Arabidopsis thaliana

Arabidopsis thaliana (A-ra-bi-dóp-sis tha-li-á-na; thale cress, mouse-ear cress or arabidopsis) is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics. Arabidopsis thaliana has a rather small genome, only 157 megabase pairs (Mbp), and was thought for a long time to own the smallest genome of all flowering plants, but the smallest flowering plants' genomes are now known to belong to plants in the genus Genlisea, order Lamiales, with Genlisea margaretae, a carnivorous plant, shows a genome size of 63.4 Mbp; arabidopsis was the first plant genome to be sequenced, and is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing.

Discovery and name origin
The plant was first discovered in 1577 in the Harz Mountains by Johannes Thal (1542-1583), a physician from Nordhausen, Thüringen, Germany, who called it Pilosella siliquosa. In 1841 the plant was renamed Arabidopsis thaliana by German botanist Gustav Heynhold in honor of Thal. The genus name, Arabidopsis comes from Greek, meaning "resembling Arabis".

Habitat, morphology, and life cycle
Arabidopsis is native to Europe, Asia, and northwestern Africa. It is an annual (rarely biennial) plant, usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, with a few leaves also on the flowering stem. The basal leaves are green to slightly purplish in color, 1.5–5 cm long and 2–10 mm broad, with an entire to coarsely serrated margin; the stem leaves are smaller and unstalked, usually with an entire margin. Leaves are covered with small, unicellular hairs (called trichomes). The flowers are 3 mm in diameter, arranged in a corymb; their structure is that of the typical Brassicaceae. The fruit is a siliqua 5–20 mm long, containing 20–30 seeds. Roots are simple in structure, with a single primary root that grows vertically downwards, later producing smaller lateral roots. These roots form interactions with rhizosphere bacteria such as Bacillus megaterium.

Arabidopsis can complete its entire life cycle in six weeks. The central stem that produces flowers grows after about three weeks, and the flowers naturally self-pollinate. In the lab, arabidopsis may be grown in Petri plates or pots, under fluorescent lights or in a greenhouse.

Use as a model organism
By the beginning of 1900s, A. thaliana had begun to be used in some developmental studies. The first collection of its mutants was made around 1945. It is now widely used for studying plant sciences, including genetics, evolution, population genetics, and plant development. It plays the role in plant biology that mice and fruit flies (Drosophila) play in animal biology. Although A. thaliana has little direct significance for agriculture, it has several traits that make it a useful model for understanding the genetic, cellular, and molecular biology of flowering plants.

The small size of its genome makes Arabidopsis thaliana useful for genetic mapping and sequencing &mdash; with about 157 megabase pairs and five chromosomes, arabidopsis has one of the smallest genomes among plants. It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative. The most up-to-date version of the A. thaliana genome is maintained by the Arabidopsis Information Resource (TAIR). Much work has been done to assign functions to its 27,000 genes and the 35,000 proteins they encode.

The plant's small size and rapid life cycle are also advantageous for research. Having specialized as a spring ephemeral, it has been used to found several laboratory strains that take about six weeks from germination to mature seed. The small size of the plant is convenient for cultivation in a small space, and it produces many seeds. Further, the selfing nature of this plant assists genetic experiments. Also, as an individual plant can produce several thousand seeds, each of the above criteria leads to A. thaliana being valued as a genetic model organism.

Plant transformation in arabidopsis is routine, using Agrobacterium tumefaciens to transfer DNA to the plant genome. The current protocol, termed "floral-dip", involves simply dipping a flower into a solution containing Agrobacterium, the DNA of interest, and a detergent. This method avoids the need for tissue culture or plant regeneration.

The arabidopsis gene knockout collections are a unique resource for plant biology made possible by the availability of high-throughput transformation and funding for genomics resources. The site of T-DNA insertions has been determined for over 300,000 independent transgenic lines, with the information and seeds accessible through online T-DNA databases. Through these collections, insertional mutants are available for most genes in arabidopsis.

Finally, the plant is well suited for light microscopy analysis. Young seedlings on the whole, and their roots in particular, are relatively translucent. This, together with their small size, facilitates live cell imaging using both fluorescence and confocal laser scanning microscopy. By wet mounting seedlings in water or in culture media, plants may be imaged uninvasively, obviating the need for fixation and sectioning and allowing time-lapse measurements. Fluorescent protein constructs can be introduced through transformation. The developmental stage of each cell can be inferred from its location in the plant or by using fluorescent protein markers, allowing detailed developmental analysis.

TAIR and NASC are curated sources for diverse arabidopsis genetic and molecular biology information, and also provide numerous links, for example, to databases that store the results of hundreds of genome-wide gene expression profile experiments. Seed and DNA stocks can be obtained from NASC or the Arabidopsis Biological Resource Center.

