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Timing of CAB expression 1 is a
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
that in ''
Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally ...
'' is encoded by the TOC1
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
. 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 (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
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 the ...
, 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 that directly inhibits transcription of morning loop genes LHY and CCA1. 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 reporter, firefly ( 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'' (), from Ancient Greek δρόσος (''drósos''), meaning "dew", and φίλος (''phílos''), meaning "loving", is a genus of fly, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or p ...
'' 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 repressilator—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) ''
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 ...
'' mutants with constitutive (always turned on) toc1
gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...
, 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, papaya,
cucumber The cucumber (''Cucumis sativus'') is a widely-cultivated creeping vine plant in the family Cucurbitaceae that bears cylindrical to spherical fruits, which are used as culinary vegetables.strawberry The garden strawberry (or simply strawberry; ''Fragaria × ananassa'') is a widely grown Hybrid (biology), hybrid plant cultivated worldwide for its fruit. The genus ''Fragaria'', the strawberries, is in the rose family, Rosaceae. The fruit ...
,
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. Soy is a staple crop, the world's most grown legume, and an important animal feed. Soy is a key source o ...
, lotus,
apple An apple is a round, edible fruit produced by an apple tree (''Malus'' spp.). Fruit trees of the orchard or domestic apple (''Malus domestica''), the most widely grown in the genus, are agriculture, cultivated worldwide. The tree originated ...
,
peach The peach (''Prunus persica'') is a deciduous tree first domesticated and Agriculture, cultivated in China. It bears edible juicy fruits with various characteristics, most called peaches and the glossy-skinned, non-fuzzy varieties called necta ...
, 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,
tomato The tomato (, ), ''Solanum lycopersicum'', is a plant whose fruit is an edible Berry (botany), berry that is eaten as a vegetable. The tomato is a member of the nightshade family that includes tobacco, potato, and chili peppers. It originate ...
,
potato The potato () is a starchy tuberous vegetable native to the Americas that is consumed as a staple food in many parts of the world. Potatoes are underground stem tubers of the plant ''Solanum tuberosum'', a perennial in the nightshade famil ...
,
grape vine ''Vitis'' (grapevine) is a genus of 81 accepted species of vining plants in the flowering plant family Vitaceae. The genus consists of species predominantly from the Northern Hemisphere. It is economically important as the source of grapes, bot ...
, and
chickpea The chickpea or chick pea (''Cicer arietinum'') is an annual plant, annual legume of the family (biology), family Fabaceae, subfamily Faboideae, cultivated for its edible seeds. Its different types are variously known as gram," Bengal gram, ga ...
. * 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 ''
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 ...
'', TOC1 is located in the nucleus and employs a pseudo-receiver (PR) domain 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 amin ...
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, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein Proteins are large biomolecules and macromolecules that comp ...
. Through its CCT domain, TOC1 is able to directly bind
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
, 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 repressilator 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 ''
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 ...
'' 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 or abscisin II) 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 ...
, 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 (: stomata, from Greek language, Greek ''στόμα'', "mouth"), also called a stomate (: stomates), is a pore found in the Epidermis (botany), epidermis of leaves, stems, and other organs, that controls the rate of gas exc ...
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, 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. Missense mutations change amino acids, which in turn alt ...
in the kelch domain of the protein and effectively cause a ztl
null mutation A null allele is a nonfunctional allele (a variant of a gene) caused by a genetic mutation. Such mutations can cause a complete lack of production of the associated gene product or a product that does not function properly; in either case, the al ...
, 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 Circadian rhythm Arabidopsis thaliana genes