Plant Biology PhD research projects

Supervisor: Lichman, Dr. Benjamin R.

Applications are currently open for a fully funded structural biology/enzyme engineering studentship at the White Rose BBSRC DTP on C-C bond forming enzymes from plants. The project is a collaboration with Prof Gideon Grogan in the Department of Chemistry. 


Self-funded PhD applications are very welcome. Please contact me to discuss potential research topics.

Supervisor: Hartley, Professor Sue

Plant defence vs Insect defence: impacts of plant quality on insect immune systems (2015-16)

Insects defend themselves against pathogens and parasites with an immune system, but key aspects of insect immunity remain unknown, including how immune function is affected by diet. Insect herbivores often consume a diet low in protein and high in plant toxins; such a diet may compromise their immune system by reducing the resources that can be allocated to it. Many grasses, including vital crops such as rice and wheat, use silicon as a defence. Silicon reduces the ability of herbivores to digest protein, but the effect of this on their immune systems has not been tested. Silicon also increases the development time of insects, increasing their exposure to invasive enemies at a time when their immune systems may less effective.

This project aims to:

(i) Assess the impacts of silicon in the diet on the immune function of insect herbivores by rearing them on plants containing different amounts/types of silicon defences and their immune function.

(ii) Understand how silicon affects the vulnerability of different types of insect herbivores to parasitoid attack.

Strategies for compromising insect immunity could lead to the development of novel sustainable pest control methods, vital when climate change may increase the frequency and severity of pest outbreaks

Supervisor: Bruce, Professor Neil C

Mining composting communities for new lignocellulose mobilising enzymes (2015-16)

From both a fundamental and industrial biotech viewpoint understanding the deconstruction of lignocellulose in soil and compost is of central importance. In the natural environments microbial communities can efficiently degrade or modify lignin to enable the effective enzymatic hydrolysis of the polysaccharides present in plant cell walls. Globally, this is important for cycling carbon in the environment and as potential sources of biocatalysts for efforts at converting plant biomass into biofuels and commodity chemicals. The objectives of this project are to use metatranscriptomics and proteomics to determine gene- and protein-centred details to determine new mechanisms and improved methods of lignocellulose deconstruction in mixed microbial communities from composting cereal straw. The project will use proteomics analysis to interrogate the secretome of microbial communities in composting cereal straw and metatranscriptomics will be used to explore the expression of genes associated with lignocellulose digestion. To identify new linocellulose degrading enzymes, the peptide sequences from the proteomics analysis will be used to probe the metatranscriptomic library for full and partial coding sequences. These coding sequences will be cloned, expressed and the recombinant proteins characterised.

Co-directors:Simon McQueen-Mason

Supervisor: Mackinder, Luke Dr

Self-funded PhD applications are welcome.

Supervisor: Davis, Professor Seth

How to set a circadian clock: structural mechanism of ELF3-ELF4 clock-protein action in transcriptional repression  (2015-16)

The circadian clock drives genome-scale transcription to coordinate most of growth and development. As the time the sun rises changes every day, mechanisms exist to reset this clock in a process called entrainment. Here a project is proposed to unravel the clock-resetting mechanism. Using a combination of biochemical and cellular experiments, one would examine the spatial-temporal function of the key hub protein ELF3. One would monitor the global, genome-wide binding of this chromatin-associated factor to define its transcriptional target genes. Next an exploration of where and how the ligand ELF4 activates ELF3, and how light-perception represses this, would be examined. Efforts to solve by crystallography the structure of the ELF4 / ELF3 repression complex will be undertaken and, in parallel, associated in vitro biophysics of complex assembly will be elucidated. Taken together this project is envisaged to provide the mechanistic basis of a clock-resetting mechanism in plants.

References: Anwer et al. eLife e02206 (2014); Herrero et al. Plant Cell 24: 428–443 (2012); Levdikov et al. Proc. Natl. Acad. Sci. USA 109, 5441-5445 (2012); Kolmos et al. Plant Cell 23: 3230-3246 (2011)

Co directors: Tony Wilkinson Department: Chemistry

Supervisor: Maathuis, Dr Frans

Plant Arsenic Biomonitors (2015-16)

Arsenic (As) is a Class 1 carcinogen with no minimum threshold intake. Arsenic poisoning affects more than 100 million people worldwide, particularly in south Asia. Recent studies have identified foods, especially rice, as an important source of inorganic As intake by humans posing a potentially significant health risk for people on a rice-based diet living anywhere in the world1,2). The main reason for this phenomenon is the much greater efficiency with which rice accumulates As, compared to other cereal crops. In the worst affected areas, build-up of As in soil has also resulted in significant yield losses due to As toxicity. Since rice is a staple food for about half of the world population, there is an urgent need to develop strategies to limit As contamination, and an early warning system to signal the onset of As accumulation would be highly beneficial.

