In silico characterization, structural modeling, and molecular docking of GabP in citrus and its potential role in GABA uptake

Abstract

Abstract GABA shunt is an important metabolic hub that plays a key role in plant growth, development, and response. Although a functional connection between GABA shunt and the TCA cycle via a mitochondrial GABA permease (gabP) gene was reported previously from model plants, this connection in non-model plants, such as citrus, is poorly studied. Herein, we used bioinformatics and multi-omics for in-silico characterization, structural modeling, and ligand-receptor binding profile of GABA transport carrier (CsgabP) from the non-model plant, Valencia sweet orange (Citrus sinensis) and to explore their potential role(s) in GABA uptake and citrus response to Huanglongbing. Genome-wide analysis showed that the citrus genome encodes for two putative CsgabP proteins (CsgabP-1 [521 aa] and CsgabP-2 [419 aa]) that were relatively highly homologous to each other and homologous to amino acid permease BAT1 proteins from other plant species. Primary structures of both CsgabPs showed high similarity and conserved sequences between them. CsgabPs are highly hydrophobic integral transmembrane transporter proteins with internal hydrophilic N- and C-terminal ends and depend on 9–12 transmembrane segments. The crystallographic three-dimensional (3D) structures of both CsgabPs were predicted and confirmed using AlphaFold as a monomer with 100% coverage, but not experimentally determined crystallographic structures. Targeted metabolomics showed that CsgabP was upregulated upon GABA supplementation in healthy and ‘Candidatus Liberibacter asiaticus’-infected citrus plants. Likewise, CsgabP was involved in citrus response(s) to different biotic stress including infection with ‘Ca. L. asiaticus’ or infestation with its vector, Diaphorina citri. These findings probably clarify the molecular and functional connection between the GABA shunt and the TCA cycle in non-model plants such as citrus.