''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small
flowering plant
Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (), commonly called angiosperms. The term "angiosperm" is derived from the Greek words ('container, vessel') and ('seed'), and refers to those plants th ...
native to
Eurasia
Eurasia (, ) is the largest continental area on Earth, comprising all of Europe and Asia. Primarily in the Northern and Eastern Hemispheres, it spans from the British Isles and the Iberian Peninsula in the west to the Japanese archipelago a ...
and
Africa
Africa is the world's second-largest and second-most populous continent, after Asia in both cases. At about 30.3 million km2 (11.7 million square miles) including adjacent islands, it covers 6% of Earth's total surface area ...
.
''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land.
A
winter annual
An annual plant is a plant that completes its biological life cycle, life cycle, from germination to the production of seeds, within one growing season, and then dies. The length of growing seasons and period in which they take place vary accor ...
with a relatively short lifecycle, ''A. thaliana'' is a popular
model organism
A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...
in
plant biology
Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek wo ...
and genetics. For a complex multicellular
eukaryote
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
, ''A. thaliana'' has a relatively small
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
around 135 mega
base pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...
s.
It was the first plant to have its genome sequenced, and is a popular tool for understanding the
molecular biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...
of many plant traits, including
flower
A flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants (plants of the division Angiospermae). The biological function of a flower is to facilitate reproduction, usually by providing a mechani ...
development and
light sensing.
Description
![194 Arabidopsis thaliana, Turritis glabra](https://upload.wikimedia.org/wikipedia/commons/6/6d/194_Arabidopsis_thaliana%2C_Turritis_glabra.jpg)
''Arabidopsis thaliana'' is an
annual
Annual may refer to:
* Annual publication, periodical publications appearing regularly once per year
**Yearbook
** Literary annual
* Annual plant
* Annual report
* Annual giving
* Annual, Morocco, a settlement in northeastern Morocco
* Annuals (b ...
(rarely
biennial
Biennial means (an event) lasting for two years or occurring every two years. The related term biennium is used in reference to a period of two years.
In particular, it can refer to:
* Biennial plant, a plant which blooms in its second year and th ...
) plant, usually growing to 20–25 cm tall.
The
leaves
A leaf (plural, : leaves) is any of the principal appendages of a vascular plant plant stem, stem, usually borne laterally aboveground and specialized for photosynthesis. Leaves are collectively called foliage, as in "autumn foliage", wh ...
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
trichome
Trichomes (); ) are fine outgrowths or appendages on plants, algae, lichens, and certain protists. They are of diverse structure and function. Examples are hairs, glandular hairs, scales, and papillae. A covering of any kind of hair on a pla ...
s. The
flower
A flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants (plants of the division Angiospermae). The biological function of a flower is to facilitate reproduction, usually by providing a mechani ...
s are 3 mm in diameter, arranged in a
corymb
Corymb is a botanical term for an inflorescence with the flowers growing in such a fashion that the outermost are borne on longer pedicels than the inner, bringing all flowers up to a common level. A corymb has a flattish top with a superficial re ...
; their structure is that of the typical
Brassicaceae
Brassicaceae () or (the older) Cruciferae () is a medium-sized and economically important family of flowering plants commonly known as the mustards, the crucifers, or the cabbage family. Most are herbaceous plants, while some are shrubs. The le ...
. The
fruit
In botany, a fruit is the seed-bearing structure in flowering plants that is formed from the ovary after flowering.
Fruits are the means by which flowering plants (also known as angiosperms) disseminate their seeds. Edible fruits in particu ...
is a
siliqua
The siliqua (plural ''siliquae'') is the modern name given (without any ancient evidence to confirm the designation) to small, thin, Roman silver coins produced in the 4th century A.D. and later. When the coins were in circulation, the Latin wo ...
5–20 mm long, containing 20–30
seed
A seed is an embryonic plant enclosed in a protective outer covering, along with a food reserve. The formation of the seed is a part of the process of reproduction in seed plants, the spermatophytes, including the gymnosperm and angiospe ...
s.
[Flora of NW Europe]
''Arabidopsis thaliana''
[Blamey, M. & Grey-Wilson, C. (1989). ''Flora of Britain and Northern Europe''. ][Flora of Pakistan]
''Arabidopsis thaliana''
[Flora of China]
''Arabidopsis thaliana''
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
The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microor ...
bacteria such as ''
Bacillus megaterium
''Bacillus megaterium'' is a rod-like, Gram-positive, mainly aerobic spore forming bacterium found in widely diverse habitats.De Vos, P. ''et al.'' Bergey's Manual of Systematic Bacteriology: Volume 3: The Firmicutes. ''Springer'' (2009) It has ...
''.
''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.
Taxonomy
The plant was first described in 1577 in the
Harz Mountains
The Harz () is a highland area in northern Germany. It has the highest elevations for that region, and its rugged terrain extends across parts of Lower Saxony, Saxony-Anhalt, and Thuringia. The name ''Harz'' derives from the Middle High German ...
by (1542–1583), a physician from
Nordhausen Nordhausen may refer to:
* Nordhausen (district), a district in Thuringia, Germany
** Nordhausen, Thuringia, a city in the district
**Nordhausen station, the railway station in the city
* Nordhouse, a commune in Alsace (German: Nordhausen)
* Narost ...
,
Thüringen
Thuringia (; german: Thüringen ), officially the Free State of Thuringia ( ), is a state of central Germany, covering , the sixth smallest of the sixteen German states. It has a population of about 2.1 million.
Erfurt is the capital and larg ...
, Germany, who called it ''Pilosella siliquosa''. In 1753,
Carl Linnaeus
Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his ennoblement in 1761 as Carl von Linné Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalised binomial nomenclature, the ...
renamed the plant ''Arabis thaliana'' in honor of Thal. In 1842, German botanist
Gustav Heynhold
Gustav Heynhold (or ''Gustav Heinhold''; 1800–1860) was a German botanist who worked at the botanic gardens of Dresden and Frankfurt
Frankfurt, officially Frankfurt am Main (; Hessian: , "Frank ford on the Main"), is the most populous c ...
erected the new genus ''Arabidopsis'' and placed the plant in that genus. The
generic
Generic or generics may refer to:
In business
* Generic term, a common name used for a range or class of similar things not protected by trademark
* Generic brand, a brand for a product that does not have an associated brand or trademark, other ...
name, ''
Arabidopsis
''Arabidopsis'' (rockcress) is a genus in the family Brassicaceae. They are small flowering plants related to cabbage and mustard. This genus is of great interest since it contains thale cress (''Arabidopsis thaliana''), one of the model organi ...
