Dokument

Summary:
The fixation of inorganic carbon and the conversion to organic molecules is a prerequisite for life and the foundation of the carbon cycle on Earth. Since the industrial revolution, this carbon cycle has become inbalanced and consequently the atmospheric carbon dioxide (CO2) concentration is increasing and is a major cause of global warming. On the contrary, atmospheric CO2 can also be considered as an important carbon feedstock of the future. However, human society has not yet come up with a viable solution to convert this inorganic atmospheric CO2 back into reduced carbon compounds and is still relying on natural CO2 fixation. Nature has evolved multiple solutions to reduce CO2 and incorporate it into organic molecules. The involved pathways differ in their cofactor requirements and are often limited to anoxic conditions. Many attempts have been made to improve natural carbon fixation to a more energy efficient process, but showed little success. The emerging field of synthetic biology offers an alternative approach by designing novel pathways for the fixation of CO2. Although, several such artificial pathways have been designed, none of them have been realized so far. This reveals an existing gap between the design and the realization and implementation of such a synthetic CO2 fixation pathway. In this work we designed several synthetic oxygen-tolerant CO2 fixation pathways in a bottom-up approach, by freely combining enzymes from different biological sources. The pathways were designed around an efficient central carboxylase from the family of enoyl-CoA carboxylases/reductases. Some members of this family belong to the most efficient carboxylases known so far, do not accept oxygen as a substrate and only require the ubiquitous NADPH as co-substrate. The theoretical analysis of thermodynamic and energetic properties of the designed pathways for CO2 fixation also showed that they are comparable or even more energy efficient than naturally occurring oxygen-tolerant CO2-fixing pathways. We were able to realize two of these cycles in vitro and investigated their efficiencies for the fixation of inorganic CO2 into organic molecules. We established the Crotonyl-CoA/EThylmalonyl-CoA/Hydroxybutyryl-CoA (CETCH) and HydrOxyPropionyl-CoA/Acrylyl-CoA (HOPAC) cycle in vitro and their CO2 fixation efficiencies were increased in several rounds of optimization. In this process, we energized the systems by ATP- and NADPH-regeneration modules, applied the principle of metabolic proofreading to recycle undesired side products and engineered several enzymes to efficiently catalyze desired reactions. The CETCH cycle in its current version 5.4 is a reaction network of 17 enzymes originating from nine different organisms of all three domains of life. It converts CO2 into organic molecules at a rate of 5 nmol CO2 per minute and mg enzyme. In comparison, the HOPAC cycle in its current version 4.1 comprises 15 enzymes originating from eight different organisms. A stepwise incorporation of 13CO2 into the intermediates of both synthetic pathway confirmed a continuous operation for multiple rounds of conversion. During the development of the synthetic cycles for CO2 fixation, we solved a novel crystal structure of a key enzyme for both pathways, the methylsuccinyl-CoA dehydrogenase. This is a member of the well described family of flavin dependent acyl-CoA dehydrogenases. We elucidated the substrate specificity of the enzyme for (2S)-methylsuccinyl-CoA, which represents a complex substrate amongst the acyl-CoA dehydrogenase family. In summary, this study laid the foundation for the development of artificial pathways for the fixation of CO2 and narrow the gap between theoretical design of synthetic CO2 fixation pathways and their application in vivo. The CETCH and HOPAC cycle expands the solution space beyond the six naturally evolved CO2 fixation pathways by two man-made alternative that are thermodynamically more efficient than the CBB cycle of plants.

Bibliographie / References

1. T. J. Erb et al., (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Mol. Microbiol. 73, 992-1008 (2009).
2. S. Djordjevic et al., 3-Dimensional Structure of Butyryl-Coa Dehydrogenase from Megasphaera-Elsdenii. Biochemistry 34, 2163-2171 (1995).
3. R. Teufel et al., 3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J. Bacteriol. 191, 4572-4581 (2009).
4. I. A. Berg et al., A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318, 1782-1786 (2007).
5. S. Herter et al., A bicyclic autotrophic CO2 fixation pathway in Chloroflexus aurantiacus. J. Biol. Chem. 277, 20277-20283 (2002).
