Advances: Excellance in Research and Training in Plant and Microbial Science

EXCELLENCE IN RESEARCH AND TRAINING IN PLANT AND MICROBIAL SCIENCE

Issue 9: Autumn 2007

JIC and TSL are powerhouses for the training of the next generation of bioscience researchers, exemplified in this edition of Advances, where the breakthroughs we report come from the work of outstanding PhD students and young Post-Doctoral researchers. Securing and further developing the skills base is a key element of our mission, and our holistic approach to training is highlighted in the central feature.

One of the lead scientists at the Sainsbury Laboratory since it's foundation in 1988, David Baulcombe, has taken up the Chair in Botany at the University of Cambridge, thus returning to the city where he started his independent research career. David and his team have been seminal contributors to the discovery of RNA interference (RNAi), and the understanding of the mechanisms of RNAi-based plant genetic regulation which is spurring development of new medical treatments, and transformed our understanding of cellular behaviour. His contribution has been outstanding and our collaborations in the burgeoning field of epigenetics will continue to flourish.

It is vitally important that we capture our breakthroughs and put them to use. Important patents for enhancing disease resistance have been granted to Plant Bioscience Ltd (PBL) in the USA. The gene, Sad1 cloned by Anne Osbourn with co-workers at the Sainsbury Laboratory, encodes the first step in a pathway producing antimicrobial compounds. Several other patents have been assigned to PBL, who have also supported the setting up of another spin-out company, Procarta Biosystems with the intellectual resource of microbiologists Michael McArthur and Mervyn Bibb. Procarta offers the biotechnology and life science industries strain improvement services based on technology developed at JIC.

The new Earth and Life Systems Alliance between JIC and the University of East Anglia has an initial focus on three areas of environmental biology - the genetic basis of diversity, agricultural transitions and geochemical cycles, with the potential to make a massive, agenda-setting change to the Grand Challenge of Living with Climate Change. The alliance has quickly generated substantial enthusiasm and engagement from a cadre of outstanding researchers. Seeding new developments as ideas emerge and momentum increases is the optimal path for world-class new science. Significant resources from both UEA and JIC will back the initiative.

Chris Lamb
Director, John Innes Centre

Understanding flowering plant evolution

Moss genes provided fuse for plant life explosion

Physcomitrella patens - the plant on the right has had its rooting genes turned off

The genes that control the development of root hairs on plants are also found in moss, a finding that changes our understanding of how the plants we see today evolved over 400 Million years ago. Plants use roots to anchor themselves, and to absorb nutrients. Root hairs are single cells that grow from the roots and greatly increase the root’s surface area. In a paper published in Science, Liam Dolan’s team describe the discovery of a pair of genes that are required for root hairs to grow. When these genes were turned off, plants produced hairless roots.

Not all plants have roots. Evolutionarily ancient plants such as mosses instead grow cells called caulonema and rhizoids. Caulonemal cells increase the surface area for nutrient absorption, and rhizoids provide anchorage. The team found that the genes that control root hair growth are very similar to the genes that regulate the development of caulonema and rhizoids in the moss Physcomitrella patens. In fact, they were able to replace the genes they turned off in plants with the equivalent genes from moss, and produce hairy roots.

This study shows that genes from one stage in the life cycle were recruited by their descendants into another part of the life cycle. The development of root hairs helped the evolution of larger plants by increasing their nutrient uptake ability and anchorage. The results give us a model for the genetic changes that underpinned the dramatic changes in plant stature that occurred during the Devonian explosion 400 Million years ago.

