Jarvis Lab

Vacancies

 
 
Postdoc Positions  
 
We have space and projects available in our laboratory for researchers able to bring their own funding. We have core funding to cover laboratory costs, if necessary, but applicants must obtain funding to cover their living expenses. Some examples of the postdoctoral fellowships that are available are shown below, and we are happy to support all competitive applications. If you would like to apply, please contact Professor Jarvis in the first instance.
 
 
  Newton International Fellowships: http://www.newtonfellowships.org/  
  European Molecular Biology Organization (EMBO) Long-Term Fellowships: http://www.embo.org/funding-awards/fellowships  
  Human Frontier Science Program (HFSP) Long-Term Fellowships: http://www.hfsp.org/funding  
  Marie Curie Fellowships: http://ec.europa.eu/research/mariecurieactions/  
  Japan Society for the Promotion of Science (JSPS) Study Abroad Fellowships: http://www.jsps.go.jp/j-ab/index.html  
   
PhD (DPhil) Studentships  
 
Projects in the following or other related areas are available. Application procedures are described here, but candidates should in the first instance contact Professor Jarvis by e-mail.

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

 
Area 1 Mechanisms controlling the biogenesis and functions of chloroplasts in plants: protein transport and the ubiquitin-proteasome system  
  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.
 
 
Area 2 Elucidating the role of the Omp85/BamA-related protein OEP80 in chloroplast β-barrel biogenesis  
  Chloroplasts belong to a diverse family of plant organelles termed plastids [1]. Chloroplasts are responsible for photosynthesis and many essential biosynthetic functions. As photosynthesis is the only significant mechanism of energy-input into the biosphere, chloroplasts are extremely important, not just to plants but to animals and mankind alike. Development of chloroplasts (and other plastids) depends on the import of thousands of nucleus-encoded proteins from the cytosol. Such protein import is mediated by multiprotein complexes in the plastid envelope membranes termed TOC and TIC (for Translocon at the Outer/Inner envelope membrane of Chloroplasts) [1,2].

The outer membrane of chloroplasts (like those of bacteria and mitochondria) contains β-barrel channel proteins. One of these proteins, Toc75, forms the main translocation pore of the TOC complex [2,3]. Recent work in bacteria and mitochondria identified Omp85-type proteins (BamA in bacteria; Sam50 in mitochondria) as important mediators of the assembly of β-barrel proteins. However, little is known about the corresponding mechanisms in chloroplasts: an Omp85-type protein called OEP80 is proposed to be involved, but there is presently only limited evidence to support this hypothesis [4]. To address this hypothesis in an in vivo context, Arabidopsis plants that are OEP80-deficient will be characterized in detail. The aim will be to elucidate the role of the OEP80 protein, and to investigate the molecular mechanisms underlying the assembly of Toc75 and other β-barrels in chloroplasts.

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. Baldwin, A., Wardle, A., Patel, R., Dudley, P., Park, S.K., Twell, D., Inoue, K. and Jarvis, P. (2005) A molecular-genetic study of the Arabidopsis Toc75 gene family. Plant Physiol. 138: 715-733.
4. Huang, W. et al. (2011) In vivo analyses of the roles of essential Omp85-related proteins in the chloroplast outer envelope membrane. Plant Physiol. 157: 147-159.
 
 
Area 3 Studying chloroplast biogenesis in the basal land plant Marchantia polymorpha: Using CRISPR/Cas9 genome editing and forward genetics to assess functional conservation and seek novel components  
  This project will be co-supervised by Professor Liam Dolan (Dept. of Plant Sciences).

Chloroplasts are responsible for photosynthesis, and are the organelles that define plants [1]. They evolved as a result of an endosymbiotic relationship between a cyanobacterium and an algal progenitor, in a process that began over a billion years ago. Land plants emerged around 500 million years ago, by which time the chloroplast had already become a fully integrated component of the plant cell.

Today, >90% of the ~3000 proteins found inside chloroplasts are encoded by the nuclear genome and synthesized in the cytosol as precursors with N-terminal targeting signals called transit peptides. The import of such precursors into chloroplasts is mediated by multiprotein machines in the chloroplast envelope membranes called TOC and TIC (Translocon at the Outer/Inner envelope membrane of Chloroplasts) [2].

