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Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece Sp University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Chemical and Biomolecular Engineering -- All Chemical and Biomolecular Engineering, Faculty Papers Department of 2012 Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803 Rajib Saha Pennsylvania State University, [email protected] Alex T. Verseput The Pennsylvania State University Bertram M. Berla Washington University Thomas J. Mueller Pennsylvania State University Himadri B. Pakrasi Washington University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/chemengall Saha, Rajib; Verseput, Alex T.; Berla, Bertram M.; Mueller, Thomas J.; Pakrasi, Himadri B.; and Maranas, Costas D., "Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803" (2012). Chemical and Biomolecular Engineering -- All Faculty Papers. 48. https://digitalcommons.unl.edu/chemengall/48 This Article is brought to you for free and open access by the Chemical and Biomolecular Engineering, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Chemical and Biomolecular Engineering -- All Faculty Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Rajib Saha, Alex T. Verseput, Bertram M. Berla, Thomas J. Mueller, Himadri B. Pakrasi, and Costas D. Maranas This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/chemengall/48 Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803 Rajib Saha1, Alex T. Verseput1, Bertram M. Berla2, Thomas J. Mueller1, Himadri B. Pakrasi2,3, Costas D. Maranas1* 1 Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America, 2 Department of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, Missouri, United States of America, 3 Department of Biology, Washington University, St. Louis, Missouri, United States of America Abstract Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen) and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively) span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models. Citation: Saha R, Verseput AT, Berla BM, Mueller TJ, Pakrasi HB, et al. (2012) Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS ONE 7(10): e48285. doi:10.1371/journal.pone.0048285 Editor: John Parkinson, Hospital for Sick Children, Canada Received June 29, 2012; Accepted September 21, 2012; Published October 31, 2012 Copyright: ß 2012 Saha et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by a grant from the United States Department of Energy, Biological and Environmental Research (DOE-BER), grant DE- SC0006870. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction biochemical pathways are significant advantages of cyanobacteria as efficient platforms for harvesting solar energy and producing Cyanobacteria represent a widespread group of photosynthetic bio-products such as short chain alcohols, hydrogen and alkanes prokaryotes [1]. By contributing oxygen to the atmosphere, they [6]. played an important role in the precambrian phase [2]. The genus Cyanothece includes unicellular cyanobacteria that can Cyanobacteria are primary producers in aquatic environments fix atmospheric nitrogen. Cyanothece sp. ATCC 51142 (hereafter and contribute significantly to biological carbon sequestration, O2 Cyanothece 51142) is one of the most potent diazotrophs charac- production and the nitrogen cycle [3–5]. Their inherent photo- terized and the first to be completely sequenced [9]. Studies show synthetic capability and ease in genetic modifications are two that it can fix atmospheric nitrogen at rates higher than many significant advantages over other microbes in the industrial filamentous cyanobacteria and also accommodate the biochemi- production of valuable bioproducts [6]. In contrast to other cally incompatible processes of photosynthesis and nitrogen microbial production processes requiring regionally limited fixation within the same cell by temporally separating them [10]. cellulosic feedstocks, cyanobacteria only need CO2, sunlight, Synechocystis sp. PCC 6803 (hereafter Synechocystis 6803), the first water and a few mineral nutrients to grow [6]. Sunlight is the most photosynthetic organism with a completely sequenced genome abundant source of energy on earth. The incident solar flux onto [11], is probably the most extensively studied model organism for the USA alone is approximately 23,000 terawatts which dwarfs the photosynthetic processes [12]. It is also closely related to Cyanothece global energy usage of 3.16 terawatts [7]. Cyanobacteria perform 51142 and shares many characteristics with all Cyanothece [9]. The photosynthesis more efficiently than terrestrial plants (3–9% vs. genome of Cyanothece 51142 is about 35% larger than that of 2.4–3.7%) [8]. The short life cycle and transformability of Synechocystis 6803 mostly due to the presence of nitrogen fixation cyanobacteria combined with a detailed understanding of their and temporal regulation related genes in Cyanothece 51142 [9]. PLOS ONE | www.plosone.org 1 October 2012 | Volume 7 | Issue 10 | e48285 Comparison of Metabolic Potential of Cyanobacteria Synechocystis 6803 has been the subject of many targeted genetic in Cyanothece iCyt773. New pathways include, among many, a TCA manipulations (e.g., expression of heterologous gene products) as bypass [33], heptadecane biosynthesis [21] and detailed fatty acid a photo-biological platform for the production of valuable biosynthesis in iSyn731 and comprehensive lipid and pigment chemicals such as poly-beta-hydroxybutyrate, isoprene, hydrogen biosynthesis and pentadecane biosynthesis [21] in iCyt773. For the and biofuels [12–20]. However, genetic tools for Cyanothece 51142 first time, not only extensive gene essentiality data [34] is used to are still lacking thus hampering its wide use as a bio-production assess the quality of the developed model (i.e., iSyn731) but also strain even though it has many attractive native pathways. For the allowable model metabolic phenotypes are contrasted against example, Cyanothece 51142 can produce (in small amounts) MFA flux data [35]. The diurnal rhythm of Cyanothece metabolism pentadecane and other hydrocarbons while containing a novel is modeled for the first time via developing separate (light/dark) (though incomplete) non-fermentative pathway for producing biomass equations and regulating metabolic fluxes based on butanol [21,22]. available protein expression data over light and dark phases [36]. A breakthrough in solar biofuel production will require following one of two strategies: 1) obtaining photosynthetic strains Materials and Methods that naturally have high-throughput pathways analogous to those in known biofuel producers, or 2) creating cellular environments Measurement of Biomass Precursors conducive for heterologous enzyme function. Despite its attractive Growth conditions. Wild-type Synechocystis 6803 and Cya- capabilities including nitrogen fixation and H2 production [19], nothece 51142 were grown for several days from an initial OD730 of unfortunately genetic tools are not currently available to efficiently ,0.05 to ,0.4. Synechocystis 6803 was grown in BG-11 medium test engineering interventions directly for Cyanothece
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