RAVEN 2.0: a versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Abstract

RAVEN is a commonly used MATLAB toolbox for genome-scale metabolic model (GEM) reconstruction, curation and constraint-based modelling and simulation. Here we present RAVEN Toolbox 2.0 with major enhancements, including: (i) de novo reconstruction of GEMs based on the MetaCyc pathway database; (ii) a redesigned KEGG-based reconstruction pipeline; (iii) convergence of reconstructions from various sources; (iv) improved performance, usability, and compatibility with the COBRA Toolbox. Capabilities of RAVEN 2.0 are here illustrated through de novo reconstruction of GEMs for the antibiotic-producing bacterium Streptomyces coelicolor. Comparison of the automated de novo reconstructions with the iMK1208 model, a previously published high-quality S.coelicolor GEM, exemplifies that RAVEN 2.0 can capture most of the manually curated model. The generated de novo reconstruction is subsequently used to curate iMK1208 resulting in Sco4, the most comprehensive GEM of S. coelicolor, with increased coverage of both primary and secondary metabolism. This increased coverage allows the use of Sco4 to predict novel genome editing targets for optimized secondary metabolites production. As such, we demonstrate that RAVEN 2.0 can be used not only for de novo GEM reconstruction, but also for curating existing models based on up-todate databases. Both RAVEN 2.0 and Sco4 are distributed through GitHub to facilitate usage and further development by the community. Author summaryCellular metabolism is a large and complex network. Hence, investigations of metabolic networks are aided by in silico modelling and simulations. Metabolic networks can be derived from whole-genome sequences, through identifying what enzymes are present and connecting these to formalized chemical reactions. To facilitate the reconstruction of genome-scale models of metabolism (GEMs), we have developed RAVEN 2.0. This versatile toolbox can reconstruct GEMs fast, through either metabolic pathway databases KEGG and MetaCyc, or from homology with an existing GEM. We demonstrate RAVEN's functionality through generation of a metabolic model of Streptomyces coelicolor, an antibiotic-producing bacterium. Comparison of this de novo generated GEM with a previously manually curated model demonstrates that RAVEN captures most of the previous model, and we subsequently reconstructed an updated model of S. coelicolor: Sco4. Following, we used Sco4 to predict promising targets for genetic engineering, which can be used to increase antibiotic production.

Genome‐Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production

“…Among all the GEMs of twelve actinomycetes reconstructed so far, GEMs of nine species have been released since 2017, which stresses the increasing industrial or medical importance of actinomycetes (Table ). In particular, GEMs of several representative species have been reconstructed multiple times over the years, including Streptomyces coelicolor , Streptomyces clavuligerus , Saccharopolyspora erythraea , Streptomyces lividans , and Streptomyces tsukubaensis . Recently, two different versions of GEMs have been released for S. coelicolor , namely Sco4 and iAA1259 .…”

“…In particular, GEMs of several representative species have been reconstructed multiple times over the years, including Streptomyces coelicolor , Streptomyces clavuligerus , Saccharopolyspora erythraea , Streptomyces lividans , and Streptomyces tsukubaensis . Recently, two different versions of GEMs have been released for S. coelicolor , namely Sco4 and iAA1259 . For Sco4, GEM reconstruction was carried out by implementing the software program RAVEN Toolbox 2 where three different GEMs, each reconstructed using KEGG, MetaCyc, and a previous S. coelicolor GEM iMK1208 as a reference, respectively, were merged together, and manually curated to give an upgraded GEM Sco4.…”

“…Recently, two different versions of GEMs have been released for S. coelicolor , namely Sco4 and iAA1259 . For Sco4, GEM reconstruction was carried out by implementing the software program RAVEN Toolbox 2 where three different GEMs, each reconstructed using KEGG, MetaCyc, and a previous S. coelicolor GEM iMK1208 as a reference, respectively, were merged together, and manually curated to give an upgraded GEM Sco4. Sco4 includes description on biosynthetic pathways of a total of eleven secondary metabolites, such as flaviolin, geosmin, albaflavenone, 2‐methylisoborneol, hopane, and desferrioxamine; the previous version iMK1208 covers five secondary metabolites .…”

“…For Sco4, GEM reconstruction was carried out by implementing the software program RAVEN Toolbox 2 where three different GEMs, each reconstructed using KEGG, MetaCyc, and a previous S. coelicolor GEM iMK1208 as a reference, respectively, were merged together, and manually curated to give an upgraded GEM Sco4. Sco4 includes description on biosynthetic pathways of a total of eleven secondary metabolites, such as flaviolin, geosmin, albaflavenone, 2‐methylisoborneol, hopane, and desferrioxamine; the previous version iMK1208 covers five secondary metabolites . Reconstruction of iAA1259, based on iMK1208, includes updates in biosynthetic pathways and model annotations by incorporating identifiers from multiple databases of genes, metabolites, and reactions, which enabled integrative analysis of multi‐omics data .…”

“…iAA1259 covered an additional biosynthetic pathway of coelimycin P1 in comparison with the iMK1208 . In general, some of the commonly observed upgrades in actinomycetes’ GEMs include incorporating information from updated metabolic databases, improving gene‐protein‐reaction associations, resolution of metabolic gaps, updates in biomass compositions, and more extensive description of biosynthetic pathways of secondary metabolites (Figure ) …”