6. R. Laguna et al., Acetate-dependent photoheterotrophic growth and the differential requirement for the Calvin-Benson-Bassham reductive pentose phosphate cycle in Rhodobacter sphaeroides and Rhodopseudomonas palustris. Arch. Microbiol. 193, 151-154 (2011).
7. S. W. Ragsdale and E. Pierce, Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873-1898 (2008).
8. L. Tong, Acetyl-coenzyme A carboxylase: crucial metabolic enzyme and attractive target for drug discovery. Cell. Mol. Life Sci. 62, 1784-1803 (2005).
9. D. M. Peter et al., A Chemo-Enzymatic Road Map to the Synthesis of CoA Esters. Molecules 21, 517 (2016).
10. J. J. Kim and R. Miura, Acyl-CoA dehydrogenases and acyl-CoA oxidases. Structural basis for mechanistic similarities and differences. Eur. J. Biochem. 271, 483-493 (2004).
11. H. Huber et al., A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. Proc. Natl. Acad. Sci. U.S.A 105, 7851- 7856 (2008).
12. G. Fuchs, Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631-658 (2011).
13. M. Khomyakova et al., A methylaspartate cycle in haloarchaea. Science 331, 334-337 (2011).
14. M. Konneke et al., Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc. Natl. Acad. Sci. U.S.A 111, 8239-8244 (2014).
15. P. H. Opgenorth et al., A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system. Nat. Chem. Biol. 13, 938-942 (2017).
16. T. C. Lehman et al., An acyl-coenzyme A dehydrogenase assay utilizing the ferricenium ion. Anal. Biochem. 186, 280-284 (1990).
17. H. L. Kornberg, Anaplerotic Sequences in Microbial Metabolism. Angew. Chem. Int. Ed. Engl. 4, 558-565 (1965).
18. L. Schada von Borzyskowski et al., An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. (to be published), (2017).
19. M. C. Evans et al., A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc. Natl. Acad. Sci. U.S.A 55, 928-934 (1966).
20. R. K. Yadav et al., A Photocatalyst-Enzyme Coupled Artificial Photosynthesis System for Solar Energy in Production of Formic Acid from CO2. J. Am. Chem. Soc. 134, 11455-11461 (2012).
21. D. N. Greene et al., Artificially evolved Synechococcus PCC6301 Rubisco variants exhibit improvements in folding and catalytic efficiency. Biochem. J. 404, 517-524 (2007).
22. L. Schada von Borzyskowski et al., A set of versatile brick vectors and promoters for the assembly, expression, and integration of synthetic operons in Methylobacterium extorquens AM1 and other alphaproteobacteria. ACS Synth. Biol. 4, 430-443 (2015).
23. J. K. Kroeger et al., A spectrophotometric assay for measuring acetyl-coenzyme A carboxylase. Anal. Biochem. 411, 100-105 (2011).
24. P. H. Opgenorth et al., A synthetic biochemistry module for production of bio-based chemicals from glucose. Nat. Chem. Biol. 12, 393-395 (2016).
25. P. H. Opgenorth et al., A synthetic biochemistry molecular purge valve module that maintains redox balance. Nat. Commun. 5, 4113 (2014).
26. T. P. Korman et al., A synthetic biochemistry platform for cell free production of monoterpenes from glucose. Nat. Commun. 8, 15526 (2017).
27. B. Jobst et al., ATP-dependent carboxylation of acetophenone by a novel type of carboxylase. J. Bacteriol. 192, 1387-1394 (2010).
28. I. A. Berg et al., Autotrophic carbon fixation in archaea. Nat. Rev. Microbiol. 8, 447-460 (2010).
29. J. E. Cronan and J. Thomas, Bacterial Fatty Acid Synthesis and Its Relationships with Polyketide Synthetic Pathways. Complex Enzymes in Microbial Natural Product Biosynthesis, Part B: Polyketides, Aminocoumarins and Carbohydrates 459, 395-433 (2009).
30. H. L. Kornberg and J. G. Morris, Beta-Hydroxyaspartate pathway: a new route for biosyntheses from glyoxylate. Nature 197, 456-457 (1963).
31. M. C. Wilson and B. S. Moore, Beyond ethylmalonyl-CoA: the functional role of crotonyl-CoA carboxylase/reductase homologs in expanding polyketide diversity. Nat. Prod. Rep. 29, 72-86 (2012).
