Team:Bielefeld-CeBiTec/Project/CO2-fixation/GeneticalApproach

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Module II - Carbon Dioxide (CO2) Fixation



Genetical approach




Introduction and motivation

Our aim is to bind carbon dioxide in organic molecules using E. coli. There are many different pathways known for carbon dioxide fixation in bacteria. Most suitable for our application are the 3-hydroxypropionate bicycle and the reductive pentose phosphate cycle also called Calvin cycle. We were looking for aerobic possibilities of carbon dioxide fixation, because of the desired energy source. Electric power should be the only source of energy for our bacteria. Therefore an aerobic cultivation is required. The electrons should pass through the bacterial respiratory chain. Oxygen is needed as the final acceptor of electrons at the end of the respiratory chain. Finally we decided to construct a bacterial version of the calvin cycle which is a well understood carbon dioxide fixation mechanism in plants (Winkel, 2004; Raines, 2003). One reason for our choice was the existence of almost all essentiell enzymes in E. coli. Only enzymes for three steps are missing. The implementation of the 3-hydroxypropionate bicycle would require the heterologous expression of genes for nearly all involved enzymes. All in all would this sum up to at least 12 genes. Nevertheless we developed plans for the construction of both pathways in E. coli.



Sedoheptulose-1,7-bisphosphatase

The first missing enzyme of the Calvin cycle in E. coli is the sedoheptulose-1,7-bisphosphatase (SBPase). While this enzyme is common in plants only a few bacterial versions of it are known. One bacterial SBPase was recently identified and characterized (Stolzenberger et al. in 2013). The origin of this sequence is the thermophilic Bacillus methanolicus. B. methanolicus lives at 50°C and therefore the temperature optimum of this enzyme is also at 50°C (Stolzenberger et al., 2013). We would like to use this enzyme at 37°C in E. coli. It had not escaped our notice that this temperature difference could cause a significant reduction in activity (Peterson et al., 2007). To our best knowledge there are no better fitting bacterial enzymes available. Tierefore we decided to clone the coding sequence of glpXC into pSB1C3. This BioBrick should then be combined with a strong promotor to enable a heterologous overexpression in E. coli. We selected the T7 and Ptac promotors for this task. The T7 is at least suitable for a simple overexpression. The resulting protein could be analysed by SDS-PAGE and MALDI-TOF-MS. This methods are suitable to proof the synthesis of GlpX. There is also an enzyme assay to validate the function of protein.



Phosphoribulokinase

The next critical step of the Calvin cycle is the phosphorylation of riublose-5-phosphate. This reaction is catalyzed by the phosphoribulokinase. E. coli lacks such an enzyme. Therefore a phosphoribulokinase encoding sequence is taken from Synechococcus elongatus. It was functionally tested before (Parikh et al., 2006). The evolutionary distance between these two species is huge and the codon usage is different. Therefore we ordered the synthesis of a codong optimized sequence for E. coli(BBa_K1465201). The function of this enzyme can be analysed by the toxicity of its product. Ribulose-1,5-bisphosphate is not metabolized in the wildtype of E. coli(Parikh et al., 2006).



RubisCO

The most important step is the actual carbon dioxide fixing reaction. It is catalyzed by ribulose-1,5-bisphosphate-carboxylase/oxygenase (RubisCO) in plants. We looked for a bacterial ezymes and selected two different RuBisCOs. One is an enzyme from the carboxysome of Halothiobacillus neapolitanus (Bonacchi et al., 2011). The other one is from Synechococcus elongatus (Long et al., 2007). We decided to express both in E. coli and to make a comparison between them. To validate the enzyme function of the RubisCO we would like to coexpress it with the phosphoribulokinase. The toxicity of the PrkA should be avoided by the RubisCO activity. The produced ribulose-1,5-bisphosphate is no longer a metabolic dead end. The RubisCO should use this metabolite as substrate and thereby close this pathway. The RubisCO from H. neapolitanus is usually located in a special microcompartiment called "carboxysome"(Bonacchi et al. in 2011). Therefore we decided to construct a carboxysome in E. coli. We would like to compare the enzymatic activity inside the carboxysome and in the cytoplasm. The separation of enzymes from both compartments could be achieved by ultracentrifugation.



