Reconstruction of the Transcriptional Regulatory Network in Arabidopsis thaliana Aliphatic Glucosinolate Biosynthetic Pathway

Abstract

Aliphatic glucosinolate is an important secondary metabolite responsible in plant defense mechanism and carcinogenic activity. It plays a crucial role in plant adaptation towards changes in the environment such as salinity and drought. However, in many plant genomes, there are thousands of genes encoding proteins still with putative functions and incomplete annotations. Therefore, the genome of Arabidopsis thaliana was selected to be investigated further to identify any putative genes that are potentially involved in the aliphatic glucosinolate biosynthesis pathway, most of its gene are with incomplete annotation. Known genes for aliphatic glucosinolates were retrieved from KEGG and AraCyc databases. Three co-expression databases i.e., ATTED-II, GeneMANIA and STRING were used to perform the co-expression network analysis. The integrated co-expression network was then being clustered, annotated and visualized using Cytoscape plugin, MCODE and ClueGO. Then, the regulatory network of A. thaliana from AtRegNet was mapped onto the co-expression network to build the transcriptional regulatory network. This study showed that a total of 506 genes were co-expressed with the 61 aliphatic glucosinolate biosynthesis genes. Five transcription factors have been predicted to be involved in the biosynthetic pathway of aliphatic glucosinolate, namely SEPALLATA 3 (SEP3), PHYTOCHROME INTERACTING FACTOR 3-like 5 (AtbHLH15/PIL5), ELONGATED HYPOCOTYL 5 (HY5), AGAMOUS-like 15 (AGL15) and GLABRA 3 (GL3). Meanwhile, three other genes with high potential to be involved in the aliphatic glucosinolates biosynthetic pathway were identified, i.e., methylthioalkylmalate-like synthase 4 (MAML-4) and aspartate aminotransferase (ASP1 and ASP4). These findings can be used to complete the aliphatic glucosinolate biosynthetic pathway in A. thaliana and to update the information on the glucosinolate-related pathways in public metabolic databases.

Supplemental UV-A Affects Growth and Antioxidants of Chinese Kale Baby-Leaves in Artificial Light Plant Factory

“…UV-A radiation could stimulate the biosynthesis and accumulation of GLs in Chinese kale, which might be caused by the activation of transcription factor genes such as HY5, after the UV-A photoreceptor senses the signal. HY5 could regulate the transcription levels of sulfur assimilation genes ATPs, APK and APR, and then affect the expression of glucosinolates biosynthesis genes, e.g., SOT16, SOT17, SOT18, MAM-L, CYP79F1 and CYP79B2 [64]. From the results of this study, GLs con-tents significantly increased under UV-A might attribute to that UV-A could up-regulate the gene expressions of the key enzymes related to glucosinolates metabolites [65,66].…”

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

“…It also highlighted the in silico-based approaches that employed the ‘guilt-by-association’ (GBA) principle in identifying transporters in plant specialised metabolism. In relation to GSL biosynthesis, the GBA approach has been used to identify regulators [ 50 , 51 , 52 , 53 , 54 , 55 ] and enzymes [ 56 , 57 , 58 , 59 ]. Identifying TPs using co-expressed genes successfully defined a boron transporter candidate in A. thaliana [ 71 ].…”

“…Therefore, we propose a ‘guilt-by-association’ (GBA) approach to identify and characterise possible GSL TPs involved in GSL metabolism [ 32 ]. The GBA principle has been used to identify regulators [ 50 , 51 , 52 , 53 , 54 , 55 ] and enzymes [ 56 , 57 , 58 , 59 ] involved in GSL biosynthesis. Detailed information on most of the molecular components related to GSL biosynthesis and metabolism can be found in SuCComBase, which is accessible at (accessed on 16 December 2021) [ 60 ].…”

Effects of Plant Hormones, Metal Ions, Salinity, Sugar, and Chemicals Pollution on Glucosinolate Biosynthesis in Cruciferous Plant

“…A large number of studies have shown that GSL biosynthesis is a complex process, which is regulated by multiple layers comprising genetic sites, developmental processes, transcription, and synthetic products ( Barco and Clay, 2019 ; Meier et al, 2019 ). At present, the biosynthetic framework roadmap of GSL is basically clear in A. thaliana , and most regulatory genes in related pathways are known, but the specific functions of these regulatory genes are not fully elucidated ( Ashari et al, 2018 ; Vo et al, 2018 ). In this process, MYB transcription factors play an important role in the regulation of GSL formation.…”