Issue 12: Winter 2008-9

 

It is timely to share with readers that JIC research going forward will provide three research powerhouses, together with integrated clusters for delivering economic impact, and embedded specialist science platforms.

• plant growth and development - aligned to HM Treasury’s Grand Challenges on ‘Global Food Security and BioEnergy’
• plant perception and response to the environment – ‘Living with Environmental Change’
• understanding and exploiting plant and microbial metabolism – ‘Health Ageing and BioEnergy’

More details will be announced via the website in due course.

We continue progression of the Norwich Science and Innovation Partnership to build on pillars of excellence in research. Two areas of focus are the Earth & Life Systems Alliance leading to exciting collaborations in agenda-setting plant and microbial biology at JIC and environmental science at the University of East Anglia, and the development of the plant natural products area with the Institute of Food Research, and with impact more broadly through to UEA in the farm to fork to population and clinic continuum.

Finally, I would like to congratulate David Baulcombe, until recently a project leader at The Sainsbury Laboratory, who has received the Lasker Award for Basic Medical Research for the discovery of the microRNAs that regulate gene function. These RNAs govern a multitude of activities in animals and plants, and have been implicated in a wide range of diseases. I am delighted that David has been recognised for this hugely influential research which is a splendid example of the broad impact of plant research. Our leading- edge science has greatly benefitted from the close working relationship between JIC and TSL, and we look forward to continuing close collaboration with David following his recent move to the University of Cambridge.

I am also delighted to share with you the detailed announcement of the launch of our 100th anniversary celebrations, here in Norwich in September 2009 (see below).

Chris Lamb FRS
Director, John Innes Centre

Registrations open for the first of the JI Centenary Events

The focus of the John Innes Centenary Year (September 2009-July 2010) is a celebration of the legacy of William Bateson, who coined the term ‘genetics’, founded the John Innes Horticultural Institution, and determined that genetics would be the central subject of our research.

We are launching the events with a Centenary Symposium ‘Genetics 100 Years On’ which will begin with a prestigious History of Genetics Day on Wednesday 9th September. An international line-up of science historians will cover topics including the background behind the founding of the Institution in 1909, the role of women in the JIHI workforce in the early years, Bateson’s contributions to evolutionary theory, and JII’s place in the history of genetics from the inter-war years to the atomic age. They will be joined by JIC Emeriti Mike Gale and Keith Chater and Science Philosopher, Sabina Leonelli who between them will cover JIC’s contribution to the modern sciences of crop genetics, bacterial genetics and Arabidopsis research - history in the making! This event will be accompanied by a major exhibition, drawing on the John Innes Foundation Historical Collections.

During the evening of 9th September, Nobel Laureate Professor Sir Paul Nurse FRS will deliver the Bateson Lecture. He will be followed by international speakers in fields that impact on the future of medicine, plant and microbial science, and our understanding of evolution, reflecting on the various areas of human interest that have been transformed by a genetics approach, examining where these areas are now and where they might be in the next 100 years.

‘JI Alumni Day’ will follow on Saturday 12th September, bringing together former staff to share their memories, catch up with what goes on today, and of course to have some fun. A ‘Discovery Day’ on Sunday 13th September will complete the launch celebrations. This is an open day providing the public with an opportunity to learn about the work of JIC. There will be an opportunity to tour the history of genetics exhibition, follow a ‘centenary trail’ around the site and to view selected laboratories. The programme will include fun activities with a genetics theme for children of all ages - guaranteed to inspire!

Registration for the History of Genetics Day, the Symposium and the JI Alumni Day is online, at www.jic.ac.uk/centenary

Purple tomatoes - a GM research tool with world-wide appeal

Scientists at JIC have expressed two genes for production of anthocyanins in tomato fruit which originated from the garden flower Antirrhinum (snapdragon).

Cathie Martin and post-doctoral scientist Eugenio Butelli had a distinct objective in developing these lines of tomato - to provide a research tool to establish whether phytonutrients of the class to which anthocyanins belong can offer health promoting or protecting effects in a dietary context. While there is a considerable body of epidemiological and cell-based evidence to support this idea, material that could provide the proper control (for example, berries without anthocyanins) was always missing. Genetic modification offers the opportunity to develop isogenic lines having, or not having, large amounts of a particular phytonutrient (in this case, anthocyanins).

Their Italian collaborators were able to show that supplying anthocyanins at significant levels in a dietary context over relatively long periods of time had a significant impact on the health of cancer- prone mice.

Their data support the arguments for inclusion of foods containing high levels of anthocyanins in all long-term dietary regimens. Next steps are to seek funding for a long-term intervention study with human volunteers.

This EU funded research outcome provide a positive example of GM application with consumer benefit. Over 50 requests for seed have been received from the general public, farmers and breeding companies. Our research has been reported very positively worldwide including BBC TV Horizon, the BBC Radio 4 Today programme, CNN, CBS, ABC and the UK tabloid and broadsheet daily and Sunday newspapers, and has already had a societal impact in the UK, helping re-frame the GM debate.