Objectives: We will generate crop plants that to report on their As status. To accomplish this we will use an arsenic sensor and a reporter. For the sensor, we will make use of the promoter of a gene that responds to As, the cytochrome P450 (Os01g43710) is an excellent candidate, and link this to a gene that when expressed provides an easily distinguished colour marker as reporter. For the latter, anthocyanins (red-purple pigments) are ideal. This approach will result in plants that will turn red whenever As toxicity presents itself.

Co director: Michael Schultze

Improving Arsenic tolerance in Rice (2015-16)

Project and background:  Arsenic (As) is a metalloid, which occurs ubiquitously in nature. It is found predominantly as inorganic arsenate and arsenite. Arsenate, as a phosphate analogue, has detrimental effects on phosphate metabolism but arsenite is even more toxic due to its high reactivity with sulfhydryl groups of proteins. As such As is classified as a group 1 carcinogen and there is large concern about human contact with As which occurs through drinking of contaminated water and via the food chain because in many areas crop growth depends on usage of As contaminated irrigation water. It is estimated that more than 100 million people are exposed to toxic levels of As.

Arsenic contamination through consumption of crops is particularly prevalent where rice is concerned: Rice is the staple of billions, it is produced in many south east Asian countries that have high levels of As in their aquifers, and rice translocates a relatively high proportion of As to its edible part, the grain.

No specific As efflux mechanism has been identified in plants. You will use a GWAS (genome wide association studies) approach to identify As efflux mechanisms. To assess if As efflux in plants can be augmented, and whether this has positive effects on plant growth, you will express heterologous systems such as ACR3 from Saccharomyces cerevisiae and/or use transgenic approaches (e.g. overexpression, genome editing) to alter activity of putative As efflux mechanisms in rice. Transgenic rice will be evaluated for As tolerance and As content level in various tissues such as roots, leaves and in seeds. This project will train the candidate in whole plant physiology, molecular biology and crop biotechnologies such as cereal transformation.

Improving Rice Salt and Drought Tolerance (2015-16)

Background: Salinity and drought stress are a major and global detriment to agricultural production. Their negative impact on crop production is exacerbated by sensitivity of major crops such as wheat and rice, a growing human population and climate change. For both salt and drought stress, the manipulation at the transcript level of single transporter genes in rice has shown that its tolerance can be significantly improved in this way. This includes altering expression of K+ transporters such as TPKs and AKTs and Na+ transporters such as NHXs and HKTs. However, the multigenic nature of salt and drought stress means that the expression of multiple transporters needs altering to optimise stress resistance. Such ‘stacking’ or ‘pyramiding’ of traits has hardly been attempted in rice abiotic stress.

Work plan and aims: This project envisages combining the positive effects that were observed by the manipulation of single genes to further improve salt and drought tolerance in rice. We will focus initially on genes for which transgenics are already available in the lab (vacuolar channels TPKa and TPKb, the K+ uptake and translocation systems AKT1 and SKOR and the Na+ transporter HKT2;1). Lines will be crossed and/or retransformed to generate multiple transgenics. Retransformation may include the use of tissue specific promoters. State of the art genome editing will also be applied to alter activity of specific genes. Using growth assays and mineral content analysis, lines will be assessed for synergistic phenotypes regarding tolerance to salt and drought stress.

Supervisor: Jones, Dr Louise

Novel Regulators of Seedling Growth (2015-16)

RNA polymerase (pol) III synthesizes noncoding RNAs that are essential for growth, e.g. tRNA and 5S rRNA.  Elevated tRNA expression has been shown to stimulate cell proliferation and organismal growth in fruitflies.  In yeast and animal cells, transcription by pol III is tightly linked to growth conditions, sometimes through epigenetic changes: it is suppressed in quiescent/dormant cells by transcriptional inhibitors; growth stimuli inactivate these inhibitors and induce direct activators of pol III transcription.  In Arabidopsis, transcription, methylation and compaction of 5S rRNA genes is regulated during seed development and germination.  It is not yet known if tRNA expression is controlled in a similar way to 5S rRNA in plants, although precedents from other organisms predict that this is the case. The project will have four main objectives: 1. Determine how tRNA expression is regulated when Arabidopsis seeds exit dormancy; 2. Test the hypothesis that loss of dormancy triggers epigenetic changes in tRNA genes; 3.  Test if tRNA genes in Arabidopsis are regulated by homologues of transcription factors that regulate pol III transcription in animal cells (e.g. MYC, MAF1, RB); 4.  Test if manipulating tRNA expression can influence seedling growth.

Co directors: Professor Bob White and Professor Ian Graham