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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-HUSSEIN1,2*
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
Received: 30 May 2018 /Accepted: 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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*Corresponding author; email: zeti.hussein@ukm.edu.my
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