Saithong Treenut, Rongsirikul Oratai, Kalapanulak Saowalak, Chiewchankaset Porntip, Siriwat Wanatsanan, Netrphan Supatcharee, Suksangpanomrung Malinee, Meechai Asawin, Cheevadhanarak Supapon
Bioinfromatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 10150 Bangkok, Thailand.
BMC Syst Biol. 2013 Aug 10;7:75. doi: 10.1186/1752-0509-7-75.
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.
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.
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). This work is considered a big step in the quantitative modeling pipeline aiming to investigate the dynamic regulation of starch biosynthesis in cassava roots.
木薯是一种著名的淀粉质块根作物，用于食品、饲料和生物燃料生产。然而，木薯淀粉生产过程背后的理解尚不可得。
在这项工作中，我们利用最近发布的基因组信息，并采用后基因组方法，使用多个植物模板重建木薯淀粉生物合成的代谢途径。通过采用简约重建框架和集体验证步骤确保了途径重建的质量。我们重建的途径以信息图的形式呈现，该图描述了途径的所有重要信息，以及交互式图，便于将组学数据整合到代谢途径中。此外，为了证明重建途径不仅仅是示意性呈现的优势，该途径可用于纳入从木薯根的各个发育阶段获得的基因表达数据。我们的结果在转录水平上展示了淀粉生物合成途径在根发育不同阶段的不同活性，其中该途径的活性在成熟贮藏根发育过程中更高。
为了扩展其应用，重建的淀粉生物合成途径的交互式图可在SBI小组网站（http://sbi.pdti.kmutt.ac.th/?page_id=33）下载。这项工作被认为是旨在研究木薯根中淀粉生物合成动态调控的定量建模流程中的一大步。