'', comes from
Greek
Greek may refer to:
Greece
Anything of, from, or related to Greece, a country in Southern Europe:
*Greeks, an ethnic group.
*Greek language, a branch of the Indo-European language family.
**Proto-Greek language, the assumed last common ancestor ...
, meaning "resembling ''
Arabis
''Arabis'' ,''Sunset Western Garden Book,'' 1995:606–607 or rockcress, is a genus of flowering plants, within the family Brassicaceae.
Description
The species are herbaceous, annual or perennial plants, growing to 10–80 cm tall, usu ...
''" (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.
Distribution and habitat
''A. thaliana'' is native to Europe, Asia, and Africa, and its geographic distribution is rather continuous from the
Mediterranean
The Mediterranean Sea is a sea connected to the Atlantic Ocean, surrounded by the Mediterranean Basin and almost completely enclosed by land: on the north by Western and Southern Europe and Anatolia, on the south by North Africa, and on the e ...
to
Scandinavia
Scandinavia; Sámi languages: /. ( ) is a subregion#Europe, subregion in Northern Europe, with strong historical, cultural, and linguistic ties between its constituent peoples. In English usage, ''Scandinavia'' most commonly refers to Denmark, ...
and
Spain
, image_flag = Bandera de España.svg
, image_coat = Escudo de España (mazonado).svg
, national_motto = ''Plus ultra'' (Latin)(English: "Further Beyond")
, national_anthem = (English: "Royal March")
, i ...
to
Greece
Greece,, or , romanized: ', officially the Hellenic Republic, is a country in Southeast Europe. It is situated on the southern tip of the Balkans, and is located at the crossroads of Europe, Asia, and Africa. Greece shares land borders with ...
. 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.]
Use as a model organism
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
Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek wo ...
, including genetics
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar wor ...
, evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
, population genetics, and plant development. Although ''A. thaliana'' has little direct significance for agriculture, several of its traits make it a useful model for understanding the genetic, cellular, and molecular biology of flowering plants.
The first mutant in ''A. thaliana'' was documented in 1873 by Alexander Braun
Alexander Carl Heinrich Braun (10 May 1805 – 29 March 1877) was a German botanist from Regensburg, Bavaria. His research centered on the morphology of plants.
Biography
He studied botany in Heidelberg, Paris and Munich. In 1833 he began teachi ...
, describing a double flower phenotype (the mutated gene was likely ''Agamous
Agamous (AG) is a homeotic gene and MADS-box transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from D ...
'', 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
An X-ray, or, much less commonly, X-radiation, is a penetrating form of high-energy electromagnetic radiation. Most X-rays have a wavelength ranging from 10 picometers to 10 nanometers, corresponding to frequencies in the range 30&nb ...
mutagenesis
Mutagenesis () is a process by which the genetic information of an organism is changed by the production of a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using la ...
. Laibach continued his important contributions to ''A. thaliana'' research by collecting a large number of accessions (often questionably referred to as "ecotype
In evolutionary ecology, an ecotype,Greek: ''οίκος'' = home and ''τύπος'' = type, coined by Göte Turesson in 1922 sometimes called ecospecies, describes a genetically distinct geographic variety, population, or race within a species, ...
s"). 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
George P. Rédei (June 14, 1921 – November 10, 2008) was a Hungarian plant biologist, professor, author and member of the Hungarian Academy of Sciences.
Biography
George Rédei was born June 14, 1921, in Vienna, Austria, to Kalman and Margit ...
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
Göttingen (, , ; nds, Chöttingen) is a college town, university city in Lower Saxony, central Germany, the Capital (political), capital of Göttingen (district), the eponymous district. The River Leine runs through it. At the end of 2019, t ...
, 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
Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn (North American and Australian English), is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. Th ...
, petunia
''Petunia'' is genus of 20 species of flowering plants of South American origin. The popular flower of the same name derived its epithet from the French, which took the word ''petun'', meaning "tobacco," from a Tupi–Guarani language. A tende ...
, and tobacco
Tobacco is the common name of several plants in the genus '' Nicotiana'' of the family Solanaceae, and the general term for any product prepared from the cured leaves of these plants. More than 70 species of tobacco are known, but the ...
. 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 ''A. thaliana'' as a model plant was 1986, in which T-DNA
The transfer DNA (abbreviated T-DNA) is the transferred DNA of the tumor-inducing (Ti) plasmid of some species of bacteria such as ''Agrobacterium tumefaciens'' and ''Agrobacterium rhizogenes(actually an Ri plasmid)''. The T-DNA is transferred fr ...
-mediated transformation
Transformation may refer to:
Science and mathematics
In biology and medicine
* Metamorphosis, the biological process of changing physical form after birth or hatching
* Malignant transformation, the process of cells becoming cancerous
* Trans ...
and the first cloned ''A. thaliana'' gene were described.
Genomics
Nuclear genome
Due to the small size of its genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
, and because it is diploid
Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectively ...
, ''Arabidopsis thaliana'' is useful for genetic mapping and sequencing
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...
— with about 157 megabase pairs and five chromosome
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
s, ''A. thaliana'' has one of the smallest genomes among plants. It was long thought to have the smallest genome of all flowering plants, but that title is now considered to belong to plants in the genus ''Genlisea
''Genlisea'' ( ) is a genus of carnivorous plants also known as corkscrew plants. The 30 or so species grow in wet terrestrial to semi-aquatic environments distributed throughout Africa and Central and South America. The plants use highly modifi ...
