What is Arabidopsis thaliana?

Natural History

Although common as an introduction into America and Australia, Arabidopsis thaliana (often referred to simply by its genus name, Arabidopsis) is found in the wild throughout Europe, the Mediterranean, the East African highlands, and eastern and central Asia (where it probably originated). Since Arabidopsis is a low winter annual (standing about thirty-five centimeters, according to the Missouri Botanical Garden), it flowers in disturbed habitats from March through May. Arabidopsis was first described by Johannes Thal (hence the thaliana as the specific epithet) in the sixteenth century in Germany’s Harz Mountains, but he named it Pilosella siliquosa. Undergoing systematic revisions and several name changes, the little plant was finally called Arabidopsis thaliana in 1842.

Several characteristics of Arabidopsis make it a useful model organism. First, it has a short life cycle; it goes from germination of a seed to seed production in only six weeks to three months (different strains have different generation times). Each individual plant is prolific, yielding thousands of seeds. Genetic crosses are easy to do, for Arabidopsis normally self-crosses (so recessive mutations are easily made homozygous and expressed), but it is also possible to outcross. Second, the plants are small, comprising a flat rosette of leaves from which emerges a flower stalk that grows up to about 35 centimeters (13.8 inches) high. These plants are easy to grow and manipulate, so many genetic screens can be done on petri dishes with a thousand seedlings examined inside just one dish. Also, the genome of Arabidopsis is relatively small, with 125 million base pairs (Mbp), about 33,600 genes, and five chromosomes containing all the requisite information to encode an entire plant (similar to the functional complexity of the fruit fly
Drosophila melanogaster
, long a favorite model organism among geneticists). Yet in comparison to the genome of corn (Zea mays), which the National Center for Biotechnology Information estimated in 2009 to be at least 2,400 Mbp, Arabidopsis has a genome almost twenty times smaller. The sequence of the Arabidopsis genome was completed in 2000. Furthermore, Arabidopsis is easily transformed using the standard vector
Agrobacterium tumefaciens. to introduce foreign genes. In the floral-dip method, immature flower clusters are dipped into a solution of Agrobacterium containing the DNA to be introduced and a detergent. The flowers then develop seeds, which are collected and studied. This transformation method is rapid because there is no need for tissue culture and plant regeneration. Arabidopsis is easy to study under the light microscope because young seedlings and roots are somewhat translucent. There are collections of T-DNA (transfer DNA from Agrobacterium) tagged strains and insertional mutation strains. There are also a large number of other mutant lines and genomic resources available for Arabidopsis at stock centers, and a cooperative multinational research community of academic, government, and industrial laboratories exists, all working with Arabidopsis.

History of Experimental Work with Arabidopsis

The earliest report of a mutant probably was made in 1873 by A. Braun, and Freidrich Laibach first compiled the unique characteristics of Arabidopsis thaliana as a model organism for genetics in 1943 (publishing the correct chromosome number of five much earlier, in 1907, later confirmed by other investigators). Erna Reinholz (a student of Laibach) submitted her thesis in 1945, published in 1947, on the first collection of x-ray–induced mutants. Peter Langridge established the usefulness of Arabidopsis in the laboratory in the 1950s, as did George Redei and other researchers, including J. H. van der Veen in the Netherlands, J. Veleminsky in Czechoslovakia, and G. Robbelen in Germany in the 1960s.

Maarten Koorneef and his coworkers published the first detailed genetic map for Arabidopsis in 1983. A genetic map allows researchers to observe approximate positions of genes and regulatory elements on chromosomes. The 1980s saw the first steps in analysis of the genome of Arabidopsis. Tagged mutant collections were developed. Physical maps, with distances between genes in terms of DNA length, based on restriction fragment length polymorphisms (RFLPs), were also made. The physical maps allow genes to be located and characterized, even if their identities are not known.

In the 1990s, scientists outlined long-range plans for Arabidopsis through the Multinational Coordinated Arabidopsis Genome Research Project, which called for genetic and physiological experimentation necessary to identify, isolate, sequence, and understand Arabidopsis genes. In the United States, the National Science Foundation (NSF), US Department of Energy (DOE), and Agricultural Research Service (ARS) funded work done at Albany directed by Athanasios Theologis. NSF and DOE funds went also to Stanford, Philadelphia, and four other US laboratories. Worldwide communication among laboratories and shared databases (particularly in the United States, Europe, and Japan) were established. Transformation methods became much more efficient, and a large number of Arabidopsis mutant lines, gene libraries, and genomic resources have been made and are now available to the scientific community through public stock centers. The expression of multiple genes has been followed, too. Teresa Mozo provided the first comprehensive physical map of the Arabidopsis genome, published in 1999; she used overlapping fragments of cloned DNA. These fundamental data provide an important resource for map-based gene cloning and genome analysis. The Arabidopsis Genome Initiative, an international effort to sequence the complete Arabidopsis genome, was created in the mid-1990s, and the results of this massive undertaking were published on December 14, 2000, in Nature.

Comparative Genomics

With full sequencing of the genome of Arabidopsis completed, the first catalog of genes involved in the life cycle of a typical plant became available, and the investigational emphasis shifted to functional and comparative genomics. Scientists began looking at when and where specific genes are expressed in order to learn more about how plants grow and develop in general, how they survive in the changing environment, and how the gene networks are controlled or regulated. Potentially, this research can lead to improved crop plants that are more nutritious, more resistant to pests and disease, less vulnerable to crop failure, and capable of producing higher yields with less damage to the natural environment. Since many more people die from malnutrition in the world than from diseases, the Arabidopsis genome takes on a much more important consideration than one might think. Of course, plants are fundamental to all ecosystems, and their energy input into those systems is essential and critical.

