A protocol for generating a high-quality genome-scale metabolic reconstruction

Abstract

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have developed over the past 10 years. These reconstructions represent structured knowledge-bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates myriad computational biological studies including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics, and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge-bases. Here, we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction as well as common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

“…22). New content can be added to an AGORA reconstruction manually or automatically, for example, using rBioNet 15 , which is compatible with the COBRA toolbox 8 and ensures all QC/QA measures defined by the community as described by Thiele and Palsson (2010) 9 . The "Feedback" tab provides contact information to the VMH developers regarding improvements to any resources available on the VMH webpage, where additions to any resource will be upheld by the VMH developers.…”

“…Gaps in the draft reconstruction are automatically filled, building a metabolic reconstruction whose condition-specific models can carry flux through a defined biomass objective function. We refined the draft reconstructions using rBioNet 15 and performed quality control and quality assurance (QC/QA) tests, including the verification of reaction directionality and mass and charge balance Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota r e s o u r c e (Online Methods and Supplementary Note 1) to ensure that the reconstructions meet the quality standards set by Thiele and Palsson (2010) 9 . We expanded the reconstructions by refining gut-microbiota-specific and central metabolic subsystems, and curated all of the reconstructions by reference to 236 publications, two reference books (Supplementary Table 1), and comparative genomics analyses (Online Methods and Supplementary Table 2).…”

“…GENREs are assembled using the genome sequence and experimental information 9 . These reconstructions form the basis for the development of condition-specific metabolic models whose functions are simulated and validated by comparison with experimental results.…”

“…Manual curation of draft reconstructions is time consuming because it involves an extensive literature review and experimental validation of metabolic functions 9 .…”

Cattle genomics and its implications for future nutritional strategies for dairy cattle

“…There are two ways of applying metabolic reconstruction to decipher underlying mechanism of metabolic regulations: (i) development of mathematical models to simulate the behavior of a specific cellular system with genetic or physiological pertubation (Thiele and Palsson, 2010); and (ii) integration of high-throughput '-omics' data to discover biological signatures in nutritional, physiological and/or pathological responses (Loor, 2010;Peddinti et al, 2010). Ruminant nutritionists are familiar with the former approach; mathematical modeling of metabolism.…”