32. S. M. Glueck et al., Biocatalytic carboxylation. Chem. Soc. Rev. 39, 313-328 (2010).
33. T. J. Erb and J. Zarzycki, Biochemical and synthetic biology approaches to improve photosynthetic CO2-fixation. Curr. Opin. Chem. Biol. 34, 72-79 (2016).
34. B. Kuchler et al., Biochemical characterization of a variant human medium-chain acyl-CoA dehydrogenase with a disease-associated mutation localized in the active site. Biochem. J. 337 ( Pt 2), 225-230 (1999).
35. B. M. van Vugt-Lussenburg et al., Biochemical similarities and differences between the catalytic [4Fe-4S] cluster containing fumarases FumA and FumB from Escherichia coli. PLoS One 8, e55549 (2013).
36. L. Rosgaard et al., Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants. J. Biotechnol. 162, 134-147 (2012).
37. L. Brennan and P. Owende, Biofuels from microalgae-A review of technologies for production, processing, and extractions of biofuels and co-products. Renew. Sust. Energ. Rev. 14, 557-577 (2010).
38. E. Holler et al., Biological and Biosynthetic-Properties of Poly-L-Malate. FEMS Microbiol. Lett. 103, 109-118 (1992).
39. Y. A. Chan et al., Biosynthesis of polyketide synthase extender units. Nat. Prod. Rep. 26, 90- 114 (2009).
40. A. Chang et al., BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res. 43, D439-446 (2015).
41. R. M. Cuellar-Franca and A. Azapagic, Carbon capture, storage and utilisation technologies: A critical analysis and comparison of their life cycle environmental impacts. J. CO2 Util. 9, 82-102 (2015).
42. J. B. McKinlay and C. S. Harwood, Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria. Proc. Natl. Acad. Sci. U.S.A 107, 11669-11675 (2010).
43. T. J. Erb, Carboxylases in natural and synthetic microbial pathways. Appl. Environ. Microbiol. 77, 8466-8477 (2011).
44. T. J. Erb et al., Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase. Proc. Natl. Acad. Sci. U.S.A 106, 8871-8876 (2009).
45. M. Hugler et al., Characterization of acetyl-CoA/propionyl-CoA carboxylase in Metallosphaera sedula. Carboxylating enzyme in the 3-hydroxypropionate cycle for autotrophic carbon fixation. Eur. J. Biochem. 270, 736-744 (2003).
46. G. Antranikian et al., Characterization of ATP citrate lyase from Chlorobium limicola. J. Bacteriol. 152, 1284-1287 (1982).
47. V. de Lorenzo et al., Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol. Rev. 39, 96-119 (2015).
48. H. Holo, Chloroflexus-Aurantiacus Secretes 3-Hydroxypropionate, a Possible Intermediate in the Assimilation of CO2 and Acetate. Arch. Microbiol. 151, 252-256 (1989).
49. R. K. Thauer, Citric-acid cycle, 50 years on. Modifications and an alternative pathway in anaerobic bacteria. Eur. J. Biochem. 176, 497-508 (1988).
50. IPCC, "Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change," (IPCC: Geneva, Switzerland, 2014).
51. S. Bhattacharyya et al., Combined quantum mechanical and molecular mechanical simulations of one-and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl- CoA dehydrogenase, and cholesterol oxidase. J Phys Chem A 111, 5729-5742 (2007).
52. S. Galanie et al., Complete biosynthesis of opioids in yeast. Science 349, 1095-1100 (2015).
53. M. Kitagawa et al., Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12, 291-299 (2005).
54. J. Mackenzie et al., Controlling electron transfer in Acyl-CoA oxidases and dehydrogenases: a structural view. J. Biol. Chem. 281, 31012-31020 (2006).
55. Y. Savir et al., Cross-species analysis traces adaptation of Rubisco toward optimality in a low- dimensional landscape. Proc. Natl. Acad. Sci. U.S.A 107, 3475-3480 (2010).
56. A. M. Gotto and H. L. Kornberg, Crystalline tartronic semialdehyde reductase from Pseudomonas ovalis Chester. Biochim. Biophys. Acta 48, 604-605 (1961).
