Arabidopsis has several features, such as rapid growth and small size, that make it an ideal experimental model for plant biology research. But such natural qualities alone are not enough to make it a popular organism for experimental work. Equally important to researchers is the rapid development of new tools which allow a detailed probing of the plant's genome. In the past few years, Arabidopsis researchers have produced a variety of such tools including synthetic DNA markers for mapping the genome, a collection of new mutants, specialized transformation techniques, and a large collection of partially sequenced complementary DNAs, which represent genes that are expressed.

Another important resource is the combined collection of genetic maps, which were developed from information generated in many collaborating laboratories. The maps are of critical importance for gene cloning and genetic analysis. Also significant is the establishment of databases, stock centers, and other research infrastructures which allow rapid dissemination of information and easy exchange of ideas and materials. Progress on development of these research tools was outlined in the third annual progress report for the Multinational Coordinated Arabidopsis thaliana Genome Research Project (NSF 93-173). Their further development is described in the next section of this report.

All of these research tools and resources allow scientists to dissect the Arabidopsis genome systematically. This has resulted in the identification of individual genes and their functions and -- more generally -- a better understanding of plant processes.

This section offers specific examples of how studies of Arabidopsis have greatly improved our understanding of disease resistance, root development, and other plant processes. The pace of Arabidopsis research has accelerated so much in the past year that it is not possible to summarize all recent, significant advances in this report. Thus, the following highlights are meant to be illustrative rather than comprehensive.

1. Scientific Highlights

Resistance to Microbial Pathogens

Because the study of how pathogens attack plants involves the study of two organisms, it is useful to manipulate both the pathogen and its host genetically in order to tease apart various aspects of plant-pathogen interactions. The basic strategy is to identify and study Arabidopsis mutants that show either enhanced or reduced resistance to a particular pathogen. A goal is to apply the knowledge obtained with Arabidopsis to crop plants which may be genetically engineered to have increased resistance to important agricultural pathogens.

Plant breeders and plant pathologists have long known that certain varieties of crops are more resistant than others to particular viral, bacterial, or fungal pathogens. Indeed, breeding for disease resistance is a major goal of most plant-breeding programs. However, this is time consuming. Also, it involves many crosses - and may be only partially effective. Although individual genes which confer disease resistance have been identified by this process, until this year too few of them had been cloned to gain detailed insight into how these genes actually work at a molecular level. The molecular cloning this past year of an Arabidopsis resistance gene, called RPS2, has significantly added to our understanding of how this gene, and similar ones, work.

Unlike resistance genes in crop plants that were found largely in natural wild populations, the Arabidopsis RPS2 disease-resistance gene was found by mutagenizing Arabidopsis plants in the laboratory. Most Arabidopsis varieties resist infection to a particular strain of the agriculturally important bacterial pathogen known as Pseudomonas syringae. Arabidopsis mutant plants that were susceptible to infection by this pathogenic P. syringae strain were therefore sought in the labs of Brian Staskawicz (Berkeley, CA) and Frederick Ausubel (Boston, MA). The susceptible Arabidopsis mutants pointed to the RPS2 gene, which was subsequently cloned in the Staskawicz and Ausubel laboratories. RPS2 encodes a novel protein containing a motif made of 14 imperfect leucine-rich repeats which is involved in protein dimerization, and a motif that binds adenosine triphosphate. Significantly, this protein likely serves as a receptor for a specific molecular ligand from the pathogen. The structure of the RPS2 protein agrees with models proposed by plant pathologists; this suggests that resistance genes encode receptors for molecular signals from the pathogens. A signal transduction cascade leads to the activation of a variety of defense responses.

