Phoenix dactylifera (date palm; Arecaceae) putative lectin homologs: Genome-wide search, architecture analysis, and evolutionary relationship

Abstract

The date palm, Phoenix dactylifera, is a vital crop in nations in the Middle East and North Africa. The date palm was thought to have outstanding traditional medicinal value because it was abundant in phytochemicals with diverse chemical structures. The date palm's ability to withstand harsh environments could be partly attributed to a class of proteins known as lectins, which are carbohydrate-binding proteins that can bind sugar moieties reversibly and without changing their chemical structures. After scanning the genome of P. dactylifera (GCF 009389715.1), this in silico study discovered 196 possible lectin homologs from 11 different families, some specific to plants. At the same time, others could also be found in other kingdoms of life. Their domain architectures and functional amino acid residues were investigated, and they yielded a 40% true-lectin with known conserved carbohydrate-binding residues. Further, their probable subcellular localization, physiochemical and phylogenetic analyses were also performed. Scanning all putative lectin homologs against the anticancer peptide (ACP) dataset found in the AntiCP2.0 webpage identified 26 genes with protein kinase receptors (Lec-KRs) belonging to 5 lectin families, which are reported to have at least one ACP motif. Our study offers the first account of Phoenix-lectins and their organization that can be used for further structural and functional analysis and investigating their potential as anticancer proteins.

Keywords: ACP; Domain rearrangements; Localization; Phoenix dactylifera; Ture lectins.

Fig. 1

Maximum likelihood analysis of lectin homologs from Phoenix dactylifera. Bootstraps were inferred from 1000 replicates. A) Nictaba family, the dark green triangle symbols represent true lectins; the Nictaba sequence from Nicotiana tabacum Nictaba lectin (AAK84134.1) was used as a reference ortholog. B) CRA family, the orange diamond symbols represent true lectins; the human GHF18 chitinase (Q9BZP6.1) was used as a reference ortholog. C) GNA family, the purple triangle symbols represent true lectins; the GNA from Galanthus nivalis Bulb lectin (P30617) was used as a reference ortholog. D) Legume family, cyan-green circle symbols represent true lectins; the. Erythrina corallodendron EcorL (1AX1) was used as a reference ortholog. E) Hevein family, the pink circle symbols represent true lectins; the Hevea brasiliensis Hevein lectin (ABW34946.1) was used as a reference ortholog. F) JRL family, lime green circle symbols represent true lectin; the Artocarpus integer Jacalin lectin (AAA32680.1) was used as a reference ortholog.

Fig. 2

Identification of true-calnexin/calreticulin lectins from Phoenix dactylifera. A) The maximum likelihood phylogenetic tree of calnexin/calreticulin. The black square blocks represent the clade of true lectins. B) Partial alignment of calnexin/calreticulin homologs. The different color one-letter codes are used to represent amino acids. The red-shaded boxes represent the conserved critical amino acids required for carbohydrate binding. The black dot represents lectins that retain all conserved amino acids needed for the binding. Lectins ID and accession numbers are shown on the left, and the number of domains that resides in the same protein is indicated after the dash. CA1X1_ARATH from Arabidopsis thaliana (P29402) was used as a reference for the alignment and an ortholog in the phylogenetic analysis.

Fig. 3

Identification of true-Malectins from Phoenix dactylifera. A) The maximum likelihood phylogenetic tree of Malectins. The red square blocks represent the clade of true-lectins. B) Partial alignment of Malectin homologs. The different color one-letter codes are used to represent amino acids. The red-shaded boxes represent the conserved critical amino acids required for carbohydrate binding. The black dot represents lectins that retain all conserved amino acids needed for the binding. Lectins ID and accession numbers are shown on the left, and the number of domains that resides in the same protein is indicated after the dash. Xenopus laevis (NP_00085212.1) was used as a reference model for the alignment and an ortholog in the phylogenetic analysis.

Fig. 4

Lectin families and true-lectin homologs representation and prevalence in Phoenix dactylifera genome. LysM: Lysin motif, GH-47: glycosyl hydrolase-47, GH–19: glycosyl hydrolase–19 (PF00182), CB–1: carbohydrate binding domain–1, PP2: Phloem protein 2, F–box (PF00646), PKinase: Protein kinase (PF00069, PF07714), S-locus glycoprotein (PF00956), and PAN2 (PF08278).

Fig. 5

Heatmap of Phoenix dactylifera lectin homologs from different families. The numbers above the heatmap blocks represent the various locations. 1: Extracellular, 2: Plasma membrane, 3: Cytoplasm, 4: ER, 5: Lysosome, 6: Mitochondria, 7: Chloroplast, 8: Vacuoles, and 9: Nucleus.

Fig. 6

Hydropathic plots for lectin models from each family. X-axis: the position of amino acids, Y-axis: the hydropathy index.