterization of PcLEA14, a Group 5 Late Embryogenesis Abundant Protein Gene from Pear (Pyrus communis)

“…The LEA14 pear homolog was confirmed to belong to the group 5C proteins of the LEA family, as shown in the phylogenetic tree analysis, and it was designated as PcLEA14 . Group 5C proteins have a unique structure [ 9 , 10 , 11 ], and although their role is unclear, they have been the subject of a small number of studies. An earlier study reported that overexpression of the same gene group in maize, ZmLEA5C , improved low-temperature stress tolerance in tobacco plant [ 2 ].…”

“…LEA proteins are classified into seven groups according to their amino acid sequences; however, group 5 proteins are considered atypical LEA proteins because of their comparatively large number of hydrophobic residues and their lack of common sequences and important motifs found in other LEA proteins [ 8 ]. Group 5C proteins have a Water Stress and Hypersensitive (WHy) response domain, and their function is expected to differ from that of other LEA proteins [ 9 , 10 , 11 ]. Although some studies have investigated the stress response of group 5C LEA proteins in herbaceous plants [ 2 , 12 , 13 , 14 ], there is limited information available on trees in which a unique functionality of the gene is expected to ensure perennially.…”

LEA Proteins and the Evolution of the WHy Domain

“…The original grouping of LEA proteins is based on common structural features, which were first identified in the prototypical cotton plant (G. hirsutum) (11), but subsequent alternative classifications have led to large inconsistencies with respect to the original taxonomy (23). LEA proteins have been variously assigned to three major groups associated with their taxonomic origins, i.e., plants, bacteria, and vertebrates (22), while other classifications yield five (23) or seven (21) major groups, with nine to 14 LEA subgroups (16,(24)(25)(26). The different classification structures have been based on the analysis of transcripts (27,28), amino acid sequences and conserved motifs (26,29,30), three-dimensional protein structures, or chemical characteristics, including in silico analyses of protein or oligonucleotide probability profiles (POPP) (16,22,23,25,26,(29)(30)(31)(32)(33).…”

Synteny-based phylogenomic networks for comparative genomics

“…A set of the DHNs are called hydrophylins because of their specific response to osmotic stress (Garay-Arroyo et al, 2000; Jaspard and Hunault, 2014). Hydrophylins play important role in protecting cell components from the adverse effects caused by low water availability due to biochemical properties such as high Glycine (Gly) content (> 6%) and low grand average hydropathy (GRAVY) (< -1) (Garay-Arroyo et al, 2000; Battaglia et al, 2008;Reyes et al, 2008).…”