'', order Lamiales
The order Lamiales (also known as the mint order) are an order in the asterid group of dicotyledonous flowering plants. It includes about 23,810 species, 1,059 genera, and is divided into about 25 families. These families include Acanthaceae, Bi ...
, with ''Genlisea tuberosa
''Genlisea tuberosa'' is a carnivorous species in the genus '' Genlisea'' (family Lentibulariaceae) that is endemic to Brazil and found only in '' campos rupestres'' vegetation. Lacking any roots, it has unpigmented bundles of "rootlike" subterr ...
'', 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
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
-coding gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
s 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.
Chloroplast genome
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
A plastome is the genome of a plastid, a type of organelle found in plants and in a variety of protoctists. The number of known plastid genome sequences grew rapidly in the first decade of the twenty-first century. For example, 25 chloroplast ...
). 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).
Mitochondrial genome
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''.
Genetics
Genetic transformation of ''A. thaliana'' is routine, using ''Agrobacterium tumefaciens
''Agrobacterium radiobacter'' (more commonly known as ''Agrobacterium tumefaciens'') is the causal agent of crown gall disease (the formation of tumours) in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Sympto ...
'' 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
Tissue culture is the growth of tissues or cells in an artificial medium separate from the parent organism. This technique is also called micropropagation. This is typically facilitated via use of a liquid, semi-solid, or solid growth medium, su ...
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 L''er'' (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 and the Arabidopsis Biological Resource Center-ABRC in Ohio, USA.
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
The University of Missouri (Mizzou, MU, or Missouri) is a public university, public Land-grant university, land-grant research university in Columbia, Missouri. It is Missouri's largest university and the flagship of the four-campus Universit ...
- 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 L''er'' collection of mutants is derived from this initial line, L''er''-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
Glabrousness (from the Latin ''glaber'' meaning "bald", "hairless", "shaved", "smooth") is the technical term for a lack of hair, down, setae, trichomes or other such covering. A glabrous surface may be a natural characteristic of all or part of ...
plants. This phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...
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.
Non-Mendelian inheritance controversy
In 2005, scientists at Purdue University
Purdue University is a public land-grant research university in West Lafayette, Indiana, and the flagship campus of the Purdue University system. The university was founded in 1869 after Lafayette businessman John Purdue donated land and money ...
proposed that ''A. thaliana'' possessed an alternative to previously known mechanisms of DNA repair
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA dam ...
, producing an unusual pattern of inheritance
Inheritance is the practice of receiving private property, Title (property), titles, debts, entitlements, Privilege (law), privileges, rights, and Law of obligations, obligations upon the death of an individual. The rules of inheritance differ ...
, 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.
Lifecycle
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.
Cellular biology
''Arabidopsis'' is often the model for study of SNAREs in plants. This has shown SNAREs to be heavily involved in vesicle trafficking
In cell biology, a vesicle is a structure within or outside a cell, consisting of liquid or cytoplasm enclosed by a lipid bilayer. Vesicles form naturally during the processes of secretion (exocytosis), uptake (endocytosis) and transport of mater ...
. Zheng et al. 1999 found an ''Arabidopsis'' SNARE called is probably essential to Golgi-vacuole
A vacuole () is a membrane-bound organelle which is present in plant and fungal cells and some protist, animal, and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic mo ...
trafficking. This is still a wide open field and plant SNAREs' role in trafficking remains understudied.
DNA repair
The DNA of plants is vulnerable to ultraviolet
Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nanometer, nm (with a corresponding frequency around 30 Hertz, PHz) to 400 nm (750 Hertz, THz), shorter than that of visible light, but longer than ...
light, and DNA repair
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA dam ...
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
Photolyases () are DNA repair enzymes that repair damage caused by exposure to ultraviolet light. These enzymes require visible light (from the violet/blue end of the spectrum) both for their own activation and for the actual DNA repair. The DN ...
.
Germination in lunar regolith
On May 12, 2022, NASA
The National Aeronautics and Space Administration (NASA ) is an independent agency of the US federal government responsible for the civil space program, aeronautics research, and space research.
NASA was established in 1958, succeeding t ...
announced that specimens of ''Arabidopsis thaliana'' had been successfully germinated and grown in samples of lunar regolith
Lunar soil is the fine fraction of the regolith found on the surface of the Moon. Its properties can differ significantly from those of terrestrial soil. The physical properties of lunar soil are primarily the result of mechanical disintegra ...
. While the plants successfully germinated and grew into seedlings, they were not as robust as specimens that had been grown in volcanic ash
Volcanic ash consists of fragments of rock, mineral crystals, and volcanic glass, created during volcano, volcanic eruptions and measuring less than 2 mm (0.079 inches) in diameter. The term volcanic ash is also often loosely used t ...
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 12 (November 14–24, 1969) was the sixth crewed flight in the United States Apollo program and the second to land on the Moon. It was launched on November 14, 1969, by NASA from the Kennedy Space Center, Florida. Commander Pete Conra ...
& Apollo 17
Apollo 17 (December 7–19, 1972) was the final mission of NASA's Apollo program, the most recent time humans have set foot on the Moon or traveled beyond low Earth orbit. Commander Gene Cernan and Lunar Module Pilot Harrison Schmitt walked on ...
were more robust than those grown in samples taken during Apollo 11
Apollo 11 (July 16–24, 1969) was the American spaceflight that first landed humans on the Moon. Commander Neil Armstrong and lunar module pilot Buzz Aldrin landed the Apollo Lunar Module ''Eagle'' on July 20, 1969, at 20:17 UTC, an ...
.
