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

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Our research is focused on the biogenesis of chloroplasts and other plastids in plants, particularly in relation to the import of nucleus-encoded proteins and the role of the ubiquitin-proteasome system. As a DPhil student in our lab, you would be part of a well-funded research group that is conducting pioneering research on molecular and cellular aspects of plant biology. Details of the DPhil project, which would fall into one of the following areas, would be defined in discussions between the student and supervisor.

Chloroplast protein import
Plastids are a diverse family of plant organelles. The family includes chloroplasts – the organelles responsible for photosynthesis – as well as 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 signals called transit peptides. Import of precursors into chloroplasts is mediated by the TOC and TIC (Translocon at the Outer/Inner envelope membrane of Chloroplasts) complexes [2]. While much progress has been made in understanding how the import machinery works, substantial gaps remain in our knowledge; for example, the mechanisms underlying the regulation of import are poorly understood. Our research seeks to achieve a more complete understanding of chloroplast protein import mechanisms, using a full spectrum of molecular, cellular, genetic, and biochemical approaches. We have brought to bear the unique advantages offered by the model plant Arabidopsis thaliana (thale cress) as an experimental system in relation to plastid protein import research. More recently, having identified potential practical applications of our work in agriculture, we have begun to also employ crop species as alternative models.

Control of plastid biogenesis by the ubiquitin-proteasome system
Our work has revealed that plastid biogenesis is directly regulated by the ubiquitin-proteasome system (UPS), defining a new and fundamentally important area of biology [3]. Using a genetic screening approach, we identified a RING-type ubiquitin E3 ligase in the plastid outer membrane called SP1 (SUPPRESSOR OF PPI1 LOCUS1) [4]. SP1 selectively targets the TOC machinery for ubiquitination and degradation. By controlling the levels of different TOC receptor isoforms, SP1 regulates which proteins are imported, and this in turn controls the plastid’s proteome, functions and developmental fate (i.e., which type of plastid is formed) [1,4]. This demonstrated for the first time that the UPS directly regulates plastid development, and revealed that plastid protein import is a dynamically regulated process. However, mechanistic details of the SP1 regulatory pathway, and the identity of other factors involved, remain to be elucidated.

Potential agricultural applications
In addition to its fundamental importance, the discovery of SP1 suggested potential applications in agriculture. In Arabidopsis, SP1 is important for developmental transitions in which plastids convert from one type to another [4]. As plastids and their interconversions are important throughout plant development, SP1 may conceivably find diverse applications, e.g., during fruit ripening in crops like tomato, when chloroplasts transform into chromoplasts, or during grain development in field crops like wheat and rice, when amyloplasts are formed [1]. Manipulating SP1 activity may allow greater control over such plastid interconversions and the associated organismal processes. Moreover, our most recent work revealed an important role for SP1 in plant abiotic stress tolerance, which it promotes by limiting the import of new photosynthetic machinery components, attenuating photosynthesis, and thus limiting the accumulation of harmful photosynthetic by-products called reactive oxygen species (ROS) [5]. Thus, SP1 may also find applications in the development of stress-tolerant crops, which is a particular priority in low- and middle-income countries where the challenges posed by climate change are a pressing concern.

References:

1. Jarvis, P. and López-Juez, E. (2013) Biogenesis and homeostasis of chloroplasts and other plastids. Nat. Rev. Mol. Cell Biol. 14:787-802.
2. Jarvis, P. (2008) Targeting of nucleus-encoded proteins to chloroplasts in plants (Tansley Review). New Phytol. 179:257-285.
3. Ling, Q. and Jarvis, P. (2013) Dynamic regulation of endosymbiotic organelles by ubiquitination. Trends Cell Biol. 23:399-408.
4. 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.
5. 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.

STUDENT PROFILE

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

Prospective students are encouraged to apply to the Oxford Interdisciplinary Bioscience DTP. International applicants are encouraged to explore scholarship options that are available to them through the University of Oxford, their home countries or organisations such as the Commonwealth Scholarship Commission.

References

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 doi: 10.1105/tpc.16.00962. [Epub ahead of print].

Flores-Pérez, Ú., Bédard, J., Tanabe, N., Lymperopoulos, P., Clarke, A.K. and Jarvis, P. (2016) Functional analysis of the Hsp93/ClpC chaperone at the chloroplast envelope. Plant Physiol. 170: 147-162.

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.

Trösch, R., Töpel, M., Flores-Pérez, Ú. and Jarvis, P. (2015) Genetic and physical interaction studies reveal functional similarities between ALBINO3 and ALBINO4 in Arabidopsis. Plant Physiol. 169: 1292-1306.

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

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