Timeless (gene)

Last updated
timeless
Identifiers
Organism D. melanogaster
Symboltim
Entrez 33571
RefSeq (mRNA) NM_164542
RefSeq (Prot) NP_722914
UniProt P49021
Other data
Chromosome 2L: 3.49 - 3.51 Mb
Search for
Structures Swiss-model
Domains InterPro

Timeless (tim) is a gene in multiple species but is most notable for its role in Drosophila for encoding TIM, an essential protein that regulates circadian rhythm. Timeless mRNA and protein oscillate rhythmically with time as part of a transcription-translation negative feedback loop involving the period (per) gene and its protein.

Contents

Discovery

In 1994, timeless was discovered through forward genetic screening performed by Jeffery L. Price while working in the lab of Michael W. Young. [1] This gene was found when they noticed an arrhythmic tim01 mutant via a P element screen. [2] [3] The tim01 mutation caused arrhythmic behavior, defined by the lack of ability to establish proper circadian rhythms. [1] In 1995, the timeless gene was cloned by Amita Sehgal and partners in the lab of Michael W. Young. [4] Unlike the Drosophila timeless gene, homologs have been discovered in other species that are non-essential for circadian rhythm. [5] The discovery of timeless followed the discovery of the period mutants in 1971 through forward genetic screening, the cloning of per in 1984, and an experiment determining that per is circadian in 1990. This occurred during a period of rapid expansion in the field of chronobiology in the 1990s.

Structure

Timeless, N-terminal
Identifiers
SymbolTIMELESS
Pfam PF04821
InterPro IPR006906
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 5MQI

The length of the coding region of the Drosophila timeless gene is 4029 base pairs, from which a 1398 amino acid protein is transcribed. [6] The gene starts at a consensus cap site upstream of a methionine codon. It contains 11 exons and 10 introns. In various Drosophila species, the timeless protein TIM contains more highly conserved functional domains and amino acid sequence than its counterpart, PER (protein encoded by per). CLD was the least conserved of these regions between D. virilis and D. melanogaster. [6] These conserved parts include: the PER interaction domain, the nuclear localization signal (NLS), cytoplasmic localization domain (CLD), N-terminal end (non-functional), and C-terminal end. [6] TIM is also known to have a basic region, which interacts with the PAS domain of the PER protein, and a central acidic region. There is also a region of unknown function near the N-terminus of the TIM protein that contains a 32 amino acid sequence that, when deleted, causes arrhythmic behavior in the fly. In various species of Drosophila, such as D. virilis and D. melanogaster, the initiating methionine for translation of the timeless gene into TIM is in different places, with the D. virilis start site downstream of the start site in D. melanogaster. [6]

Timeless homologs

timeout
Identifiers
Organism Drosophila melanogaster
Symboltim-2
UniProt Q8INH7
Search for
Structures Swiss-model
Domains InterPro
Timeout, C-terminal (PAB)
4XHT asyr r 250.jpg
Human TIMELESS PAB
Identifiers
SymbolTIMELESS_C
Pfam PF05029
InterPro IPR006906
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 4XHT

Drosophila homolog

The timeless gene is an essential component of the molecular circadian clock in Drosophila. [3] It acts as part of an autoregulatory feedback loop in conjunction with the period (per) gene product as noted in collaborative studies performed by the labs of Michael W. Young and Amita Sehgal. [7] Further studies by the labs of Young, Sehgal, Charles Weitz, and Michael Rosbash indicated that timeless protein (TIM) and period protein (PER) form a heterodimer that exhibits circadian rhythms in wild type Drosophila. [8] [9] Researchers in Rosbash's lab also showed that tim mRNA levels and TIM protein levels have circadian rhythms that are similar to those of the period (per) mRNA and its product. [8] [10] [11] Experiments done jointly by the Weitz, Young, and Sehgal labs using yeast 2-hybrid proved that TIM directly binds with PER. [12] During the early evening, PER and TIM dimerize and accumulate. Late at night, the dimer travels into the nucleus to inhibit per and tim transcription. In 1996, the teams of Sehgal, Edery, and Young found that exposure to light leads to the degradation of TIM and subsequently PER. [1] [11] [13]

The PER/TIM heterodimer negatively regulates transcription of period (per) and timeless (tim) genes. Within this negative feedback loop, first the PER/TIM heterodimers form in the cytoplasm, accumulate, and then translocate to the nucleus. [14] The complex then blocks the positive transcription factors clock (CLK) and cycle (CYC), thereby repressing the transcription of per.

