Plants: An insider’s guide

C&I Issue 3, 2008

To understand all there is to know about plants, you have to look inside them, says Arno Krotzky, managing director of Berlin-based plant science company metanomics. And where better to start than the company’s MetaMap database. The world’s biggest library of information about plant genes and their functions, MetaMap contains information on the activities of some 55 000 individual genes, including roughly 1.5m metabolic profiles – unique snapshots of the biochemical changes that occur in individual plants when certain genes are switched off or new genes are introduced.

Knowing all of this information about what plant genes do makes good business sense. BASF Plant Science, metanomics’ owner, estimates that the total global market for plant biotechnology will be worth around $50bn by 2025, with high-yielding GM crops among the biggest markets. By 2030, the UN estimates that the amount of arable land available globally per capita will have shrunk from 2200m2 in 2005 to 1800m2 by 2030 – when the world’s population is expected to hit 8.3bn. Understanding which genes are important in regulating plant growth and development will be crucial for developing new hardier GM crop varieties able to increase productivity.

Over the next decade, BASF Plant Science, together with partner company Monsanto, has committed to increase the yield of corn, soya bean, canola and cotton by 20%. Plant biotechnology will allow researchers deliver these improvements in a fraction of the time of traditional plant breeding methods, and by changing just one or two genes, argues Peter Oakley, member of the board of executive directors at BASF. Compare this, for example, with the development of modern corn varieties, he points out, which are roughly three times the size of some of the original species identified 500 years ago and have only 50% of genes in common.

Selecting which genes are important is the first step in developing a new GM crop. A typical plant species will contain something like 35 000 genes, Krotzky explains. These genes in turn define and produce the enzymes involved in carrying out thousands of chemical reactions responsible for the plant’s appearance and behaviour. A change in just a single gene leads to precise changes in the types and ratios of metabolites making up the plant’s metabolic network. ‘Metabolites are the real drivers behind plant functions and at the same time the most comprehensive, rapid and sensitive ‘diagnostic sensors’ of plant life,’ Krotzky says. ‘The addition of one gene leads to the production of a new metabolite or plant function. New metabolites are specific for new functions.’

To construct metanomics’ MetaMap database, researchers began by individually knocking out each of the genes of the humble weed Arabidopsis and looking at the changes in metabolite profiles. The next step was to introduce to the plant entirely new genes – some 20 000 of them to date – to see what new functions could be added. One of the most promising of these is a gene responsible for drought resistance in moss. Adding this new gene to Arabidopsis not only allowed the researchers to see if the same effects could be switched on in a different species, but also to look at what other effects, if any, it may have on the plant metabolism. With the proof of concept in hand, the group is now evaluating this and other similar genes in more valuable crop plants, such as corn, with the aim of delivering new drought-resistant crop varieties to the marketplace post-2012.

To date, metanomics has submitted for patent more than 150 000 gene-function relationships, Krotzky says – with an average of one major patent every five days. In a typical year, the company will study 5000–10 000 genes, involving the analysis of more than 100 000 fractionated plant samples by more than 70 mass spectrometers and robots in a continuous around the clock operation claimed as the world’s largest platform for metabolite profiling.

Each plant species produces between 50 000 and 100 000 different metabolites, Krotzky continues. Following the changes in these compounds over time involves an army of dedicated hi-tech analytical and IT equipment and skilled personnel. Even the merest fluctuation in temperature or wind direction may be enough to shift a plant’s metabolite patterns, so a stable, controlled temperature, environment is essential when trying to take measurements.

To map the sequence of metabolite changes, Krotzky explains, the physiology of a single plant is arrested in 10sec and parts of the tip, root or whole plant obtained for analysis. The first step is to separate the metabolite compounds contained in the plant samples into different fractions by extraction into various solvents, depending on whether they are fat or water-soluble etc. These fractions are then subjected to a suite of analytical techniques, either GC-MS, LC-MS/MS and other mass spectrometry technologies, generating an average of 320 000 analytical results every 24hr. ‘A single analysis can involve just 20 µL of sample, for many metabolites up to 500x more sensitive than the best human lab in the world,’ Krotzky points out. Over 1000 important target metabolites and 9000 metabolome signals – a comprehensive set of metabolites for any given genetic make-up - can be seen in parallel at any one time.

Keeping track of all these data are powerful bioinfomatics systems, notes Richard Trethewey, scientific director of metanomics. The company’s MetaMap plant function database is effectively a ‘Google-type’ search engine for plants, he explains. It contains 25 Terabytes of information or as many as 2.4 billion data points, linking the plant genes to a whole range of different metabolite networks. Available for viewing by all employees worldwide, the system operates as an internet browser allowing users to search for any relevant biochemical pathways of interest, say, for example, where to engineer a plant to increase the rate of photosynthesis, he elaborates. In addition, specialised software links the MetaMap results online to tens of thousands journal paper references, clustered into discrete blocks according to their content.

One of the main functions of the system is as a predictive tool for determining gene function, Trethewey explains: The more data that are fed into the database, the more reliable the results. Along with its metabolite profiles, metanomics holds records of complete plant, bacteria and yeast genomes, as well as profiles of yield and stress tolerance performance – the ability of the plant to withstand adverse environmental and other impacts. The company also holds information on 31m crop genes - including the complete genomes of nine crops. Several hundred genes, including the one for drought resistance and another for potato blight resistance, are currently undergoing field tests.

But helping to identify which genes are important is only part of the metanomics story. Developing a new GM trait can take anything from 10 to 12 years including approval and costs  €60-80m, according to Oakley. To secure EU approval, any new GM crop product must undergo a battery of tests to assess its nutritional value, toxicology, allergenicity and environmental impact. Does the newly introduced gene do what it says it will do or are there any side effects?

Knowledge of the plant’s metabolic profile is crucial in ensuring the plant is safe for both humans and the environment. It also means that researchers are able to switch off or remove any genes that give rise any undesirable characteristics, notes BASF Plant Science president and ceo Hans Kast.

‘Today we are in a position where we can identify which proteins cause allergies in a peanut or other substances and take them out.’

To date only one GM plant has been approved for use in the EU: bt corn for insect resistance. A decision on BASF’s Amflora potato is expected in the next few weeks. If approved, this would become the first new GM plant cleared for cultivation in the EU in more than a decade. Not intended for human consumption, Amflora’s novelty lies in the fact its starch comprises 100% amylopectin, without the amylose starch found in natural potatoes. This makes it more valuable for industrial applications in the paper, adhesive and textile industries, Kast explains.

European acceptance of GM will depend on the availability of more information to support the safety of these new plants. Databases such as MetaMap can only be helpful, and the more we understand about plant biochemistry, the more persuasive the case, GM proponents argue. Whatever the arguments for and against, it is clear that we still have a lot more to learn about plants.

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