Development
Flower development
''A. thaliana ''has been extensively studied as a model for flower development. The developing flower has four basic organs - sepal
A sepal () is a part of the flower of angiosperms (flowering plants). Usually green, sepals typically function as protection for the flower in bud, and often as support for the petals when in bloom., p. 106 The term ''sepalum'' was coined b ...
s, petal
Petals are modified Leaf, leaves that surround the reproductive parts of flowers. They are often advertising coloration, brightly colored or unusually shaped to attract pollinators. All of the petals of a flower are collectively known as the ''c ...
s, stamen
The stamen (plural ''stamina'' or ''stamens'') is the pollen-producing reproductive organ of a flower. Collectively the stamens form the androecium., p. 10
Morphology and terminology
A stamen typically consists of a stalk called the filame ...
s, and carpel
Gynoecium (; ) is most commonly used as a collective term for the parts of a flower that produce ovules and ultimately develop into the fruit and seeds. The gynoecium is the innermost whorl of a flower; it consists of (one or more) ''pistils'' ...
s (which go on to form pistil
Gynoecium (; ) is most commonly used as a collective term for the parts of a flower that produce ovules and ultimately develop into the fruit and seeds. The gynoecium is the innermost whorl of a flower; it consists of (one or more) ''pistils'' ...
s). 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
In evolutionary developmental biology, homeosis is the transformation of one organ into another, arising from mutation in or misexpression of certain developmentally critical genes, specifically homeotic genes. In animals, these developmental ge ...
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.
Observations of homeotic mutations led to the formulation of the ABC model of flower development
The ABC model of flower development is a scientific model of the process by which flowering plants produce a pattern of gene expression in meristems that leads to the appearance of an organ oriented towards sexual reproduction, a flower. There ...
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 factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The fu ...
s 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.
Leaf development
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
A leaf (plural, : leaves) is any of the principal appendages of a vascular plant plant stem, stem, usually borne laterally aboveground and specialized for photosynthesis. Leaves are collectively called foliage, as in "autumn foliage", wh ...
, the establishment of dorsiventrality, and the development of a marginal meristem
The meristem is a type of tissue found in plants. It consists of undifferentiated cells (meristematic cells) capable of cell division. Cells in the meristem can develop into all the other tissues and organs that occur in plants. These cells conti ...
. 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
Gibberellins (GAs) are plant hormones that regulate various developmental processes, including stem elongation, germination, dormancy, flowering, flower development, and leaf and fruit senescence. GAs are one of the longest-known classes of p ...
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
Dorsal (from Latin ''dorsum'' ‘back’) may refer to:
* Dorsal (anatomy), an anatomical term of location referring to the back or upper side of an organism or parts of an organism
* Dorsal, positioned on top of an aircraft's fuselage
* Dorsal co ...
(adaxial) surface of the leaf is different from the ventral (abaxial) surface.
Microscopy
''A. thaliana'' is well suited for light microscopy
Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of micr ...
analysis. Young seedlings
A seedling is a young sporophyte developing out of a plant embryo from a seed. Seedling development starts with germination of the seed. A typical young seedling consists of three main parts: the radicle (embryonic root), the hypocotyl (embry ...
on the whole, and their roots in particular, are relatively translucent. This, together with their small size, facilitates live cell imaging using both fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...
and confocal laser scanning microscopy
Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser confocal scanning microscopy (LCSM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a s ...
. By wet-mounting seedlings in water or in culture media, plants may be imaged uninvasively, obviating the need for fixation and sectioning
Involuntary commitment, civil commitment, or involuntary hospitalization/hospitalisation is a legal process through which an individual who is deemed by a qualified agent to have symptoms of severe mental disorder is detained in a psychiatric hos ...
and allowing time-lapse
Time-lapse photography is a technique in which the frequency at which film frames are captured (the frame rate) is much lower than the frequency used to view the sequence. When played at normal speed, time appears to be moving faster and thus ...
measurements. Fluorescent protein constructs can be introduced through transformation
Transformation may refer to:
Science and mathematics
In biology and medicine
* Metamorphosis, the biological process of changing physical form after birth or hatching
* Malignant transformation, the process of cells becoming cancerous
* Trans ...
. The developmental
Development of the human body is the process of growth to maturity. The process begins with fertilization, where an egg released from the ovary of a female is penetrated by a sperm cell from a male. The resulting zygote develops through mitosi ...
stage of each cell can be inferred from its location in the plant or by using fluorescent protein Fluorescent proteins include:
* Green fluorescent protein (GFP)
* Yellow fluorescent protein
Yellow fluorescent protein (YFP) is a genetic mutant of green fluorescent protein (GFP) originally derived from the jellyfish '' Aequorea victoria''. Its ...
markers, allowing detailed developmental analysis.
Physiology
Light sensing, light emission, and circadian biology
The photoreceptors phytochrome
Phytochromes are a class of photoreceptor in plants, bacteria and fungi used to detect light. They are sensitive to light in the red and far-red region of the visible spectrum and can be classed as either Type I, which are activated by far-re ...
s A, B, C, D, and E mediate red light-based phototropic
Phototropism is the growth of an organism in response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi. The cells on the plant that are farthest from the light contain a hor ...
response. Understanding the function of these receptors has helped plant biologists understand the signaling cascades that regulate photoperiodism
Photoperiodism is the physiological reaction of organisms to the length of night or a dark period. It occurs in plants and animals. Plant photoperiodism can also be defined as the developmental responses of plants to the relative lengths of light a ...
, germination
Germination is the process by which an organism grows from a seed or spore. The term is applied to the sprouting of a seedling from a seed of an angiosperm or gymnosperm, the growth of a sporeling from a spore, such as the spores of fungi, fer ...
, de-etiolation, and shade avoidance in plants. The genes ''FCA FCA may refer to:
Arts
* Federation of Canadian Artists
* Foundation for Contemporary Art, in Ghana
* Foundation for Contemporary Arts, in the United States
Business and economics
* False Claims Act, a United States federal law
* Federal Cus ...
'', '' fy'', '' fpa'', '' LUMINIDEPENDENS'' (''ld''), ''fly
Flies are insects of the Order (biology), order Diptera, the name being derived from the Ancient Greek, Greek δι- ''di-'' "two", and πτερόν ''pteron'' "wing". Insects of this order use only a single pair of wings to fly, the hindwing ...
'', '' fve'' and ''FLOWERING LOCUS C
Flowering Locus C (''FLC'') is a MADS-box gene that in late-flowering ecotypes of the plant '' Arabidopsis thaliana'' is responsible for vernalization. In a new seedling ''FLC'' is expressed, which prevents flowering. Upon exposure to cold, less ...
