Timing of CAB expression 1 is a

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, res ...

that in ''

Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter ...

'' is encoded by the TOC1

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 b ...

. TOC1 is also known as two-component response regulator-like APRR1. TOC1 was the first plant gene that, when mutated, yielded a circadian phenotype. It codes for the

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 f ...

TOC1, which affects the period of plants' circadian rhythms: built-in, malleable oscillations that repeat every 24 hours. The gene codes for a transcriptional

repressor In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. A DNA-binding repressor blocks the attachment of RNA polymerase to t ...

, TOC1, one of five pseudo-response regulators (PRR) that mediate the period of the circadian clock in plants. The TOC1 protein is involved in the clock's evening loop, which is a

repressilator The repressilator is a genetic regulatory network consisting of at least one feedback loop with at least three genes, each expressing a protein that represses the next gene in the loop. In biological research, repressilators have been used to buil ...

that directly inhibits transcription of morning loop genes LHY and

CCA1 Circadian Clock Associated 1 (CCA1) is a gene that is central to the circadian oscillator of angiosperms. It was first identified in ''Arabidopsis thaliana'' in 1993. CCA1 interacts with LHY and TOC1 to form the core of the oscillator system. CCA ...

. Toc1 gene is expressed in most plant structures and cells, and has its locus on chromosome 5.

Historical context

Discovery

The TOC1 gene was initially discovered by Prof. Andrew Millar and colleagues in 1995 while Millar was a graduate student. Millar developed an innovative forward genetic screen in which he linked a

bioluminescent Bioluminescence is the production and emission of light by living organisms. It is a form of chemiluminescence. Bioluminescence occurs widely in marine vertebrates and invertebrates, as well as in some fungi, microorganisms including some b ...

reporter, firefly (

luciferase Luciferase is a generic term for the class of oxidative enzymes that produce bioluminescence, and is usually distinguished from a photoprotein. The name was first used by Raphaël Dubois who invented the words '' luciferin'' and ''luciferase'' ...

), to expression of CAB (chlorophyll-a,b binding protein—see Light-harvesting complexes of green plants) in ''

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 organ ...

''. By measuring bioluminescence over the course of the day, Millar found CAB expression to display oscillatory patterns in constant light and to oscillate with a shorter period in toc1 mutant plants. He also mapped the toc1 gene to chromosome 5. These methods and discoveries were published in and featured on the cover of ''Science'' magazine in February 1995. Partially because the initial studies of clock genes were conducted in ''

Drosophila ''Drosophila'' () is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many speci ...

'' in the 1970s and then in mammals, it was originally thought that the plant circadian clock functioned similarly to the mammalian clock. In mammals, positive and negative regulatory elements act in feedback loops to drive circadian oscillations; namely, Per and Cry genes are activated by positive elements CLOCK and BMAL to produce proteins that, when phosphorylated, act as negative elements to inhibit the CLOCK:BMAL complex from its activating function. In this way, Per and Cry inhibit their own transcription. In contrast, Millar's group found the TOC1 protein to be a negative regulator, and the plant clock to be better modeled as a

—a system in which one gene represses another and is in turn repressed by the next, forming an interdependent, oscillating gene network. This finding was achieved through 1) ''

'' mutants with constitutive (always turned on) toc1

gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. T ...

, which showed decreased mRNA abundance in both morning loop genes prr7 and 9, cca1, and lhy and evening loop genes gi and elf4; and 2) plants with mutations in toc1 and plants in which RNAi was used to knock out toc1. These mutants with no functional toc1 showed an advanced phase for lhy, suggesting less repression in the absence of TOC1 protein. A study by Carl Strayer and colleagues found that toc1 gene's transcriptional involvement shortened circadian rhythms in constant dark in addition to constant light, and that TOC1 was circadianly regulated and involved in regulation of its own feedback loop.

Evolutionary History

* Homologs Homologs of TOC1 have been found in Lyrate rockcress,

Brassica ''Brassica'' () is a genus of plants in the cabbage and mustard family ( Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants. Crops from this genus are sometimes called ''cole c ...

papaya The papaya (, ), papaw, () or pawpaw () is the plant species ''Carica papaya'', one of the 21 accepted species in the genus '' Carica'' of the family Caricaceae. It was first domesticated in Mesoamerica, within modern-day southern Mexico and ...

cucumber Cucumber (''Cucumis sativus'') is a widely-cultivated creeping vine plant in the Cucurbitaceae family that bears usually cylindrical fruits, which are used as culinary vegetables.strawberry The garden strawberry (or simply strawberry; ''Fragaria × ananassa'') is a widely grown hybrid species of the genus '' Fragaria'', collectively known as the strawberries, which are cultivated worldwide for their fruit. The fruit is widely ap ...

soybean The soybean, soy bean, or soya bean (''Glycine max'') is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu ...

, lotus,

apple An apple is an edible fruit produced by an apple tree (''Malus domestica''). Apple trees are cultivated worldwide and are the most widely grown species in the genus '' Malus''. The tree originated in Central Asia, where its wild ancest ...

peach The peach (''Prunus persica'') is a deciduous tree first domesticated and cultivated in Zhejiang province of Eastern China. It bears edible juicy fruits with various characteristics, most called peaches and others (the glossy-skinned, n ...