The technology has been assigned to and is the subject of patent applications filed by PBL www.pbltechnology.com

Reference: An ancient mechanism controls the development of cells with a rooting function in land plants. Benoit Menand et al. (2007) Science 316 1477-1480

Funding: Natural Environment Research Council, Human Frontier Science Program Organization, BBSRC Core Strategic Grant; European Molecular Biology Organisation & Marie Curie Fellowships; Marie Curie TIPNET Network; Joint Scholarship between the University of East Anglia, China Scholarship Council & HFSPO

Collaboration: University of Lausanne and Zhejiang University, Hangzhou, P.R.China

How plants learned to respond to changing environments

The clubmoss Selaginella kraussiana is a member of the group Lycophyta, which diverged from other land plants around 400 million

Plants adapt their growth, including key steps in their life cycle such as germination and flowering, to take advantage of environmental conditions. They can also repress growth when their environment is not favourable. This involves many complex signalling pathways which are integrated by the plant growth hormone, gibberellin. Nick Harberd’s group examined the genes involved in the gibberellin signalling pathway in a wide range of plants and, in a paper in Current Biology have described how they discovered that it was not until flowering plants evolved 300 Million years ago that plants gained the ability to repress growth in response to environmental cues.

All land plants evolved from an aquatic ancestor, and it was after colonisation of the land that the gibberellin mechanism evolved. The earliest land plants to evolve were the bryophyte group, which includes liverworts, hornworts and ancestral mosses, many of which still exist today. The ancestral mosses have their own copies of the genes, but the proteins they make do not interact with each other and can’t repress growth. However, the moss proteins work the same as their more recently evolved counterparts when transferred into modern flowering plants.

The lycophyte group, which evolved 400 Million years ago, were the first plants to evolve vascular tissues for transporting water and nutrients. They also have the genes involved in the gibberellin signalling mechanism, and the products of their genes are able to interact with each other, and the hormone gibberellin. However, this still does not result in growth repression. Not until the evolution of the gymnosperms 300 Million years ago are these interacting proteins able to repress growth. The angiosperms (flowering plants) also possess the gibberellin growth repression system. This group of plants became the most dominant, and make up the majority of plant species we see today.

Evolution of this growth control mechanism appears to have happened in a series of steps, which this study associates with major stages in the evolution of today’s flowering plants. It also involves two types of evolutionary change. As well as structural changes, that allow the proteins to interact, flowering plants have also changed the range of genes that are turned on and off in response to these proteins.

Reference: Step-by-step acquisition of the gibberellin-DELLA growth-regulatory mechanism during land-plant evolution. Yuki Yasumura, Matilda Crumpton-Taylor, Sara Fuentes & Nicholas P. Harberd (2007) Current Biology 17 1225-1230

Funding: BBSRC Core Strategic Grant

Scientists find stem cell switch

Arabidopsis root meristem showing extra divisions in the quiescent centre after ethylene treatment

Poor soil structure is a problem in tropical agriculture, where soil becomes compact as it dries out.

Liam Dolan’s group have discovered how the stem cells in plant roots detect soil structure and whether it is favourable for growth. They describe in a paper in Science that the hormone, ethylene, regulates cell division in root stem cells in the model plant Arabidopsis. Ethylene is known to play a role in perceiving and communicating environmental cues. They predict that this is the mechanism plants use to detect how tough or soft the soil is around them.

As in humans, the defining characteristics of stem cells are that they are able to either regenerate themselves or produce other types of cells. Every spring, the growth in our gardens is the result of the function of stem cells. Stem cells in buds are activated to divide and give rise to the growth for that season. In roots, the team found that the division of stem cells is regulated by ethylene and they suggest that ethylene provides signals from the environment to activate cell division when the conditions are right.

We believe this is a first step towards understanding how plants respond to soil compaction. Armed with this understanding we can start to devise ways to tackle it”

Reference: Ethylene modulates stem cell division in the Arabidopsis thaliana root. Olga Ortega-Martínez, Monica Pernas, Rachel Carol & Liam Dolan (2007) Science 317 (no. 5837) 507 - 510

Funding: BBSRC Core Strategic Grant, a John Innes Foundation studentship (OO-M) and a postdoctoral fellowship from the Spanish Ministerio de Educacion y Ciencia (MP)

Potential for engineering anthocyanins

A collaborative study between JIC and the Institute of Food Research (IFR) has used pioneering functional genomic techniques to investigate anthocyanin production. Jie Luo, a JIC Post Doctoral Training Fellow, worked with IFR Post Doctoral scientists Christine Fuell and Katherine Elliott to identify enzymes able to beneficially modify anthocyanins - pigments found in plants that give some flowers, leaves and fruits their colours.