'' (''FLC'') are involved in photoperiod
Photoperiodism is the physiological reaction of organisms to the length of night or a dark period. It occurs in plants and animals. Plant photoperiodism can also be defined as the developmental responses of plants to the relative lengths of light a ...
triggering of flowering and vernalization
Vernalization (from Latin ''vernus'', "of the spring") is the induction of a plant's flowering process by exposure to the prolonged cold of winter, or by an artificial equivalent. After vernalization, plants have acquired the ability to flower, ...
. Specifically Lee et al 1994 find ''ld'' produces a homeodomain
A homeobox is a DNA sequence, around 180 base pairs long, that regulates large-scale anatomical features in the early stages of embryonic development. For instance, mutations in a homeobox may change large-scale anatomical features of the full-g ...
and Blazquez et al 2001 that ''fve'' produces a WD40 repeat
The WD40 repeat (also known as the WD or beta-transducin repeat) is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Tandem copies of these repeats typically fold togethe ...
.
The UVR8
UV-B resistance 8 (UVR8) also known as ultraviolet-B receptor UVR8 is an UV-B – sensing protein found in plants and possibly other sources.
* It is responsible for sensing ultraviolet light in the range 280-315 nm and initiating the plant ...
protein detects UV-B
Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nm (with a corresponding frequency around 30 PHz) to 400 nm (750 THz), shorter than that of visible light, but longer than X-rays. UV radiation i ...
light and mediates the response to this DNA-damaging wavelength.
''A. thaliana'' was used extensively in the study of the genetic basis of phototropism
Phototropism is the growth of an organism in response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi. The cells on the plant that are farthest from the light contain a hor ...
, chloroplast
A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
alignment, and stoma
In botany, a stoma (from Greek ''στόμα'', "mouth", plural "stomata"), also called a stomate (plural "stomates"), is a pore found in the epidermis of leaves, stems, and other organs, that controls the rate of gas exchange. The pore is bor ...
l aperture and other blue light-influenced processes. These traits respond to blue light, which is perceived by the phototropin
Phototropins are photoreceptor proteins (more specifically, flavoproteins) that mediate phototropism responses in higher plants. Phototropins can be found throughout the leaves of a plant. Along with cryptochromes and phytochromes they allow plants ...
light receptors. ''Arabidopsis'' has also been important in understanding the functions of another blue light receptor, cryptochrome
Cryptochromes (from the Greek κρυπτός χρώμα, "hidden colour") are a class of flavoproteins found in plants and animals that are sensitive to blue light. They are involved in the circadian rhythms and the sensing of magnetic fields i ...
, which is especially important for light entrainment to control the plants' circadian rhythm
A circadian rhythm (), or circadian cycle, is a natural, internal process that regulates the sleep–wake cycle and repeats roughly every 24 hours. It can refer to any process that originates within an organism (i.e., Endogeny (biology), endogeno ...
s. When the onset of darkness is unusually early, ''A. thaliana'' reduces its metabolism of starch by an amount that effectively requires division
Division or divider may refer to:
Mathematics
*Division (mathematics), the inverse of multiplication
*Division algorithm, a method for computing the result of mathematical division
Military
*Division (military), a formation typically consisting ...
.
Light responses were even found in roots, previously thought to be largely insensitive to light. While the gravitropic
Gravitropism (also known as geotropism) is a coordinated process of differential growth by a plant in response to gravity pulling on it. It also occurs in fungi. Gravity can be either "artificial gravity" or natural gravity. It is a general featu ...
response of ''A. thaliana'' root organs is their predominant tropic response, specimens treated with mutagen
In genetics, a mutagen is a physical or chemical agent that permanently changes nucleic acid, genetic material, usually DNA, in an organism and thus increases the frequency of mutations above the natural background level. As many mutations can ca ...
s 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
Janet may refer to:
Names
* Janet (given name)
* Janet (French singer) (1939–2011)
Surname
* Charles Janet (1849–1932), French engineer, inventor and biologist, known for the Left Step periodic table
* Jules Janet (1861–1945), French psych ...
of Rice University
William Marsh Rice University (Rice University) is a Private university, private research university in Houston, Houston, Texas. It is on a 300-acre campus near the Houston Museum District and adjacent to the Texas Medical Center. Rice is ranke ...
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.
On the Moon
On January 2, 2019, China's Chang'e-4 lander brought ''A. thaliana'' to the moon. A small microcosm
Microcosm or macrocosm, also spelled mikrokosmos or makrokosmos, may refer to:
Philosophy
* Microcosm–macrocosm analogy, the view according to which there is a structural similarity between the human being and the cosmos
Music
* Macrocosm (alb ...
'tin' in the lander contained ''A. thaliana'', seeds of potato
The potato is a starchy food, a tuber of the plant ''Solanum tuberosum'' and is a root vegetable native to the Americas. The plant is a perennial in the nightshade family Solanaceae.
Wild potato species can be found from the southern Unit ...
es, and silkworm
The domestic silk moth (''Bombyx mori''), is an insect from the moth family Bombycidae. It is the closest relative of ''Bombyx mandarina'', the wild silk moth. The silkworm is the larva or caterpillar of a silk moth. It is an economically imp ...
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
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
, and grow and bloom in the lunar environment.
Secondary metabolites
is an ''Arabidopsis'' root triterpene
Triterpenes are a class of chemical compounds composed of three terpene units with the molecular formula C30H48; they may also be thought of as consisting of six isoprene units. Animals, plants and fungi all produce triterpenes, including squale ...
. Potter ''et al.'', 2018 finds synthesis
Synthesis or synthesize may refer to:
Science Chemistry and biochemistry
*Chemical synthesis, the execution of chemical reactions to form a more complex molecule from chemical precursors
** Organic synthesis, the chemical synthesis of organ ...
is induced by a combination of at least 2 facts, cell-specific transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The fu ...
s (TFs) and the accessibility of the chromatin
Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in r ...
.
Plant–pathogen interactions
Understanding how plants achieve resistance is important to protect the world's food production, and the agriculture industry. Many model systems have been developed to better understand interactions between plants and bacterial
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
, fungal
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from th ...
