Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism

Abstract

Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana, the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and serves to protect high-value tissues such as reproductive tissues. This study aimed to identify potential GSL-transporter proteins (TPs) using a network-biology approach. The known A. thaliana GSL genes were retrieved from the literature and pathway databases and searched against several co-expression databases to generate a gene network consisting of 1267 nodes and 14,308 edges. In addition, 1151 co-expressed genes were annotated, integrated, and visualised using relevant bioinformatic tools. Based on three criteria, 21 potential GSL genes encoding TPs were selected. The AST68 and ABCG40 potential GSL TPs were chosen for further investigation because their subcellular localisation is similar to that of known GSL TPs (SULTR1;1 and SULTR1;2) and ABCG36, respectively. However, AST68 was selected for a molecular-docking analysis using AutoDOCK Vina and AutoDOCK 4.2 with the generated 3D model, showing that both domains were well superimposed on the homologs. Both molecular-docking tools calculated good binding-energy values between the sulphate ion and Ser419 and Val172, with the formation of hydrogen bonds and van der Waals interactions, respectively, suggesting that AST68 was one of the sulphate transporters involved in GSL biosynthesis. This finding illustrates the ability to use computational analysis on gene co-expression data to screen and characterise plant TPs on a large scale to comprehensively elucidate GSL metabolism in A. thaliana. Most importantly, newly identified potential GSL transporters can serve as molecular tools in improving the nutritional value of crops.

Understanding the Complex Functional Interplay between Glucosinolates and Cyanogenic Glycosides in Carica papaya

“…The GSL biosynthesis pathway has been elucidated by identifying various biological factors involved, such as regulators [77][78][79][80][81][82], enzymes [83][84][85], and protein transporters [86][87][88][89] that also seem to participate in the cross-talk with other essential metabolic processes such as phenylpropanoids, sulfur, and nitrogen in A. thaliana [90,91]. A comprehensive set of 113 known GSL genes were identified from the literature and using public pathway databases, encoding for transcriptional regulators, enzymes, and protein transporters [7].…”

Gene Co-Expression Network Tools and Databases for Crop Improvement

“…Although the whole genome sequence in crops is widely developed, plant gene annotation is still scarce. Previous studies have used the GCN as a source to annotate unknown and uncharacterised genes involved in specific biological roles [15,16] and to identify new genes involved in biological mechanisms [17][18][19][20][21][22]. This is due to the hypothesis that groups of genes that are co-expressed in a module may share a similar biological function [13].…”

Large scale transcriptomics analyses for gene function annotation and regulation

“…In yeast, predicted tropane alkaloid transporters from plants that were introduced to the system were able to increase efficiency in metabolite transport across organelles, resulting in a 100-fold and 7-fold increase in the final product littorine and hyoscyamine respectively (Srinivasan and Smolke, 2021). Transporters potentially involved in the process of secondary metabolite biosynthesis have also been identified through coexpression analysis (Yan et al, 2021;Harun et al, 2022).…”