Plants use this colouration to attract pollinators and as protection against various environmental stresses. Stabilised anthocyanins could have important uses as natural food colourants. At present, their use is limited because they are degraded, and become discoloured. Stable anthocyanins could replace many of the artificial colours used in a variety of foods, with the added benefit of the health-promoting activities associated with anthocyanins.

IFR Post Doctoral scientists Kath Elliott & Christine Fuell

There are hundreds of different anthocyanins found in nature, differing from each other by small chemical modifications. The research groups, led by Cathie Martin at JIC and Tony Michael at IFR, looked at acyltransferases, a group of enzymes which transfer acyl groups onto the anthocyanins. Only a few of these enzymes have been characterised, but many more must exist because of the great range of anthocyanins.

The enzymes are very versatile in their substrate specificity, and are thought to be able to evolve rapidly. Very similar enzymes appear to have evolved independently, and hence are structurally different, but function almost identically. This convergent evolution has hindered conventional approaches to identifying new genes, so a modified strategy was required.

JIC Post Doctoral Training Fellow
Jie Lui

In collaboration with Japanese research groups, they looked at the chemical structure of the major anthocyanin in Arabidopsis, and identified the exact type of acyltransferases needed to make the necessary structural modifications. Acyltransferases are part of a distinct enzyme group, which has 88 members in Arabidopsis. Analysing the genetic sequence of these 88 genes found no good candidates for the specific acyltransferases required. Instead, they looked at which of these genes were turned on when the plants were making anthocyanins in response to stress. This identified a smaller number of candidate genes.

Biochemical analysis showed that the candidates could make the necessary modifications to synthesise the major Arabidopsis anthocyanin. Enzymes functions were confirmed when the genes were transferred into tobacco. The acylation of tobacco anthocyanins caused a slight change in the colour of the tobacco flowers. The acylated anthocyanins were also more stable.

Reference: Convergent evolution in the BAHD family of acyl transferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana. Jie Luo et al. (2007) The Plant Journal 50 678-695

Funding: BBSRC AgriFood Committee (to JIC and the Institute of Food Research), BBSRC Core Strategic Grant, Ministry of Education, Japan and Japan Science & Technology Agency CREST

Collaboration: RIKEN Plant Sciences Center, Chiba University, Suntory Ltd, Shinshu University, and Ehime Women’s College, all in Japan

Securing the skills base

The Centre has a pre-eminent role in training plant and microbial scientists, both in the UK and internationally. Many of our student and post-doctoral intake choose the centre either because they have read high-impact papers in major journals, or because their supervisors and department heads are linked to JIC and The Sainsbury Laboratory through their own training and research collaboration networks.

High school students

...get ‘Inside Science’

Science degree courses have declined in popularity over the last 20 years in the UK, threatening our world-class research base. Business leaders have warned that a growing skills shortage will have serious implications for the health of the economy.

Mass spectrometry with Lionel Hill

The Norwich BioScience Institutes hosted a three day workshop in September for gifted and talented high school students, to introduce them to careers in science.

As well as hearing from leading scientists working in fields such as food allergy, genetics, crop science and microbiology, they had the opportunity to get hands-on with hi-tech equipment such as electron microscopes and mass spectrometers.

Hannah Norman won the prize for the best interpretation of ‘Perceptions of Science’. We will be tracking their progress to establish the impact of early exposure to the campus.

Perceptions of Science

Hannah Norman, a year 11 pupil at Sir John Leman School, Beccles

Science. A scary thought
Labs and chemicals, all toxic
Out of control Meddling in things we should leave alone.

Science. The wonder of the world
Living, breathing, multiplying
Watch with baited breath and widened eye
But do not touch.

Science. A power to be harnessed
Starting wars and saving lives
To learn the secrets it holds.

Science. Bewildering and Beautiful
Frightening and Familiar
Perceptions of science.

What’s yours?

…undertake their first research project

Each year, pre-university high school students also compete for the chance to undertake 4 week research projects at the centre, part of a national programme funded by the Nuffield Foundation. At the end of their projects, each student has to prepare and deliver a 5 minute Powerpoint presentation to a science audience, and answer their questions. A total of 13 students spent the summer on campus this year.