, oomycete
Oomycota forms a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, called oomycetes (). They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction of an oospore is the resul ...
, viral, and nematode
The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant-Parasitism, parasitic nematodes also known as eelworms. They are a diverse animal phylum inhab ...
pathogens. ''A. thaliana'' has been a powerful tool for the study of the subdiscipline of plant pathology
Plant pathology (also phytopathology) is the scientific study of diseases in plants caused by pathogens (infectious organisms) and environmental conditions (physiological factors). Organisms that cause infectious disease include fungus, fung ...
, that is, the interaction between plants and disease-causing pathogens
In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...
.
The use of ''A. thaliana'' has led to many breakthroughs in the advancement of knowledge of how plants manifest plant disease resistance
Plant disease resistance protects plants from pathogens in two ways: by pre-formed structures and chemicals, and by infection-induced responses of the immune system. Relative to a susceptible plant, disease resistance is the reduction of pathoge ...
. The reason most plants are resistant to most pathogens is through nonhost resistance - not all pathogens will infect all plants. An example where ''A. thaliana'' was used to determine the genes responsible for nonhost resistance is ''Blumeria graminis
''Blumeria graminis'' (commonly called barley powdery mildew or corn mildew) is a fungus that causes powdery mildew on grasses, including cereals. It is the only species in the genus ''Blumeria''. It has also been called ''Erysiphe graminis'' and ...
'', the causal agent of powdery mildew of grasses. ''A. thaliana'' mutants were developed using the mutagen
In genetics, a mutagen is a physical or chemical agent that permanently changes nucleic acid, genetic material, usually DNA, in an organism and thus increases the frequency of mutations above the natural background level. As many mutations can ca ...
ethyl methanesulfonate
Ethyl methanesulfonate (EMS) is a mutagenic, teratogenic, and carcinogenic organic compound with formula C3H8SO3. It produces random mutations in genetic material by nucleotide substitution; particularly through G:C to A:T transitions induced b ...
and screened to identify mutants with 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. thaliana'' to begin the disease process. The ''PEN'' genes were later mapped to identify the genes responsible for nonhost resistance to ''B. graminis''.
In general, when a plant is exposed to a pathogen, or nonpathogenic microbe, an initial response, known as PAMP-triggered immunity (PTI), occurs because the plant detects conserved motifs known as pathogen-associated molecular pattern
Pathogen-associated molecular patterns (PAMPs) are small molecular motifs conserved within a class of microbes. They are recognized by toll-like receptors (TLRs) and other pattern recognition receptors (PRRs) in both plants and animals. A vast arra ...
s (PAMPs). These PAMPs are detected by specialized receptors
Receptor may refer to:
*Sensory receptor, in physiology, any structure which, on receiving environmental stimuli, produces an informative nerve impulse
*Receptor (biochemistry), in biochemistry, a protein molecule that receives and responds to a n ...
in the host known as pattern recognition receptors
Pattern recognition receptors (PRRs) play a crucial role in the proper function of the innate immune system. PRRs are germline-encoded host sensors, which detect molecules typical for the pathogens. They are proteins expressed, mainly, by cells of ...
(PRRs) on the plant cell surface.
The best-characterized PRR in ''A. thaliana'' is FLS2 (Flagellin-Sensing2), which recognizes bacterial flagellin
Flagellin is a globular protein that arranges itself in a hollow cylinder to form the filament in a bacterial flagellum. It has a mass of about 30,000 to 60,000 daltons. Flagellin is the principal component of bacterial flagella, and is present ...
, a specialized organelle used by microorganisms for the purpose of motility, as well as the ligand
In coordination chemistry, a ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electr ...
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. FLS2 shows striking similarity to rice XA21, the first PRR isolated in 1995. Both flagellin and UV-C
Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nm (with a corresponding frequency around 30 PHz) to 400 nm (750 THz), shorter than that of visible light, but longer than X-rays. UV radiation i ...
act similarly to increase homologous recombination
Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may ...
in ''A. thaliana'', as demonstrated by Molinier et al. 2006. Beyond this somatic
Somatic may refer to:
* Somatic (biology), referring to the cells of the body in contrast to the germ line cells
** Somatic cell, a non-gametic cell in a multicellular organism
* Somatic nervous system, the portion of the vertebrate nervous sys ...
effect, they found this to extend to subsequent generations of the plant.
A second PRR, EF-Tu receptor (EFR), identified in ''A. thaliana'', recognizes the bacterial EF-Tu
EF-Tu (elongation factor thermo unstable) is a prokaryotic elongation factor responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome. It is a G-protein, and facilitates the selection and binding of an aa-tRNA to th ...
protein, the prokaryotic elongation factor used in protein synthesis
Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside Cell (biology), cells, homeostasis, balancing the loss of cellular proteins (via Proteolysis, degradation or Protein targeting, export) through the product ...
, 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
''Nicotiana benthamiana'', colloquially known as benth or benthi, is a species of ''Nicotiana'' indigenous to Australia. It is a close relative of tobacco.
A synonym for this species is ''Nicotiana suaveolens'' var. ''cordifolia'', a descrip ...
'', tobacco plant that does not recognize EF-Tu, thereby permitting recognition of bacterial EF-Tu thereby confirming EFR as the receptor of EF-Tu.
Both FLS2 and EFR use similar signal transduction
Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellula ...
pathways to initiate PTI. ''A. thaliana'' has been instrumental in dissecting these pathways to better understand the regulation of immune responses, the most notable one being the mitogen-activated protein kinase
A mitogen-activated protein kinase (MAPK or MAP kinase) is a type of protein kinase that is specific to the amino acids serine and threonine (i.e., a serine/threonine-specific protein kinase). MAPKs are involved in directing cellular responses to ...
(MAP kinase) cascade. Downstream responses of PTI include callose
Callose is a plant polysaccharide. Its production is due to the glucan synthase-like gene (GLS) in various places within a plant. It is produced to act as a temporary cell wall in response to stimuli such as stress or damage. Callose is composed ...
deposition, the oxidative burst
Respiratory burst (or oxidative burst) is the rapid release of the reactive oxygen species (ROS), superoxide anion () and hydrogen peroxide (), from different cell types.
