Arabidopsis thaliana is a small
flowering plantThe flowering plants , also known as Angiospermae or Magnoliophyta, are the most diverse group of land plants. Angiosperms are seed-producing plants like the gymnosperms and can be distinguished from the gymnosperms by a series of synapomorphies...
native to
EuropeEurope is, by convention, one of the world's seven continents. Comprising the westernmost peninsula of Eurasia, Europe is generally 'divided' from Asia to its east by the watershed divides of the Ural and Caucasus Mountains, the Ural River, the Caspian and Black Seas, and the waterways connecting...
,
AsiaAsia is the world's largest and most populous continent, located primarily in the eastern and northern hemispheres. It covers 8.7% of the Earth's total surface area and with approximately 3.879 billion people, it hosts 60% of the world's current human population...
, and northwestern
AfricaAfrica is the world's second largest and second most populous continent, after Asia. At about 30.2 million km² including adjacent islands, it covers 6% of the Earth's total surface area and 20.4% of the total land area...
. A spring
annualAn annual plant is a plant that usually germinates, flowers, and dies in a year or season. True annuals will only live longer than a year if they are prevented from setting seed...
with a relatively short life cycle, arabidopsis is popular as a
model organismA model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
in plant biology and genetics.
Arabidopsis thaliana has a rather small
genomeIn modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
, only 157
megabase pairsIn molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
(Mbp), and was thought for a long time to have the smallest genome of all flowering plants, but the smallest flowering plants' genomes now known belong to plants in the genus
GenliseaGenlisea is a genus of carnivorous plants also known as corkscrew plants. The 21 species grow in wet terrestrial to semi-aquatic environments distributed throughout Africa and Central and South America. The plants use highly modified underground leaves to attract, trap and digest minute...
, order
LamialesLamiales is an order in the asterid group of dicotyledonous flowering plants. It includes approximately 11,000 species divided into about 20 families...
, with
Genlisea margaretaeGenlisea margaretae is a carnivorous species in the genus Genlisea native to areas of Madagascar, Tanzania, and Zambia. It has pale bundles of root-like organs up to about 20 cm long under ground that attract, trap, and digest protozoans. These organs are subterranean leaves, which lack chlorophyll...
, a carnivorous plant, showing a genome size of 63.4 Mbp. Arabidopsis was the first plant genome to be sequenced, and is a popular tool for understanding the
molecular biologyMolecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
of many plant traits, including
flowerA flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants . The biological function of a flower is to effect reproduction, usually by providing a mechanism for the union of sperm with eggs...
development and
light sensingPhototropism is directional growth in which the direction of growth is determined by the direction of the light source. In other words, it is the growth and response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi...
.
Discovery and name origin
The plant was first discovered in 1577 in the Harz Mountains by Johannes Thal (1542–1583), a physician from
NordhausenNordhausen is a town at the southern edge of the Harz Mountains, in the state of Thuringia, Germany. It is the capital of the district of Nordhausen...
, Thüringen, Germany, who called it
Pilosella siliquosa. In 1841 the plant was renamed
Arabidopsis thaliana by German botanist
Gustav HeynholdGustav Heynhold was a German botanist.In 1841, he renamed Arabis thaliana as Arabidopsis thaliana Heynh. in honour of Johannes Thal.His author abbreviation is Heynh.-Works:...
in honor of Thal. The genus name,
Arabidopsis comes from Greek, meaning "resembling
ArabisArabis , or rockcress, is a genus of flowering plants, within the family Brassicaceae, subfamily Brassicoideae.Though traditionally recognized as a large genus with many Old World and New World members, more recent evaluations of the relationships among these species using genetic data suggest that...
".
Habitat, morphology, and life cycle
Arabidopsis is native to
EuropeEurope is, by convention, one of the world's seven continents. Comprising the westernmost peninsula of Eurasia, Europe is generally 'divided' from Asia to its east by the watershed divides of the Ural and Caucasus Mountains, the Ural River, the Caspian and Black Seas, and the waterways connecting...
