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

Abstract

BackgroundCassava 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.ResultsIn 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.ConclusionsTo 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.

The industrial applications of cassava: current status, opportunities and prospects

“…G1P can be utilized in cellular structure development (cell wall biosynthesis), energy production (respiration) or macromolecule synthesis and accumulation (starch biosynthesis) . According to the KEGG (http://www.genome.jp/kegg) and PMN (http://www.plantcyc.org/) reference pathway databases, starch biosynthesis comprises 270 starch‐related proteins: 141 proteins are annotated in sucrose and starch metabolic reactions, while 129 proteins are involved in the Calvin cycle …”

“…Biosynthesis pathway of cassava starch: Ru5p, ribulose‐5‐phosphate; RuBP, ribulose‐1,5‐bisphosphate; 3PGA, 3‐phosphate‐glycerate; BPGA, 1,3‐bisphospho‐glycerate; GA3p, glyceraldehyde‐3‐phosphate; FBP, fructose‐1,6‐phosphate; F6P, fructose‐6‐phosphate.…”

“…15,16 Therefore this review summarizes current knowledge on the system biology, economic importance, nutritional value and applications of cassava and cassava-based industrial wastes in an attempt to better understand, integrate and utilize cassava information resources for cassava researchers. 31,78 Ru5p, ribulose-5-phosphate; RuBP, ribulose-1,5-bisphosphate; 3PGA, 3-phosphate-glycerate; BPGA, 1,3-bisphospho-glycerate; GA3p, glyceraldehyde-3-phosphate; FBP, fructose-1,6-phosphate; F6P, fructose-6-phosphate.…”

Cassava shrunken-2 homolog MeAPL3 determines storage root starch and dry matter content and modulates storage root postharvest physiological deterioration

“…In cassava, homologs of bt2 and sh2 have been cloned and their expression pattern determined by northern blot analysis in different tissues (Munyikwa et al 2001). Presence of multiple isoforms of APL genes in cassava is expected (Saithong et al 2013;Dong et al 2019;Tappiban et al 2019), and would be consistent with monocot and dicot plant species (Ballicora et al 2004). In the present study, we identified five isoforms of cassava APL genes (MeAPL1-MeAPL5) from the cassava genome and characterized their functional significance in starch biosynthesis in storage roots using virus induced gene silencing (VIGS).…”

Evaluación De La Expresión De Genes Implicados en La Biosíntesis De Almidón en Diferentes Variedades De Yuca

“…En yuca, hasta hace poco, sólo algunos de los genes responsables habían sido descritos. Sin embargo con la reciente liberación de la secuencia completa del genoma (Prochnik et al, 2012) fue posible reconstruir la ruta metabólica completa (Saithong et al, 2013). Este estudio mostró que existe un alto grado de conservación en los genes y, en general, en toda la ruta metabólica del almidón de yuca con otras especies como Arabidopsis, arroz, maíz, ricino y papa.…”