Nuffield students and their supervisors

The next stages

Funding is available from a variety of sources to support bench-based training whilst students are at university in the UK. JIC welcomes funded students onto campus during the vacation between their 2nd and 3rd year – but competition is fierce and places are limited.

Dr Mike Merrick (Chair of Graduate Studies Committee) with two of the 2007 PhD students

Over the years we have trained and nurtured a substantial number of the world’s best plant and microbial scientists and the Centre provides a dynamic, stimulating and friendly environment for PhD training amongst a thriving research community. In October each year the arrival of the post-graduate student intake gives new impetus to our science. For many of our alumni, their association with us starts when they arrive as PhD students. In total we welcomed 16 newcomers to JIC and the Sainsbury Laboratory this October.

Webpages: www.jic.ac.uk/students/

We offer two distinct PhD routes, one of which is the prestigious 4 year Rotation in which students take three mini research projects in their first year to provide a strong research base from which to undertake their chosen research project. In addition to a broad range of scientific skills, students achieve a Certificate in Professional Studies after attending an 8-module course on issues such as science communication and time management.

PhD student profiles

Nicole Steinmetz studied at the Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen, Germany, prior to joining JIC as a Marie Curie EST Fellow where she studied the Cowpea mosaic virus and its potential for the development of novel materials or devices at the nanoscale.

“Although I was not previously trained in chemistry or materials science I have enjoyed the challenges of mastering a new area of study. During the past three years I have published or submitted seven papers and two review articles.”

Whilst at JIC, she won the Bryan Harrison Award at the International Conference on Advances in Plant Virology, participated in the Meeting of Nobel prize winners in Lindau, Germany, was a Finalist in the European Young Chemists Award, and won the Biosciences Federation Science Communication ‘New Researcher’ Award.

Nicole’s next appointment is as a post-doctoral scientist in the Dept. of Cell Biology at the Scripps Research Institute in California, using viral nanoparticles as tools for bioimaging and targeted drug delivery.

Matilda Crumpton-Taylor and Sara Fuentes are PhD student co-authors of a paper in Current Biology featured in this issue of Advances.

Olga Ortega-Martínez (undertaking a PhD supported by the John Innes Foundation) is lead author on the paper on stem cell switching published in Science, and featured in this edition of Advances.

Amy Strange won the prize for the best talk at the 13th European Meeting of PhD Students in Evolutionary Ecology in Lund, Sweden this August. The five day meeting was attended by over 60 students from all over Europe, each of whom gave a 10 minute talk on their project and answered 5 minutes of questions.

Post-Doctoral Training Fellows

The next stage of training at JIC is the BBSRC’s Post-Doctoral Opportunities Scheme, aimed at the most exceptional post-doctoral candidates who would be credible candidates for fellowships from EMBO, Marie Curie, the Human Frontiers Science Program or similar international or national programmes. We would expect, for example, that a recent PhD graduate would have one or more papers with a significant impact in their field. The ethos of the scheme is to help new scientists develop the knowledge and skills (field-specific, analytical and transferable) necessary for their development as a research scientist, whilst allowing them the opportunities to attain personal development pertinent to their chosen career pathways.

PDTFs Benoit Menand and Jie Luo are first authors of two papers featured in this edition of Advances. Jie’s first year at JIC was funded by a visiting scholarship from China Scholarship Council and he currently has leave of absence from his permanent position in China at Huazhong University of Science and Technology to continue his fellowship. Benoit is leaving JIC this Autumn, to start work as a young group leader at the Laboratoire de Génétique et Biophysique des Plantes (Luminy Univesity, Marseille) funded by CNRS (Centre National de la Recherche Scientifique). He will be working on the evolution of signalling pathways that control plant growth and development in response to abiotic stress (particularly nutrient starvation) in land plants. Monica Pernas and Rachel Carol, co-authors of the recent paper on stem cell switching published in Science, were also PDTFs at JIC.

We keep in touch with ‘leavers’ via our world-wide alumni network.