,
AsiaAsia is the world's largest and most populous continent, located primarily in the eastern and northern hemispheres. It covers 8.7% of the Earth's total surface area and with approximately 3.879 billion people, it hosts 60% of the world's current human population...
, and northwestern
AfricaAfrica is the world's second largest and second most populous continent, after Asia. At about 30.2 million km² including adjacent islands, it covers 6% of the Earth's total surface area and 20.4% of the total land area...
. It is an
annualAn annual plant is a plant that usually germinates, flowers, and dies in a year or season. True annuals will only live longer than a year if they are prevented from setting seed...
(rarely
biennialA biennial plant is a flowering plant that takes two years to complete its biological lifecycle. In the first year the plant grows leaves, stems, and roots , then it enters a period of dormancy over the colder months. Usually the stem remains very short and the leaves are low to the ground, forming...
) plant, usually growing to 20–25 cm tall. The
leavesA leaf is an organ of a vascular plant, as defined in botanical terms, and in particular in plant morphology. Foliage is a mass noun that refers to leaves as a feature of plants....
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
trichomeTrichomes are fine outgrowths or appendages on plants and certain protists. These are of diverse structure and function. Examples are hairs, glandular hairs, scales, and papillae.- Algal trichomes :...
s). The
flowerA flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants . The biological function of a flower is to effect reproduction, usually by providing a mechanism for the union of sperm with eggs...
s are 3 mm in diameter, arranged in a corymb; their structure is that of the typical
BrassicaceaeBrassicaceae, a medium sized and economically important family of flowering plants , are informally known as the mustards, mustard flowers, the crucifers or the cabbage family....
. The
fruitIn broad terms, a fruit is a structure of a plant that contains its seeds.The term has different meanings dependent on context. In non-technical usage, such as food preparation, fruit normally means the fleshy seed-associated structures of certain plants that are sweet and edible in the raw state,...
is a siliqua 5–20 mm long, containing 20–30
seedA seed is a small embryonic plant enclosed in a covering called the seed coat, usually with some stored food. It is the product of the ripened ovule of gymnosperm and angiosperm plants which occurs after fertilization and some growth within the mother plant...
s. Roots are simple in structure, with a single primary root that grows vertically downwards, later producing smaller lateral roots. These roots form interactions with
rhizosphereThe rhizosphere is the narrow region of soil that is directly influenced by root secretions and associated soil microorganisms. Soil which is not part of the rhizosphere is known as bulk soil. The rhizosphere contains many bacteria that feed on sloughed-off plant cells, termed rhizodeposition, and...
bacteria such as
Bacillus megateriumBacillus megaterium is a rod-shaped, Gram-positive, endospore forming, species of bacteria used as a soil inoculant in agriculture and horticulture.Bacterium is arranged into the streptobacillus form....
.
Arabidopsis can complete its entire life cycle in six weeks. The central stem that produces flowers grows after about three weeks, and the flowers naturally self-pollinate. In the lab, arabidopsis may be grown in Petri plates or pots, under fluorescent lights or in a greenhouse.
Use as a model organism
By the beginning of 1900s,
A. thaliana had begun to be used in some developmental studies. The first collection of its mutants was made around 1945. It is now widely used for studying plant sciences, including
geneticsGenetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
,
evolutionEvolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
, population genetics, and plant development. It plays the role in plant biology that mice and
fruit flies (Drosophila)Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
play in animal biology. Although
A. thaliana has little direct significance for agriculture, it has several traits that make it a useful model for understanding the genetic, cellular, and molecular biology of flowering plants.
The small size of its
genomeIn modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
makes
Arabidopsis thaliana useful for genetic mapping and
sequencingIn genetics and biochemistry, sequencing means to determine the primary structure of an unbranched biopolymer...
— with about 157 megabase pairs and five
chromosomeA chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
s, arabidopsis has one of the smallest genomes among plants. It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative. The most up-to-date version of the
A. thaliana genome is maintained by the Arabidopsis Information Resource (TAIR). Much work has been done to assign functions to its 27,000
geneA gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s and the 35,000 proteins they encode.
