Sains Malaysiana 47(12)(2018): 2993–3002

http://dx.doi.org/10.17576/jsm-2018-4712-08

 

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

(Pembinaan Semua Jaringan Pengawal Atur Transkripsi Tapak Jalan Biosintesis

Glukosinolat Alifatik dalam Arabidopsis thaliana)

KHALIDAH-SYAHIRAH ASHARI¹, MUHAMMAD-REDHA ABDULLAH-ZAWAWI², SARAHANI HARUN² & ZETI-AZURA MOHAMED-HUSSEIN^1,2*

 

¹Centre for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

²Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

Diserahkan: 30 Mei 2018 /Diterima: 19 September 2018

 

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.

 

Keywords: Aliphatic glucosinolate biosynthesis; co-expression analysis; regulatory network

 

ABSTRAK

Glukosinolat alifatik merupakan metabolit sekunder penting di dalam mekanisme pertahanan tumbuhan dan aktiviti karsinogen. Glukosinolat juga penting di dalam penyesuaian terhadap persekitaran seperti kemasinan dan kemarau. Namun begitu dalam kebanyakan genom tumbuhan, masih banyak fungsi gen yang mengekod protein adalah putatif dan tidak lengkap. Oleh itu, genom Arabidopsis thaliana telah dipilih untuk dikaji dengan lebih mendalam untuk mengenal pasti gen putatif yang berpotensi terlibat di dalam tapak jalan biosintesis glukosinolat alifatik. Gen biosintetik glukosinolat alifatik telah dikumpul daripada pangkalan data KEGG dan AraCyc manakala pangkalan data ATTED-II, GeneMANIA dan STRING digunakan dalam analisis pengekspresan bersama. Integrasi jaringan pengekspresan bersama telah dilakukan dengan menggunakan perisian Cytoscape, MCODE dan ClueGO. Kesemua gen pengekspresan bersama yang terlibat dipetakan menggunakan set data jaringan pengawal atur daripada pangkalan data AtRegNet. Hasil kajian ini berjaya mengenal pasti 506 gen yang telah diekspreskan bersama dengan 61 gen biosintetik glukosinolat alifatik. Lima faktor transkripsi telah berjaya dikenal pasti dan didapati terlibat di dalam mengawal atur biosintetis glukosinolat alifatik iaitu SEPALLATA 3 (SEP3), PHYTOCHROME INTERACTING FACTOR 3-like 5 (AtbHLH15/PIL5), ELONGATED HYPOCOTYL 5 (HY5), AGAMOUS-like 15 (AGL15) dan GLABRA 3 (GL3). Kajian ini mengukuhkan lagi penglibatan gen berpotensi di dalam tapak jalan biosintesis glukosinolat alifatik melalui penemuan gen methylthioalkylmalate-like synthase 4 (MAML-4) dan aspartate aminotransferase (ASP4 dan ASP1) menggunakan kaedah yang telah dijalankan.

 

Kata kunci: Analisis pengekspresan bersama; biosintesis glukosinolat alifatik; jaringan pengawal atur

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*Pengarang untuk surat-menyurat; email: zeti.hussein@ukm.edu.my