Brassicaceae отбасының модельдік өсімдігі: Arabidopsis thaliana

Model plant species in the family Brassicaceae

Arabidopsis thaliana, the thale cress, mouse ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally considered a weed. A winter annual with a relatively short lifecycle, A. thaliana is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a relatively small genome of around 135 megabase pairs. It was the first plant to have its genome sequenced, and is an important tool for understanding the molecular biology of many plant traits, including flower development and light sensing.

Arabidopsis thaliana is an annual (rarely biennial) plant, usually growing to 20–25 cm tall. Roots are simple in structure, with a single primary root that grows vertically downward, later producing smaller lateral roots. These roots form interactions with rhizosphere bacteria such as Bacillus megaterium. A. thaliana can complete its entire lifecycle in six weeks. The central stem that produces flowers grows after about 3 weeks, and the flowers naturally self pollinate. In the lab, A. thaliana may be grown in Petri plates, pots, or hydroponics, under fluorescent lights or in a greenhouse.

The plant was first described in 1577 in the Harz Mountains by Johannes Thal [de] (1542–1583), a physician from Nordhausen, Thüringen, Germany, who called it Pilosella siliquosa. In 1753, Carl Linnaeus renamed the plant Arabis thaliana in honor of Thal. In 1842, German botanist Gustav Heynhold erected the new genus Arabidopsis and placed the plant in that genus. The generic name, Arabidopsis, comes from Greek, meaning "resembling Arabis" (the genus in which Linnaeus had initially placed it). Thousands of natural inbred accessions of A. thaliana have been collected from throughout its natural and introduced range. These accessions exhibit considerable genetic and phenotypic variation, which can be used to study the adaptation of this species to different environments. It also appears to be native in tropical alpine ecosystems in Africa and perhaps South Africa. It has been introduced and naturalized worldwide, including in North America around the 17th century. A. thaliana readily grows and often pioneers rocky, sandy, and calcareous soils. It is generally considered a weed, due to its widespread distribution in agricultural fields, roadsides, railway lines, waste ground, and other disturbed habitats, but due to its limited competitive ability and small size, it is not categorized as a noxious weed. Like most Brassicaceae species, A. thaliana is edible by humans in a salad or cooked, but it does not enjoy widespread use as a spring vegetable.

Botanists and biologists began to research A. thaliana in the early 1900s, and the first systematic description of mutants was done around 1945. A. thaliana is now widely used for studying plant sciences, including genetics, evolution, population genetics, and plant development. Although A. thaliana the plant has little direct significance for agriculture, A. thaliana the model organism has revolutionized our understanding of the genetic, cellular, and molecular biology of flowering plants. The first mutant in A. thaliana was documented in 1873 by Alexander Braun, describing a double flower phenotype (the mutated gene was likely Agamous, cloned and characterized in 1990). Friedrich Laibach (who had published the chromosome number in 1907) did not propose A. thaliana as a model organism, though, until 1943. His student, Erna Reinholz, published her thesis on A. thaliana in 1945, describing the first collection of A. thaliana mutants that they generated using X ray mutagenesis. Laibach continued his important contributions to A. thaliana research by collecting a large number of accessions (often questionably referred to as "ecotypes"). With the help of Albert Kranz, these were organised into a large 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 A. thaliana 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 A. thaliana research community dates to a newsletter called Arabidopsis Information Service, established in 1964. The first International Arabidopsis Conference was held in 1965, in Göttingen, Germany. In the 1980s, A. thaliana started to become widely used in plant research laboratories around the world. It was one of several candidates that included maize, petunia, and tobacco.

[[File:Plastomap of Arabidopsis thaliana. svg|thumb|Chloroplast genome map of A. thaliana: and five chromosomes, A. thaliana has one of the smallest genomes among plants. but that title is now considered to belong to plants in the genus Genlisea, order Lamiales, with Genlisea tuberosa, a carnivorous plant, showing a genome size of approximately 61 Mbp. 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. The genome encodes ~27,600 protein coding genes and about 6,500 non coding genes. However, the Uniprot database lists 39,342 proteins in their Arabidopsis reference proteome. Among the 27,600 protein coding genes 25,402 (91.8%) are now annotated with "meaningful" product names, although a large fraction of these proteins is likely only poorly understood and only known in general terms (e. g. as "DNA binding protein without known specificity"). Uniprot lists more than 3,000 proteins as "uncharacterized" as part of the reference proteome.

The plastome of A. thaliana is a 154,478 base pair long DNA molecule, a size typically encountered in most flowering plants (see the list of sequenced plastomes). It comprises 136 genes coding for small subunit ribosomal proteins (rps, in yellow: see figure), large subunit ribosomal proteins (rpl, orange), hypothetical chloroplast open reading frame proteins (ycf, lemon), proteins involved in photosynthetic reactions (green) or in other functions (red), ribosomal RNAs (rrn, blue), and transfer RNAs (trn, black).

The mitochondrial genome of A. thaliana is 367,808 base pairs long and contains 57 genes. There are many repeated regions in the Arabidopsis mitochondrial genome. The largest repeats recombine regularly and isomerize the genome. Like most plant mitochondrial genomes, the Arabidopsis mitochondrial genome exists as a complex arrangement of overlapping branched and linear molecules in vivo.

