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BMC Bioinformatics

, 12:343

Networks analysis

Abstract

BackgroundThe numerous diverse metabolic pathways by which plant compounds can be produced make it difficult to predict how colour pigmentation is lost for different tissues and plants. This study employs mathematical and in silico methods to identify correlated gene targets for the loss of colour pigmentation in plants from a whole cell perspective based on the full metabolic network of Arabidopsis. This involves extracting a self-contained flavonoid subnetwork from the AraCyc database and calculating feasible metabolic routes or elementary modes EMs for it. Those EMs leading to anthocyanin compounds are taken to constitute the anthocyanin biosynthetic pathway ABP and their interplay with the rest of the EMs is used to study the minimal cut sets MCSs, which are different combinations of reactions to block for eliminating colour pigmentation. By relating the reactions to their corresponding genes, the MCSs are used to explore the phenotypic roles of the ABP genes, their relevance to the ABP and the impact their eliminations would have on other processes in the cell.

ResultsSimulation and prediction results of the effect of different MCSs for eliminating colour pigmentation correspond with existing experimental observations. Two examples are: i two MCSs which require the simultaneous suppression of genes DFR and ANS to eliminate colour pigmentation, correspond to observational results of the same genes being co-regulated for eliminating floral pigmentation in Aquilegia and; ii the impact of another MCS requiring CHS suppression, corresponds to findings where the suppression of the early gene CHS eliminated nearly all flavonoids but did not affect the production of volatile benzenoids responsible for floral scent.

ConclusionsFrom the various MCSs identified for eliminating colour pigmentation, several correlate to existing experimental observations, indicating that different MCSs are suitable for different plants, different cells, and different conditions and could also be related to regulatory genes. Being able to correlate the predictions with experimental results gives credence to the use of these mathematical and in silico analyses methods in the design of experiments. The methods could be used to prioritize target enzymes for different objectives to achieve desired outcomes, especially for less understood pathways.

List of Abbreviations Used3-UGTAnthocyanidin 3-O-glucosyltransferase

ABPAnthocyanin Biosynthetic Pathway

ANSAnthocyanidin synthase

CfConnectivity in the full network

CsConnectivity in the subnetwork

CHIChalcone isomerise

CHSChalcone synthase

CNACellNetAnalyzer

Cycy: cyanidin-3-O-glucoside

DFRDihydroflavonol reductase

EMElementary Mode

F3HFlavanone 3-hydroxylase

F3-HFlavanone 3-hydroxylase

FBAFlux Balance Analysis

fcfragility coefficient

FLSFlavonol synthase

LDOXLeucoanthocyanidin dioxygenase

MCSMinimal Cut Set

MPAMetabolic Pathway Analysis

Pgpg: pelargonidin-3-O-glucoside

UDPGUDP-glycosyltransferase.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-12-343 contains supplementary material, which is available to authorized users.

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Autor: Sangaalofa T Clark - Wynand S Verwoerd

Fuente: https://link.springer.com/







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