, western poplar (

populus ''Populus'' is a genus of 25–30 species of deciduous flowering plants in the family Salicaceae, native to most of the Northern Hemisphere. English names variously applied to different species include poplar (), aspen, and cottonwood. The we ...

castor bean ''Ricinus communis'', the castor bean or castor oil plant, is a species of perennial flowering plant in the spurge family, Euphorbiaceae. It is the sole species in the monotypic genus, ''Ricinus'', and subtribe, Ricininae. The evolution of ...

tomato The tomato is the edible berry of the plant ''Solanum lycopersicum'', commonly known as the tomato plant. The species originated in western South America, Mexico, and Central America. The Mexican Nahuatl word gave rise to the Spanish word ...

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 Uni ...

grape vine ''Vitis'' (grapevine) is a genus of 79 accepted species of vining plants in the flowering plant family Vitaceae. The genus is made up of species predominantly from the Northern Hemisphere. It is economically important as the source of grapes, ...

, and

chickpea The chickpea or chick pea (''Cicer arietinum'') is an annual legume of the family Fabaceae, subfamily Faboideae. Its different types are variously known as gram" or Bengal gram, garbanzo or garbanzo bean, or Egyptian pea. Chickpea seeds are h ...

. * Polymorphisms 21 polymorphisms have been found in ''Arabidopsis'', including substitutions, insertions, and deletions.

Protein characteristics

Structural motifs

Like the other four PRR proteins found in ''

'', TOC1 is located in the nucleus and employs a pseudo-receiver (PR)

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 * ...

in the

N-terminus The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...

and a CONSTANS, CONSTANS-LIKE, and TOC1 (CCT) domain at the

C-terminus The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein i ...

. Through its CCT domain, TOC1 is able to directly bind DNA, and the PR domain is responsible for transcriptional repression activity.

Functions and interactions

TOC1 binds to the G-box and EE-motif promoter regions of genes involved in both the morning and evening transcription-translation feedback loops that drive the plant circadian clock; these genes include PRR7 and 9, CCA1, and LHY in the morning feedback loop and GI and ELF4 in the evening loop. Discrete induction of TOC1 gene expression results in reduced CCA1 and PRR9 expression, indicating that TOC1 plays a repressive rather than stimulatory role in regulating circadian gene expression. Repression of morning loop genes lhy and cca1 was predicted by computational modeling and was the piece of evidence needed to re-define toc1's role in the plant clock as part of a triple negative-component

model rather than a positive/negative-element system of the sort seen in mammals. The binding pattern of TOC1's CCT domain exhibits circadian oscillations, with maximum binding to G-box and EE motifs—promoter regions that bind transcription factors—occurring at CT15 in the plant's early subjective night. It was shown through the loss of binding rhythms in ''

'' mutants with constitutive TOC1 expression that oscillations in TOC1 binding are regulated by the protein's abundance. TOC1 also appears to be involved in a feedback loop with

abscisic acid Abscisic acid (ABA) is a plant hormone. ABA functions in many plant developmental processes, including seed and bud dormancy, the control of organ size and stomatal closure. It is especially important for plants in the response to environmental s ...

, a key plant hormone involved in development and stress response. '' Arabidopsis '' plants to which varying amounts of ABA were applied showed corresponding differences in TOC1 expression and in circadian period length. Through computational modeling of this feedback loop, TOC1 was shown to be a clock-based influence on patterns of

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 bo ...

opening and closure, which has traditionally been described as a mainly ABA-regulated process.

Post-translational modifications

Over the circadian cycle, TOC1 is differentially

phosphorylated In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...

, with peak phosphorylation occurring during the night. In the highly phosphorylated state, TOC1 has a higher binding affinity to the F-box protein ZEITLUPE (ZTL). In addition to controlling TOC1 - ZTL interactions, phosphorylation of the N-terminus of TOC1 protein increases interaction with PRR3, one of the five PRR proteins found in ''Arabidopsis''. From studies with ztl-1 mutants, which have a single

missense mutation In genetics, a missense mutation is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. It is a type of nonsynonymous substitution. Substitution of protein from DNA mutations Missense m ...

in the kelch domain of the protein and effectively cause a ztl null mutation, TOC1 protein has been found to be stabilized and TOC1 cycling largely eliminated. While phosphorylation of TOC1 protein stabilizes interactions with ZTL, it also increases TOC1's affinity for PRR3. This ultimately protects TOC1 from ZTL-mediated degradation. PRR3 acts as a competitive inhibitor for the ZTL-TOC1 interaction, as binding of TOC1 to PRR3 results in decreased TOC1 substrate availability for ZTL-dependent degradation. This results in an enhanced amplitude of TOC1 cycling, implying that stable TOC1 cycling is dependent upon ZTL degradation in addition to transcriptional regulation controls.

Agricultural use

To most efficiently use environmental resources such as light, plants generally synchronize their circadian rhythms to match the period of the environment. In a study published in 2005, it was shown that plants whose circadian period matched the period of the light-dark cycle in its environment had increased photosynthesis and growth. Using this knowledge, botanists can take advantage of a mutation in the toc1 gene that has been shown to decrease the period of a plant. It is plausible that these toc1 mutants can easily be used to produce plants in a shorter amount of time, with a smaller amount of energy.

References

External links

* {{cite web , url = http://www.wikigenes.org/e/gene/e/836259.html , title = TOC1 - two-component response regulator-like APRR1 , publisher = WikiGenes Chronobiology Arabidopsis thaliana genes