Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway

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 enc...

Full description

Bibliographic Details
Main Authors:	Khalidah-Syahirah Ashari, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun, Zeti-Azura Mohamed-Hussein
Format:	Article
Language:	English
Published:	Penerbit Universiti Kebangsaan Malaysia 2018
Online Access:	http://journalarticle.ukm.my/12920/ http://journalarticle.ukm.my/12920/ http://journalarticle.ukm.my/12920/1/08%20Khalidah-Syahirah%20Ashari.pdf

id	ukm-12920
recordtype	eprints
spelling	ukm-129202019-05-15T11:01:32Z http://journalarticle.ukm.my/12920/ Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway Khalidah-Syahirah Ashari, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun, Zeti-Azura Mohamed-Hussein, 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. Penerbit Universiti Kebangsaan Malaysia 2018-12 Article PeerReviewed application/pdf en http://journalarticle.ukm.my/12920/1/08%20Khalidah-Syahirah%20Ashari.pdf Khalidah-Syahirah Ashari, and Muhammad-Redha Abdullah-Zawawi, and Sarahani Harun, and Zeti-Azura Mohamed-Hussein, (2018) Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway. Sains Malaysiana, 47 (12). pp. 2993-3002. ISSN 0126-6039 http://www.ukm.my/jsm/malay_journals/jilid47bil12_2018/KandunganJilid47Bil12_2018.html
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Kebangasaan Malaysia
building	UKM Institutional Repository
collection	Online Access
language	English
description	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.
format	Article
author	Khalidah-Syahirah Ashari, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun, Zeti-Azura Mohamed-Hussein,
spellingShingle	Khalidah-Syahirah Ashari, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun, Zeti-Azura Mohamed-Hussein, Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway
author_facet	Khalidah-Syahirah Ashari, Muhammad-Redha Abdullah-Zawawi, Sarahani Harun, Zeti-Azura Mohamed-Hussein,
author_sort	Khalidah-Syahirah Ashari,
title	Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway
title_short	Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway
title_full	Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway
title_fullStr	Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway
title_full_unstemmed	Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway
title_sort	reconstruction of the transcriptional regulatory network in arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway
publisher	Penerbit Universiti Kebangsaan Malaysia
publishDate	2018
url	http://journalarticle.ukm.my/12920/ http://journalarticle.ukm.my/12920/ http://journalarticle.ukm.my/12920/1/08%20Khalidah-Syahirah%20Ashari.pdf
first_indexed	2023-09-18T20:03:41Z
last_indexed	2023-09-18T20:03:41Z
_version_	1777407016708341760

Reconstruction of the transcriptional regulatory network in Arabidopsis thaliana aliphatic glucosinolate biosynthetic pathway

Similar Items