INTERNATIONAL MENTORING

JIC is keen to encourage science and mentor outstanding scientists from less developed countries, and a programme is being established that will allow an expansion of our involvement in collaborative projects that support international development. Scientist-in-charge, Lesley Boyd envisages that, through external funding, scientists from less developed countries will be able to spend time working on a project that addresses a problem of relevance to their home country, supported by one or more research groups working within a similar research area at the centre.

Bringing scientists together

As part of our commitment to post-graduate education and training we organise and contribute to courses all over the world. This year JIC jointly sponsored the first of an annual series of summer schools on Applied Molecular Microbiology with the Rudjer Boskovic Institute in Zagreb. Thirty-eight PhD students and early post-doctoral researchers, representing twenty nationalities, attended the course entitled “Microbial Genomics and Secondary Metabolites” at the Mediterranean Institute for Life Sciences.

The course consisted of lively poster sessions, and a series of lectures. This included a review of metagenomics by JIC’s Mervyn Bibb, who illustrated the concepts of DNA isolation, heterologous expression and product detection with some of the experiences of biotechnology company Diversa (now part of the Verenium Corporation) in searching for novel antibiotics. David Hopwood reviewed recent advances in the total synthesis and expression of unnatural polyketide synthase gene clusters to make novel molecules. Following on from this year’s success, planning is underway for next year’s course.

Capturing breakthroughs

Important patents for enhancing disease resistance

Plant Bioscience Ltd (PBL) have recently been granted a US patent on a gene, cloned by Anne Osbourn with co-workers at the Sainsbury Laboratory. The gene, Sad1, encodes the first step in a pathway producing antimicrobial compounds in oats, called avenacins. These compounds are only found in oats and confer broad spectrum disease resistance on the plant. Transferred to other species, these genes may be able to confer resistance to plants that are unable to produce avenacins, such as wheat and barley, and so protect them from diseases including take-all (an important fungal disease that infects roots, disrupting their ability to take up nutrients and water and so severely reducing yield).

Avenacins belong to a group of chemicals called triterpenoids, which have a variety of functions in plants including pest resistance and palatability to animals. Some have also been found to have important pharmaceutical, nutritional and anti-cancer properties. PBL have recently applied for two other patents covering further genes in the oat avenacin synthesis pathway that may be useful as tools for altering the chemical structure of triterpenoids. These modified triterpenoids may also improve the plant’s flavour or increase its nutritional value.

Oats produce avenacins specifically in the epidermal cells of the root tip and lateral roots. This localised production is brought about by tightly regulating the expression of the genes in the avenacin synthesis pathway. The gene promoter, which controls the gene expression, is the subject of a fourth patent application assigned to PBL. This root-specific promoter was shown to be effective when transferred into Arabidopsis and rice, and so could be used as a genetic tool for targeting gene expression to the roots in transgenic plants.

Any interested parties should contact Lars von Borke at PBL – lars@pbltechnology.com

Avenacin A-1

Procarta Biosystems

Molecular microbiologists Michael McArthur and Mervyn Bibb are the scientific co-founders of Procarta Biosystems Ltd. The new company, based in our bioincubator, offers strain improvement services based on technology developed at JIC, which enables efficient genetic optimisation of metabolic pathways. Procarta will also be developing new proprietary therapeutic agents for overcoming antibiotic resistance in pathogenic microorganisms, widely recognised as an extremely serious problem for the healthcare industry. Procarta has received financial backing from PBL.

GIMA awards

19 July 2007

The Vital Earth™ product range was runner-up in the 2007 Garden Industry Manufacturer’s Association Awards – Growing Aids category. The composts, endorsed by the John Innes Foundation, are based on UK sourced environmentally sustainable materials.

Earth and Life Systems – the new Alliance

ELSA The Earth and Life Systems Alliance (ELSA) is a unique multi-disciplinary Alliance integrating world-class expertise in biological, earth and social sciences to tackle the challenges posed by a changing climate.

ELSA is a major strategic collaboration between JIC and the School of Environmental Science at UEA, Norwich. The research agenda of the Alliance is focussed around three research ‘pillars’ which are fully described on the new website.

	Biodiversity in the face of global environmental change
	Agricultural transitions under climate change
	Elemental systems that sustain life and the planet

Discussions with UEA, led by Caroline Dean, and development of the pillars has been underway for most of this year. The first formal meeting of ELSA scientists took place at JIC in September.

