Professor Alison Smith
Find out more about Alison Smith and her Group or email Alison.Smith@plantsci.cam.ac.uk
Project titles:
- Algal-Bacterial Symbiosis - the one stop vitamin shop
- Regulation of gene expression by vitamin B12 in algae
- Metabolic engineering in algae with riboswitches
- Growing algae outdoors - can algal-bacterial symbioses provide the means to reduce contamination?
- Developing a microdroplet platform for development of microalgal biotechnology
- Network models for biosynthetic pathways in higher plants
Project Title: Algal-Bacterial Symbiosis - the one stop vitamin shop
Supervisor: Prof. Alison Smith
Project outline:
Algae are responsible for fixing more CO2 than land plants. We have found that, unlike higher plants, many eukaryotic algae have an obligate requirement for vitamin B12 (cobalamin) for their metabolism, and that surprisingly, they have to obtain it from bacteria (Croft et al (2005) Nature 438: 90-93). We have established a model system for investigating the interaction between algae and bacteria. The growth of the B12 auxotroph Lobomonas rostrata can be supported in coculture by several rhizobial species of bacteria, which supply it with cobalamin, in return for fixed carbon. L. rostrata is related to Chlamydomonas reinhardtii the model green alga whose genome sequence is known, which does not have an obligate requirement for vitamin B12, but will use it if available, and can take up the vitamin in cocultures with the same bacterial species.
This project seeks to investigate how C. reinhardtii, and its related vitamin B12 auxotrophs, associate and communicate with bacteria. Through a variety of biochemical and molecular techniques, including the analysis of gene and protein expression coupled with mutagenesis, the project aims to elucidate the mechanisms used to pass vitamin B12 from the bacterium to the alga, thus providing a clue to the mechanism of this remarkable symbiosis.
See Research or email: Alison.Smith@plantsci.cam.ac.uk
Project Title: Regulation of gene expression by vitamin B12 in algae
Supervisor: Prof. Alison Smith
Project outline:
Over half of all microalgae require an external source of vitamin B12, which they use as a cofactor for the essential enzyme methionine synthase (METH). Other species, such as the green alga Chlamydomonas reinhardtii do not require the vitamin because they have an alternative form of methionine synthase, METE. However if B12 is available, C. reinhardtii uses METH in preference, and the gene for METE is switched off at the level of transcription, probably via repression of the promoter (Croft et al (2005) Nature 438: 90-93). A similar situation is found in the completely unrelated diatom, Phaeodactylum tricornutum.
The aim of this project is to study the regulation of METE gene expression in the two algae, firstly to establish which region of the gene is responsible for the repression by B12, and then to identify possible transcription factors or other proteins that might be involved. At the same time, the potential to use this repressible system to regulate transgene expression in these algae will be investigated. The project will thus provide training in algal molecular biology and biotechnology.
See Research or email: Alison.Smith@plantsci.cam.ac.uk
Project Title: Metabolic engineering in algae with riboswitches
Supervisor: Prof. Alison Smith
Project outline:
There is increasing interest in exploitation of microalgae for biofuel, and as a platform for the production of high value chemicals. However, there is only one algal species for which metabolic engineering is routine, namely the model green alga Chlamydomonas reinhardtii, and even for this species the range of molecular tools are limited. One particularly important requirement is to be able to regulate expression of any transgene. We have been investigating the potential for expressing a novel biosynthetic pathway in the chloroplast of C. reinhardtii. Vitamin B12 is only made by prokaryotes and requires over 20 different enzymes for its synthesis. We have generated C. reinhardtii lines with varying numbers (up to 10) of B12 biosynthesis genes in the chloroplast, and have demonstrated transcription of the genes.
The project will be to build on this study, to optimize expression of the enzyme proteins in the chloroplast, in particular to explore a novel way of regulating expression of the transgenes using riboswitches, which are elements in mRNA that respond to binding of metabolites or other small ligands, resulting in alteration of expression of the mRNA. We have recently found riboswitches in C. reinhardtii and in several other algae (Croft et al (2007) Proc. Natl Acad Sci USA 104: 20770-20775).
Thus tools developed as part of this project may facilitate metabolic engineering in other algal species. The student will become familiar with concepts of metabolic engineering, biosynthetic pathways, metabolite profiling and riboswitches.
See Research or email: Alison.Smith@plantsci.cam.ac.uk
Project Title: Growing algae outdoors - can algal-bacterial symbioses provide the means to reduce contamination?