Remarkably, RPS2 is similar to the product of the RPP5 gene of Arabidopsis, which confers resistance to the fungal pathogen Peronospora parasitica. The RPP5 gene has recently been cloned by Jonathan Jones (Norwich, UK). Moreover, the two Arabidopsis resistance genes RPS2 and RPP5 are also similar to the N gene of tobacco, which confers resistance to tobacco mosaic virus; the L6 gene of flax, which confers resistance to the fungal rust pathogen Melamspora lini; and the Cf9 gene of tomato, which confers resistance to the fungal pathogen Cladosporium fulvum. The cloning of these resistance genes, all within the last 12 months, is a major accomplishment.

Root Development

The promise of the Arabidopsis root as a model for plant organ formation began to be realized this year. The attractive features of this root for developmental studies include its simple architecture, transparency, and continuous developmental program. Laboratories at the John Innes Centre (Norwich, UK), University of Utrecht, New York University, University of Michigan, and National Institute of Basic Biology (Japan) -- among others -- have made significant contributions. Noteworthy was the publication of a cell lineage map of the Arabidopsis embryonic root and root meristem by Ben Scheres' laboratory (Utrecht, The Netherlands): It was the first complete root fate map to be generated for any species.

A variety of Arabidopsis mutations that affect root development have also been described recently. They are being used to better understand how roots develop. For example, mutants have been identified in Philip Benfey's laboratory (New York, NY) in which the radial pattern of embryonic root meristem is disrupted. Also, mutants have been found in the laboratories of Scott Poethig (Philadelphia, PA); Keith Roberts (Norwich, UK); and John Schiefelbein (Ann Arbor, MI) in which the signaling process, which specifies the fate of epidermal cells to form root hairs, has been disrupted.

Flower Development

Floral growth begins with development from a vegetative meristem, which produces leaves, to an inflorescence meristem which may branch to form several floral meristems, each of which develops into a separate flower. Then, each floral meristem undergoes developmental controls; these determine the formation of floral organs such as petals, sepals, and stamens.

During the past year, there have been three noteworthy advances in understanding flower development. First, interactions among the meristem identity genes, which control the fate of the meristems, have been clarified. Second, molecular confirmation has been obtained for the regulation of a number of meristem and organ identity genes by other genes. Third, regulation of floral homeotic genes (organ identity genes) by the meristem identity genes has been demonstrated. In the wake of these advances, there are now more than a dozen laboratories working in this area worldwide.

Light Signal Transduction

Genetic analysis of Arabidopsis has shown that light responses are not endpoints of a linear signal pathway. Instead, they are the result of the integration of a variety of input signals through a complex network of interacting signals. Two main classes of genes in the light signal transduction pathways have been identified. Photoreceptor genes encode either red-/far red- light receptors (phytochromes) or a putative blue-light receptor; signal transduction pathway genes encode proteins that carry signal from the photoreceptors.

Studies in the laboratories of Peter Quail (Albany, CA), Nick Harberd (Norwich, UK), and Joanne Chory (La Jolla, CA) show distinct and overlapping roles for two phytochromes in the control of light-regulated responses. The two phytochromes appear to be partly redundant, and absorption of light by either phytochrome A or B leads to plant responses. Mutants have shown which response is due to each phytochrome. Mutants have also helped uncover a role for the Pr form of phytochrome B in the control of germination and shoot gravitropism. Previously, it was thought that this phytochrome had no biological activity.

The chemical nature of a blue-light receptor in plants was previously unknown, but has been revealed by the cloning of the Arabidopsis HY4 gene in Anthony Cashmore's lab (Philadelphia, PA). The predicted protein is similar to photolyases, which are known to be flavin-binding proteins. These results suggest a mechanism by which blue-light photoreceptors trigger a physiological response in higher plants. In addition, a variety of mutations have been isolated that affect the entire morphogenetic program of young seedlings in the dark.