Reference: Butelli, E. et al. (2008) Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nature Biotechnology 26 1301-1308

Funding: EU funding from ProFood profood.ipk-gatersleben.de, FLORA www.flora-flavonoids.eu/sito/cms2 and BBSRC Core Strategic Grant

Collaboration: European institute of Oncology, Milan, Italy; Leibnitz Institute of Plant genetics and Crop Plant Research, Gatersleben, Germany; Plant Research International and Centre for BioSystems Genomics, Wageningen, The Netherlands

Checkpoints in division

The process of cell division is tightly regulated to ensure that the cell’s genome is correctly copied and distributed to daughter cells. Checkpoints in the process of division are used as a form of ‘quality control’, where the cycle of cell division is halted unless certain criteria are met. One such checkpoint is the correct association of sets of chromosomes to the mitotic spindle, which is used to pull the replicated sets of chromosomes apart. Animal cells which fail at this checkpoint are usually eliminated, to prevent cells becoming cancerous. Robert Sablowski has been investigating how these quality controls operate in plants, by disrupting microtubules which play key roles in growth and division.

Microtubules are components of the structural framework, or cytoskeleton, within cells, that form into different arrays during the cycle of cell division. They are made from protein sub-units of cx- and ß-tubulin, and are dynamic in nature, constantly adding or losing tubulin sub-units. The researchers blocked the function of a protein, PLP3, which is responsible for ensuring tubulin sub-units are correctly folded. Mis-folded sub-units cannot form microtubules. This provides a way of triggering cell division checkpoints, to see if plants exhibit the same controls as animal cells.

Plant cell division is mostly seen in the meristem and during early development of organs. Later organ growth is based on cell elongation. The loss of PLP3 function caused severe disruption to cell division during early organ development. Chromosomes failed to segregate correctly, cell walls were only partially formed and cells were enlarged and misshapen, resulting in deformed seedlings with severely arrested development. All of these defects are linked to disruption of the microtubule arrays.

Despite the severe disruption to cell division, however, the meristem was still able to grow and produce viable cells; it was able to tolerate defects in cell division and disrupted cellular organisation. This may be one reason why polyploidy (having more than two sets of chromosomes) has evolved in many plant species.

Reference: Mar Castellano, M. & Sablowski, R. (2008) Phosducin-like protein 3 is required for microtubule-dependent steps of cell division but not for meristem growth in Arabidopsis. The Plant Cell 20 969-981

Funding: Long-term EMBO Fellowship; Intra-European Marie- Curie fellowship (MEIF-CT-2003- 503985); BBSRC Core Strategic Grant

ONE SYSTEM - two different relationships

A JIC combination of biological and mathematical approaches has provided a novel explanation for the mechanisms of multi- functionality in signalling pathways.

Plants have symbiotic relationships with micro-organisms, which benefit both partners. Leguminous plants, such as peas and beans, form nodules on their roots which house rhizobia, bacteria which are able to “fix” nitrogen. Many plants, including legumes, form another symbiotic relationship with a type of soil fungus, which helps the plants absorb nutrients, particularly phosphate. These arbuscular mycorrhizal fungi are very different to rhizobia, and produce very different reactions in the plants. Although both symbiotic relationships activate and use several of the same plant genes, it is only now that a JIC team, led by Giles Oldroyd and Allan Downie, have discovered how the one system can manage two different relationships.

Calcium spiking in a Medicago root hair cell injected with a calcium responsive dye

Nitrogen-fixing rhizobia produce a chemical, known as Nod factor, which is detected by root hair cells in legumes. The legume root signalling pathway responsible for perception of Nod factor uses oscillations in calcium levels to transduce the signal in cells. The fact that several genes in this signalling pathway are also required for mycorrhizal symbiosis suggested that mycorrhizal fungi were likely to activate calcium spiking in root hair cells. The researchers monitored calcium levels when mycorrhizal fungi were present and found, for the first time, that mycorrhizal fungi activate calcium spiking, but the pattern produced is different to that induced by Nod factor. This creates a quandary: how can the same signalling pathway be activated differentially to produce alternative calcium responses?

Computational and Systems Biologists Saul Hazledine and Richard Morris then analysed the mycorrhizal and Nod factor- induced calcium responses, and found that they were both chaotic in nature. Stochasticity and randomness are not the only explanations for the seemingly erractic and noisy signals observed in these calcium oscillations. Often a fairly simple set of equations can give rise to what is termed ‘deterministic chaos’, allowing the system to produce a vast range of different behaviours with minimal energetic effort. Chaotic systems are intrinsically flexible and are particularly sensitive to small changes in the nature of the input. Likewise, the symbiosis signalling pathway must be sufficiently flexible to allow differential responses to rhizobia and mycorrhizal fungi; such flexibility may be provided through this chaotic component within the signalling pathway. The chaotic nature of the signalling pathway implies that only minor differences between the means of activation would be necessary in order to produce the differential calcium responses observed.