Supervisor: Prof. Alison Smith
Project outline:
There are many challenges to be overcome before growth of microalgae at an industrial scale will be economic and sustainable. Although there are commercial microalgal ventures, most of the products are high value, and so cultivation is at relatively small scale, and with little requirement to optimize energy input. Most operations are in photobioreactors (PBRs), enclosed systems that allow good control of growth conditions (temperature, pH, nutrient supply, etc), and minimise problems with contamination. However, life cycle analysis - an approach used by chemical engineers to assess the efficiency of an overall process - indicates that the energy inputs associated with PBRs far exceed the energetic value of the extracted biodiesel. In contrast, growth in open ponds or raceways results in a small but significant reduction in energy compared to that from fossil-derived diesel (Stephenson et al (2010) Energy & Fuels 24: 4062-4077). On the other hand, a major problem with these open systems is one of contamination, eg by predators, competing algae, or bacteria. Thus crop protection is recognised as an essential feature of any industrial-scale operation for the production of microalgae. This project will address the question whether growing algae with mutualistic bacteria offers a better solution to contamination than strict monocultures. The aim would be to establish a number of combinations of algae/bacteria/predators and then analyse the productivity of the cultures and robustness to contamination, both experimentally and by mathematical modeling, as well as additional life-cycle analyses.
See Research or email: Alison.Smith@plantsci.cam.ac.uk
Project Title: Developing a microdroplet platform for development of microalgal biotechnology
Supervisor: Prof. Alison Smith
Project outline:
This is a joint project with Professor Alison Smith's algal molecular biology group in Plant Sciences and Professor Chris Abell's Microdroplet group in Chemistry, building on our initial work to apply microdroplet technology to the study and analysis of algal growth. Microdroplets are typically 20-100 micron water droplets carried through a microfluidic device in an oil stream [Pan et al (2011) Integrative Biol 3: 1043-1051]. The Microdroplet group have developed devices capable of trapping algal cells in droplets, where they can be grown, analysed and sorted at rates of up to 10 kHz. Optical detection allows the number of cells to be monitored, whilst fluorescence measurements can be used to quantify chlorophyll content, secretion of key compounds (though coupled assays), and lipid accumulation (by dye staining). The project will develop these specifically formatted experimental platforms to carry out high-throughput screening of algal strains, for example natural populations o r mutagenised libraries to detect strains with specific properties, for example those that have desirable properties for biotechnological purposes, such as high lipid content. Because millions of cells can be analysed in a short time, the technology could also be adapted to identified transgenic cells expressing a particular reporter gene, without the need for a selectable marker. The student will receive multidisciplinary training in research in the areas of microfabrication and lab-on-a-chip, and their application to algal biotechnological and microbial interactions. Suitable candidates would have background in many disciplines, including chemistry, chemical engineering, biochemistry or plant/algal biology, but must be prepared to work at the interface between physical sciences and biology.
See Research or email: Alison.Smith@plantsci.cam.ac.uk
Project Title: Network models for biosynthetic pathways in higher plants
Supervisor: Prof. Alison Smith
Project outline:
One of the most important and complex biosynthetic pathways in plants is that for tetrapyrroles - chlorophyll, haem, sirohaem and phytochromobilin. It must be tightly regulated to ensure correct assemble of the cofactors with their cognate apoproteins, and also because many of the intermediates are phototoxic, and therefore must not accumulate (Moulin et al (2008) Proc Natl Acad Sci USA, 105: 15178-15183). Because of its complexity and the number of genes involved - the biosynthetic enzymes and apoproteins comprise over 1% of the Arabidopsis genome - the tetrapyrrole pathway lends itself to a systems approach. Fortunately, it has many features that make it an ideal system with which to carry out studies of a subcellular network, and to develop and test mathematical tools that can be also used more widely in systems biology: all the genes are known, the concentrations of the intermediates and end-products can be measured with a good accuracy, there are several well-characterised Arabidopsis mutants available, and the behaviour of the pathway can be tested experimentally using a variety of genomics approaches.
We have used both microarray and metabolomics data to begin to construct a model to describe the pathway and its interactions with other cellular processes during seedling development. In collaboration with Dr John Ward, University of Loughborough, the aim of the current project will be to extend the model of the pathway, estimate parameters and subsequently study the response of the pathway to different treatments and in defined mutants. Thus the student will have an opportunity both to construct mathematical models and to test the design in practice by collecting experimental data, which will in turn be used to refine the models. The project is suitable for students with a strong background in mathematics, physics or mathematical biology; biologists and biochemists with an interest in mathematics are also encouraged to apply.
See Research or email: Alison.Smith@plantsci.cam.ac.uk