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.
Highlights
Cyanobacteria are photoautotrophic prokaryotes that exhibit robust growth under diverse environmental conditions with minimal nutritional requirements
Genome-scale models (GSMs) are the collection of gene to protein to reaction associations (GPRs), charge and elementally balanced reactions, and constraints on molecular functions found within a cell [1,2,3,4]
Since Cyanothece ATCC 51142 is closely related to all five Cyanothece species discussed in this paper [12], it was used in the development of the reconstructions for five organisms, Cyanothece PCC 7424, 7425, 7822, 8801, and 8802, as iCyc792, iCyn731, iCyj826, iCyp752, and iCyh755 respectively
Summary
Cyanobacteria 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 reconstruction of quality genome-scale metabolic models for organisms with limited annotation resources remains a challenging task. Genome-scale models (GSMs) are the collection of gene to protein to reaction associations (GPRs), charge and elementally balanced reactions, and constraints on molecular functions found within a cell [1,2,3,4]. The objective of this study is to expediently generate models for a collection of members of a genus, using as a foundation an existing high-quality metabolic model for a representative member of the genus, while integrating information from a range of available sources
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