Reference: Kosuta, S. et al. (2008) Differential and chaotic calcium signatures in the symbiosis signaling pathway of legumes. Proceedings of the National Academy of Sciences 105 (28) 9823-9828 doi:10.1073/pnas.0803499105

Funding: BBSRC Core Strategic Gran; Royal Society Wolfson Research Council award; BBSRC David Phillips Fellowship

Speeding up resistance gene identification

Scientists from TSL, with Dutch and US colleagues, have developed a method to accelerate the identification and isolation of genes that could be used to make potatoes resistant to Phytophthora. Current methods of discovering resistance genes are too slow and do not lead to sustainable resistance, because Phytophthora can easily adapt. The best strategy to make potatoes resistant to Phytophthora is to develop so-called broad spectrum resistance. The newly developed method is aimed at the identification of interactions between genes of both the pathogen and the potato. By using a set of effectors (proteins that are secreted by Phytophthora into the plant during infection), and testing these for recognition by a diverse set of wild relatives of the potato, scientists can relatively quickly identify and isolate the genes that are crucial for recognition and resistance. The team tested 54 effectors (of an estimated 500 effectors in total) on a large set of wild potato species. In many cases, this led to a reaction known as the hypersensitive response, where programmed cell death is initiated on recognition of an effector protein. In the case of one effector (IPiO), recognition was found in three wild species, Solanum stoloniferum, S. papita and S. bulbocastanum. This indicated that all three species had the resistance gene. Realising that the resistance genes from the three species had to be very similar and using their knowledge of the previously isolated resistance gene from S. bulbocastanum, they were able to quickly isolate the resistance genes in S. papita and S. stoloniferum.

Reference: Vleeshouwers, V. G. A. A. et al. (2008) Effector genomics accelerates discovery and functional profiling of potato disease resistance and Phytophthora infestans avirulence genes. PLoS ONE 3(8): e2875. doi:10.1371/journal.pone.0002875

Funding: Gatsby Charitable Foundation; Wageningen UR Plant Breeding; Czech University of Agriculture; Center of Biosystems Genomics; NSF Plant Genome Research Program grant DBI-0211659

Collaboration: Wageningen UR Plant Breeding; Laboratory of Phytopathology, Wageningen University; Department of Plant Pathology, Ohio State University

Wageningen University press release (in Dutch): www.wur.nl/NL/nieuwsagenda/nieuws/Phyth080806.htm

 

FOCUS ON VIRAL NANOPARTICLES

SIRV2 nanoparticle - Image by Kim Findlay, JIC

The development of tuneable thin film assemblies and arrays that contain (bio) nanoparticles is an emerging field in bionanosciences / nanotechnology. Functional molecules such as proteins, nucleic acids, metallic and semiconducting nanoparticles, redox-active moieties and virus particles may be incorporated into the ultrathin films and arrays, with great potential for applications ranging from biomedicine to electronics.

Researchers at JIC led by David Evans are exploring the utilisation of viral nanoparticles (VNPs) as tools and building blocks for materials science. VNPs are ideally sized, can be produced in large quantities, and some are very stable and robust. They can self-assemble with very high precision, but are also amenable to modification by chemical means or genetic engineering.

Some applications of VNPs require them to withstand extremely harsh conditions. Uses in electrical systems may expose them to high temperatures, and biomedical uses can involve exposure to highly acidic conditions. VNPs able to remain functional in these conditions are therefore desirable. Evans’ team, working with colleagues in the USA and France, identified viruses from the hot acidic sulphurous springs in Iceland. One of these, SIRV2, was assessed for its suitability for use as a viral nanobuilding block.

SIRV2 is a virus that infects Sulfolobus islandicus, a single-celled microorganism that grows optimally at 80°C and at pH 3, and it was also able to withstand other harsh environments created in the laboratory. This shows that the rigid, rod-shaped SIRV2 virus capsule must be very stable, an important characteristic for use as a nanobuilding block. To be potentially useful as a VNP, the viral capsule also needs to be open to modification or decoration with functional chemical groups.

The researchers found that, depending on the chemistry used, modifications could be targeted specifically to the ends of the virus particle, to its body, or both. This spatially- controlled modification is unique to this VNP, and opens up new possibilities when the nanobuilding blocks are built up into arrays or layers. Since the virus body and ends can be selectively labelled it is expected that arrays with different physical properties can be fabricated, for example by aligning particles body-to-body versus self-assembly end-to-end. This option is not possible with other rod- shaped VNPs.

Evans’ interest in array architecture has also led him to collaborate with the Institute of Food Research’s Tim Noel and Roger Parker to address the question of whether the shape of the VNPs influences the overall structures of the arrays. They found that sphere-like particles showed rapid adsorption kinetics and were retained within the arrays whereas, in stark contrast, rod-like particles showed slow adsorption kinetics and were excluded from the arrays, and floated atop the array architecture in an ordered arrangement.

