Arabidopsis thaliana: Wikis

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Arabidopsis thaliana
Scientific classification
Kingdom: Plantae
(unranked): Angiosperms
(unranked): Eudicots
(unranked): Rosids
Order: Brassicales
Family: Brassicaceae
Genus: Arabidopsis
Species: A. thaliana
Binomial name
Arabidopsis thaliana
(L.) Heynh.
Synonyms

Arabis 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.[1] A spring annual with a relatively short life cycle, Arabidopsis is popular as a model organism in plant biology and genetics. Its genome is one of the smallest plant genomes[2] and was the first plant genome to be sequenced. Arabidopsis is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing.

Contents

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 colour, 1.5–5 cm long and 2–10 mm broad, with an entire to coarsely serrated margin; the stem leaves are smaller, 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.[3][4][5][6] 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.[7]

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.[8]

Use as a model organism

By the beginning of 1900s, Arabidopsis thaliana had begun to be used in some developmental studies. The first collection of its mutants were made around 1945.[9]. However, Arabidopsis thaliana was designated as a model organism only in 1998[10]. It is now widely used for studying plant sciences, including genetics, evolution, population genetics, and plant development.[11][12][13] It plays the role for agricultural sciences that mice and fruit flies (Drosophila) play in animal biology. Although Arabidopsis 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 — with about 157 million base pairs[14] 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.[15] The most up-to-date version of the Arabidopsis thaliana genome is maintained by The Arabidopsis Information Resource (TAIR).[16] Much work has been done to assign functions to its 27,000 genes and the 35,000 proteins they encode.[17]

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 Arabidopsis 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.[18][19] 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.[20] 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.[21] 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 as well as seed and DNA stocks, and also provide numerous links, for example, to databases that store the results of hundreds of genome-wide gene expression profile experiments.

History of Arabidopsis research

A double flower mutant of Arabidopsis, first documented in 1873.

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).[22] However, it was not until 1943 that Friedrich Laibach (who had published the chromosome number in 1907) proposed Arabidopsis as a model organism.[23] 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 Arabidopsis 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.[23] 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.[24][25]

Research

The ABC model of flower development was developed through study of Arabidopsis.
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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 — 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.[26] 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.[27] 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.[28]

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 that the roots also show positive phototropism. [29]

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 that the record may be RNA-based[30] Since then, alternative models have been proposed which would explain the phenotype without requiring a new model of inheritance[31][32] More recently the whole phenomenon is being challenged as a being a simple artifact of pollen contamination.[33] "When Jacobsen took great pains to isolate the plants, he couldn't reproduce the [reversion] phenomenon", notes Steven Henikoff.[34] 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.[35]

Multigen

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.