The plant's small size and rapid life cycle are also advantageous for research. Having specialized as a spring ephemeral, it has been used to found several laboratory strains that take about six weeks from germination to mature seed. The small size of the plant is convenient for cultivation in a small space, and it produces many seeds. Further, the selfing nature of this plant assists genetic experiments. Also, as an individual plant can produce several thousand seeds, each of the above criteria leads to
A. thaliana being valued as a genetic model organism.
Plant
transformationIn molecular biology transformation is the genetic alteration of a cell resulting from the direct uptake, incorporation and expression of exogenous genetic material from its surroundings and taken up through the cell membrane. Transformation occurs naturally in some species of bacteria, but it can...
in arabidopsis is routine, using
Agrobacterium tumefaciensAgrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of dicot. It is a rod shaped, Gram negative soil bacterium...
to transfer DNA to the plant genome. The current protocol, termed "floral-dip", involves simply dipping a flower into a solution containing
Agrobacterium, the DNA of interest, and a detergent. This method avoids the need for
tissue cultureTissue culture is the growth of tissues or cells separate from the organism. This is typically facilitated via use of a liquid, semi-solid, or solid growth medium, such as broth or agar...
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 microscopyConfocal laser scanning microscopy is a technique for obtaining high-resolution optical images with depth selectivity. The key feature of confocal microscopy is its ability to acquire in-focus images from selected depths, a process known as optical sectioning...
. By wet mounting seedlings in water or in culture media, plants may be imaged uninvasively, obviating the need for
fixationIn the fields of histology, pathology, and cell biology, fixation is a chemical process by which biological tissues are preserved from decay, thereby preventing autolysis or putrefaction...
and
sectioningDissection is usually the process of disassembling and observing something to determine its internal structure and as an aid to discerning the functions and relationships of its components....
and allowing
time-lapseTime-lapse photography is a cinematography technique whereby the frequency at which film frames are captured is much lower than that which will be used to play the sequence back. When replayed at normal speed, time appears to be moving faster and thus lapsing...
measurements. Fluorescent protein constructs can be introduced through
transformationIn molecular biology transformation is the genetic alteration of a cell resulting from the direct uptake, incorporation and expression of exogenous genetic material from its surroundings and taken up through the cell membrane. Transformation occurs naturally in some species of bacteria, but it can...
. The
developmentalPlant morphology or phytomorphology is the study of the physical form and external structure of plants. This is usually considered distinct from plant anatomy, which is the study of the internal structure of plants, especially at the microscopic level...
stage of each cell can be inferred from its location in the plant or by using
fluorescent proteinThe green fluorescent protein is a protein composed of 238 amino acid residues that exhibits bright green fluorescence when exposed to blue light. Although many other marine organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the...
markers, allowing detailed
developmental analysisDevelopmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and "morphogenesis", which is the process that gives rise to tissues, organs and anatomy.- Related fields of study...
.
TAIR and
NASC are curated sources for diverse arabidopsis genetic and molecular biology information, and also provide numerous links, for example, to
databases that store the results of hundreds of genome-wide gene expression profile experiments. Seed and DNA stocks can be obtained from NASC or the
Arabidopsis Biological Resource Center.
History of Arabidopsis research
The first mutant in arabidopsis was documented in 1873 by
Alexander BraunAlexander Carl Heinrich Braun was a German botanist from Regensburg, Bavaria.He studied botany in Heidelberg, Paris and Munich. In 1833 he began teaching botany at the Polytechnic School of Karlsruhe, staying there until 1846...