Reference: Steinmetz, N. F. et al. (2008) Site- specific and spatially controlled addressability of a new viral nanobuilding block: Sulfolobus islandicus rod-shaped virus. Advanced Functional Materials 18 3478-3486

Reference: Steinmetz, N. F. et al. (2008) Layer-by-layer assembly of viral nanoparticles and polyelectrolytes: the film architecture is different for spheres versus rods. ChemBioChem 9 1662-1670

Funding: EU Grant Marie Curie Early Stage Training CT-2004- 504273; the Biotechnology and Biological Sciences Research Council through Responsive Mode and Core Strategic Grant, and NIH (CA112075)

Collaboration: The Scripps Research Institute, California and the Institut Pasteur, Paris

Life science specimens under the microscope

JIC’s Head of Microscopy Kim Findlay continues our tradition of leading-edge support for science in microscopy techniques.

The Bioimaging team moved into a new, purpose-built facility in the Biffen building this year, along with a new transmission EM, a Tecnai G2 20 Twin purchased from FEI (formerly Philips Electron Optics Division). This 200kV instrument has a digital camera and full electron tomography capabilities, which involves taking a succession of images whilst tilting the specimens through increasing angles, which can then be combined to form a three-dimensional image of the specimen.

This replaces our two existing Jeol TEMs which were both over 20 years old. This represents the culmination of capital estate works funded through BBSRC under JIC’s Capital Rationalisation Plan, and the installation of microscopy equipment purchased in part through the BBSRC’s Research Equipment Initiative, with Norwich Research Park-wide financial support.

Function and redundancy of chaplin cell surface proteins

Working in collaboration with the Department of Biology and Institute for Infectious Disease Research, McMaster University, Canada, JIC scientists in Mark Buttner’s Group have been examining the chaplins, a group of proteins which help streptomycetes attach to the surface of host plants. These ‘hydrophobins’ are highly surface-active and are capable of dramatically reducing surface tension at the colony air-water interface.

Germinating spores in soil-dwelling streptomycetes outgrow in the aqueous environment to form a vegetative mycelium in which secondary metabolites such as antibiotics are produced. Specialised reproductive structures (aerial hyphae) are then formed, differentiating into unigenomic spores. Vegetative hyphae are hydrophilic; aerial hyphae and spores are hydrophobic. The chaplins are a family of eight secreted proteins that are critical for raising aerial hyphae in Streptomyces coelicolor. They can be separated into two main groups: the long chaplins (ChpA to -C) and the short chaplins (ChpD to -H). The short chaplins can be further subdivided on the basis of their abilities to form intramolecular disulphide bonds: ChpD, -F, -G, and -H contain two Cys residues, while ChpE has none.

The team constructed a “minimal chaplin strain” containing only chpC, chpE, and chpH, which raised a substantial aerial mycelium. This strain was used to examine the roles of specific chaplins. Within this strain, the Cys-containing ChpH was identified as the major polymerisation unit contributing to aerial hyphal formation and assembly of an intricate rodlet ultrastructure on the aerial surfaces, and the two Cys residues were determined to be critical for its function. The long chaplin, ChpC, augmented aerial hyphal formation and rodlet assembly, most likely by anchoring the short chaplins to the cell surface, whilst ChpE was essential for the viability of wild- type S. coelicolor.

Interestingly, the lethal effects of a chpE null mutation could be suppressed by the loss of the other chaplins, the inactivation of the twin arginine translocation (Tat) secretion pathway, or the loss of the rodlins (another group of hydrophobins).

Reference: Di Berardo, C. et al. (2008) Function and redundancy of the chaplin cell surface proteins in aerial hypha formation, rodlet assembly, and viability in Streptomyces coelicolor. Journal of Bacteriology 190 5879-5889

Funding: Canada Research Chairs program; Canadian Institutes of Health; BBSRC grant 208/EGH16080

 

Sugar-coated antibiotics

Many antibiotics have a variety of different carbohydrate molecules attached to them, which can help the antibiotic to be taken up by the target organism or overcome resistance. By manipulating the sugar, it may be possible to restore the usefulness of antibiotics to which resistance has developed.

Rob Field and David Lawson from the John Innes Centre have recently studied the structure and function of an enzyme which is involved in decorating antibiotics with sugar molecules. The enzyme is derived from a little studied species of Streptomyces bacteria, which produces the antibiotic tylosin. Specifically, the enzyme modifies a sugar molecule before it is attached to tylosin backbone. By working out how the enzyme works, it may be possible to use it to make unnatural sugars, with different properties.

They are not yet near to a market product, but trying to understand at a fundamental level how these sugars are made. By modelling the enzyme, and comparing it with related enzymes, they have been able to identify the key features important for its function, and to propose the biochemical basis for its action.