See also

References

  1. ^ Germplasm Resources Information Network: Arabidopsis thaliana
  2. ^ .. Arabidopsis has been reported to have the smallest genome known among flowering plants (Leutwileret al., 1984). In oursurveyArabidopsis ...
  3. ^ Flora of NW Europe: Arabidopsis thaliana
  4. ^ Blamey, M. & Grey-Wilson, C. (1989). Flora of Britain and Northern Europe. ISBN 0-340-40170-2
  5. ^ Flora of Pakistan: Arabidopsis thaliana
  6. ^ Flora of China: Arabidopsis thaliana
  7. ^ López-Bucio J, Campos-Cuevas JC, Hernández-Calderón E, et al (2007). "Bacillus megaterium rhizobacteria promote growth and alter root-system architecture through an auxin- and ethylene-independent signaling mechanism in Arabidopsis thaliana". Mol. Plant Microbe Interact. 20 (2): 207–17. doi:10.1094/MPMI-20-2-0207. PMID 17313171. 
  8. ^ D.W. Meinke, J.M. Cherry, C. Dean, S.D. Rounsley, M. Koornneef (1998). "Arabidopsis thaliana: A Model Plant for Genome Analysis". Science 282 (5389): 662–682. doi:10.1126/science.282.5389.662+. 
  9. ^ [1] TAIR: About [[Arabidopsis]]
  10. ^ Fink G (1998). "Anatomy of a Revolution". Genetics 149: 473–477. 
  11. ^ Rensink WA, Buell CR (2004). "Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species". Plant Physiol. 135 (2): 622–9. doi:10.1104/pp.104.040170. PMID 15208410. 
  12. ^ Coelho SM, Peters AF, Charrier B, et al (2007). "Complex life cycles of multicellular eukaryotes: new approaches based on the use of model organisms". Gene 406 (1-2): 152–70. doi:10.1016/j.gene.2007.07.025. PMID 17870254. 
  13. ^ Platt A, Horton M, Huang YS, Li Y, Anastasio AE, et al (2010). "The scale of population structure in Arabidopsis thaliana". PLoS Gen. 6 (2). doi:10.1371/journal.pgen.1000843. http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000843. 
  14. ^ Bennett, M. D., Leitch, I. J., Price, H. J., & Johnston, J. S. (2003). "Comparisons with Caenorhabditis (100 Mb) and Drosophila (175 Mb) Using Flow Cytometry Show Genome Size in Arabidopsis to be 157 Mb and thus 25% Larger than the Arabidopsis Genome Initiative Estimate of 125 Mb". Annals of Botany 91: 547–557. doi:10.1093/aob/mcg057. PMID 12646499. 
  15. ^ The Arabidopsis Genome Initiative (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature 408: 796–815. doi:10.1038/35048692. PMID 11130711. 
  16. ^ "TAIR - Genome Annotation:". http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp. 
  17. ^ "Integr8 - A.thaliana Genome Statistics:". http://www.ebi.ac.uk/integr8/OrganismStatsAction.do;jsessionid=08E9058B5B688A4F7FF7D161CB9E36A4?orgProteomeId=3. 
  18. ^ Clough SJ, Bent AF (1998). "Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana". Plant J 16 (6): 735-743. doi:10.1046/j.1365-313x.1998.00343.x. PMID 10069079. 
  19. ^ Zhang X, Henriques R, Lin SS, Niu QW, Chua NH (2006). "Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method". Nat Protoc 1 (2): 641–6. doi:10.1038/nprot.2006.97. PMID 17406292. 
  20. ^ Moreno N, Bougourd S, Haseloff J and Fiejo JA. 2006. Chapter 44: Imaging Plant Cells. In: Pawley JB (Editor). Handbook of Biological Confocal Microscopy - 3rd edition. SpringerScience+Business Media, New York. p769-787
  21. ^ Shaw S (2006). "Imaging the live plant cell". The Plant Journal 45: 573–598. doi:10.1111/j.1365-313X.2006.02653.x. 
  22. ^ M.F. Yanofsky, H. Ma, J.L. Bowman, G.N. Drews, K.A. Feldmann & E.M. Meyerowitz (1990). "The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors". Nature 346: 35–39. doi:10.1038/346035a0. PMID 1973265. http://www.nature.com/nature/journal/v346/n6279/abs/346035a0.html. 
  23. ^ a b E.M. Meyerowitz (2001). "Prehistory and History of Arabidopsis Research". Plant Physiology 125: 15–19. doi:10.1038/346035a0. PMID 11154286. http://www.plantphysiol.org/cgi/content/full/125/1/15. 
  24. ^ Lloyd AM, Barnason AR, Rogers SG, Byrne MC, Fraley RT, Horsch RB (1986). "Transformation of Arabidopsis thaliana with Agrobacterium tumefaciens". Science 234: 464–466. doi:10.1126/science.234.4775.464. PMID 17792019. 
  25. ^ Chang C, Meyerowitz EM (1986). "Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene". Proc Natl Acad Sci USA 83: 1408–1412. doi:10.1073/pnas.83.5.1408. PMID 2937058. 
  26. ^ Coen, Henrico S.; Elliot M. Meyerowitz (1991). "The war of the whorls: Genetic interactions controlling flower development". Nature 353: 31–37. doi:10.1038/353031a0. PMID 1715520. 
  27. ^ Sullivan JA, Deng XW (2003). "From seed to seed: the role of photoreceptors in Arabidopsis development". Dev. Biol. 260 (2): 289–97. doi:10.1016/S0012-1606(03)00212-4+. PMID 12921732. 
  28. ^ Más P (2005). "Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development". Int. J. Dev. Biol. 49 (5-6): 491–500. doi:10.1387/ijdb.041968pm. PMID 16096959. http://www.intjdevbiol.com/paper.php?doi=10.1387/ijdb.041968pm. 
  29. ^ Ruppel NJ, Hangarter RP, Kiss JZ (2001). "Red-light-induced positive phototropism in Arabidopsis roots". Planta 212 (3): 424–30. doi:10.1007/s004250000410+. PMID 11289607. 
  30. ^ Lolle SJ, Victor JL, Young JM, Pruitt RE (2005). "Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis". Nature 434: 505–9. doi:10.1038/nature03380. PMID 15785770. Washington Post summary.
  31. ^ Chaudhury, A. (2005). "Hothead healer and extragenomic information". Nature 437: E1–E2. doi:10.1038/nature04062. PMID 16136082. 
  32. ^ Comai L, Cartwright RA (2005). "A toxic mutator and selection alternative to the non-Mendelian RNA cache hypothesis for hothead reversion". Plant Cell 17: 2856–8. doi:10.1105/tpc.105.036293. PMID 16267378. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16267378.  summary
  33. ^ Peng P., et al. (2006). "Plant genetics: Increased outcrossing in hothead mutants". Nature 443: E8–E9. doi:10.1038/nature05251+. PMID 17006468. 
  34. ^ Pennisi E (2006). "Genetics. Pollen contamination may explain controversial inheritance". Science 313: 1864. doi:10.1126/science.313.5795.1864. PMID 17008492. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=17008492. 
  35. ^ Lolle S. J., et al. (2006). "Increased outcrossing in hothead mutants (Reply)". Nature 443: E8–E9. doi:10.1038/nature05252. PMID 17006468. 