, describing a
double flowerDouble Flower Football Association is a Hong Kong football club and plays in Hong Kong Second Division League. It was a very successful team in 1990s under the name Instant-Dict .-Events:...
phenotype (the mutated gene was likely
Agamous, cloned and characterized in 1990). However, not until 1943 did Friedrich Laibach (who had published the chromosome number in 1907) propose arabidopsis as a model organism. His student, Erna Reinholz, published her thesis on arabidopsis in 1945, describing the first collection of arabidopsis mutants that they generated using
X-rayX-radiation is a form of electromagnetic radiation. X-rays have a wavelength in the range of 0.01 to 10 nanometers, corresponding to frequencies in the range 30 petahertz to 30 exahertz and energies in the range 120 eV to 120 keV. They are shorter in wavelength than UV rays and longer than gamma...
mutagenesisMutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures...
. Laibach continued his important contributions to arabidopsis research by collecting a large number of
ecotypeIn 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 species , which is adapted to specific environmental conditions.Typically, ecotypes...
s. With the help of Albert Kranz, these were organised into the current ecotype collection of 750 natural accessions of
A. thaliana from around the world.
In the 1950s and 1960s,
John LangridgeJohn George Langridge was a cricketer who played for Sussex. His obituary in Wisden called him "one of the best English cricketers of the 20th century never to play a Test match"....
and
George RédeiGeorge P. Rédei was a Hungarian-born plant biologist, professor, author and member of the Hungarian Academy of Sciences.- Biography :...
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
GöttingenGöttingen is a university town in Lower Saxony, Germany. It is the capital of the district of Göttingen. The Leine river runs through the town. In 2006 the population was 129,686.-General information:...
, 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
maizeMaize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
,
petuniaPetunia is a widely cultivated genus of flowering plants of South American origin, closely related with tobacco, cape gooseberries, tomatoes, deadly nightshades, potatoes and chili peppers; in the family Solanaceae. The popular flower derived its name from French, which took the word petun, meaning...
and
tobaccoTobacco is an agricultural product processed from the leaves of plants in the genus Nicotiana. It can be consumed, used as a pesticide and, in the form of nicotine tartrate, used in some medicines...
. 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
geneA gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
to be cloned and published.
Characterized ecotypes and mutant lines of arabidopsis serve as experimental material in laboratory studies. The most commonly used background lines are L
er, or Landsberg erecta, and Col, or Columbia. Other background lines less-often cited in the scientific literature are Ws, or Wassilewskija, C24, Cvi, or Cape Verde Islands, Nossen, etc. (see for ex.) Series of mutants, named L
er-x, Col-x, have been obtained and characterized; mutant lines are generally available through stock centers, of which best known are the Nottingham Arabidopsis Stock Center-NASC and the Arabidopsis Biological Resource Center-ABRC in Ohio, USA.
The Col or Columbia ecotype was selected, as an agronomically performant line, by Rédei, within a (nonirradiated) population of seeds named Landsberg he received from Laibach. Columbia is the ecotype sequenced in the Arabidopsis Genome Initiative. The L
er or Landsberg erecta line was selected by Rédei from within a Landsberg population on which he had performed some X-ray mutagenesis experiments. As the L
er collection of mutants is derived from this initial line, L
er-0 does not correspond to the Landsberg ecotype which is named La-0.
Research
Flower development
Arabidopsis has been extensively studied as a model for flower development. The developing flower has four basic organs:
sepalA sepal is a part of the flower of angiosperms . Collectively the sepals form the calyx, which is the outermost whorl of parts that form a flower. Usually green, sepals have the typical function of protecting the petals when the flower is in bud...
s,
petalPetals are modified leaves that surround the reproductive parts of flowers. They often are brightly colored or unusually shaped to attract pollinators. Together, all of the petals of a flower are called a corolla. Petals are usually accompanied by another set of special leaves called sepals lying...
s,
stamenThe stamen is the pollen producing reproductive organ of a flower...
s, and
carpelGynoecium is most commonly used as a collective term for all carpels in a flower. A carpel is the ovule and seed producing reproductive organ in flowering plants. Carpels are derived from ovule-bearing leaves which evolved to form a closed structure containing the ovules...
s (which go on to form
pistilGynoecium is most commonly used as a collective term for all carpels in a flower. A carpel is the ovule and seed producing reproductive organ in flowering plants. Carpels are derived from ovule-bearing leaves which evolved to form a closed structure containing the ovules...
s). 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. MeyerowitzElliot Meyerowitz is an American biologist.He is George W. Beadle Professor of Biology, Division of Biology at the California Institute of Technology, he served as Chair of the Biology Division from 2000 to 2010....