57. K. P. Battaile et al., Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with acetoacetyl-CoA: comparison with other acyl-CoA dehydrogenases. J. Biol. Chem. 277, 12200-12207 (2002).
58. C. S. Huang et al., Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase. Nature 466, 1001-1005 (2010).
59. L. Diacovich et al., Crystal structure of the beta-subunit of acyl-CoA carboxylase: structure- based engineering of substrate specificity. Biochemistry 43, 14027-14036 (2004).
60. Z. Fu et al., Crystal structures of human glutaryl-CoA dehydrogenase with and without an alternate substrate: structural bases of dehydrogenation and decarboxylation reactions. Biochemistry 43, 9674-9684 (2004).
61. J. J. Kim et al., Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Proc. Natl. Acad. Sci. U.S.A 90, 7523-7527 (1993).
62. A. Bar-Even et al., Design and analysis of synthetic carbon fixation pathways. Proc. Natl. Acad. Sci. U.S.A 107, 8889-8894 (2010).
63. C. A. Hutchison et al., Design and synthesis of a minimal bacterial genome. Science 351, 1414- U1473 (2016).
64. U. Barenholz et al., Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points. Elife 6, (2017).
65. G. G. Tcherkez et al., Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized. Proc. Natl. Acad. Sci. U.S.A 103, 7246-7251 (2006).
66. M. R. Parikh et al., Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli. Protein Eng. Des. Sel. 19, 113-119 (2006).
67. R. G. Rosenthal et al., Direct evidence for a covalent ene adduct intermediate in NAD(P)H- dependent enzymes. Nat. Chem. Biol. 10, 50-55 (2014).
68. H. S. Toogood et al., Dynamics driving function: new insights from electron transferring flavoproteins and partner complexes. FEBS J. 274, 5481-5504 (2007).
69. I. A. Berg, Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl. Environ. Microbiol. 77, 1925-1936 (2011).
70. M. Enquist-Newman et al., Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature 505, 239-243 (2014).
71. P. Kiefer et al., eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. Bioinformatics 29, 963-964 (2013).
72. C. Dellomonaco et al., Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals. Nature 476, 355-359 (2011).
73. K. Hoelsch et al., Engineering of formate dehydrogenase: synergistic effect of mutations affecting cofactor specificity and chemical stability. Appl. Microbiol. Biotechnol. 97, 2473-2481 (2013).
74. Y. K. Wang et al., Enhanced production of Ca(2)(+)-polymalate (PMA) with high molecular mass by Aureobasidium pullulans var. pullulans MCW. Microb. Cell. Fact. 14, 115 (2015).
75. G. Strauss and G. Fuchs, Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle. Eur. J. Biochem. 215, 633-643 (1993).
76. S. W. Ragsdale, Enzymology of the wood-Ljungdahl pathway of acetogenesis. Ann. N. Y. Acad. Sci. 1125, 129-136 (2008).
77. A. Flamholz et al., eQuilibrator--the biochemical thermodynamics calculator. Nucleic Acids Res. 40, D770-775 (2012).
78. C. L. Linster et al., Ethylmalonyl-CoA decarboxylase, a new enzyme involved in metabolite proofreading. J. Biol. Chem. 286, 42992-43003 (2011).
79. T. J. Erb et al., Ethylmalonyl-CoA mutase from Rhodobacter sphaeroides defines a new subclade of coenzyme B12-dependent acyl-CoA mutases. J. Biol. Chem. 283, 32283-32293 (2008).
80. J. Ormerod, 'Every dogma has its day'*: a personal look at carbon metabolism in photosynthetic bacteria. Photosynthesis Res. 76, 135-143 (2003).
81. N. L. Gale and J. V. Beck, Evidence for the Calvin cycle and hexose monophosphate pathway in Thiobacillus ferrooxidans. J. Bacteriol. 94, 1052-1059 (1967).
82. F. Jacob, Evolution and tinkering. Science 196, 1161-1166 (1977).
83. L. Schada von Borzyskowski et al., Evolutionary history and biotechnological future of carboxylases. J. Biotechnol. 168, 243-251 (2013).