External links


Wikispecies

Up to date as of January 23, 2010

From Wikispecies

Arabidopsis thaliana

Taxonavigation

Classification System: APG II (down to family level)

Main Page
Cladus: Eukaryota
Regnum: Plantae
Cladus: Angiospermae
Cladus: Eudicots
Cladus: core eudicots
Cladus: Rosids
Cladus: Eurosids II
Ordo: Brassicales
Familia: Brassicaceae
Genus: Arabidopsis
Species: Arabidopsis thaliana

Name

Arabidopsis thaliana, (L.) Heynh.

References

USDA, NRCS. 2006. The PLANTS Database, 6 March 2006 (http://plants.usda.gov). Data compiled from various sources by Mark W. Skinner. National Plant Data Center, Baton Rouge, LA 70874-4490 USA.

Vernacular names

Deutsch: Acker-Schmalwand, Schotenkresse
English: Thale Cress, Mouse-ear Cress
Español: Oruga
Français: Arabette des Dames, Arabette de Thalius, Arabidopsis de Thalius, Arabette Rameuse, Fausse Arabette
Italiano: Arabetta Comune
Nederlands: Zandraket
‪Norsk (bokmål)‬: Vårskrinneblom
Polski: Rzodkiewnik Pospolity
Svenska: Backtrav

Simple English

Arabidopsis thaliana
File:Arabidopsis
Scientific classification
Kingdom: Plantae
(unranked) Eudicots
(unranked) Rosids
Order: Brassicales
Family: Brassicaceae
Genus: Arabidopsis
Species: A. thaliana
Binomial name
Arabidopsis thaliana
(L.) Heynh.
File:Arabidopsis thaliana
Synonyms

Arabis thaliana

Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. It is widely used as a model organism in plant genetics. Arabidopsis is a member of the mustard (Brassicaceae) family, which includes cultivated species such as cabbage and radish.

It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative.[1] The most up-to-date version of the Arabidopsis thaliana genome is maintained by The Arabidopsis Information Resource (TAIR).[2]

Much work has been done to find out what its 27,000 genes and 35,000 proteins do.[3] Arabidopsis is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing.

References

  1. The Arabidopsis Genome Initiative (2000). [Expression error: Unexpected < operator "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana"]. Nature 408 (6814): 796–815. doi:10.1038/35048692. PMID 11130711. 
  2. "TAIR - Genome Annotation:". http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp. 
  3. "Integr8 - A.thaliana Genome Statistics:". http://www.ebi.ac.uk/integr8/OrganismStatsAction.do;jsessionid=08E9058B5B688A4F7FF7D161CB9E36A4?orgProteomeId=3. 

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