Constraint-based modeling analysis of the metabolism of two Pelobacter species. BMC Syst Biol 4:e174

Genomatica Inc., 10520 Wateridge Circle, San Diego, CA, USA.
BMC Systems Biology (Impact Factor: 2.44). 12/2010; 4(1):174. DOI: 10.1186/1752-0509-4-174
Source: PubMed


Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells.
In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models.
We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community.

18 Reads
  • Source
    • "Manual curation can then be reserved for certain key steps. Some of these models only include additional reactions beyond those retrieved from the curated models if the reactions are required for biomass production [58,60,61]. This restricts the inclusion of reactions unique to either that organism or a subset of organisms that the reference models do not belong to. "
    [Show abstract] [Hide abstract]
    ABSTRACT: 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 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. Here 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. Our 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.
    BMC Systems Biology 12/2013; 7(1):142. DOI:10.1186/1752-0509-7-142 · 2.44 Impact Factor
  • Source
    • "The complete genome sequence of P. carbinolicus has led to the discoveries that it expresses c-type cytochromes [8] and that it utilizes Fe(III) as a terminal electron acceptor indirectly via reduction of S° [9]. In silico metabolic models have been constructed for P. carbinolicus and P. propionicus[10], their genomes have been compared to those of acetate-oxidizing, non-fermentative Geobacteraceae[11], and a shortage of histidyl-tRNA caused by the CRISPR locus has been proposed to account for the loss of some ancestral genes such as multiheme c-type cytochromes by the P. carbinolicus genome [12]. However, there are many features of the P. carbinolicus genome that these studies have not addressed. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. Results Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires. Conclusions Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.
    BMC Genomics 12/2012; 13(1):690. DOI:10.1186/1471-2164-13-690 · 3.99 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The demonstrated advantages of polymer insulators have been verified by field experience, and these products are becoming widely accepted for suspension and horizontal line post applications. The use of polymer station posts has been comparatively small and mostly limited to bus support applications. This document reviews the characteristics of polymer posts for vertical break switch applications. Information is presented which indicates that polymer station posts may be used as direct replacements for porcelain station posts in transmission class switch installations
    Transmission and Distribution Construction and Live Line Maintenance, 1995. ESMO-95 Proceedings., Seventh International Conference on; 01/1995
Show more

Preview (3 Sources)

18 Reads
Available from