84. G. Wachtershauser, Evolution of the 1st Metabolic Cycles. Proc. Natl. Acad. Sci. U.S.A 87, 200- 204 (1990).
85. M. W. Keller et al., Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide. Proc. Natl. Acad. Sci. U.S.A 110, 5840-5845 (2013).
86. T. Fukui et al., Expression and characterization of (R)-specific enoyl coenzyme A hydratase involved in polyhydroxyalkanoate biosynthesis by Aeromonas caviae. J. Bacteriol. 180, 667- 673 (1998).
87. D. L. Falcone and F. R. Tabita, Expression of endogenous and foreign ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) genes in a RubisCO deletion mutant of Rhodobacter sphaeroides. J. Bacteriol. 173, 2099-2108 (1991).
88. M. Mattozzi et al., Expression of the sub-pathways of the Chloroflexus aurantiacus 3- hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. Metab. Eng. 16, 130-139 (2013).
89. P. Emsley et al., Features and development of Coot. Acta. Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
90. C. Hold et al., Forward design of a complex enzyme cascade reaction. Nature Communications 7, (2016).
91. S. Billerbeck et al., From understanding to designing enzymatic networks. FEBS J. 277, 23-23 (2010).
92. A. M. Appel et al., Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation. Chem. Rev. 113, 6621-6658 (2013).
93. F. R. Tabita et al., Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol. Mol. Biol. Rev. 71, 576-599 (2007).
94. J. K. Rogers and G. M. Church, Genetically encoded sensors enable real-time observation of metabolite production. Proc. Natl. Acad. Sci. U.S.A 113, 2388-2393 (2016).
95. E. Rodriguez and H. Gramajo, Genetic and biochemical characterization of the alpha and beta components of a propionyl-CoA carboxylase complex of Streptomyces coelicolor A3(2). Microbiology 145 ( Pt 11), 3109-3119 (1999).
96. A. Kaplun et al., Glyoxylate carboligase lacks the canonical active site glutamate of thiamine- dependent enzymes. Nat. Chem. Biol. 4, 113-118 (2008).
97. C. J. Paddon et al., High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496, 528-532 (2013).
98. D. M. Etheridge et al., Historical CO2 records from the Law Dome DE08, DE08-2, and DSS ice cores. In Trends: A Compendium of Data on Global Change. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tenn., U.S.A, (1989).
99. E. M. Nichols et al., Hybrid bioinorganic approach to solar-to-chemical conversion. Proc. Natl. Acad. Sci. U.S.A 112, 11461-11466 (2015).
100. T. V. Nguyen et al., Identification of isobutyryl-CoA dehydrogenase and its deficiency in humans. Mol. Genet. Metab. 77, 68-79 (2002).
101. I. Olsen and J. M. Merrick, Identification of propionate as an endogenous CO2 acceptor in Rhodospirillum rubrum and properties of purified propionyl-coenzyme A carboxylase. J. Bacteriol. 95, 1774-1778 (1968).
102. J. Zarzycki et al., Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. U.S.A 106, 21317-21322 (2009).
103. M. Volpers et al., Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro- Autotrophy. PLoS One 11, e0157851 (2016).
104. P. M. Shih et al., Introduction of a synthetic CO2-fixing photorespiratory bypass into a cyanobacterium. J. Biol. Chem. 289, 9493-9500 (2014).
105. S. Liu and A. Steinbuchel, Investigation of poly(beta-L-melic acid) production by strains of Aureobasidium pullulans. Appl. Microbiol. Biotechnol. 46, 273-278 (1996).
106. B. Willibald et al., Is beta-poly(L-malate) synthesis catalysed by a combination of beta-L-malyl- AMP-ligase and beta-poly(L-malate) polymerase? Eur. J. Biochem. 265, 1085-1090 (1999).
107. L. Diacovich et al., Kinetic and structural analysis of a new group of Acyl-CoA carboxylases found in Streptomyces coelicolor A3(2). J. Biol. Chem. 277, 31228-31236 (2002).
108. D. M. Peter, Substrate Promiscuity, Kinetics and Engineering of Enoyl-CoA Carboxylases/Reductases. Doctoral Thesis, ETH Zurich, Switzerland, (2016).