. 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 factorIn molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s 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 plantThe flowering plants , also known as Angiospermae or Magnoliophyta, are the most diverse group of land plants. Angiosperms are seed-producing plants like the gymnosperms and can be distinguished from the gymnosperms by a series of synapomorphies...
s.
Light sensing
The photoreceptors
phytochromePhytochrome is a photoreceptor, a pigment that plants use to detect light. It is sensitive to light in the red and far-red region of the visible spectrum. Many flowering plants use it to regulate the time of flowering based on the length of day and night and to set circadian rhythms...
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
photoperiodismPhotoperiodism is the physiological reaction of organisms to the length of day or night. It occurs in plants and animals.Photoperiodism can also be defined as the developmental responses of plants to the relative lengths of the light and dark periods...
,
germinationGermination is the process in which a plant or fungus emerges from a seed or spore, respectively, and begins growth. The most common example of germination is the sprouting of a seedling from a seed of an angiosperm or gymnosperm. However the growth of a sporeling from a spore, for example the...
, de-etiolation and
shade avoidanceShade avoidance is a set of responses that plants display when they are subjected to the shade of another plant. It often includes elongation, altered flowering time, increased apical dominance and altered partitioning of resources...
in plants.
Arabidopsis was used extensively in the study of the genetic basis of
phototropismPhototropism is directional growth in which the direction of growth is determined by the direction of the light source. In other words, it is the growth and response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi...
,
chloroplastChloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...
alignment, and stomatal aperture and other blue light-influenced processes. These traits respond to blue light, which is perceived by the
phototropinPhototropins are photoreceptor proteins that mediate phototropism responses in higher plants. Along with cryptochromes and phytochromes they allow plants to respond and alter their growth in response to the light environment...
light receptors.
Arabidopsis has also been important in understanding the functions of another blue light receptor,
cryptochromeCryptochromes are a class of blue light-sensitive flavoproteins found in plants and animals. Cryptochromes are involved in the circadian rhythms of plants and animals, and in the sensing of magnetic fields in a number of species...
, which is especially important for light entrainment to control the plants
circadian rhythmA circadian rhythm, popularly referred to as body clock, is an endogenously driven , roughly 24-hour cycle in biochemical, physiological, or behavioural processes. Circadian rhythms have been widely observed in plants, animals, fungi and cyanobacteria...
s.
Light response was even found in roots, which were thought not to be particularly sensitive to light. While
gravitropicGravitropism is a turning or growth movement by a plant or fungus in response to gravity. Charles Darwin was one of the first to scientifically document that roots show positive gravitropism and stems show negative gravitropism. That is, roots grow in the direction of gravitational pull and stems...
response of
Arabidopsis root organs is their predominant tropic response, specimens treated with
mutagenIn genetics, a mutagen is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level. As many mutations cause cancer, mutagens are therefore also likely to be carcinogens...
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 the roots also show positive phototropism.
Non-Mendelian inheritance
In 2005, scientists at
Purdue UniversityPurdue University, located in West Lafayette, Indiana, U.S., is the flagship university of the six-campus Purdue University system. Purdue was founded on May 6, 1869, as a land-grant university when the Indiana General Assembly, taking advantage of the Morrill Act, accepted a donation of land and...
proposed that
Arabidopsis possessed an alternative to previously known mechanisms of
DNA repairDNA repair refers to 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 UV light and radiation can cause DNA damage, resulting in as many as 1...
, which one scientist called a "parallel path of
inheritanceMendelian inheritance is a scientific description of how hereditary characteristics are passed from parent organisms to their offspring; it underlies much of genetics...
