Evolution and structural diversification of<i>Nictaba</i>-like lectin genes in food crops with a focus on soybean (<i>Glycine max</i>)

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

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“…These conclusions are in correspondence with a previous study, in which Nictaba homologs from 15 plant genomes were analyzed [30]. …”

Section: Resultssupporting

confidence: 92%

“…This again supports the idea that the F-box and Nictaba domain evolved together, and have diverged from an ancestral protein, as suggested in a previous study [30]. …”

Section: Resultssupporting

confidence: 91%

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Holle

Schutter

Eggermont

et al. 2017

IJMS

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“…Besides Nictaba, which appears as the prototype of a group of closely related lectins [263,264], other groups of stress inducible lectins in the nucleocytoplasmic compartment have been identified, such as the Euonymus europaeus EUL-related lectins [170,265] and the group of mannose-binding jacalin-related lectins [221,266]. Among the stress inducible cytoplasmic/nuclear lectins identified so far, Nictaba belonging to the Nictaba-related lectins [267], Orysata belonging to the jacalin-related lectins [268], and OrysaEULD1A belonging to the EUL-related lectins [269], all readily interact with high-mannose glycan structures (Table 7).…”

Section: Functions Of Mannose-specific Lectinsmentioning

confidence: 99%

Overview of the Structure–Function Relationships of Mannose-Specific Lectins from Plants, Algae and Fungi

Barre

Bourne

Damme

et al. 2019

IJMS

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To date, a number of mannose-binding lectins have been isolated and characterized from plants and fungi. These proteins are composed of different structural scaffold structures which harbor a single or multiple carbohydrate-binding sites involved in the specific recognition of mannose-containing glycans. Generally, the mannose-binding site consists of a small, central, carbohydrate-binding pocket responsible for the “broad sugar-binding specificity” toward a single mannose molecule, surrounded by a more extended binding area responsible for the specific recognition of larger mannose-containing N-glycan chains. Accordingly, the mannose-binding specificity of the so-called mannose-binding lectins towards complex mannose-containing N-glycans depends largely on the topography of their mannose-binding site(s). This structure–function relationship introduces a high degree of specificity in the apparently homogeneous group of mannose-binding lectins, with respect to the specific recognition of high-mannose and complex N-glycans. Because of the high specificity towards mannose these lectins are valuable tools for deciphering and characterizing the complex mannose-containing glycans that decorate both normal and transformed cells, e.g., the altered high-mannose N-glycans that often occur at the surface of various cancer cells.

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“…However, the three-dimensional conformations and sugar-recognition modes of Nictaba and mammalian Fbs1 differ considerably (Mizushima et al., 2004; Schouppe et al., 2010). Arabidopsis and crops such as soybean express dozens of F-box/Nictaba proteins (Delporte et al., 2015; Van Holle et al., 2017), but to date only an Arabidopsis F-box/Nictaba protein, At2g02360, has been characterized. The expression of At2g02360 is up-regulated after treatment with salicylic acid, heat stress, or infection with Pseudomonas syringae.…”

Section: Mechanism Of N-glycan Recognition By Sugar-recognizing F-boxmentioning

confidence: 99%

Sugar-Recognizing Ubiquitin Ligases: Action Mechanisms and Physiology

2019

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F-box proteins, the substrate recognition subunits of SKP1–CUL1–F-box protein (SCF) E3 ubiquitin ligase complexes, play crucial roles in various cellular events mediated by ubiquitination. Several sugar-recognizing F-box proteins exist in both mammalian and plant cells. Although glycoproteins generally reside outside of cells, or in organelles of the secretory pathway, these lectin-type F-box proteins reside in the nucleocytoplasmic compartment. Mammalian sugar-recognizing F-box proteins commonly bind to the innermost position of N-glycans through a unique small hydrophobic pocket in their loops. Two cytosolic F-box proteins, Fbs1 and Fbs2, recognize high-mannose glycans synthesized in the ER, and SCF Fbs1 and SCF Fbs2 ubiquitinate excess unassembled or misfolded glycoproteins in the ERAD pathway by recognizing the innermost glycans, which serve as signals for aberrant proteins. On the other hand, endomembrane-bound Fbs3 recognizes complex glycans as well as high-mannose glycans, and SCF Fbs3 ubiquitinates exposed glycoproteins in damaged lysosomes fated for elimination by selective autophagy. Plants express stress-inducible lectin-type F-box proteins recognizing a wider range of N- and O-glycans, suggesting that the roles of mammalian and plant lectin-type F-box proteins have diverged over the course of evolution to recognize species-specific targets with distinct functions. These sugar-recognizing F-box proteins interpret glycans in the cytosol as markers of unwanted proteins and organelles, and degrade them via the proteasome or autophagy.

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Evolution and structural diversification ofNictaba-like lectin genes in food crops with a focus on soybean (Glycine max)

Cited by 8 publications

References 85 publications

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Overview of the Structure–Function Relationships of Mannose-Specific Lectins from Plants, Algae and Fungi

Sugar-Recognizing Ubiquitin Ligases: Action Mechanisms and Physiology

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