109. M. Hugler et al., Malonyl-coenzyme A reductase from Chloroflexus aurantiacus, a key enzyme of the 3-hydroxypropionate cycle for autotrophic CO2 fixation. J. Bacteriol. 184, 2404-2410 (2002).
110. A. Besrat et al., Mammalian metabolism of glutaric acid. J. Biol. Chem. 244, 1461-1467 (1969).
111. J. V. Rodrigues and C. M. Gomes, Mechanism of superoxide and hydrogen peroxide generation by human electron-transfer flavoprotein and pathological variants. Free Radic Biol Med 53, 12- 19 (2012).
112. S. Ghisla et al., Mechanistic studies with general acyl-CoA dehydrogenase and butyryl-CoA dehydrogenase: evidence for the transfer of the beta-hydrogen to the flavin N(5)-position as a hydride. Biochemistry 23, 3154-3161 (1984).
113. J. Zarzycki et al., Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. J. Bacteriol. 190, 1366-1374 (2008).
114. R. K. Thauer et al., Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6, 579-591 (2008).
115. W. Bonacci et al., Modularity of a carbon-fixing protein organelle. Proc. Natl. Acad. Sci. U.S.A 109, 478-483 (2012).
116. J. Sambrook and D. W. Russel, Molecular Cloning, a Laboratory Manual. (Cold Spring Harbor Laboratory Press, ed. 3, 2001).
117. R. J. Ellis, Most Abundant Protein in the World. Trends Biochem. Sci. 4, 241-244 (1979).
118. J. A. Rollin et al., New biotechnology paradigm: cell-free biosystems for biomanufacturing. Green Chem. 15, 1708-1719 (2013).
119. S. A. Ensign et al., New roles for CO2 in the microbial metabolism of aliphatic epoxides and ketones. Arch. Microbiol. 169, 179-187 (1998).
120. C. Lerma-Ortiz et al., 'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites. Biochem. Soc. Trans. 44, 961-971 (2016).
121. K. Izai et al., Novel fatty acid beta-oxidation enzymes in rat liver mitochondria. I. Purification and properties of very-long-chain acyl-coenzyme A dehydrogenase. J. Biol. Chem. 267, 1027- 1033 (1992).
122. F. L. Crane and H. Beinert, On the mechanism of dehydrogenation of fatty acyl derivatives of coenzyme A. II. The electron-transferring flavoprotein. J. Biol. Chem. 218, 717-731 (1956).
123. F. L. Crane et al., On the mechanism of dehydrogenation of fatty acyl derivatives of coenzyme A. I. The general fatty acyl coenzyme A dehydrogenase. J. Biol. Chem. 218, 701-706 (1956).
124. M. Bujara et al., Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis. Nat. Chem. Biol. 7, 271-277 (2011).
125. M. D. Winn et al., Overview of the CCP4 suite and current developments. Acta. Crystallogr. D Biol. Crystallogr. 67, 235-242 (2011).
126. B. W. Carlson and L. L. Miller, Oxidation of Nadh by Ferrocenium Salts -Rate-Limiting One- Electron Transfer. J. Am. Chem. Soc. 105, 7453-7454 (1983).
127. E. Noor et al., Pathway thermodynamics highlights kinetic obstacles in central metabolism. PLoS Comput. Biol. 10, e1003483 (2014).
128. P. D. Adams et al., PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta. Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
129. K. Schuhle and G. Fuchs, Phenylphosphate carboxylase: a new C-C lyase involved in anaerobic phenol metabolism in Thauera aromatica. J. Bacteriol. 186, 4556-4567 (2004).
130. G. Bowes et al., Phosphoglycolate Production Catalyzed by Ribulose Diphosphate Carboxylase. Biochem. Biophys. Res. Commun. 45, 716-722 (1971).
131. I. Yacoby et al., Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro. Proc. Natl. Acad. Sci. U.S.A 108, 9396-9401 (2011).
132. B. Nocek et al., Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria. Proc. Natl. Acad. Sci. U.S.A 105, 17730-17735 (2008).