". It was observed in
mutationIn molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
s of the
HOTHEADHOTHEAD is a gene in Arabidopsis thaliana that encodes an flavin adenine dinucleotide-containing oxidoreductase. It is involved in the creation of the carpel during the formation of flowers, through the fusion of epidermal cells...
gene. Plants mutant in this gene exhibit organ fusion, and
pollenPollen is a fine to coarse powder containing the microgametophytes of seed plants, which produce the male gametes . Pollen grains have a hard coat that protects the sperm cells during the process of their movement from the stamens to the pistil of flowering plants or from the male cone to the...
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 polymorphismA single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...
s. The initial hypothesis proposed the record may be
RNARibonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
-based Since then, alternative models have been proposed which would explain the
phenotypeA phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
without requiring a new model of inheritance. More recently, the whole phenomenon is being challenged as a being a simple artifact of pollen contamination. "When Jacobsen took great pains to isolate the plants, he couldn't reproduce the [reversion] phenomenon", notes Steven Henikoff. In response to the new finding, Lolle and Pruitt agree that Peng
et al. did observe cross-pollination, but note that some of their own data, such as double reversions of both mutant genes to the regular form, cannot be explained by cross-pollination.
Plant–pathogen interactions
It is important to understand how plants achieve resistance to protect the world's food production as well as the agricultural industry. Many model systems have been developed to better understand interactions between plants and bacterial, fungal, oomycete,
viralA virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
and
nematodeThe nematodes or roundworms are the most diverse phylum of pseudocoelomates, and one of the most diverse of all animals. Nematode species are very difficult to distinguish; over 28,000 have been described, of which over 16,000 are parasitic. It has been estimated that the total number of nematode...
pathogens.
Arabidopsis thaliana has been successfully implemented in the study of the subdicipline of plant pathology, that is, the interaction between plants and disease-causing pathogens.
| Pathogen type | Example in Arabidopsis thaliana |
| Bacteria |
Pseudomonas syringaePseudomonas syringae is a rod shaped, Gram-negative bacterium with polar flagella. It is a plant pathogen which can infect a wide range of plant species, and exists as over 50 different pathovars, all of which are available to legitimate researches via international culture collections such as the...
, Xanthomonas campestrisBlack rot, caused by the bacterium Xanthomonas campestris pv. campestris , is considered the most important and most destructive disease of crucifers, infecting all cultivated varieties of brassicas worldwide . This disease was first described by botanist and entomologist Harrison Garman in...
|
| Fungi |
Colletotrichum destructivum Colletotrichum destructivum is a plant pathogen.- External links :* *...
, Botrytis cinereaBotrytis cinerea is a necrotrophic fungus that affects many plant species, although its most notable hosts may be wine grapes. In viticulture, it is commonly known as botrytis bunch rot; in horticulture, it is usually called grey mould or gray mold.The fungus gives rise to two different kinds of...
, Golovinomyces orontii |
| Oomycete |
Hyaloperonospora arabidopsidis Hyaloperonospora arabidopsidis is a species from the family Peronosporaceae. It is an obligate parasite and the causal agent of the downy mildew of the plant model organism Arabidopsis thaliana...
|
| Viral |
Cauliflower mosaic virus (CaMV)Cauliflower mosaic virus is the type member of the caulimoviruses, one of the six genera in the Caulimoviridae family, pararetroviruses that infect plants...
, tomato mosaic virus (TMV)Tobacco mosaic virus is a positive-sense single stranded RNA virus that infects plants, especially tobacco and other members of the family Solanaceae. The infection causes characteristic patterns on the leaves . TMV was the first virus to be discovered...
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| Nematode |
Meloidogyne incognita, Heterodera schachtiiHeterodera is a genus of nematodes in the family Heteroderidae. Members of the genus are obligate parasites and different species attack different crops, often causing great economic damage...
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The use of
A. thaliana has led to many breakthroughs in the advancement of knowledge of how plants manifest
plant disease resistancePlant disease resistance is crucial to the reliable production of food, and it provides significant reductions in agricultural use of fuel, land, water and other inputs. There are numerous examples of devastating plant disease impacts , as well as recurrent severe plant disease issues...
