Evolution-guided engineering of plant organelles for crop improvement

Lead Research Organisation: University of Oxford
Department Name: Interdisciplinary Bioscience DTP

Abstract

Plant cell organelles are specialised to carry out fundamental processes necessary for cellular function. Broadly, their core functions are conserved: whether it is to convert sunlight into sugar in the chloroplast or to break down that sugar into energy in the mitochondria. However, these subcellular organelles have been evolving independently for millions of years in different plant lineages and so differences exist in the protein complement of organelles between modern day plant species. My DPhil project aims to analyse and exploit these differences between extant species to discover how the protein complement of subcellular organelles has evolved during plant evolution and to determine whether changes in organellar protein content can provide new insight into the biology of major evolutionary events (for example the evolution of C4 photosynthesis). The second phase of my DPhil project will utilise this evolutionary analysis to attempt to perform evolution-guided engineering of crop plants. Here, it is hypothesised that if a protein is targeted to a new subcellular location during its evolution in one or more plant lineages (without subsequent loss) then it is likely conferring a selective advantage in this new location. I will test this hypothesis by identifying proteins that have undergone a change subcellular localisation during evolution in one or more plant lineages and assessing whether a benefit can be gained by replicating this change in species for whom it has not occurred. If this is the case, then the relocalisation of these proteins to or from subcellular organelles such as the chloroplast or mitochondria could be a potential mechanism by which we can improve crop species.
In summary, this project will provide new insight into how subcellular organelles have evolved in different plant lineages and potentially provide a new paradigm for crop improvement through evolutionary-guided engineering.

BBSRC priority areas:
1) Data driven biology 2) Food nutrition and health 3) Sustainably enhancing agricultural production 4) Systems approaches to the biosciences

AFS, ENWW

Publications

10 25 50

Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011224/1 01/10/2015 31/03/2024
1757774 Studentship BB/M011224/1 01/10/2016 31/03/2021
 
Description Plant cells contain specialised subcellular compartments known as organelles. The functioning of these organelles relies upon the import of 1000s proteins from the cell cytosol which is coordinated by the presence of short target signals located within an organelle protein sequence. This research set out to study how organelle evolution has been affected by changes in the subcellular localisation of proteins via the gain or loss of these target signals. To do this we used computational methods to interrogate whole-proteome data for a wide range of plant species and to identify in which gene families, and when, ancestral changes in protein localisation occurred. Thus far this research has revealed:
- That changes in protein targeting to organelles has been pervasive throughout the evolution of plants. This is important as it reveals that the organellar proteome has not been static since the origin of land plants but has been constantly evolving and diversifying in different plant lineages.
- That the majority of changes that have happened to the chloroplast and mitochondrion involve proteins with post-translational or post-transcriptional regulatory functions. This is important as it makes the surprising discovery that the major energy organelles have not been modifying their metabolic repertoire since early plant evolution, but instead have been evolving through changes in their control mechanisms. Thus, the evolutionary history of the chloroplast and mitochondrion is a story of altered regulatory capacity rather than altered metabolic function.
- That changes in protein localisation to and from the different plant cell organelles happen at a higher rate following gene duplication. This is important as it uncovers a novel role for gene duplication in the evolution of plant cell organelles.

Furthermore, this research has culminated in a dataset mapping ancestral changes in protein localisation across all gene families for these 42-plant species. We hope that the provision of this data will prove a valuable tool for the research community.
Exploitation Route The presence of organelles in the cell is a hallmark feature of eukaryote organisms. While there has been much research interest in the early evolution and establishment of organelles in the eukaryotic cell, much less is known about how they have evolved and diversified in different lineages since. Here we focus on the proteomic evolution of plant cell organelles, but this research has the potential to inform and stimulate research in other domains of eukaryotic life too. In the plant community, the data generated by this research will hopefully serve as a tool for researchers interested in the evolution of proteins and/or organelles across different plant species. In particular, there is intense research surrounding the evolution of chloroplast proteins in different plant species, given that these organelles are the main site of plant photosynthesis and there is much interest (in both academic and non-academic groups) in strategies for the improvement of photosynthesis in crop plants. This research takes a novel approach in the identification of the changes that occurred during the evolution of the chloroplast in different plant groups and data produced by this study has the potential to drive the discovery of key targets for crop innovation.
Sectors Agriculture, Food and Drink
URL https://doi.org/10.1093/molbev/msz275