This work featured on the front cover of the journal, ChemBioChem

Reference: Tello, M. et al. (2008) Tyl1a, a TDP-6- deoxy-D-xylo-4-hexulose 3,4- isomerase from Streptomyces fradiae: structure prediction, mutagenesis and solvent Isotope incorporation experiments to investigate reaction mechanism. ChemBioChem 8 1295-1302

Funding: Norwich Research Park Studentship; EPSRC Grant Number GR/S820046/01; BBSRC Grant Number: B19400; BBSRC Core Strategic Grant

Collaboration: University of East Anglia; Biotica, Cambridge - www.biotica.com

Sowing a future for peas

While many compounds have been reported to change in laboratory-based drought stress experiments, few studies have identified how such compounds change in crops under field conditions. New research from Claire Domoney and colleagues at JIC, and the Central Science Laboratory could help breeders to develop pea varieties able to withstand drought stress and climate change. The research which analysed plants grown under glasshouse and simulated field conditions, also shows that the composition of crops is likely to change with the climate.

The researchers used NMR spectroscopy to produce a profile of the levels of the many different small molecules or metabolites in pea plant leaves. This profile, known as the metabolome, was then compared with that future for peas from plants subjected to controlled drought stress. The study found several key plant metabolites increased under drought stress, some of which had not previously been shown to be involved.

Less water, especially at critical times in the growing season, means lower yield and quality. This new information could be used to identify varieties of pea and other pulse crops that are more tolerant to changes in water availability.

Drought stress also induced changes in compounds that could have an impact on taste and flavour. Changes in climate are likely to alter the characteristics of commercial crops and could possibly affect their value. Peas and other legumes make a valuable contribution to sustainable food production by fixing nitrogen in the soil for the next crop, reducing the need for nitrogen fertiliser.

Reference: Charlton, A. J. et al. (2008) Responses of the pea (Pisum sativum L.) leaf metabolome to drought stress assessed by nuclear magnetic resonance spectroscopy.Metabolomics 4(4) 1573-3882

Funding: DEFRA Pulse Crop Genetic Improvement Network www.pcgin.org and the EU Grain Legumes Integrated Project www.eugrainlegumes.org

The Arabidopsis Reactome

New ways of capturing and representing biological knowledge are needed to enable individual researchers to remain abreast of relevant discoveries and to permit computational approaches for interpreting the large volumes of diverse data generated by modern biological research. JIC systems-, cell- and metabolic biologists were key to the establishment of the online knowledgebase called ‘Arabidopsis Reactome’. Its curated and imported pathways currently cover ~8% of the proteome.

Arabidopsis Reactome events have been electronically projected onto five other predicted plant proteomes. Such a system allows the visualisation and interpretation of high- throughput data, hypothesis formulation in systems biology, and is a useful learning resource. The project is open access, open source, and open to contributions! www.arabidopsisreactome.org

Reference:Tsesmetzis, N. et al. (2008) Arabidopsis Reactome: a foundation knowledgebase for plant systems biology. The Plant Cell 20 1426-1436

Funding: BBSRC Bioinformatics and e-Science Initiative; EU (Arabidopsis GROwth Network integrating Omics technologies); US National Institutes of Health; EU 6th Framework Programme; NIH Cell Migration Consortium and EBI Industry programme

Collaboration: European Bioinformatics Institute, Cambridge; Cold Spring Harbor Laboratory, New York; School of Medicine, New York University Grant

Regulatory framework for GM pharmaceuticals

The production of pharmaceutical proteins in plants has a number of potential advantages over conventional mammalian and bacterial methods, including lower costs and scalability of agricultural production compared to cell culture based fermentation methods and the absence of human pathogens. The use of genetically modified plants to synthesise proteins that are subsequently processed, regulated and sold as pharmaceuticals are set to challenge two very different, established regulatory frameworks, one concerning GM plants and the other concerning the development of biotechnology-derived drugs. The products nearing commercial viability will ultimately help to road test and fine-tune these evolving regulations, and may help to reduce regulatory uncertainties. Penny Sparrow and colleagues from the EU 6th Framework project ‘Pharma-Planta’ have recently reviewed the current state of the regulatory framework in several different countries and discuss recent changes in a paper in Trends in Biotechnology. They highlight the need for further regulatory development and make the case for international regulatory harmonisation.

www.pharma-planta.org

Reference:Spök, A. et al. (2008) Evolution of a regulatory framework for pharmaceuticals derived from genetically modified plants. Trends in Biotechnology 26(9) 506-17

Funding: EU 6th Framework Programme (Pharma-Planta)

Collaboration: Inter-University Research Centre for Technology, Work and Culture, Graz, Austria; Dept. of Biology, University of York; Fraunhofer IME, Aachen, Germany; St George’s Hospital Medical School, London

Transforming barley - simple and efficient

As well as being widely grown throughout the world, barley has been used as a model for studying the genetics of wheat, which has a large and complicated genome. Wendy Harwood’s group at JIC have developed a simple new method for transforming barley at a much higher efficiency than ever before, opening up opportunities for functional genomics research in this important crop species.

