ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses

Harun, Sarahani; Rohani, Emelda Rosseleena; Ohme‐Takagi, Masaru; Goh, Hoe-Han; Mohamed‐Hussein, Zeti‐Azura

doi:10.1007/s10265-021-01257-9

Cited by 12 publications

(11 citation statements)

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“…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 ].…”

Section: Discussionmentioning

confidence: 99%

“…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 ].…”

Section: Introductionmentioning

confidence: 99%

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

Harun

Afiqah‐Aleng

Hadi

et al. 2022

Life

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Harun

Afiqah‐Aleng

Hadi

et al. 2022

Life

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“…Further functional analysis was performed using chimeric repressor gene silencing technology (CRES-T) and gene expression analysis using qPCR. The over-expression of downstream aliphatic GSL genes ( UGT74C1 and IPMI1 ) in the ADAP-SRDX line indicated the possibility of ADAP as a negative regulator in aliphatic GSL biosynthesis via a feedback mechanism ( Harun et al, 2021 ). A total of thirteen potential genes ( Table 3 ) were identified from the top six significant analysis that is known as IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1 , and At3g14220 .…”

Section: Discussionmentioning

confidence: 99%

“…Previously, we have successfully identified a novel GSL gene ADAP ( Table S1 ) in the GSL biosynthesis via the similar approach and carried out an experimental validation of its involvement in the biosynthesis ( Harun et al, 2021 ). Thirteen potential GSL genes from the top six significant clusters: IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1 , and At3g14220 were identified from the GSL enriched clusters.…”

Section: Discussionmentioning

confidence: 99%

Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach

Harun

Afiqah‐Aleng

Karim

et al. 2021

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Background Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset. Methods We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher’s exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher’s exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters. Results The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clustering approach in identifying potential GSL genes which cannot be found from the standard similarity search.

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“…These secondary metabolites are used by plants as a defense mechanism against herbivores and different pathogens, and afford benefits to consumers. Each subtype of GLS has its precursors and is synthesized independently; however, all biosynthetic pathways follow the same general steps in the following order: side-chain elongation, formation of core molecule structure, and secondary modification [64,65]. SeMet can be used as a precursor of aliphatic GLS in place of Met, and the resulting (methylseleno) glucosinolates, as well as their Se-containing aglycons, are supposed to possess superior bioactivity as anticancer and antimicrobial agents compared to GLS [36,37].…”

Section: Selenium Metabolism In Plantsmentioning

confidence: 99%

The Relevance of Plant-Derived Se Compounds to Human Health in the SARS-CoV-2 (COVID-19) Pandemic Era

et al. 2021

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Dietary selenium (Se)-compounds accumulated in plants are essential for human metabolism and normal physiological processes. Inorganic and organic Se species can be readily absorbed by the human body, but are metabolized differently and thus exhibit distinct mechanisms of action. They can act as antioxidants or serve as a source of Se for the synthesis of selenoproteins. Selenocysteine, in particular, is incorporated at the catalytic center of these proteins through a specific insertion mechanism and, due to its electronic features, enhances their catalytic activity against biological oxidants. Selenite and other Se-organic compounds may also act as direct antioxidants in cells due to their strong nucleophilic properties. In addition, Se-amino acids are more easily subjected to oxidation than the corresponding thiols/thioethers and can bind redox-active metal ions. Adequate Se intake aids in preventing several metabolic disorders and affords protection against viral infections. At present, an epidemic caused by a novel coronavirus (SARS-CoV-2) threatens human health across several countries and impacts the global economy. Therefore, Se-supplementation could be a complementary treatment to vaccines and pharmacological drugs to reduce the viral load, mutation frequency, and enhance the immune system of populations with low Se intake in the diet.

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ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses

Cited by 12 publications

References 67 publications

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

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

Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach

The Relevance of Plant-Derived Se Compounds to Human Health in the SARS-CoV-2 (COVID-19) Pandemic Era

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