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

Abstract

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). This work is considered a big step in the quantitative modeling pipeline aiming to investigate the dynamic regulation of starch biosynthesis in cassava roots.

Figure 1

The overview of the methodology. The pathway reconstruction protocol is divided into three steps: (Panel 1) finding the cassava orthologous sequences through the similarity search technique, (Panel 2) defining the confidence of the cassava sequence annotation as well as the pathway reconstruction, and (Panel 3) visualizing the resulting pathway.

Figure 2

The reconstructed pathway of the carbon dioxide fixation process in cassava presented on the SmartDraw platform. The number in the orange boxes denotes the EC number of the enzymes which is possibly a product of the genes below, denoted as the 12-digit ID. The colored dots beside each gene ID indicate the plant templates from which the genes were annotated: green – Arabidopsis, red – maize, pink – rice, violet – castor bean, and orange – potato. The background colors of the dots represent the matching quality of the sequence alignment: highest in yellow to lower in blue and the lowest in white. The following two columns describe the match (MS) and conservation (CS) scores, respectively. The box marks the reactions that are relevant to the C4-photosynthesis pathway found in a typical C4-plant.

Figure 3

The reconstructed pathway of the sucrose synthesis process in cassava presented on the SmartDraw platform. The number in the orange boxes denotes the EC number of the enzymes which is possibly a product of the genes below, denoted as the 12-digit ID. The colored dots beside each gene ID indicate the plant templates from which the genes were annotated: green – Arabidopsis, red – maize, pink – rice, violet – castor bean, and orange – potato. The background colors of the dots represent the matching quality of the sequence alignment: highest in yellow to lower in blue and the lowest in white. The following two columns describe the match (MS) and conservation (CS) scores, respectively.

Figure 4

The reconstructed pathway of the starch synthesis process in cassava presented on the SmartDraw platform. The number in the orange boxes denotes the EC number of the enzymes which is possibly a product of the genes below, denoted as the 12-digit ID. The colored dots beside each gene ID indicate the plant templates from which the genes were annotated: green – Arabidopsis, red – maize, pink – rice, violet – castor bean, and orange – potato. The background colors of the dots represent the matching quality of the sequence alignment: highest in yellow to lower in blue and the lowest in white. The following two columns describe the match (MS) and conservation (CS) scores, respectively.

Figure 5

The example of the pathway map that includes the results of the protein motif analysis. The functional motifs of the proteins were examined through the Conserved Domain Database (CDD) web tool from the NCBI database (http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi). The protein motifs contained in the analyzed sequences are presented in two levels: specific hit domain (dark blue - indicates a highly confident annotation fit to a specific motif in the NCBI repository) and superfamily (light blue - indicates a collection of the motifs that are found redundantly among the homologous proteins). See the detailed definition and types of identified motifs in [41,42].

Figure 6

The scheme plotting the relationship between the match score (MS) and conservation score (CS). The shadow region refers to the theoretical range of both confidence scores (MS and CS) and the circles indicate the scores of sequences whose identification was supported by the experiment. The regions A, B, and C refer to the area in the MS-CS plot having different levels of confidence: A – low, B – high, and C – extremely high.

Figure 7

The integrated map of the carbon dioxide fixation process presented on the VANTED platform. The microarray data measuring gene expression in fibrous, developmental and mature roots of cassava were integrated into the reconstructed pathway. The height of the bar graph indicates the level of gene expression, while the colors denote the types of roots: black - fibrous root, dark grey - developmental root, and light grey - mature root.

Figure 8

The integrated map of the sucrose synthesis process presented on the VANTED platform. The microarray data measuring gene expression in fibrous, developmental and mature roots of cassava were integrated into the reconstructed pathway. The height of the bar graph indicates the level of gene expression, while the colors denote the types of roots: black - fibrous root, dark grey - developmental root, and light grey - mature root.

Figure 9

The integrated map of the starch synthesis process presented on the VANTED platform. The microarray data measuring gene expression in fibrous, developmental and mature roots of cassava were integrated into the reconstructed pathway. The height of the bar graph indicates the level of gene expression, while the colors denote the types of roots: black - fibrous root, dark grey - developmental root, and light grey - mature root.