The method was tested by John Innes Foundation PhD student Jo Bartlett, who produced hundreds of transgenic lines using pBRACT vectors created at JIC. It is based on an Agrobacterium-mediated infection of immature embryos, producing a transformation efficiency of at least 25%. Most existing barley transformation techniques are less than 10% efficient, or are too complex for high- throughput use.

This method is the most efficient and straightforward barley transformation protocol developed to date. It is a useful tool for studying a particular target gene, by over-expressing or silencing it to provide proof of that gene’s function in crop plants. It also provides a way to generate large populations of genetic mutants, as has been done in species such as Arabidopsis and rice, where the development of such resources has greatly aided functional genetics studies. These resources allow researchers to search for important genes, and look at their functions.

Through the BRACT programme, barley transformation is now being offered as a service, and other laboratories are being trained to use the technology. At JIC, Paul Nicholson has identified Arabidopsis genes that increase susceptibility to the fungal pathogen Fusarium graminearum. He is using the barley transformation system to translate this work from model to crop, to see if reducing the expressions of these genes also make barley and wheat resistant to this toxin-producing fungus.

Chris Ridout is also investigating innate resistance in barley, with a view to developing durable resistance to a wide range of pathogens. Other laboratories are interested in testing out genes that help with drought tolerance.

Reference:Bartlett, J. G. et al. (2008) High-throughput Agrobacterium- mediated barley transformation. Plant Methods 4(22) doi:10.1186/1746-4811-4-22 or www.plantmethods.com/content/4/1/22

Funding: John Innes Foundation studentship; the EU Socrates/Erasmus funding scheme; DEFRA; BBSRC Core Strategic Grant

www.bract.org

BrachyTag

new tools for Brachypodium functional genomics

The purple false brome (Brachypodium distachyon) is a promising model system for the structural and functional genomics of temperate grasses (particularly wheat and barley) because of its physical, genetic and genome attributes, and sequencing of the inbred, community standard line Bd21 started in 2007.

Philippe Vain and colleagues at JIC have developed a facile, efficient and rapid transformation system for Bd21 using Agrobacterium-mediated transformation of compact embryogenic calli (CEC) derived from immature embryos, which will facilitate large-scale functional genomics research in this model system.

His team is supported by the BBSRC Tools and Development Fund as they construct and test new improved tools to switch off genes and to study their expression - scientists worldwide will have to introduce foreign DNA into Brachypodium around 200,000-times to be sure to hit and switch-off all of its genes at least once. Tens of thousands of unproductive DNA insertions may be avoided using this new technology, speeding up research in the area.

All the tools constructed during the new BrachyTAG project will be made available to all scientists in the UK and worldwide using the internet and scientific publications. Philippe and his team seek further financial support to underpin their initiative, and companies and philanthropic organisations will be invited to sponsor ‘inactivated genes’.

Reference:Vain, P. et al. (2008) Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnology Journal 6 236-245

Funding: BBSRC Core Strategic Grant

 

How do cyclomodulins work?

Mark Banfield has won funding from BBSRC to investigate the structure and function of a protein, originally identified in the food-borne pathogens Enteropathogenic E. coli (EPEC) and Enterohaemorrhagic E. coli (EHEC), that is able to change the properties of the host cell during infection. This protein, ‘Cif’, interferes with progression of the host cell cycle, irreversibly stopping it in its tracks. Cell cycle arrest by Cif is not achieved by activation of the DNA damage pathway but by a novel, as yet uncharacterised mechanism. Proteins that modulate the cell cycle are one of the most targeted set of molecules by the pharmaceutical industry. Investigating how a bacterially-derived protein interferes with the eukaryotic cell cycle is important for understanding the molecular details of this system, and in the long-term may identify new routes for novel therapeutics.

Fine-scale Phylogeny

Now that we are able to sequence parts of genomes, or in some cases whole genomes, it is commonplace for biologists to construct evolutionary trees using DNA data, a new approach, called ‘Phylogenetics’, has grown around building such trees. Thanks to recent large-scale genome sequencing projects, which have revealed the DNA codes of many organisms, including very closely related ones such as various yeast strains (or sub- species), we now have data available to construct far more detailed phylogenies. Some DNA sequences, such as the rDNA sequences, vary within genomes as well as between them, which will enable us to uncover the relationships between closely related organisms, such as our yeast strains, much more clearly than we have been able to do before now. However, new tools will be required to carry out the analytical processes involved.

The BBSRC Tools and Resources Development will support Jo Dicks and colleagues as they build a new mathematical tool to analyse rDNA sequence variation and dynamics at the most basic level. The tool will be applied to yeast and, if possible, plant data, allowing much more detailed phylogenies to be constructed than hitherto possible. Yeast genomes provide excellent models for understanding genome dynamics in plants and in other eukaryotic genomes, including humans. Their new tool can also be used by scientists who wish to analyse datasets of other species groups.