. The reason most plants are resistant to most pathogens is through nonhost resistance. This is, not all pathogens will infect all plants. An example where
A. thaliana was used to determine the genes responsible for non-host resistance is
Blumeria graminisBlumeria graminis 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 Oidium monilioides or Oidium tritici.-Systematics:Previously B...
, the causal agent of powdery mildew of grasses.
A. thaliana mutants were developed using the mutagen
ethyl methanesulfonate and screened to determine which mutants had increased infection by
B. graminis. The mutants with higher infection rates are referred to as PEN mutants due to the ability of
B. graminis to penetrate
A. thalaina to begin the disease process. The PEN genes were later mapped to identify the genes responsible for nonhost resistance to
B. graminis.
Generally, when a plant is exposed to a pathogen, or
nonpathogenicIn ecology, commensalism is a class of relationship between two organisms where one organism benefits but the other is neutral...
microbe, there is an initial response, known as PAMP-triggered immunity (PTI), because the plant detects conserved motifs known as Pathogen-associated molecular patterns (PAMPs). These PAMPs are detected by specialized receptors in the host known as pattern recognition receptors (PRRs) on the plant cell surface.
The best characterized PRR in
A. thaliana is FLS2 (Flagellin-Sensing2) which recognizes bacterial
flagellinFlagellin is a protein that arranges itself in a hollow cylinder to form the filament in bacterial flagellum. It has a mass of about 30,000 to 60,000 daltons...
, a specialized organelle used by microorganisms for the purpose of motility, as well as the
ligandIn biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In a narrower sense, it is a signal triggering molecule, binding to a site on a target protein.The binding occurs by intermolecular forces, such as ionic bonds, hydrogen...
flg22, which comprises the 22 amino acids recognized by FLS2. Discovery of FLS2 was facilitated by the identification of an
A. thaliana ecotype, Ws-0, that was unable to detect flg22, leading to the identification of the gene encoding FLS2.
A second PRR, EFR (EF-Tu receptor), has been identified in
A. thaliana which recognizes the bacterial
EF-TuEF-Tu is one of the prokaryotic elongation factors.The prokaryotic factor EF-Tu mediates the entry of the aminoacyl-tRNA into a free site of the ribosome. EF-Tu functions by binding an aminoacylated, or charged, tRNA molecule in the cytoplasm...
protein, the prokaryotic elongation factor used in protein synthesis, as well as the laboratory-used ligand elf18. Using
Agrobacterium-mediated transformation, a technique that takes advantage of the natural process by which
Agrobacterium transfers genes into host plants, the EFR gene was transformed into
Nicotiana benthamianaNicotiana benthamiana is a close relative of tobacco and species of Nicotiana indigenous to Australia.The herbaceous plant is found amongst rocks on hills and cliffs throughout the northern regions of Australia. Variable in height and habit, the species may be erect and up to 1.5 metres or...
, 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 transductionSignal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response...
pathways to initiate PTI.
A. thaliana has been instrumental in dissecting these pathways to better understand the regulation of immune responses, most notably the
mitogen-activated protein kinaseMitogen-activated protein kinases are serine/threonine-specific protein kinases that respond to extracellular stimuli and regulate various cellular activities, such as gene expression, mitosis, differentiation, proliferation, and cell survival/apoptosis.-Activation:MAP kinases are activated...
(MAP kinase) cascade. Downstream responses of PTI include
calloseCallose is a plant polysaccharide. It is composed of glucose residues linked together through β-1,3-linkages, and is termed a β-glucan. It is thought to be manufactured at the cell wall by callose synthases and is degraded by β-1,3-glucanases. It is laid down at plasmodesmata, at the cell...
deposition, the oxidative burst, and transcription of defense-related genes.