This is usually utilised for mammalian immunological defence, but also pla ...
, 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), which 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 guardee protein in a hypothesis known as the guard hypothesis. The first R-gene cloned in ''A. thaliana'' was ''RPS2'' (resistance to ''Pseudomonas syringae'' 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
The type III secretion system (T3SS or TTSS), also called the injectisome, is one of the bacterial secretion systems used by bacteria to secrete their effector proteins into the host's cells to promote virulence and colonisation. The T3SS is a ...
of ''P. syringae'' pv. ''tomato'' strain DC3000. Recognition of avrRpt2 by RPS2 occurs via the guardee protein RIN4, which is cleaved. Recognition of a pathogen effector leads to a dramatic immune response known as the hypersensitive response
Hypersensitive response (HR) is a mechanism used by plants to prevent the spread of infection by microbial pathogens. HR is characterized by the rapid death of cells in the local region surrounding an infection and it serves to restrict the growt ...
, in which the infected plant cells undergo cell death to prevent the spread of the pathogen.
Systemic acquired resistance Systemic acquired resistance (SAR) is a "whole-plant" resistance response that occurs following an earlier localized exposure to a pathogen. SAR is analogous to the innate immune system found in animals, and although there are many shared aspects b ...
(SAR) is another example of resistance that is better understood in plants because of research done in ''A. thaliana''. Benzothiadiazol (BTH), a salicylic acid
Salicylic acid is an organic compound with the formula HOC6H4CO2H. A colorless, bitter-tasting solid, it is a precursor to and a metabolite of aspirin (acetylsalicylic acid). It is a plant hormone, and has been listed by the EPA Toxic Substance ...
(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 levels are recognized by nonexpresser of PR genes 1 (''NPR1'') due to redox change in the cytosol, resulting in the reduction of ''NPR1. NPR1'', which usually exists in a multiplex (oligomeric) state, becomes monomeric (a single unit) upon reduction. When NPR1 becomes monomeric, it translocates to the nucleus, where it interacts with many TGA transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The fu ...
s, and is able to induce pathogen-related genes such as ''PR1''. Another example of SAR would be the research done with transgenic tobacco plants, which express bacterial salicylate hydroxylase, nahG gene, requires the accumulation of SA for its expression
Although not directly immunological, intracellular transport
Intracellular transport is the movement of vesicles and substances within a cell. Intracellular transport is required for maintaining homeostasis within the cell by responding to physiological signals. Proteins synthesized in the cytosol are dist ...
affects susceptibility by incorporating - or being tricked into incorporating - pathogen particles. For example, the '' Dynamin-related protein 2b/ drp2b'' gene helps to move invaginated material into cells, with some mutants increasing ''PstDC3000
''Pseudomonas syringae'' is a rod-shaped, Gram-negative bacterium with polar flagella. As a plant pathogen, it can infect a wide range of species, and exists as over 50 different pathovars, all of which are available to researchers from intern ...
'' virulence even further.
Evolutionary aspect of plant-pathogen resistance
Plants are affected by multiple pathogens
In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...
throughout their lifetimes. In response to the presence of pathogens, plants have evolved receptors on their cell surfaces to detect and respond to pathogens. ''Arabidopsis thaliana'' is a model organism used to determine specific defense mechanisms of plant-pathogen resistance. These plants have special receptors on their cell surfaces that allow for detection of pathogens and initiate mechanisms to inhibit pathogen growth. They contain two receptors, FLS2 (bacterial flagellin receptor) and EF-Tu (bacterial EF-Tu protein), which use signal transduction pathways to initiate the disease response pathway. The pathway leads to the recognition of the pathogen causing the infected cells to undergo cell death to stop the spread of the pathogen. Plants with FLS2 and EF-Tu receptors have shown to have increased fitness in the population. This has led to the belief that plant-pathogen resistance is an evolutionary mechanism that has built up over generations to respond to dynamic environments, such as increased predation and extreme temperatures.
''A. thaliana'' has also been used to study SAR.
This pathway uses benzothiadiazol, a chemical inducer, to induce transcription factors, mRNA, of SAR genes. This accumulation of transcription factors leads to inhibition of pathogen-related genes.
Plant-pathogen interactions are important for an understanding of how plants have evolved to combat different types of pathogens that may affect them. Variation in resistance of plants across populations is due to variation in environmental factors. Plants that have evolved resistance, whether it be the general variation or the SAR variation, have been able to live longer and hold off necrosis of their tissue (premature death of cells), which leads to better adaptation and fitness for populations that are in rapidly changing environments. In the future, comparisons of the pathosystem A pathosystem is a subsystem of an ecosystem and is defined by the phenomenon of parasitism. A plant pathosystem is one in which the host species is a plant. The parasite is any species in which the individual spends a significant part of its lifesp ...
s of wild populations + their coevolved
In biology, coevolution occurs when two or more species reciprocally affect each other's evolution through the process of natural selection. The term sometimes is used for two traits in the same species affecting each other's evolution, as well ...
pathogens with wild-wild hybrids of known parentage may reveal new mechanisms of balancing selection Balancing selection refers to a number of selective processes by which multiple alleles (different versions of a gene) are actively maintained in the gene pool of a population at frequencies larger than expected from genetic drift alone. Balancing ...
. In life history theory
Life history theory is an analytical frameworkVitzthum, V. (2008). Evolutionary models of women's reproductive functioning. ''Annual Review of Anthropology'', ''37'', 53-73 designed to study the diversity of life history strategies used by differen ...
we may find that ''A. thaliana'' maintains certain alleles due to pleitropy between plant-pathogen effects and other traits, as in livestock
Livestock are the domesticated animals raised in an agricultural setting to provide labor and produce diversified products for consumption such as meat, eggs, milk, fur, leather, and wool. The term is sometimes used to refer solely to animals ...
.