133. P. C. Hinkle, P/O ratios of mitochondrial oxidative phosphorylation. Biochim. Biophys. Acta 1706, 1-11 (2005).
134. S. Friedmann et al., Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188, 2646-2655 (2006).
135. B. E. Alber and G. Fuchs, Propionyl-coenzyme A synthase from Chloroflexus aurantiacus, a key enzyme of the 3-hydroxypropionate cycle for autotrophic CO2 fixation. J. Biol. Chem. 277, 12137-12143 (2002).
136. A. de Marco, Protocol for preparing proteins with improved solubility by co-expressing with molecular chaperones in Escherichia coli. Nat. Protoc. 2, 2632-2639 (2007).
137. B. Sohling and G. Gottschalk, Purification and characterization of a coenzyme-A-dependent succinate-semialdehyde dehydrogenase from Clostridium kluyveri. Eur. J. Biochem. 212, 121- 127 (1993).
138. Y. Ikeda et al., Purification and characterization of short-chain, medium-chain, and long-chain acyl-CoA dehydrogenases from rat liver mitochondria. Isolation of the holo-and apoenzymes and conversion of the apoenzyme to the holoenzyme. J. Biol. Chem. 260, 1311-1325 (1985).
139. U. Gehring and D. I. Arnon, Purification and properties of -ketoglutarate synthase from a photosynthetic bacterium. J. Biol. Chem. 247, 6963-6969 (1972).
140. D. Seigneurin-Berny et al., Purification of intact chloroplasts from Arabidopsis and spinach leaves by isopycnic centrifugation. Curr. Protoc. Cell Biol. Chapter 3, Unit 3 30 (2008).
141. K. M. Yu et al., Recent advances in CO2 capture and utilization. ChemSusChem 1, 893-899 (2008).
142. D. R. Ort et al., Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc. Natl. Acad. Sci. U.S.A 112, 8529-8536 (2015).
143. S. P. Long et al., Rising atmospheric carbon dioxide: plants FACE the future. Annu. Rev. Plant Biol. 55, 591-628 (2004).
144. R. J. Spreitzer and M. E. Salvucci, Rubisco: structure, regulatory interactions, and possibilities for a better enzyme. Annu. Rev. Plant Biol. 53, 449-475 (2002).
145. D. M. Peter et al., Screening and Engineering the Synthetic Potential of Carboxylating Reductases from Central Metabolism and Polyketide Biosynthesis. Angew. Chem. Int. Ed. Engl. 54, 13457-13461 (2015).
146. Y. Ikeda et al., Separation and properties of five distinct acyl-CoA dehydrogenases from rat liver mitochondria. Identification of a new 2-methyl branched chain acyl-CoA dehydrogenase. J. Biol. Chem. 258, 1066-1076 (1983).
147. S. U. Bajad et al., Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J. Chromatogr. A 1125, 76-88 (2006).
148. N. E. Kreel and F. R. Tabita, Serine 363 of a Hydrophobic Region of Archaeal Ribulose 1,5- Bisphosphate Carboxylase/Oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis Affects CO2/O2 Substrate Specificity and Oxygen Sensitivity. PLoS One 10, e0138351 (2015).
149. K. Kajala et al., Strategies for engineering a two-celled C(4) photosynthetic pathway into rice. J. Exp. Bot. 62, 3001-3010 (2011).
150. S. Wischgoll et al., Structural basis for promoting and preventing decarboxylation in glutaryl- coenzyme a dehydrogenases. Biochemistry 49, 5350-5357 (2010).
151. R. P. McAndrew et al., Structural basis for substrate fatty acyl chain specificity: crystal structure of human very-long-chain acyl-CoA dehydrogenase. J. Biol. Chem. 283, 9435-9443 (2008).
152. J. Ruprecht et al., Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. J. Biol. Chem. 284, 29836-29846 (2009).
153. K. A. Tiffany et al., Structure of human isovaleryl-CoA dehydrogenase at 2.6 A resolution: structural basis for substrate specificity. Biochemistry 36, 8455-8464 (1997).
154. D. M. Anstrom et al., Structure of the Escherichia coli malate synthase G:pyruvate:acetyl- coenzyme A abortive ternary complex at 1.95 A resolution. Protein Sci. 12, 1822-1832 (2003).