In flowering plants, the TOC complex comprises a channel-forming molecule (Toc75) and multiple receptors in two families (Toc159, Toc34) that recognize precursor proteins as they arrive at the chloroplast surface. Composition of the TOC complex is controlled by a “master regulator” protein called SP1 [3]. The SP1 gene was identified using a forward-genetic approach in the model flowering plant, Arabidopsis thaliana: we screened for extragenic suppressors of a pale-yellow TOC receptor mutant, identifying suppressor mutants by their greener appearance [4]. SP1 is a ubiquitin E3 ligase in the chloroplast outer membrane that targets TOC components for ubiquitination and degradation by the ubiquitin-proteasome system. By controlling protein import in this way, SP1 enables reconfiguration of chloroplast functions in response to developmental and environmental cues [3,4].

Bryophytes, comprising liverworts, mosses and hornworts, are the earliest diverging group of land plants. The liverwort Marchantia polymorpha is an emerging model system for plant biology research [5], which because of its basal position in the land plants enables important evolutionary questions to be addressed. Marchantia has several distinguishing features, such as the dominance of the haploid gametophyte generation over the diploid sporophyte during its life cycle. The latter point, in combination with its low genetic redundancy, means that Marchantia is particularly well suited to forward-genetic screening based on phenotype analysis. Moreover, advanced techniques for generating targeted gene knockouts (including homologous recombination and CRISPR/Cas9 approaches [6,7]) have been successfully applied in Marchantia.

We sequenced the Marchantia genome [8], and bioinformatic analyses indicated the presence of genes encoding SP1 and all major TOC components. The aims of this project will be to elucidate the functions of these genes, assessing the extent of functional conservation with flowering plants, and to seek entirely new components involved in chloroplast protein biogenesis that eluded detection previously due the higher genetic redundancy in flowering plant models:

1. Reverse genetics. Using CRISPR/Cas9 genome editing [6,7], we will generate knockout or knockdown mutants for SP1 and all TOC genes. The phenotypes of the mutants will then be characterized in detail (e.g., in relation to protein import capacity) to elucidate the extent to which the functions of the genes have been conserved during land plant evolution. Functional relationships between the components will be assessed by generating and characterizing all relevant double mutant combinations.

2. Forward genetics. Based on the results from 1, we will establish a forward-genetic screening strategy to identify entirely novel factors involved in chloroplast protein import. We predict that TOC mutants will have visible, pale-yellow phenotypes caused by defective chloroplast biogenesis [2]. This will enable us to conduct a suppressor screen analogous to that which led to the identification of SP1 in Arabidopsis [3]: we will screen for greener plants following UV mutagenesis. The suppressor mutants will be characterized in detail, and the mutated genes will be identified by whole-genome sequencing.

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., Huang, W., Baldwin, A. and Jarvis, P. (2012) Chloroplast biogenesis is regulated by direct action of the ubiquitin-proteasome system. Science 338:655-659.
4. 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..
5. Ishizaki, K. (2016) Molecular genetic tools and techniques for Marchantia polymorpha research. Plant Cell Physiol. 57:262-270.
6. Ishizaki, K. (2013) Homologous recombination-mediated gene targeting in the liverwort Marchantia polymorpha L. Sci. Rep. 3:1532.
7. Sugano, S. et al. (2014) CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol. 55:475-481.
8. Honkanen, S. et al. (2016) The mechanism forming the cell surface of tip-growing rooting cells is conserved among land plants. Curr. Biol. 26:3238-3244.
 

 
Area 4 Assembling the photosynthetic machinery in plant chloroplasts: Elucidating the novel “STIC-dependent” pathway of protein transport to thylakoids using proteomics  
 

This project will be co-supervised by Professor Shabaz Mohammed (Advanced Proteomics Facility, Dept. of Biochemistry).

Chloroplasts are the organelles that define plants. Along with many other functions, these organelles are responsible for photosynthesis (the process whereby sunlight energy is harnessed to power the cellular activities of life), and consequently they are essential for plant growth, and for the myriad ecosystems that depend on plants.

The development of chloroplasts depends on the import of thousands of nucleus-encoded proteins from the cytosol [1,2]. Such import is mediated by multiprotein complexes in the chloroplast envelope membranes termed TOC and TIC (Translocon at the Outer/Inner membrane of Chloroplasts). The TIC complex mediates inner membrane transport, and provides the ATP-dependent driving force for the process. A critical component of the TIC complex is the co-chaperone Tic40, which regulates internal chaperones at the conclusion of the import process [3,4]. Upon exiting the TIC machinery, many imported proteins (e.g., components of the photosynthetic machinery) engage additional sorting pathways that direct them to the internal thylakoid membranes, where the light-dependent reactions of photosynthesis take place [1].

