ArticleBMC systems biology2013
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 34 citations in OpenAlex.
- Terpene-based biofuels production: a revolutionizing role of cyanobacteria through metabolic engineering, opportunities and challenges.Archives of microbiology · 2026Review
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling.PLoS computational biology · 2021Article
- Genome-scale metabolic reconstruction of the non-model yeastMetabolic engineering communications · 2020Article
- Biochemical Characteristics and a Genome-Scale Metabolic Model of an Indian Euryhaline Cyanobacterium with High Polyglucan Content.Metabolites · 2020Article
- A comprehensive genome-scale model forMetabolic engineering communications · 2019Article
- New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering.Frontiers in bioengineering and biotechnology · 2019Review
- Thermodynamic Constraints Improve Metabolic Networks.Biophysical journal · 2017Article
- Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973.Scientific reports · 2017Article
- Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects.Life (Basel, Switzerland) · 2016Review
- From cyanochemicals to cyanofactories: a review and perspective.Microbial cell factories · 2016Review
- Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach.Frontiers in bioengineering and biotechnology · 2016Review
- Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production.Metabolites · 2015Review
- Transparency in metabolic network reconstruction enables scalable biological discovery.Current opinion in biotechnology · 2015Review
- Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model.Biotechnology for biofuels · 2014Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCyanobacteria are photoautotrophic prokaryotes that exhibit robust growth under diverse environmental conditions with minimal nutritional requirements. They can use solar energy to convert CO2 and other reduced carbon sources into biofuels and chemical products. The genus Cyanothece includes unicellular nitrogen-fixing cyanobacteria that have been shown to offer high levels of hydrogen production and nitrogen fixation. The reconstruction of quality genome-scale metabolic models for organisms with limited annotation resources remains a challenging task.
resultsHere we reconstruct and subsequently analyze and compare the metabolism of five Cyanothece strains, namely Cyanothece sp. PCC 7424, 7425, 7822, 8801 and 8802, as the genome-scale metabolic reconstructions iCyc792, iCyn731, iCyj826, iCyp752, and iCyh755 respectively. We compare these phylogenetically related Cyanothece strains to assess their bio-production potential. A systematic workflow is introduced for integrating and prioritizing annotation information from the Universal Protein Resource (Uniprot), NCBI Protein Clusters, and the Rapid Annotations using Subsystems Technology (RAST) method. The genome-scale metabolic models include fully traced photosynthesis reactions and respiratory chains, as well as balanced reactions and GPR associations. Metabolic differences between the organisms are highlighted such as the non-fermentative pathway for alcohol production found in only Cyanothece 7424, 8801, and 8802.
conclusionsOur development workflow provides a path for constructing models using information from curated models of related organisms and reviewed gene annotations. This effort lays the foundation for the expedient construction of curated metabolic models for organisms that, while not being the target of comprehensive research, have a sequenced genome and are related to an organism with a curated metabolic model. Organism-specific models, such as the five presented in this paper, can be used to identify optimal genetic manipulations for targeted metabolite overproduction as well as to investigate the biology of diverse organisms.
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