Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration

BMC Systems Biology

Supapon Cheevadhanarak⁵  Asawin Meechai⁴  Malinee Suksangpanomrung¹  Supatcharee Netrphan¹  Wanatsanan Siriwat³  Porntip Chiewchankaset²  Saowalak Kalapanulak²  Oratai Rongsirikul³  Treenut Saithong² 

[1] National Center for Genetic Engineering and Biotechnology, 10120 Pathumthani, Thailand;Systems Biology and Bioinformatics Research Group (SBI), Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, 10150 Bangkok, Thailand;Bioinfromatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, 10150 Bangkok, Thailand;Department of Chemical Engineering, King Mongkut’s University of Technology Thonburi, 10140 Bangkok, Thailand;Division of Biotechnology, School of Bioresources and Technology, King Mongkut’sBangkok, Thailand

关键词: Starch biosynthesis;    Metabolic pathway reconstruction;    Data integration;    Cassava;   

Others  :  1142456
DOI  :  10.1186/1752-0509-7-75

 received in 2013-03-05, accepted in 2013-08-05,  发布年份 2013

【 摘 要 】

Background

Cassava is a well-known starchy root crop utilized for food, feed and biofuel production. However, the comprehension underlying the process of starch production in cassava is not yet available.

Results

In this work, we exploited the recently released genome information and utilized the post-genomic approaches to reconstruct the metabolic pathway of starch biosynthesis in cassava using multiple plant templates. The quality of pathway reconstruction was assured by the employed parsimonious reconstruction framework and the collective validation steps. Our reconstructed pathway is presented in the form of an informative map, which describes all important information of the pathway, and an interactive map, which facilitates the integration of omics data into the metabolic pathway. Additionally, to demonstrate the advantage of the reconstructed pathways beyond just the schematic presentation, the pathway could be used for incorporating the gene expression data obtained from various developmental stages of cassava roots. Our results exhibited the distinct activities of the starch biosynthesis pathway in different stages of root development at the transcriptional level whereby the activity of the pathway is higher toward the development of mature storage roots.

Conclusions

To expand its applications, the interactive map of the reconstructed starch biosynthesis pathway is available for download at the SBI group’s website (http://sbi.pdti.kmutt.ac.th/?page_id=33 webcite). This work is considered a big step in the quantitative modeling pipeline aiming to investigate the dynamic regulation of starch biosynthesis in cassava roots.

【 授权许可】

   
2013 Saithong et al.; licensee BioMed Central Ltd.

【 图 表 】

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