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Mechanisms controlling the biogenesis and functions of chloroplasts in plants: protein transport, CHLORAD, and the ubiquitin-proteasome system

  • Full or part time
  • Application Deadline
    Friday, January 24, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Link to group webpage:

Our research is focused on the biogenesis and homeostasis of chloroplasts (and other plastids) in plants. Particular areas of interest are the import into chloroplasts of nucleus-encoded proteins, and the ubiquitin-dependent proteolysis of chloroplast components via a recently discovered process called CHLORAD (chloroplast-associated protein degradation). As a DPhil student in our group, you would be part of a well-funded research team that is conducting pioneering research in this field. Details of the project, which would fall into one of the following areas, would be defined through discussions between the student and supervisor.

Chloroplast protein import

Plastids are a diverse family of plant organelles with numerous functions that are vital for plant growth. The family includes chloroplasts (responsible for photosynthesis), and a range of non-photosynthetic variants such as starch-containing amyloplasts in seeds, tubers and roots, carotenoid-rich chromoplasts in flowers and fruits, and chloroplast-precursor organelles in dark-grown plants called etioplasts [1]. Most plastid proteins are encoded by the nuclear genome and synthesized in the cytosol as precursors with N-terminal targeting peptides. Import of precursors into chloroplasts is mediated by the TOC and TIC (Translocon at the Outer/Inner envelope membrane of Chloroplasts) complexes [1]. While much progress has been made in understanding how the import machinery works, substantial knowledge gaps remain; for example, the mechanisms underlying the regulation of import are poorly understood. We seek to understand these protein transport systems mechanistically, and in particular their proteolytic regulation via CHLORAD. To do this, we apply a full spectrum of molecular, cellular, genetic, and biochemical approaches, and we study the model plant Arabidopsis thaliana as well as a range of crop species.

Control of plastid biogenesis by the ubiquitin-proteasome system

A recent highlight of our work was the discovery that plastids are directly regulated by the ubiquitin-proteasome system; this defined a new and fundamentally important area of cell biology [2]. Originally we identified a ubiquitin E3 ligase in the plastid outer membrane called SP1, and showed that it targets the protein import (TOC) machinery for degradation [3]. More recently, we revealed that SP1 is part of a broader system, named CHLORAD, which incorporates a protein ‘retrotranslocation’ system that acts to extract target proteins from chloroplasts so that they may be degraded within the cytosolic proteasome. By regulating the protein import machinery, CHLORAD controls the plastid’s proteome, functions and developmental fate (e.g., which plastid variant is formed) [1,3,4]. However, many mechanistic details of the CHLORAD pathway remain to be elucidated; this is a major focus of our research.

Potential agricultural applications

Our discovery of CHLORAD suggested novel crop improvement strategies. CHLORAD is required for developmental transitions in which plastids change function [3,4], and so it potentially has diverse agricultural applications, e.g., during fruit ripening in crops like tomato, when chloroplasts transform into chromoplasts, or during grain development in crops like wheat and rice, when amyloplasts are formed [1]. Manipulating CHLORAD activity may allow for greater control over such processes. Moreover, our work also revealed an important role for CHLORAD in plant abiotic stress responses, which it promotes by attenuating photosynthesis so as to limit accumulation of harmful reactive oxygen species [4,5]. Thus, manipulating CHLORAD may also enable development of stress-tolerant crops, which is a particular priority in low/middle-income countries and in the context of climate change [6]. We are exploring these possibilities in on-going experiments in our laboratory.


This project would suit candidates with a strong background in one or more of the following areas: biological sciences, molecular biology, cell biology, biochemistry, bioinformatics, genetics.

Funding Notes

There are two main routes into the Department of Plant Sciences Graduate Programme dictated by different funding mechanisms: If, after discussion with a potential supervisor, you decide that one of these programmes is right for you, you will need to apply directly to the relevant programme.

Option 1: Applying via a Doctoral Training Programme
Option 2: Applying directly to the Plant Sciences DPhil research programme

In depth guidance is available here: View Website


1. Jarvis, P., López-Juez, E. (2013) Nat. Rev. Mol. Cell Biol. 14: 787-802.
2. Ling, Q., Jarvis, P. (2013) Trends Cell Biol. 23: 399-408.
3. Ling, Q., Huang, W., Baldwin, A., Jarvis, P. (2012) Science 338: 655-659.
4. Ling, Q. et al. (2019) Science 363: eaav4467.
5. Ling, Q., Jarvis, P. (2015) Curr. Biol. 25: 2527-2534.


Ling, Q., Broad, W., Trösch, R., Töpel, M., Demiral Sert, T., Lymperopoulos, P., Baldwin, A. and Jarvis, R.P. (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science 363: eaav4467.

Wu, G.Z., Meyer, E.H., Richter, A.S., Schuster, M., Ling, Q., Schöttler, M.A., Walther, D., Zoschke, R., Grimm, B., Jarvis, R.P. and Bock, R. (2019) Control of retrograde signalling by protein import and cytosolic folding stress. Nat. Plants 5: 525-538.

Bédard, J., Trösch, R., Wu, F., Ling, Q., Flores-Pérez, Ú., Töpel, M., Nawaz, F. and Jarvis, P. (2017) Suppressors of the chloroplast protein import mutant tic40 reveal a genetic link between protein import and thylakoid biogenesis. Plant Cell 29: 1726-1747.

Ling, Q. and Jarvis, P. (2015) Regulation of chloroplast protein import by the ubiquitin E3 ligase SP1 is important for stress tolerance in plants. Curr. Biol. 25:2527-2534.

Ling, Q. and Jarvis, P. (2013) Dynamic regulation of endosymbiotic organelles by ubiquitination. Trends Cell Biol. 23: 399-408.

Jarvis, P. and López-Juez, E. (2013) Biogenesis and homeostasis of chloroplasts and other plastids. Nat. Rev. Mol. Cell Biol. 14: 787-802.

Ling, Q., Huang, W., Baldwin, A. and Jarvis, P. (2012) Chloroplast biogenesis is regulated by direct action of the ubiquitin-proteasome system. Science 338: 655-659.

How good is research at University of Oxford in Biological Sciences?

FTE Category A staff submitted: 223.80

Research output data provided by the Research Excellence Framework (REF)

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