Phytoplasmas – tiny genome, immense importance

Saskia Hogenhout has won responsive mode funding from BBSRC to work on phytoplasmas, bacterial plant pathogens that have been associated with massive yield losses of crops worldwide. They can be particularly devastating for high-value production crops, such as blackberry, apple and pear productions in the United Kingdom; grape vines in southern Europe; and palm trees in Africa, the Caribbean Islands, Florida and Mexico. They are also prevalent in wild plant species, and are associated with losses of native plants unique to some areas. These bacteria are transmitted from plant to plant by phloem-feeding insects (leafhoppers, planthoppers and psyllids) and are predominantly dependent on their plant and insect hosts for dispersal in nature. They have the unique ability to invade and replicate in their plant and insect hosts. Some phytoplasmas, including Aster Yellows phytoplasma strain Witches’ broom (AY-WB), manipulate plant species to become better hosts for phloem-feeding insects, including insects that normally do not survive on these species.

Genome sequencing and subsequent bioinformatics analyses have revealed that phytoplasmas produce a range of effector proteins, of which some target plant cell nuclei and can perturb plant processes. Saskia will be focusing on the characterisation of some of the effector proteins of AY-WB to determine whether these effector proteins are involved in symptom development and in increased attractiveness of plants to insect vectors.

There is a general concern that phytoplasma disease incidence will increase in the future. An increase is expected in more intensive farming approaches in which crops may be grown all year round. Furthermore, global warming will extend the leafhopper breeding season and increase leafhopper survival during the warmer winters. Coincidentally, vector populations have probably also increased because of a reduction in pesticide use.

Witches’ broom = growth of a dense mass of shoots from a single point

Late blight resistance and elevated flavonoid composition – a new concept in potato improvement

JIC’s Cathie Martin and TSL’s Jonathan Jones have received ‘Follow-on Funding’ from the BBSRC to combine two highly important quality traits to appeal to both producers and consumers of potato. Current BBSRC funding supports isolation of resistance genes that will be deployed to enhance blight control. Flavonoids are health- promoting natural antioxidants, but potatoes – though a major dietary component – contain only low levels. Flavonoids can be elevated substantially using transcription factors identified at the John Innes Centre through BBSRC funding. The team is producing potato lines that combine late blight resistance with enhanced flavonoid content and nutritional/health value, using constructs with no bacterial antibiotic resistance genes. These improved potato lines will form the basis of a new spin-out company from TSL and JIC, to exploit the global potential of varieties with novel traits produced using cisgenic technology.

Seed funding to Procarta

Procarta Biosystems, the company ‘spun-out’ of the John Innes Centre in 2008 with the assistance of PBL to develop a technology designed to defeat antibiotic-resistant superbugs, has received significant seed funding.

The Rainbow Seed Fund and the Iceni Seedcorn Fund have invested £320,000 to allow Procarta to further develop its DNA decoy technology, which aims to restore antibiotic efficacy against resistant superbugs, such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin- resistant Enterococcus (VRE). Procarta’s pioneering approach to combating the threat of superbugs is based on Transcription Factor Decoys (TFDs). TFDs are short pieces of DNA which inactivate the resistance genes the bacteria need to counter antibiotics. This new funding will initially allow Procarta to generate pre-clinical data to validate the TFD approach and develop a product pipeline as potential therapies for numerous pathogenic bacteria. Procarta Biosystems is based in the Norwich Bio-Incubator on the JIC campus.

New crop data generated by JIC transformation resource

PBL has funded, through its Technology Development Programme (TDP), several projects led by Penny Sparrow to generate crop data in Brassica with four of PBL’s yield and stress traits. Most recently, Penny has completed work on the eIF2alpha translation factor which originated from Don Roth’s laboratory at the University of Wyoming. The results generated through this work show a significant increase in harvest index in transgenic Brassica containing a version of the eIF2alpha gene, demonstrating the potential benefit of increasing yield in crops with this gene. Over the last two years the JIC research team have provided to PBL an outstanding resource for proving the benefit of a number of genes from PBL’s yield and stress portfolio. The projects, which include the recently licensed Flavodoxin gene, have had clear benefit in communicating the strength of PBL’s trait portfolio to the AgBiotech industry and have resulted in an increased commercial uptake of these technologies.

For more information from PBL, please contact Dr Lars von Borcke at lars@pbltechnology.com

Validation of trait prediction

Many species exhibit increased growth rates, reach larger sizes and, in the cases of crops and farm animals, produce higher yields when grown as hybrids (“hybrid vigour”) but breeding for this trait is both intractable and expensive. Building upon our breakthroughs in understanding the molecular basis of this phenomenon, Ian Bancroft’s Group have developed a technology that permits the quantitative prediction of hybrid vigour, and, funded by PBL’s TDP scheme, demonstrated its utility in maize. They anticipate applicability in a wide range of crops, and even in livestock. However, in both species tested so far, the studies have used collections representing broad ranges of genetic diversity rather than realistic breeding material. With BBSRC follow-on funding they will validate the technology for use in breeding programmes using winter oilseed rape, which is one of the crops most closely related to their model species, Arabidopsis thaliana. This will add further support to their patent application and provide key data for demonstrating the utility of the technology to potential licensees.