Already the genetic research on Arabidopsis has boosted production of staple crops such as wheat, tomatoes, and rice. The genetic basis for every economically important trait in plants—whether pest resistance, vegetable oil production, or even wood quality in paper products—has been under intense scrutiny in Arabidopsis.

Although Arabidopsis is considered a weed, it is closely related to a number of vegetables, including broccoli, cabbage, brussels sprout, and cauliflower, which are very important to humans nutritionally and economically. A mutation observed in Arabidopsis has resulted in its floral structures assuming the basic shape of a head of cauliflower. This mutation in Arabidopsis, not surprisingly, is referred to simply as “cauliflower” and was isolated by Martin Yanofsky’s laboratory. The analogous gene from the cauliflower plant was examined, and it was discovered the cauliflower plant already had a mutation in this gene. From the study of Arabidopsis, therefore, researchers have uncovered why a head of cauliflower looks the way it does.

In plants, there is an ethylene-signaling pathway (ethylene is a plant hormone) that regulates fruit ripening, plant senescence, and leaf abscission. The genes necessary for the ethylene-signaling pathway have been identified in Arabidopsis, including genes coding for the ethylene receptors. As expected, a mutation in these ethylene receptors would cause the Arabidopsis plant to be unable to sense ethylene. Ethylene receptors have now been uncovered from other plant species from the knowledge gained from Arabidopsis. Harry Klee’s laboratory, for example, has found a tomato mutation in the ethylene receptor, which prevents ripening. When the mutant Arabidopsis receptor is expressed in other plants, moreover, the transformed plants also exhibit this insensitivity to ethylene and the lack of ensuing processes associated with it. Therefore, the mechanism of ethylene perception seems to be conserved in plants, and modifying ethylene receptors can induce change in a plant.

Once the sequence of Arabidopsis was determined, there was a coordinated effort to determine the functions of the genome (functional genetics). The Arabidopsis Information Resource (TAIR) is an online repository of Arabidopsis genomic data. The November 2010 TAIR 10 Arabidopsis genome annotation indicated 27,416 protein-coding genes, 4,827 pseudogenes or transposable elements, and 1,359 noncoding RNAs, for a total of 33,602 genes. There are ongoing studies of the genome to determine the patterns of transcription, epigenetic (methylation) patterns, proteomics, and metabolic profiling. Arabidopsis is a model organism for plant molecular biology and genetics, for the understanding of plant flower development, and for determining how plants sense light. Ongoing Arabidopsis projects include determining genome-wide transcription networks of TGA factors (transcription regulators), an analysis throughout the genome of novel Arabidopsis genes predicted by comparative genomics, and completing the expression catalog of the Arabidopsis transcriptome using real-time PCR (RT-PCR). The e-journal The Arabidopsis Book (TAB), produced by the American Society of Plant Biologists, summarizes the current understanding of Arabidopsis biology. TAB includes articles on such subjects as cell cycle division, peroxisome biogenesis, seed dormancy and germination, guard cell signal transduction, the cytoskeleton, mitochondrial biogenesis, and meiosis.

Advances in evolutionary biology and medicine are expected from Arabidopsis research, too. Robert Martienssen of Cold Spring Harbor Laboratory has indicated the completion of the Arabidopsis genome sequence has a major impact on human health as well as plant biology and agriculture. Surprisingly, some Arabidopsis genes are extremely similar or even identical to human genes linked to certain illnesses. No doubt there are many more mysteries to unravel with the proteome analysis of Arabidopsis (analysis of how proteins function in the plant), and the biological role of the tens of thousands of Arabidopsis genes will keep scientists busy for some time to come.

Key Terms




Brassicaceae


:

the mustard family, a large, cosmopolitan family of plants with many wild species, some of them common weeds, including widely cultivated edible plants like cabbage, cauliflower, radish, rutabaga, turnip, and mustard




genetic map

:

a “map” showing distances between genes in terms of recombination frequency




TILLING (targeting induced local lesions in genomes)

:

a method used to create mutations throughout the genome by chemical mutagenesis, followed by the polymerase chain reaction (PCR) method to amplify regions of the genome, denaturing high-pressure liquid chromatography (HPLC) to screen for mutants, and finally determining the phenotype





Bibliography

Borevitz, Justin O., and Joseph R. Ecker. “Plant Genomics: The Third Wave.” Annual Review of Human Genetics 5 (2004): 443–77. Print.

Griffiths, Anthony J. F., Susan R. Wessler, Sean B. Carroll, and John Doebley. Introduction to Genetic Analysis. 10th ed. New York: Freeman, 2012. Print.

MacLachlan, Allison. "One More Way Plants Help Human Health." Inside Life Science. National Institute of General Medical Sciences, National Institutes of Health, 19 Nov. 2012. Web. 21 July 2014.

Memelink, Johan. “The Use of Genetics to Dissect Plant Secondary Pathways.” Current Opinion in Plant Biology 8 (2005): 230–35. Print.

Salinas, Julio, and José J. Sánchez-Serrano, eds. Arabidopsis Protocols. 3rd ed. New York: Humana, 2014. Print.

TAIR. "Genome Snapshot." Arabidopsis.org. Phoenix Bioinformatics Corp., 22 Nov. 2010. Web. 21 July 2014.

Zhang, X., et al. “Agrobacterium-Mediated Transformation of Arabidopsis thaliana Using Floral Dip Method.” Nature Protocols 1.2 (2006): 641–46. Print.