Show simple item record

dc.contributor.authorClark, Sangaalofaen
dc.contributor.authorVerwoerd, Wynand S.en
dc.identifier.citationClark, S. & Verwoerd, W. (2011). A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants. BMC Bioinformatics, 12(343). Retrieved from
dc.description.abstractThe 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 selfcontained 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. Simulation 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. From 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.en
dc.description.sponsorshipLincoln University.en
dc.publisherBMC Bioinformatics.en
dc.relationThe original publication is available from - BMC Bioinformatics. - -
dc.rights© 2011 Clark and Verwoerd; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.subjectminimal cut setsen
dc.subjectcolour pigmentationen
dc.subjectcorrelated gene targetsen
dc.subjectmetabolic pathwaysen
dc.subject.meshSystems Biologyen
dc.subject.meshGenes, Regulatoren
dc.subject.meshMetabolic Networks and Pathwaysen
dc.subject.meshBiosynthetic Pathwaysen
dc.titleA systems approach to identifying correlated gene targets for the loss of colour pigmentation in plantsen
dc.typeJournal Article
lu.contributor.unitLincoln Universityen
lu.contributor.unitFaculty of Agriculture and Life Sciencesen
lu.contributor.unitDepartment of Wine, Food and Molecular Biosciencesen
dc.subject.anzsrc06 Biological Sciencesen
dc.subject.anzsrc08 Information and Computing Sciencesen
dc.subject.anzsrc01 Mathematical Sciencesen
dc.relation.isPartOfBMC Bioinformaticsen
pubs.organisational-group/LU/Agriculture and Life Sciences
pubs.organisational-group/LU/Agriculture and Life Sciences/WFMB

Files in this item

Default Thumbnail

This item appears in the following Collection(s)

Show simple item record

Creative Commons Attribution
Except where otherwise noted, this item's license is described as Creative Commons Attribution