Encapsulated mimics and real-time PCR controls

New molecular techniques for disease diagnostics are highly sensitive but can be prone to failure. When screening for infectious diseases, false- negative results due to assay failure are a major problem; to this end George Lomonossof and Nick Montague have produced internal assay controls using engineered Cowpea Mosaic Virus to mimic a diagnostic target, with synthetic sequence elements from the diagnostic target disease added into the virus genome. The JIC technology has been evaluated in veterinary diagnostic applications, and has attracted interest from commercial testing and reagent manufacturing companies. Nick is working alongside PBL to commercialise the mimics, and has received a Royal Society of Edinburgh/BBSRC Enterprise Fellowship which enables researchers to concentrate on, and be actively involved in, commercialising research that was largely funded by BBSRC.

Mark Banfield (Biological Chemistry) spent a week in Westminster with Ian Gibson MP on the Royal Society ‘Scientist-MP pairing scheme’ and Ian made a return visit to Mark’s lab. Dr Gibson commented “The John Innes Centre is internationally well known, producing internationally important science and scientists, and I particularly admire the dedication and enthusiasm of the young people in the lab, and their desire to advance their skills, knowledge and interest in their subject. Without scientific research and a knowledge of how things work then policy decisions in science would be much poorer”. He helped to start the scheme in 2001, and has taken part in it every year

Centenary Planting

Gordon Rowley, 87, former Keeper of the Roses when JIHI was at Bayfordbury, Hertfordshire, heels in ‘John Innes’, a new rose bred by Beales Roses, Attleborough to commemorate the JI Centenary.

Joining him from left to right were former colleague and friend Ellis Marks, Steve Rawsthorne, Science Operations Manager at JIC, Peter Beales of Beales Roses, Peter Innes, John Innes Foundation Trustee and descendant of John Innes, Brian Snoad, also a former colleague and friend from Bayfordbury days and Sarah Wilmot, JI-100 Outreach Curator.

Allaboutwheat

Funded by the BBSRC, the John Innes Centre and the Institute of Food Research have developed an exhibition and website on the history of wheat and the impact this important crop has had on mankind and the planet. The exhibition, currently on display at Gressenhall Farm & Workhouse in Norfolk, was established to encourage dialogue and to educate about the process of growing wheat, and to gain a better understanding of the needs of consumers and growers. www.allaboutwheat.info

Cereals 2008

JIC and the National Institute for Agricultural Botany, Cambridge again joined forces to present work to the plant breeding and farming community at the UK specialist cereals event in Lincolnshire.

40 years at JIC

In 1968, JIC Emeritus David Hopwood and four of his group transferred from the University of Glasgow to the then John Innes Institute. Helen Kieser, his technician, worked in the Streptomyces Group from 1968 to 2005, and was awarded a PhD in 1999. Since 2005 she has been Lab Manager for the JIC’s Bateson Building, a role which allows science to continue to benefit from her outstanding skills and experience.

InCrops launched

The John Innes Centre is InCrops a partner in a new venture based at the University of East Anglia that will develop novel uses for crops to reduce our dependency on man-made products in a bid to tackle climate change.

Innovation in Crops, or InCrops, has received more than million from the East of England Development Agency (EEDA) and the European Union to develop an enterprise hub linking the region’s top researchers with businesses looking to develop new products. The five-year, £4 million project will use the region’s scientific expertise to create new plant –based products such as bio-plastics and packaging. It will also look at using plants in innovative ways such as using hemp for building and car components. www.incropsproject.co.uk
Press release: www.uea.ac.uk/home/services/units/mac/comm/media/press/ 2008/nov/homepagenews/incropsinitiative

Metabomeeting 2009

The European Forum for practitioners from academia, government and Metabomeeting industry that discusses the techniques and applications of metabolic profiling (metabolomics/metabonomics) will take place at the Norwich BioScience Institutes Conference facilities (5th-8th July). The meeting, co-organised by JIC, the Institute of Food Research and the Metabolic Profiling Forum, follows on from the highly successful meetings at the University of Cambridge, Imperial College London and the Ecole Normale Supérieure de Lyon.
www.thempf.org/MM09/general_info.html or contact Lionel Hill (lionel.hill@jic.ac.uk)

DNA Detangler

International scientists working on new drug discovery targets for cancer and bacterial diseases met at JIC this year to share their latest findings. Visitors attending Topo2008 all work in the field of topoisomerases, enzymes that act on the double strands of DNA to stop them becoming tangled. Without topoisomerases, cells die as they replicate. One way of stopping diseased cells from growing is to inhibit topoisomerases, for example to stop the uncontrolled cell division characteristic of cancer. As well as sharing fundamental research findings, the scientists showcased how their work is being translated into the discovery of new drugs.