History of Arabidopsis research
The first mutant in arabidopsis was documented in 1873 by Alexander Braun, describing a double flower phenotype (the mutated gene was likely Agamous, cloned and characterized in 1990). However, not until 1943 did Friedrich Laibach (who had published the chromosome number in 1907) propose arabidopsis as a model organism. His student, Erna Reinholz, published her thesis on arabidopsis in 1945, describing the first collection of arabidopsis mutants that they generated using X-ray mutagenesis. Laibach continued his important contributions to arabidopsis research by collecting a large number of ecotypes. With the help of Albert Kranz, these were organised into the current ecotype collection of 750 natural accessions of A. thaliana from around the world.

In the 1950s and 1960s, John Langridge and George Rédei played an important role in establishing arabidopsis as a useful organism for biological laboratory experiments. Rédei wrote several scholarly reviews instrumental in introducing the model to the scientific community. The start of the arabidopsis research community dates to a newsletter called Arabidopsis Information Service (AIS), established in 1964. The first International Arabidopsis Conference was held in 1965, in Göttingen, Germany.

In the 1980s, arabidopsis started to become widely used in plant research laboratories around the world. It was one of several candidates that included maize, petunia and tobacco. The latter two were attractive, since they were easily transformable with the then current technologies, while maize was a well-established genetic model for plant biology. The breakthrough year for arabidopsis as the preferred model plant came in 1986, when T-DNA-mediated transformation was first published, and this coincided with the first gene to be cloned and published.

Characterized ecotypes and mutant lines of arabidopsis serve as experimental material in laboratory studies. The most commonly used background lines are Ler, or Landsberg erecta, and Col, or Columbia. Other background lines less-often cited in the scientific literature are Ws, or Wassilewskija, C24, Cvi, or Cape Verde Islands, Nossen, etc. (see for ex. ) Series of mutants, named Ler-x, Col-x, have been obtained and characterized; mutant lines are generally available through stock centers, of which best known are the Nottingham Arabidopsis Stock Center-NASC and the Arabidopsis Biological Resource Center-ABRC in Ohio, USA. The Col or Columbia ecotype was selected, as an agronomically performant line, by Rédei, within a (nonirradiated) population of seeds named Landsberg he received from Laibach. Columbia is the ecotype sequenced in the Arabidopsis Genome Initiative. The Ler or Landsberg erecta line was selected by Rédei from within a Landsberg population on which he had performed some X-ray mutagenesis experiments. As the Ler collection of mutants is derived from this initial line, Ler-0 does not correspond to the Landsberg ecotype which is named La-0.

Flower development
Arabidopsis has been extensively studied as a model for flower development. The developing flower has four basic organs: sepals, petals, stamens, and carpels (which go on to form pistils). These organs are arranged in a series of whorls: four sepals on the outer whorl, followed by six petals inside this, six stamens, and a central carpel region. Homeotic mutations in Arabidopsis result in the change of one organ to another &mdash; in the case of the Agamous mutation, for example, stamens become petals and carpels are replaced with a new flower, resulting in a recursively repeated sepal-petal-petal pattern.

Observations of homeotic mutations led to the formulation of the ABC model of flower development by E. Coen and E. Meyerowitz. According to this model, floral organ identity genes are divided into three classes: class A genes (which affect sepals and petals), class B genes (which affect petals and stamens), and class C genes (which affect stamens and carpels). These genes code for transcription factors that combine to cause tissue specification in their respective regions during development. Although developed through study of Arabidopsis flowers, this model is generally applicable to other flowering plants.

Light sensing
The photoreceptors phytochrome A, B, C, D and E mediate red light-based phototropic response. Understanding the function of these receptors has helped plant biologists understand the signalling cascades that regulate photoperiodism, germination, de-etiolation and shade avoidance in plants.

Arabidopsis was used extensively in the study of the genetic basis of phototropism, chloroplast alignment, and stomatal aperture and other blue light-influenced processes. These traits respond to blue light, which is perceived by the phototropin light receptors. Arabidopsis has also been important in understanding the functions of another blue light receptor, cryptochrome, which is especially important for light entrainment to control the plants circadian rhythms.

Light response was even found in roots, which were thought not to be particularly sensitive to light. While gravitropic response of Arabidopsis root organs is their predominant tropic response, specimens treated with mutagens and selected for the absence of gravitropic action showed negative phototropic response to blue or white light, and positive response to red light, indicating the roots also show positive phototropism.

Non-Mendelian inheritance
In 2005, scientists at Purdue University proposed that Arabidopsis possessed an alternative to previously known mechanisms of DNA repair, which one scientist called a "parallel path of inheritance". It was observed in mutations of the HOTHEAD gene. Plants mutant in this gene exhibit organ fusion, and pollen can germinate on all plant surfaces, not just the stigma. After spending over a year eliminating simpler explanations, it was indicated that the plants "cached" versions of their ancestors' genes going back at least four generations, and used these records as templates to correct the HOTHEAD mutation and other single nucleotide polymorphisms. The initial hypothesis proposed the record may be RNA-based Since then, alternative models have been proposed which would explain the phenotype without requiring a new model of inheritance. More recently, the whole phenomenon is being challenged as a being a simple artifact of pollen contamination. "When Jacobsen took great pains to isolate the plants, he couldn't reproduce the [reversion] phenomenon", notes Steven Henikoff. In response to the new finding, Lolle and Pruitt agree that Peng et al. did observe cross-pollination, but note that some of their own data, such as double reversions of both mutant genes to the regular form, cannot be explained by cross-pollination.