Research in ''A. thaliana'' suggests that the immunity regulator protein family EDS1 in general co-evolved with the CC family of nucleotide-bindingleucine-rich-repeat-receptors (NLRs). Xiao et al. 2005 have shown that the powdery mildew
Powdery mildew is a fungal disease that affects a wide range of plants. Powdery mildew diseases are caused by many different species of ascomycete fungi in the order Erysiphales. Powdery mildew is one of the easier plant diseases to identify, as ...
immunity mediated by ''A. thaliana''s RPW8 (which has a CC domain
Domain may refer to:
Mathematics
*Domain of a function, the set of input values for which the (total) function is defined
**Domain of definition of a partial function
**Natural domain of a partial function
**Domain of holomorphy of a function
* Do ...
) is dependent on two members of this family: '' EDS1'' itself and ''PAD4
Protein-arginine deiminase type-4, is a human protein which in humans is encoded by the ''PADI4'' gene. The protein as an enzyme, specifically protein-arginine deiminase, a type of hydrolase.
Molecular biology
The human gene is found on the sho ...
''.
'' RESISTANCE TO PSEUDOMONAS SYRINGAE 5/RPS5'' is a disease resistance protein which guards '' AvrPphB SUSCEPTIBLE 1/PBS1''. ''PBS1'', as the name would suggest, is the target of '' AvrPphB'', an effector
Effector may refer to:
*Effector (biology), a molecule that binds to a protein and thereby alters the activity of that protein
* ''Effector'' (album), a music album by the Experimental Techno group Download
* ''EFFector'', a publication of the El ...
produced by ''Pseudomonas syringae'' pv. ''phaseolicola''.
Other research
Ongoing research on ''A. thaliana'' is being performed on the International Space Station
The International Space Station (ISS) is the largest modular space station currently in low Earth orbit. It is a multinational collaborative project involving five participating space agencies: NASA (United States), Roscosmos (Russia), JAXA ...
by the European Space Agency
, owners =
, headquarters = Paris, Île-de-France, France
, coordinates =
, spaceport = Guiana Space Centre
, seal = File:ESA emblem seal.png
, seal_size = 130px
, image = Views in the Main Control Room (1205 ...
. The goals are to study the growth and reproduction of plants from seed to seed in microgravity
The term micro-g environment (also μg, often referred to by the term microgravity) is more or less synonymous with the terms ''weightlessness'' and ''zero-g'', but emphasising that g-forces are never exactly zero—just very small (on the I ...
.
Plant-on-a-chip devices in which ''A. thaliana'' tissues can be cultured in semi-''in vitro'' conditions have been described. Use of these devices may aid understanding of pollen-tube guidance and the mechanism of sexual reproduction in ''A. thaliana.''
Researchers at the University of Florida
The University of Florida (Florida or UF) is a public land-grant research university in Gainesville, Florida. It is a senior member of the State University System of Florida, traces its origins to 1853, and has operated continuously on its ...
were able to grow the plant in lunar soil
Lunar soil is the fine fraction of the regolith found on the surface of the Moon. Its properties can differ significantly from those of terrestrial soil. The physical properties of lunar soil are primarily the result of mechanical disintegra ...
originating from the Sea of Tranquillity
Mare Tranquillitatis (Latin ''tranquillitātis'', the Sea of Tranquillity or Sea of Tranquility; see spelling differences) is a lunar mare that sits within the Tranquillitatis basin on the Moon. It is the first location on another world to be v ...
.
Self-pollination
''A. thaliana'' is a predominantly self-pollinating plant with an outcrossing rate estimated at less than 0.3%. An analysis of the genome-wide pattern of linkage disequilibrium suggested that self-pollination evolved roughly a million years ago or more. Meioses that lead to self-pollination are unlikely to produce significant beneficial genetic variability. However, these meioses can provide the adaptive benefit of recombinational repair of DNA damages during formation of germ cells at each generation. Such a benefit may have been sufficient to allow the long-term persistence of meioses even when followed by self-fertilization. A physical mechanism for self-pollination in ''A. thaliana'' is through pre-anthesis autogamy, such that fertilisation takes place largely before flower opening.
Databases and other resources
* TAIR and NASC: curated sources for diverse genetic and molecular biology information, links to gene expression databases etc.
* Arabidopsis Biological Resource Center
The Arabidopsis Biological Resource Center (ABRC) was established at Ohio State University in September, 1991. Primary support for the ABRC is provided by a National Science Foundation grant. The mission of the ABRC is to acquire, preserve and dis ...
(seed and DNA stocks)
* Nottingham Arabidopsis Stock Centre
The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Project and the wider research community. It is based in the School of Biosciences at the University of Nottingham's Su ...
(seed and DNA stocks)
* Artade database
See also
* ''A. thaliana'' responses to salinity
*BZIP intron plant
The bZIP intron plant is an unconventional bZIP intron in plants located in the mRNA of bZIP60 orthologs. The consensus RNA structure is very similar to the animal variant with short, usually 23 nt intron defined by the loop regions of the cons ...
* The Thaliana Bridge, installed in 2021 at Harlow Carr
Harlow is a large town and local government district located in the west of Essex, England. Founded as a new town, it is situated on the border with Hertfordshire and London, Harlow occupies a large area of land on the south bank of the upper ...
was inspired by the work of the botanical scientist Rachel Leech
Rachel Leech (3 June 1936 – 23 December 2017) was Professor of Plant Sciences at the University of York, UK. Her research focused on chloroplasts and she was a leader in the field of understanding their development and function. She was also on ...
and represents the sequence of an ''Arabidopsis thaliana'' chromosome.
References
External links
*
Arabidopsis transcriptional regulatory map
The Arabidopsis Information Resource (TAIR)
What Makes Plants Grow? The Arabidopsis genome knows
Featured article in Genome News Network
The Arabidopsis book
- A comprehensive review published yearly related to research in ''Arabidopsis''
A. thaliana protein abundance
The Arabidopsis Information Portal (Araport)
{{Use dmy dates, date=January 2015
Flora of Europe
Flora of Asia
Flora of Africa
Flora of Lebanon
Plant models
Plants described in 1753
Taxa named by Carl Linnaeus
Space-flown life
Edible plants
Plant cognition
thaliana