Carboxysome

The carboxysome ensures an efficient carbon fixation reaction under aerobic conditions. The concentration of carbon dioxide is selectively increased inside the carboxysome (Reinhold et al., 1991; Dou et al., 2008; Mangan and Brenner, 2014). The gene cluster of the carboxysome contains many illegal restriction sites. Because of this we decided to order synthesis of some parts of the sequence to delete this recognition sites. By synthesizing we are able to optimize the codon usage for expression in E. coli.



Summary

If it is possible to enable the whole cycle in E. coli the cells should be able to grow with electricity as energy source and carbon dioxide as sole carbon source. As a backup we think of feeding a pentose sugar (xylose) to support the Calvin cycle in case the efficiency of the newly created electroautotrophic metabolism is not high enough.

References
  • Winkel, B. S. J. „Metabolic Channeling in Plants“. Annual Review of Plant Biology 55 (2004): 85–107. doi:10.1146/annurev.arplant.55.031903.141714.
  • Raines, C. A. „The Calvin Cycle Revisited“. Photosynthesis Research 75, Nr. 1 (2003): 1–10. doi:10.1023/A:1022421515027.
  • Stolzenberger, Jessica, Steffen N. Lindner, Marcus Persicke, Trygve Brautaset, und Volker F. Wendisch. „Characterization of Fructose 1,6-Bisphosphatase and Sedoheptulose 1,7-Bisphosphatase from the Facultative Ribulose Monophosphate Cycle Methylotroph Bacillus Methanolicus“. Journal of Bacteriology 195, Nr. 22 (November 2013): 5112–22. doi:10.1128/JB.00672-13.
  • Peterson, Michelle E., Roy M. Daniel, Michael J. Danson, und Robert Eisenthal. „The dependence of enzyme activity on temperature: determination and validation of parameters“. Biochemical Journal 402, Nr. Pt 2 (1. März 2007): 331–37. doi:10.1042/BJ20061143.
  • Bonacci, Walter, Poh K. Teng, Bruno Afonso, Henrike Niederholtmeyer, Patricia Grob, Pamela A. Silver, und David F. Savage. „Modularity of a Carbon-Fixing Protein Organelle“. Proceedings of the National Academy of Sciences 109, Nr. 2 (1. Oktober 2012): 478–83. doi:10.1073/pnas.1108557109.
  • Long, Benedict M., Murray R. Badger, Spencer M. Whitney, und G. Dean Price. „Analysis of Carboxysomes from Synechococcus PCC7942 Reveals Multiple Rubisco Complexes with Carboxysomal Proteins CcmM and CcaA“. Journal of Biological Chemistry 282, Nr. 40 (10. Mai 2007): 29323–35. doi:10.1074/jbc.M703896200.
  • Reinhold et al., 1990. A model for inorganic carbon fluxes and photosynthesis in cyanobacterial carboxysomes. Canadian Journal of Botany, vol. 69, pp. 984-988
  • Dou, Zhicheng, Sabine Heinhorst, Eric B. Williams, C. Daniel Murin, Jessup M. Shively, und Gordon C. Cannon. „CO2 Fixation Kinetics of Halothiobacillus Neapolitanus Mutant Carboxysomes Lacking Carbonic Anhydrase Suggest the Shell Acts as a Diffusional Barrier for CO2“. The Journal of Biological Chemistry 283, Nr. 16 (18. April 2008): 10377–84. doi:10.1074/jbc.M709285200.
  • Mangan, Niall M, und Michael P Brenner. „Systems analysis of the CO2 concentrating mechanism in cyanobacteria“. eLife 3 (29. April 2014). doi:10.7554/eLife.02043.

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