Plant–pathogen interactions
It is important to understand how plants achieve resistance to protect the world's food production as well as the agricultural industry. Many model systems have been developed to better understand interactions between plants and bacterial, fungal, oomycete, viral and nematode pathogens. Arabidopsis thaliana has been successfully implemented in the study of the subdicipline of plant pathology, that is, the interaction between plants and disease-causing pathogens.

The use of A. thaliana has led to many breakthroughs in the advancement of knowledge of how plants manifest plant disease resistance. The reason most plants are resistant to most pathogens is through nonhost resistance. This is, not all pathogens will infect all plants. An example where A. thaliana was used to determine the genes responsible for non-host resistance is Blumeria graminis, the causal agent of powdery mildew of grasses. A. thaliana mutants were developed using the mutagen ethyl methanesulfonate and screened to determine which mutants had increased infection by B. graminis. The mutants with higher infection rates are referred to as PEN mutants due to the ability of B. graminis to penetrate A. thalaina to begin the disease process. The PEN genes were later mapped to identify the genes responsible for nonhost resistance to B. graminis.

Generally, when a plant is exposed to a pathogen, or nonpathogenic microbe, there is an initial response, known as PAMP-triggered immunity (PTI), because the plant detects conserved motifs known as Pathogen-associated molecular patterns (PAMPs). These PAMPs are detected by specialized receptors in the host known as pattern recognition receptors (PRRs) on the plant cell surface.

The best characterized PRR in A. thaliana is FLS2 (Flagellin-Sensing2) which recognizes bacterial flagellin, a specialized organelle used by microorganisms for the purpose of motility, as well as the ligand flg22, which comprises the 22 amino acids recognized by FLS2. Discovery of FLS2 was facilitated by the identification of an A. thaliana ecotype, Ws-0, that was unable to detect flg22, leading to the identification of the gene encoding FLS2.

A second PRR, EFR (EF-Tu receptor), has been identified in A. thaliana which recognizes the bacterial EF-Tu protein, the prokaryotic elongation factor used in protein synthesis, as well as the laboratory-used ligand elf18. Using Agrobacterium-mediated transformation, a technique that takes advantage of the natural process by which Agrobacterium transfers genes into host plants, the EFR gene was transformed into Nicotiana benthamiana, tobacco plant that does not recognize EF-Tu, thereby permitting recognition of bacterial EF-Tu there by confirming EFR as the receptor of EF-Tu.

Both FLS2 and EFR use similar signal transduction pathways to initiate PTI. A. thaliana has been instrumental in dissecting these pathways to better understand the regulation of immune responses, most notably the mitogen-activated protein kinase (MAP kinase) cascade. Downstream responses of PTI include callose deposition, the oxidative burst, and transcription of defense-related genes.

PTI is able to combat pathogens in a nonspecific manner. A stronger and more specific response in plants is that of effector-triggered immunity (ETI). ETI is dependent upon the recognition of pathogen effectors, proteins secreted by the pathogen that alter functions in the host, by plant resistance genes (R-genes), often described as a gene-for-gene relationship. This recognition may occur directly or indirectly via a guard protein in a hypothesis known as the guard hypothesis. The first R-gene cloned in A. thaliana was RPS2 (resistance to Pseudomonas syringe 2), which is responsible for recognition of the effector avrRpt2. The bacterial effector avrRpt2 is delivered into A. thaliana via the Type III secretion system of P. syringae pv tomato strain DC3000. Recognition of avrRpt2 by RPS2 occurs via the guard protein RIN4. Recognition of a pathogen effector leads to a dramatic immune response known as the hypersensitive response, in which the infected plant cells undergo cell death to prevent the spread of the pathogen.

Systemic acquired resistance (SAR) is another example of resistance which is better understood in plants because of research done in A. thaliana. Benzothiadiazol (BTH), a salicylic acid (SA) analog, has been used historically as an antifungal compound in crop plants. BTH, as well as SA, has been shown to induce SAR in plants. The initiation of the SAR pathway was first demonstrated in A. thaliana in which increased SA level are recognized by NPR1 (nonexpresser of PR genes 1) due to pH changes in the cytosol, resulting in the reduction of NPR1. NPR1, which usually exists in a multiplex (oligomerized state), becomes monomeric (a single unit) upon reduction. When NPR1 becomes monomeric, it translocates to the nucleus, were it interacts with many TGA transcription factors, and is able to induce pathogen-related genes such as PR1.

Multigenerational
Ongoing research on Arabidopsis thaliana is being performed on the International Space Station by the European Space Agency. The goals are to study the growth and reproduction of plants from seed to seed in microgravity.