PTI is able to combat pathogens in a nonspecific manner. A stronger and more specific response in plants is that of effector-triggered immunity (ETI). ETI is dependent upon the recognition of pathogen effectors, proteins secreted by the pathogen that alter functions in the host, by plant
resistance genes (R-genes)Resistance genes are genes in plant genomes that convey plant disease resistance against pathogens by producing R proteins. The main class of R-genes consist of a nucleotide binding domain and a leucine rich repeat domain and are often referred to as R-genes. Generally, the NB domain binds...
, often described as
a gene-for-gene relationshipThe gene-for-gene relationship was discovered by Harold Henry Flor who was working with rust of flax . Flor was the first scientist to study the genetics of both the host and parasite and to integrate them into one genetic system...
. This recognition may occur directly or indirectly via a guard protein in a hypothesis known as the guard hypothesis. The first R-gene cloned in
A. thaliana was RPS2 (resistance to
Pseudomonas syringe 2), which is responsible for recognition of the effector avrRpt2. The bacterial effector avrRpt2 is delivered into
A. thaliana via the Type III secretion system of
P. syringae pv tomato strain DC3000. Recognition of avrRpt2 by RPS2 occurs via the guard protein RIN4. Recognition of a pathogen effector leads to a dramatic immune response known as the
hypersensitive responseThe hypersensitive response is a mechanism, used by plants, to prevent the spread of infection by microbial pathogens. The HR is characterized by the rapid death of cells in the local region surrounding an infection. The HR serves to restrict the growth and spread of pathogens to other parts of...
, in which the infected plant cells undergo cell death to prevent the spread of the pathogen.
Systemic acquired resistanceThe systemic acquired resistance 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 there is evidence that SAR in plants and innate immunity in animals may be evolutionarily...
(SAR) is another example of resistance which is better understood in plants because of research done in
A. thaliana. Benzothiadiazol (BTH), a
salicylic acid (SA)Salicylic acid is a monohydroxybenzoic acid, a type of phenolic acid and a beta hydroxy acid. This colorless crystalline organic acid is widely used in organic synthesis and functions as a plant hormone. It is derived from the metabolism of salicin...
analog, has been used historically as an antifungal compound in crop plants. BTH, as well as SA, has been shown to induce SAR in plants. The initiation of the SAR pathway was first demonstrated in
A. thaliana in which increased SA level are recognized by NPR1 (nonexpresser of PR genes 1) due to pH changes in the cytosol, resulting in the
reductionRedox reactions describe all chemical reactions in which atoms have their oxidation state changed....
of NPR1. NPR1, which usually exists in a multiplex (oligomerized state), becomes monomeric (a single unit) upon reduction. When NPR1 becomes monomeric, it translocates to the nucleus, were it interacts with many TGA
transcription factorIn molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s, and is able to induce pathogen-related genes such as PR1.
Multigenerational
Ongoing research on
Arabidopsis thaliana is being performed on the
International Space StationThe International Space Station is a habitable, artificial satellite in low Earth orbit. The ISS follows the Salyut, Almaz, Cosmos, Skylab, and Mir space stations, as the 11th space station launched, not including the Genesis I and II prototypes...
by the
European Space AgencyThe European Space Agency , established in 1975, is an intergovernmental organisation dedicated to the exploration of space, currently with 18 member states...
. The goals are to study the growth and reproduction of plants from seed to seed in microgravity.
See also
- Arabidopsis Biological Resource Center
The Arabidopsis Biological Resource Center was established at The Ohio State University in September, 1991. Primary support for the ABRC is provided by a National Science Foundation grant...
- Botany
Botany, plant science, or plant biology is a branch of biology that involves the scientific study of plant life. Traditionally, botany also included the study of fungi, algae and viruses...
- Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
- Non-Mendelian inheritance
Non-Mendelian inheritance is a general term that refers to any pattern of inheritance in which traits do not segregate in accordance with Mendel’s laws. These laws describe the inheritance of traits linked to single genes on chromosomes in the nucleus. In Mendelian inheritance, each parent...
- Nottingham Arabidopsis Stock Centre
The Nottingham Arabidopsis Stock Centre provides seed and information resources to the International Arabidopsis Genome Project and the wider research community...
External links