Mutant plants lacking the Tic40 protein are pale-yellow due to defective protein transport and retarded chloroplast development [3]. To identify novel factors involved in chloroplast protein transport, we employed forward genetics: we screened for extragenic suppressors of the tic40 mutant. The suppressor mutants were considerably greener and more developed than tic40 plants, and they identified the STIC1 and STIC2 (SUPPRESSOR OF TIC40) genes. Recent work revealed that the STIC1 gene encodes a member of the Alb3/Oxa1/YidC family of membrane protein integrases, located in the thylakoid membrane, and that STIC2 encodes a protein of unknown function related to bacterial protein YbaB [5]. Moreover, it was shown that the STIC1 and STIC2 proteins together define a novel protein-transport pathway leading from the TIC apparatus, at the envelope, to the thylakoid membranes. While this was a significant breakthrough, significant questions remain unanswered. For example, what are the clients of this STIC-dependent pathway? – in other words, which proteins does it deliver to the thylakoids? And, what other factors act in the STIC pathway? The latter is an important question as it seems highly unlikely that STIC1/2 act alone.

To address these questions, we propose to take two different proteomics approaches. The first question will be addressed using an isobaric tag-based quantitative proteomics approach called TMT (tandem mass tagging; Thermo Fisher) [6]. In this work, chloroplasts will be isolated from wild-type and stic1 and stic2 mutant plants, and then an analysed using TMT to determine which proteins, specifically, are depleted in the mutants. Proteins found to be depleted in both stic mutants, relative to wild type, will be candidate clients of the STIC pathway, and will be verified as such in subsequent experimental analyses.

The second question will be addressed by applying an affinity purification approach called tandem affinity purification (TAP), or similar [7,8]. Chloroplasts isolated from plant lines expressing TAP-tagged STIC1 or STIC2 proteins (these plant lines have already been generated) will be subjected to gentle lysis and membrane-solubilization prior to affinity-purification of the STIC-containing complexes. The components of these purified STIC complexes will then be identified by mass spectrometry, paving the way for a range of molecular, genetic and cell biological approaches to elucidate the functions of the identified components, and of the STIC pathway generally.

At the conclusion of this project, it is expected that we will have a greatly improved level of understanding of an important new pathway of thylakoid protein biogenesis in plant chloroplasts.

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. Kovacheva, S., Bédard, J., Patel, R., Dudley, P., Twell, D., Ríos, G., Koncz, C. and Jarvis, P. (2005) In vivo studies on the roles of Tic110, Tic40 and Hsp93 during chloroplast protein import. Plant J. 41:412-428.
4. Bédard, J., Kubis, S., Bimanadham, S. and Jarvis, P. (2007) Functional similarity between the chloroplast translocon component, Tic40, and the human co-chaperone, Hip. J. Biol. Chem. 282:21404-21414.
5. 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.
6. Rose, C.M. et al. (2016) Highly multiplexed quantitative mass spectrometry analysis of ubiquitylomes. Cell Syst. 3:395-403.e4.
7. Rohila, J.S., Chen, M., Cerny, R. and Fromm, M.E. (2004) Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J. 38:172-181.
8. Low, T.Y., Peng, M., Magliozzi, R., Mohammed, S., Guardavaccaro, D. and Heck, A.J. (2014) A systems-wide screen identifies substrates of the SCFβTrCP ubiquitin ligase. Sci Signal. 7(356):rs8.
 

 
 
 
  Self-Funded Students  
  Funded studentships are available within the University (and may be applied for as described above), but we also encourage applications from students able to bring their own funding. Candidates will need to obtain scholarship funding to cover their own living expenses, and fees charged by the University of Oxford.
 
 
  Web Links  
  Graduate Study in the Department of Plant Sciences: http://www.plants.ox.ac.uk/graduates  
  The British Council: http://www.britishcouncil.org/home  
  Commonwealth Scholarship Commission (CSC): http://cscuk.dfid.gov.uk/  
 
 
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 Last updated: Sept 2017
 Paul Jarvis