Design and in vitro realization of carbon-conserving photorespiration
Devin L. TrudeauChristian Edlich-MuthJan ZarzyckiMarieke ScheffenMoshe GoldsmithOlga KhersonskyZiv AvizemerSarel J. FleishmanCharles A. R. CottonTobias J. ErbDan S. Tawfik, and Arren Bar-Even

Photorespiration limits plant carbon fixation by releasing CO2 and using cellular resources to recycle the product of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation, 2-phosphoglycolate. We systematically designed synthetic photorespiration bypasses that combine existing and new-to-nature enzymatic activities and that do not release CO2. Our computational model shows that these bypasses could enhance carbon fixation rate under a range of physiological conditions. To realize the designed bypasses, a glycolate reduction module, which does not exist in nature, is needed to be engineered. By reshaping the substrate and cofactor specificity of two natural enzymes, we established glycolate reduction to glycolaldehyde. With the addition of three natural enzymes, we observed recycling of glycolate to the key Calvin Cycle intermediate ribulose 1,5-bisphosphate with no carbon loss.


Daring metabolic designs for enhanced plant carbon fixation
Arren Bar-Even
Plant Science, Volume 273, August 2018, Pages 71-83 –   LINK

Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., “low hanging fruit”. Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco’s catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon. While the barriers to implement these elaborated metabolic architectures are quite significant, if we truly want to revolutionize carbon fixation, only daring engineering efforts will lead the way.


A short history of RubisCO: the rise and fall (?) of Nature’s predominant CO2 fixing enzyme.
Erb TJ, Zarzycki J
Current Opinion in Biotechnology Volume 49, February 2018, Pages 100-107 –  LINK

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is arguably one of the most abundant proteins in the biosphere and a key enzyme in the global carbon cycle. Although RubisCO has been intensively studied, its evolutionary origins and rise as Nature’s most dominant carbon dioxide (CO2)-fixing enzyme still remain in the dark. In this review we will bring together biochemical, structural, physiological, microbiological, as well as phylogenetic data to speculate on the evolutionary roots of the CO2-fixation reaction of RubisCO, the emergence of RubisCO-based autotrophic CO2-fixation in the context of the Calvin-Benson-Bassham cycle, and the further evolution of RubisCO into the ‘RubisCOsome’, a complex of various proteins assembling and interacting with the enzyme to improve its operational capacity (functionality) under different biological and environmental conditions.


Enzyme engineering: reaching the maximal catalytic efficiency peak.
Goldsmith M, Tawfik DS
Current Opinion in Structural Biology Volume 47, December 2017, Pages 140-150. –  LINK

The practical need for highly efficient enzymes presents new challenges in enzyme engineering, in particular, the need to improve catalytic turnover (kcat) or efficiency (kcat/KM) by several orders of magnitude. However, optimizing catalysis demands navigation through complex and rugged fitness landscapes, with optimization trajectories often leading to strong diminishing returns and dead-ends. When no further improvements are observed in library screens or selections, it remains unclear whether the maximal catalytic efficiency of the enzyme (the catalytic ‘fitness peak’) has been reached; or perhaps, an alternative combination of mutations exists that could yield additional improvements. Here, we discuss fundamental aspects of the process of catalytic optimization, and offer practical solutions with respect to overcoming optimization plateaus.


Synthetic metabolism: metabolic engineering meets enzyme design
Erb TJ, Jones PR, Bar-Even A.
Current Opinion in Chemical Biology, Volume 37, April 2017, Pages 56-62  –  LINK

Metabolic engineering aims at modifying the endogenous metabolic network of an organism to harness it for a useful biotechnological task, for example, production of a value-added compound. Several levels of metabolic engineering can be defined and are the topic of this review. Basic ‘copy, paste and fine-tuning’ approaches are limited to the structure of naturally existing pathways. ‘Mix and match’ approaches freely recombine the repertoire of existing enzymes to create synthetic metabolic networks that are able to outcompete naturally evolved pathways or redirect flux toward non-natural products. The space of possible metabolic solution can be further increased through approaches including ‘new enzyme reactions’, which are engineered on the basis of known enzyme mechanisms. Finally, by considering completely ‘novel enzyme chemistries’ with de novo enzyme design, the limits of nature can be breached to derive the most advanced form of synthetic pathways. We discuss the challenges and promises associated with these different metabolic engineering approaches and illuminate how enzyme engineering is expected to take a prime role in synthetic metabolic engineering for biotechnology, chemical industry and agriculture of the future.


Biochemical and synthetic biology approaches to improve photosynthetic CO2-fixation. 
Erb TJ, Zarzycki J.  
Current Opinion in Chemical Biology, Volume 34, October 2016, Pages 72–79  –   LINK

There is an urgent need to improve agricultural productivity to secure future food and biofuel supply. Here, we summarize current approaches that aim at improving photosynthetic CO2-fixation. We critically review, compare and comment on the four major lines of research towards this aim, which focus on (i) improving RubisCO, the CO2-fixing enzyme in photosynthesis, (ii) implementing CO2-concentrating mechanisms, (iii) establishing synthetic photorespiration bypasses, and (iv) engineering synthetic CO2-fixation pathways.