ELSA – www.elsa-uk.net - pioneering research for a changing environment

Communication in Rhizobia

A single Rhizobium colony (in white) inducing a streak of a biosensor bacterium (a modified Chromobacterium violaceum strain) to produce a purple pigment due to rhizobially-made quorum-sensing signals

In a critical review, Allan Downie and colleagues have examined how rhizobia can communicate with each other using low molecular weight signals (N-acyl homoserine lactones) to optimise their ability to form nitrogen-fixing nodules on legumes.

Much of this work was done at JIC and forms a critical component of the research knowledge. However in addition they reviewed the evidence from work at JIC and elsewhere that the plant ‘tunes in’ to this conversation and seems to respond to the same signals that the bacteria use for their conversation. There is even some evidence that the plant may be able to make equivalent (but chemically different) signals that can be detected by the bacterial communication systems and in some cases can even interfere with the bacterial conversations.

Reference: Quorum-sensing regulation in rhizobia and its role in symbiotic interactions with legumes. Maria Sanchez-Contreras et al. (2007) Philosophical Transaction of the Royal Society B 362 1149-1163

Funding: Research on rhizobia at JIC is funded by the BBSRC

JIC SCIENTIST NAMED
Plant Cell Editor-in-Chief

Cathie Martin - appointed as editor-in-chief of The Plant Cell Cathie Martin from the Department of Metabolic Biology has been appointed as editor-in-chief of The Plant Cell from January, 2008 succeeding University of Arizona plant scientist, Rich Jorgensen. The Plant Cell is the science journal of the American Society of Plant Biologists, with the highest impact factor (9.868) of primary research journals in plant biology. Cathie has been a member of the Editorial Board since 2001. As Editor-in-Chief, her vision for the journal includes maintaining and enhancing the strength of the editorial board, continuing emphasis on high scientific standards and publishing ‘full stories’, broadening the scope of the journal (for example, to include more high quality work in evolutionary development, structural and comparative genomics, biotechnology, and studies in non-model plant species), and expanding the publication of reviews, commentaries, and opinion pieces.

Cereals 2007

This year we were guests on the National Institute of Botany stand as part of the JIC/NIAB Alliance, and demonstrated to visitors the wide ranging effects of mutation on phenotype in the spring wheat Paragon, and how research at JIC uses this information in research to produce improved wheat for the 21st Century. There was huge public interest with discussions typically centred round the recognised need for future proofing which our research could potentially provide the agricultural industry, and how our Germplasm facility enables us to make use of past variation as well as the novel forms in our plot demonstration.

See website: www.jic.ac.uk/GERMPLAS

Science in Society award

The Science, Art and Writing (SAW) project conceived by JIC scientist Anne Osbourn has received funding from BBSRC to enable the SAW Trust to take ten science projects into local schools.

Scientists representing different facets of science will each assemble a collection of thought-provoking images based on their research areas (for example, the inside of a leaf, starch grains, photosynthesis) and will design experiments around their chosen themes, with support from experts at the SAW Trust. The images will also be used to brief poets and artists with experience in working in schools on SAW projects.

Each science theme will be used to run a 1 day SAW project in a local primary school. The scientists will lead a practical science session on their research area, using the images as an integral part of their introduction. This will be followed by poetry and art, led by the poets and artists. The creative output of these projects (poetry and artwork on scientific themes) will be celebrated in an event for all those involved and published in hard copy and on the SAW website www.sawtrust.org

Elected to RSC Council

Dave Evans of the Department of Biological Chemistry has been elected to the Dalton Council of the Royal Society of Chemistry.

Dalton Council is responsible for setting RSC policy in areas related to inorganic chemistry. His term of office is initially for three years and he hopes to use his wide experience to provide a viewpoint that reflects those of scientists working in multidisciplinary research at the interface with chemistry.

Outstanding venue for science events

Our conference facilities are being marketed under the Norwich BioScience Institutes banner at www.venue-norwich.info - we are looking to attract more scientific conferences to the venue and look forward to discussing possibilities, particularly for international science conferences.