Evolution-guided engineering of enhanced photosynthesis
Lead Research Organisation:
University of Oxford
Department Name: Interdisciplinary Bioscience DTP
Abstract
Photosynthesis is the biological reaction which converts gaseous CO2 and sunlight into the sugars which are used to support growth and development. However, despite the central importance of this process, the type of photosynthesis utilized by the vast majority of plants and agricultural crops (called C3 photosynthesis) is typically inefficient. In this D.Phil project, I will identify and test strategies to improve the photosynthetic performance of C3 plants using evolution as a guide, by exploiting the natural variation which exists in photosynthesis and photosynthesis-related traits across the plant kingdom. This goal will be achieved through completion of both exploratory and applied aspects of this project.
In the exploratory phase of this research, I will study how photosynthesis has been evolving during the diversification of land plants by interrogating publicly available datasets in the context of the plant phylogenetic tree. Specifically, I will first elucidate the evolution of the principal CO2-fixing enzyme in photosynthesis ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), which is widely acknowledged as a crucial bottleneck to photosynthetic efficiency and thus represents a crucial area of interest. I will then investigate the evolution of a broader array of anatomical, ultrastructural, biochemical and physiological traits which are related to plant photosynthetic performance. In combination, this research will provide a core understanding of the mechanisms by which photosynthesis is evolving along the major plant clades and will help elucidate the constraints on these processes. Whilst interesting from a fundamental perspective, this mechanistic understanding gained will also be invaluable in inspiring targets for crop improvement (both within and outside of this specific project).
Next, in the more applied aspect of this work, I aim to optimise the biochemical CO2 fixation pathway as a means to increase plant photosynthetic rate. To achieve this, I will first identify a small number of sequence changes which have naturally evolved in enzymes of this pathway (including RuBisCO), and are associated either directly or indirectly with increased flux through this scheme. This task will be undertaken using a number of bioinformatic tools, including ancestral state reconstruction, machine learning, and selection analysis. Mutations thus identified will be introduced into enzymes from agriculturally important crops, and the resulting enzyme variants will be tested for improved function using in vitro assays. If time allows, promising sequence changes will then be engineered in plants using site-directed mutagenesis in order to examine whether an improvement in photosynthesis can be achieved. If successful, this technology will ultimately serve as a precise means to enhance the productivity and yields of agricultural crops.
In the exploratory phase of this research, I will study how photosynthesis has been evolving during the diversification of land plants by interrogating publicly available datasets in the context of the plant phylogenetic tree. Specifically, I will first elucidate the evolution of the principal CO2-fixing enzyme in photosynthesis ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), which is widely acknowledged as a crucial bottleneck to photosynthetic efficiency and thus represents a crucial area of interest. I will then investigate the evolution of a broader array of anatomical, ultrastructural, biochemical and physiological traits which are related to plant photosynthetic performance. In combination, this research will provide a core understanding of the mechanisms by which photosynthesis is evolving along the major plant clades and will help elucidate the constraints on these processes. Whilst interesting from a fundamental perspective, this mechanistic understanding gained will also be invaluable in inspiring targets for crop improvement (both within and outside of this specific project).
Next, in the more applied aspect of this work, I aim to optimise the biochemical CO2 fixation pathway as a means to increase plant photosynthetic rate. To achieve this, I will first identify a small number of sequence changes which have naturally evolved in enzymes of this pathway (including RuBisCO), and are associated either directly or indirectly with increased flux through this scheme. This task will be undertaken using a number of bioinformatic tools, including ancestral state reconstruction, machine learning, and selection analysis. Mutations thus identified will be introduced into enzymes from agriculturally important crops, and the resulting enzyme variants will be tested for improved function using in vitro assays. If time allows, promising sequence changes will then be engineered in plants using site-directed mutagenesis in order to examine whether an improvement in photosynthesis can be achieved. If successful, this technology will ultimately serve as a precise means to enhance the productivity and yields of agricultural crops.
Organisations
People |
ORCID iD |
| Gail Preston (Primary Supervisor) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011224/1 | 01/10/2015 | 31/03/2024 | |||
| 2269836 | Studentship | BB/M011224/1 | 01/10/2019 | 31/03/2024 |
| Description | A part of my DPhil research investigates the mechanisms which explain why rubisco (the CO2 fixing enzyme in photosynthesis) is inefficient, a perplexing limitation of this specific enzyme which comes at the detriment of the growth and productivity of photosynthetic organisms. To resolve this long-standing question, I have successfully applied a novel method of analysis which interrogates in parallel both the kinetic trait data (i.e., information describing various parameters of enzyme efficiency) and phylogenetic data (i.e., information describing enzyme evolutionary history) from a large number of plant rubiscos. Results emanating from this work have demonstrated that in contrast to previous beliefs, the inefficiency of rubisco is not a product of inherent antagonistic trade-offs thought to exist between its kinetic traits (the "catalytic trade-off" model of rubisco). Instead, results from this revised analysis show that the predominant limitation on rubisco efficiency is likely associated with a slow pace of rubisco adaptive evolution. This research now published in Molecular Biology and Evolution is therefore noteworthy. First, this work publicizes an improved "phylogenetically informed" method for comparative analysis of enzyme kinetics which would do well to be adopted more widely in the enzyme literature. Next, this work has led to a fruitful collaboration with rubisco researchers at the Australia National University, Canberra, which will be helpful for subsequent parts of my DPhil research. Finally, this specific work has generated a body of evidence which has considerably improved our fundamental understanding of the evolutionary constrains which act on rubisco adaptation and performance. |
| Exploitation Route | As described above, my published research output to date has demonstrated that the principal explanation for the inefficiency of rubisco is an inherent slow rate of the enzyme's molecular evolution. Thus, in forging this novel theory of rubisco adaptation, this work naturally opens the door to various subsequent areas of academic research interest. First, from a fundamental research perspective, the obvious follow-up question to investigate would be to answer why rubisco is evolving slowly. In addition, given that it should be feasible in the current era of synthetic biology to overcome the slow rate of evolution in rubisco via experimental means, this work also creates substantial optimism for applied research in rubisco engineering for the goal of enhancing crop productivity. Thus, it would be exciting to see the respective progress which is achieved in these two regards over coming years. |
| Sectors | Agriculture, Food and Drink,Environment |
| URL | https://academic.oup.com/mbe/article/38/7/2880/6178800 |