Genome-wide metabolic network reconstruction of the picoalga Ostreococcus

Abstract

The green picoalga Ostreococcus is emerging as a simple plant model organism, and two species, O. lucimarinus and O. tauri, have now been sequenced and annotated manually. To evaluate the completeness of the metabolic annotation of both species, metabolic networks of O. lucimarinus and O. tauri were reconstructed from the KEGG database, thermodynamically constrained, elementally balanced, and functionally evaluated. The draft networks contained extensive gaps and, in the case of O. tauri, no biomass components could be produced due to an incomplete Calvin cycle. To find and remove gaps from the networks, an extensive reference biochemical reaction database was assembled using a stepwise approach that minimized the inclusion of microbial reactions. Gaps were then removed from both Ostreococcus networks using two existing gap-filling methodologies. In the first method, a bottom-up approach, a minimal list of reactions was added to each model to enable the production of all metabolites included in our biomass equation. In the second method, a top-down approach, all reactions in the reference database were added to the target networks and subsequently trimmed away based on the sequence alignment scores of identified orthologues. Because current gap-filling methods do not produce unique solutions, a quality metric that includes a weighting for phylogenetic distance and sequence similarity was developed to distinguish between gap-filling results automatically. The draft O. lucimarinus and O. tauri networks required the addition of 56 and 70 reactions, respectively, in order to produce the same biomass precursor metabolites that were produced by our plant reference database.

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

“…Photosynthetic organisms are represented at the microalgal level by Chlamydomonas reinhardtii (Boyle and Morgan, 2009;Chang et al, 2011) and Ostreococcus spp. (Krumholz et al, 2012). For plants, there are now several models of Arabidopsis (Arabidopsis thaliana; Poolman et al, 2009;de Oliveira Dal'Molin et al, 2010;Mintz-Oron et al, 2012), and these are currently undergoing a process of collaborative reconciliation.…”

Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model

“…By this process, we restricted the directionality of 36 reactions and removed 2,055 reactions from the model (Table II). Upon the resolution of thermodynamically infeasible cycles, attempts were made to unblock the remaining blocked core reactions and biomass formation by adding reactions from similar organisms (Krumholz et al, 2012) and model organisms (i.e. rice ssp.…”

Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks

“…For instance, adding an internal reaction incurs a lower cost than adding a transporter. Bottom-up gap filling works well for well annotated genomes, but for networks that require extensive gap filling, a top-down approach is more robust (29). In the more recently developed top-down methods, all gap-filling reactions are added, followed by the successive preferential removal of unneeded gap-filling reactions with little or no sequence similarity in the genome of the organism for which the network is reconstructed (14,29,30).…”

“…Bottom-up gap filling works well for well annotated genomes, but for networks that require extensive gap filling, a top-down approach is more robust (29). In the more recently developed top-down methods, all gap-filling reactions are added, followed by the successive preferential removal of unneeded gap-filling reactions with little or no sequence similarity in the genome of the organism for which the network is reconstructed (14,29,30). Prioritization of the removal of reactions without sequence similarity minimizes the inclusion of locally (enzymes with an associated sequence that is not present in the target genome) and globally (reactions without sequence association) orphaned reactions.…”