Golden harvests

Technologists are used to trade-offs. Better sensitivity means worse specificity. Higher purity means lower yield. And for plants, greater tolerance to stress means stunted growth. Kazuo Shinozaki and Kazuko Yamaguchi-Shinozaki, a husband-wife team, and colleagues at RIKEN Plant Science Center (Yokohama, Japan), demonstrated that the last trade-off can be overcome¹.

By the late 1990s, many genes that protect plants against harsh environmental conditions had been identified, but researchers balked at the prospect of transferring genes one by one into transgenic plants. Shinozaki and colleagues engineered Arabidopsis thaliana to constitutively overexpress the transcription factor DREB1A, which they had previously found to upregulate several genes in response to cold and dehydration. The transgenic plants showed remarkable increases in tolerance to freezing, water stress and salinity, but the plants were dwarf in phenotype. The researchers got around this by expressing the protective gene just when it was needed. When they used the promoter from a dehydration-induced gene to control expression of DREB1A, the resulting plants were even more stress tolerant than constitutively active transgenics and furthermore, grew to a normal size.

“The DREB1A transcription factor is a master switch of stress-inducible gene expression,” explains Shinozaki. Though the research was carried out in A. thaliana, he says, “our method [for] molecular breeding of abiotic stress tolerance can be applied to real breeding of crops and trees.” Shinozaki's colleagues and collaborators are currently using these new insights to probe stress responses in a wide variety of crop plants, including rice, wheat, tobacco, corn, petunia, poplar, canola, tomato, tea, and soybean. It's possible that farmers breeding crops for higher yields have, over the centuries, selected variants less likely to express protective transcription factors². Now, plant scientists have insights on how to tweak coordinated gene expression systems to improve stress tolerance.

Kazuo Shinozaki and Kazuko Yamaguchi-Shinozaki of RIKEN Plant Science Center showed that overexpression of transcription factor DREB1A confers remarkable increases in plant tolerance to freezing, water stress and salinity.

Although creating more stress-tolerant crops is likely to benefit farmers everywhere, public mistrust of agricultural biotechnology remains a constraint to acceptance and expansion of the field. This is fuelled by the view that large agribusiness is the primary beneficiary of some of the current crop of transgenics, such as those displaying insect- and pesticide-resistance. Efforts to produce low trans fat soybean oils or to enhance the nutritional content of products are therefore likely to be of increasing importance, but will require more complex genetic engineering than was previously required for single gene traits (e.g., in certain Bacillus thuringiensis (Bt) or herbicide-resistant crops) as well as a comprehensive analysis of plant metabolic pathways (see Box 1). In this context, the work of Rachel Drake and her colleagues at Syngenta (Basel) in enhancing β-carotene enriched rice³ (also known as 'Golden Rice') represented a significant step forward. The work continued on from a landmark study in 2000 by Ingo Potrykus and colleagues⁴ that aimed to produce a rice strain that could help alleviate vitamin A deficiencies, which can cause blindness among malnourished populations. The problem with the original paper was that the levels of β-carotene (a precursor to vitamin A) produced were too low to be a practical source of the nutrient. Drake and her colleagues examined the metabolic pathway in transgenic rice and found that the original daffodil gene for phytoene synthase was the limiting step in β-carotene accumulation. By systematically substituting the daffodil gene with homologs from other plants, the Syngenta team boosted pro-vitamin A levels in the rice by more than 20-fold, which might be enough to make a practical difference in nutrition. What's more, Syngenta has donated the rights to this rice to the Golden Rice Humanitarian Board.

Box 1: Digesting the implications of metabolomics

In 2000, Nature Biotechnology published one of the first papers demonstrating that metabolic profiling (metabolomics) could be used to compare genotypes¹. Oliver Fiehn and colleagues at Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany) developed a high-throughput way to analyze hundreds of compounds in Arabidopsis thaliana leaves and showed that differences in these small molecules can clearly distinguish different genotypes. Now he's applying these techniques for diverse applications including figuring out how cigarette smoke harms a developing fetus, finding functions for orphan plant genes, and generally mapping metabolic networks.

Key to Fiehn and colleagues' 2000 innovation was a way to volatalize metabolites so that they could be separated by gas chromatography before mass spectrometry. But although this increased the number of compounds that can be analyzed, many still are not identified by molecular structure. “You see things going up and down and you don't know the name for it,” says Fiehn, now a molecular biologist at the University of California, Davis. “This is a clear bottleneck.”

In most other areas, says Fiehn, metabolomics has surged ahead. He estimates that experiments and analyses that required three weeks in 2000 can now be completed in two days. And the faster experiments include more quality controls, catalog more compounds and permit instant comparisons across data sets. Now, Fiehn and colleagues can look at the metabolites from individual organisms, identify correlations between metabolites, elucidate metabolic networks and potentially link these networks back to genes. Best of all, says Fiehn, today's data can fuel tomorrow's experiments. “The whole idea of having data that is consistent, structured and can be queried wasn't there in 2000, but it's there today.”

Reference:

Fiehn, O. et al. Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18, 1157–1161 (2000).