Genetic transformation of A. thaliana is routine, using Agrobacterium tumefaciens to transfer DNA into the plant genome. The current protocol, termed "floral dip", involves simply dipping flowers into a solution containing Agrobacterium carrying a plasmid of interest and a detergent. This method avoids the need for tissue culture or plant regeneration. The A. thaliana 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 A. thaliana. Characterized accessions and mutant lines of A. thaliana serve as experimental material in laboratory studies. The most commonly used background lines are Ler (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.) Sets of closely related accessions named Col 0, Col 1, etc., have been obtained and characterized; in general, mutant lines are available through stock centers, of which best known are the Nottingham Arabidopsis Stock Center NASC
The Col 0 accession was selected by Rédei from within a (nonirradiated) population of seeds designated 'Landsberg' which he received from Laibach. Columbia (named for the location of Rédei's former institution, University of Missouri Columbia) was the reference accession sequenced in the Arabidopsis Genome Initiative. The Later (Landsberg erecta) line was selected by Rédei (because of its short stature) from a Landsberg population he had mutagenized with X rays. As the Ler collection of mutants is derived from this initial line, Ler 0 does not correspond to the Landsberg accessions, which designated La 0, La 1, etc. Trichome formation is initiated by the GLABROUS1 protein. Knockouts of the corresponding gene lead to glabrous plants. This phenotype has already been used in gene editing experiments and might be of interest as visual marker for plant research to improve gene editing methods such as CRISPR/Cas9.

In 2005, scientists at Purdue University proposed that A. thaliana possessed an alternative to previously known mechanisms of DNA repair, producing an unusual pattern of inheritance, but the phenomenon observed (reversion of mutant copies of the HOTHEAD gene to a wild type state) was later suggested to be an artifact because the mutants show increased outcrossing due to organ fusion.

The plant's small size and rapid lifecycle are also advantageous for research. Having specialized as a spring ephemeral, it has been used to found several laboratory strains that take about 6 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.

Arabidopsis is often the model for study of SNAREs in plants. This has shown SNAREs to be heavily involved in vesicle trafficking. Zheng et al. 1999 found an Arabidopsis SNARE called AtVTI1a is probably essential to Golgi vacuole trafficking. This is still a wide open field and plant SNAREs' role in trafficking remains understudied.

The DNA of plants is vulnerable to ultraviolet light, and DNA repair mechanisms have evolved to avoid or repair genome damage caused by UV. Kaiser et al. showed that in A. thaliana cyclobutane pyrimidine dimers (CPDs) induced by UV light can be repaired by expression of CPD photolyase.

On May 12, 2022, NASA announced that specimens of Arabidopsis thaliana had been successfully germinated and grown in samples of lunar regolith. While the plants successfully germinated and grew into seedlings, they were not as robust as specimens that had been grown in volcanic ash as a control group, although the experiments also found some variation in the plants grown in regolith based on the location the samples were taken from, as A. thaliana grown in regolith gathered during Apollo 12 & Apollo 17 were more robust than those grown in samples taken during Apollo 11.

A. thaliana 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 four petals inside this, six stamens, and a central carpel region. Homeotic mutations in A. thaliana result in the change of one organ to another—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. thumb|150px|The ABC model of flower development was developed through studying A. thaliana. 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 A. thaliana flowers, this model is generally applicable to other flowering plants.

Studies of A. thaliana have provided considerable insights with regards to the genetics of leaf morphogenesis, particularly in dicotyledon type plants. Much of the understanding has come from analyzing mutants in leaf development, some of which were identified in the 1960s, but were not analysed with genetic and molecular techniques until the mid 1990s. A. thaliana leaves are well suited to studies of leaf development because they are relatively simple and stable. Using A. thaliana, the genetics behind leaf shape development have become more clear and have been broken down into three stages: The initiation of the leaf primordium, the establishment of dorsiventrality, and the development of a marginal meristem. Leaf primordia are initiated by the suppression of the genes and proteins of class I KNOX family (such as SHOOT APICAL MERISTEMLESS). These class I KNOX proteins directly suppress gibberellin biosynthesis in the leaf primordium. Many genetic factors were found to be involved in the suppression of these class I KNOX genes in leaf primordia (such as ASYMMETRIC LEAVES1, BLADE ON PETIOLE1, SAWTOOTH1, etc.). Thus, with this suppression, the levels of gibberellin increase and leaf primordium initiate growth. The establishment of leaf dorsiventrality is important since the dorsal (adaxial) surface of the leaf is different from the ventral (abaxial) surface.

A. thaliana 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.

The photoreceptors phytochromes A, B, C, D, and E mediate red light based phototropic response. Understanding the function of these receptors has helped plant biologists understand the signaling cascades that regulate photoperiodism, germination, de etiolation, and shade avoidance in plants. The genes FCA, fy, are involved in photoperiod triggering of flowering and vernalization. Specifically Lee et al 1994 find ld produces a homeodomain and Blazquez et al 2001 that fve produces a WD40 repeat. 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. When the onset of darkness is unusually early, A. thaliana reduces its metabolism of starch by an amount that effectively requires division. Light responses were even found in roots, previously thought to be largely insensitive to light. While the gravitropic response of A. thaliana 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 that the roots also show positive phototropism. In 2000, Dr. Janet Braam of Rice University genetically engineered A. thaliana to glow in the dark when touched. The effect was visible to ultrasensitive cameras. Multiple efforts, including the Glowing Plant project, have sought to use A. thaliana to increase plant luminescence intensity towards commercially viable levels.

In 1990, Janet Braam and Ronald W. Davis determined that A. thaliana exhibits thigmomorphogenesis in response to wind, rain and touch. Four or more touch induced genes in A. thaliana were found to be regulated by such stimuli.

On January 2, 2019, China's Chang'e 4 lander brought A. thaliana to the moon. A small microcosm 'tin' in the lander contained A. thaliana, seeds of potatoes, and silkworm eggs. As plants would support the silkworms with oxygen, and the silkworms would in turn provide the plants with necessary carbon dioxide and nutrients through their waste, researchers will evaluate whether plants successfully perform photosynthesis, and grow and bloom in the lunar environment.