Hormone Signal Transduction

Investigators studying the action of ethylene, which is an important plant hormone, have identified mutations that alter sensitivity to exogenous ethylene. By constructing and characterizing double mutant combinations, Joseph Ecker (Philadelphia, PA) has found the order of action of various gene products. Using this approach, the ETR1 gene was shown to function before CTR1 in an ethylene response pathway. Both the ETR1 and CTR1 genes were recently cloned, leading to an ability to control the response of Arabidopsis to ethylene (Caren Chang at the California Institute of Technology and Joseph Ecker).

The past year also saw the cloning of a gene for response to abscisic acid, another important plant hormone. It was accomplished by the laboratories of Jerome Giraudat (Gif-sur-Yvette, France) and Erwin Grill (Zurich, Switzerland).

2. Commercial Benefits

As predicted, discoveries made with Arabidopsis are leading to improvements in commercial crops. For example, even though the flowers of Arabidopsis are very different from those of snapdragons, the same genes control flower development in both. And those genes that guide the synthesis of oils in Arabidopsis are closely related to those that produce oils in commercial oil crops. Indeed, this relation is being exploited to produce plants with more desirable, edible oils.

About one-third of the calories in our diets comes from soybean or other vegetable oils. However, most vegetable oils are not well-suited to food uses because they are highly polyunsaturated. For many uses, the polyunsaturated oils are chemically modified by catalytic hydrogenation; this causes many double bonds to isomerize from cis to trans. Although the nutritional consequences of these trans unsaturations are even now being debated in the medical community, there is widespread interest in developing a new method of producing less highly saturated oils. During the past several years, genes for most of the fatty acid desaturases have been cloned from Arabidopsis. These have been used, first, to identify the corresponding genes from soybean, canola, and several other crop species; and, second, to genetically engineer crop plants with reduced levels of polyunsaturation. Early results suggest that it may be possible to eliminate the need for catalytic hydrogenation and to fine tune the oil composition of some crops to better suit human nutritional needs.

Because of the rich base of genetic information about lipids, oils, and starch in Arabidopsis, this plant has also been the test organism for efforts to produce biodegradable plastics in crop plants. In the first series of experiments, several genes from the bacterium Alcaligenes eutrophus were introduced into Arabidopsis so that the gene products built up in the cytoplasm. This resulted in the accumulation of small amounts of polyhydroxybutyrate (PHB), a biodegradable plastic. Recently, the amount of PHB accumulated by Arabidopsis plants was increased about a hundredfold by transferring the three genes from A. eutrophus to transgenic Arabidopsis plants so that the gene products collected in the plastids. These plants accumulated as much as 20 percent of their dry weight as PHB. This level of accumulation is considered adequate to merit development as a possible commercial product. Based on these results, several large chemical companies have started active research programs to develop transgenic crops that produce PHB. It appears that the results obtained with Arabidopsis can also be obtained with several commercial oilseed crops: The first field trials are expected in 1995.

One of the most active areas of Arabidopsis research concerns the mechanisms by which plants sense and respond to small signal molecules or "phytohormones." The gas ethylene has been long known to affect plant growth and development: It is used to alter the ripening of fruits and vegetables and the aging of flowers. Because of this, there is broad interest in preventing plants from producing or responding to ethylene in certain situations. A new strategy for the possible manipulation of a plant's response to ethylene comes from the recent discovery of a gene in Arabidopsis which mediates the biological effects of this gas. It is thought that this gene encodes a receptor which binds ethylene and then triggers a cascade of biological responses. A mutant form of this gene has also been isolated from Arabidopsis which prevents the normal response to ethylene. In fact, it has been shown that introducing this altered, unresponsive gene into plants such as tomatoes prevents the plants from responding to ethylene. This could significantly slow down the rate of fruit-ripening or wilting of flowers, keeping them fresh longer.

Although still in the research stage, it is expected that many other recent discoveries in Arabidopsis will be rapidly applied to the improvement of plants. Most promising is the recent cloning of specific disease-resistance genes which, in turn, should lead to new mechanisms for engineered disease resistance. On another front, the progress in characterizing genes for flower development will permit the production of new horticultural varieties.