155. K. P. Battaile et al., Structures of isobutyryl-CoA dehydrogenase and enzyme-product complex: comparison with isovaleryl-and short-chain acyl-CoA dehydrogenases. J. Biol. Chem. 279, 16526-16534 (2004).
156. B. Pohl et al., Studies on the reaction mechanism of general acyl-CoA dehydrogenase. Determination of selective isotope effects in the dehydrogenation of butyryl-CoA. Eur. J. Biochem. 160, 109-115 (1986).
157. N. Antonovsky et al., Sugar Synthesis from CO2 in Escherichia coli. Cell 166, 115-125 (2016).
158. T. J. Erb et al., Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. Proc. Natl. Acad. Sci. U.S.A 104, 10631- 10636 (2007).
159. H. L. Kornberg and H. A. Krebs, Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle. Nature 179, 988-991 (1957).
160. T. J. Erb et al., Synthetic metabolism: metabolic engineering meets enzyme design. Curr. Opin. Chem. Biol. 37, 56-62 (2017).
161. T. J. Erb et al., The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-Malyl-coenzyme A (CoA)/{beta}-methylmalyl-CoA lyase and (3S)- Malyl-CoA thioesterase. J. Bacteriol. 192, 1249-1258 (2010).
162. L. G. Ljungdahl, The autotrophic pathway of acetate synthesis in acetogenic bacteria. Annu. Rev. Microbiol. 40, 415-450 (1986).
163. M. S. Sevinc et al., The cysteines of catalase HPII of Escherichia coli, including Cys438 which is blocked, do not have a catalytic role. Eur. J. Biochem. 230, 127-132 (1995).
164. N. J. Watmough and F. E. Frerman, The electron transfer flavoprotein: ubiquinone oxidoreductases. Biochim. Biophys. Acta 1797, 1910-1916 (2010).
165. K. Schneider et al., The ethylmalonyl-CoA pathway is used in place of the glyoxylate cycle by Methylobacterium extorquens AM1 during growth on acetate. J. Biol. Chem. 287, 757-766 (2012).
166. J. A. Raven et al., The evolution of inorganic carbon concentrating mechanisms in photosynthesis. Philos. Trans. R Soc. Lond. B Biol. Sci. 363, 2641-2650 (2008).
167. D. M. Kramer and J. R. Evans, The importance of energy balance in improving photosynthetic productivity. Plant Physiol. 155, 70-78 (2011).
168. M. Calvin and A. A. Benson, The Path of Carbon in Photosynthesis. Science 107, 476-480 (1948).
169. J. A. Bassham et al., The Path of Carbon in Photosynthesis .21. The Cyclic Regeneration of Carbon Dioxide Acceptor. J. Am. Chem. Soc. 76, 1760-1770 (1954).
170. J. A. Bassham et al., The Path of Carbon in Photosynthesis .8. The Role of Malic Acid. J. Biol. Chem. 185, 781-787 (1950).
171. M. Eisenhut et al., The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants. Proc. Natl. Acad. Sci. U.S.A 105, 17199-17204 (2008).
172. M. C. Weiss et al., The physiology and habitat of the last universal common ancestor. Nat Microbiol 1, 16116 (2016).
173. M. Eisenhut et al., The plant-like C2 glycolate cycle and the bacterial-like glycerate pathway cooperate in phosphoglycolate metabolism in cyanobacteria. Plant Physiol. 142, 333-342 (2006).
174. A. Bar-Even et al., Thermodynamic constraints shape the structure of carbon fixation pathways. Biochim. Biophys. Acta 1817, 1646-1659 (2012).
175. H. L. Kornberg and J. G. Morris, The Utilization of Glycollate by Micrococcus Denitrificans: The Beta-Hydroxyaspartate Pathway. Biochem. J. 95, 577-586 (1965).
176. Y. Nakajima et al., Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase. J Biochem 131, 365-374 (2002).
177. J. R. Swartz et al., Using cell-free biology to study systems biology. Abstracts of Papers of the American Chemical Society 227, U255-U255 (2004).
178. C. Liu et al., Water splitting-biosynthetic system with CO2 reduction efficiencies exceeding photosynthesis. Science 352, 1210-1213 (2016).
179. A Portrait of the Max Planck Society. https://www.mpg.de/short-portrait, (2017).

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