As part of the circadian clock, timeless is essential for entrainment to light-dark (LD) cycles. The typical period length of free-running Drosophila is 23.9 hours, requiring adaptations to the 24-hour environmental cycle. [15] Adaptation first begins with exposure to light. This process leads to the rapid degradation of the TIM protein, allowing organisms to entrain at dawn to environmental cycles. [16]

Circadian clock of drosophila Circadian clock of drosophila.PNG
Circadian clock of drosophila

In light-dark cycles, TIM protein level decreases rapidly in late night/early morning, followed by the similar but more gradual changes in PER protein level. TIM degradation is independent of per and its protein, and releases PER from the PER/TIM complex. [8] In some cell types, the photoreceptor protein cryptochrome (CRY) physically associates with TIM and helps regulate light-dependent degradation. CRY is activated by blue light, which binds to TIM and tags it for degradation. [17] This ends the PER/TIM repression of the CLK/CYC-mediated transcription of per and tim genes, allowing per and tim mRNA to be produced to restart the cycle. [8]

This mechanism allows entrainment of flies to environmental light cues. When Drosophila receive light inputs in the early subjective night, light-induced TIM degradation causes a delay in TIM accumulation, which creates a phase delay. [17] When light inputs are received in the late subjective night, a light pulse causes TIM degradation to occur earlier than under normal conditions, leading to a phase advance. [17]

In Drosophila, the negative regulator PER, from the PER/TIM complex, is eventually degraded by a casein kinase-mediated phosphorylation cycle, allowing fluctuations in gene expression according to environmental cues. These proteins mediate the oscillating expression of the transcription factor VRILLE (VRI), which is required for behavioral rhythmicity, per and tim expression, and accumulation of PDF (pigment-dispersing factor). [16]

Gryllus bimaculatus (two-spotted cricket) homolog

Timeless does not appear to be essential for oscillation of the circadian clock for all insects. In wild type Gryllus bimaculatus,tim mRNA shows rhythmic expression in both LD and DD (dark-dark cycles) similar to that of per, peaking during the subjective night. When injected with tim double-stranded RNA (dstim), tim mRNA levels were significantly reduced and its circadian expression rhythm was eliminated. After the dstim treatment, however, adult crickets showed a clear locomotor rhythm in constant darkness, with a free-running period significantly shorter than that of control crickets injected with Discosoma sp. Red2 (DsRed2) dsRNA. These results suggest that in the cricket, tim plays some role in fine-tuning of the free-running period but may not be essential for oscillation of the circadian clock. [5]

Mammalian homolog

In 1998, researchers identified a mouse homolog and a human homolog of the Drosophilatimeless gene. [18] The exact role of TIM in mammals is still unclear,. Recent work on the mammalian timeless (mTim) in mice has suggested that the gene may not play the same essential role in mammals as in Drosophila as a necessary function of the circadian clock. [19] While Tim is expressed in the Suprachiasmatic Nucleus (SCN) which is thought to be the primary oscillator in humans, its transcription does not oscillate rhythmically in constant conditions, and the TIM protein remains in the nucleus. [19] [20]

Circadian clock of mammals Circadian clock of mammals.PNG
Circadian clock of mammals

However, mTim is shown to be necessary for embryonic development in mice, indicating a different gene function than in Drosophila. This suggests a divergence between mammalian clocks and the Drosophila clock. [19] Moreover, mammalian tim is more orthologous to the Tim-2 (Timeout) paralog of the DrosophilaTimeless gene than the actual gene itself. [21] Like tim-2, the mammalian orthologs has a C-terminal PARP1-binding (PAB) domain. The complex they from promotes homologous recombination DNA repair. [22]

The timeless protein is thought to directly connect the cell cycle with the circadian rhythm in mammals. In this model. referred to as a “direct coupling,” [23] the two cycles share a key protein whose expression exhibits a circadian pattern. The essential role of Tim in Drosophila in creating circadian rhythm is accomplished by Cry in mammals. In mammals, Cry and Per transcription is activated by the CLOCK/BMAL1 complex, and repressed by the PER/CRY complex. [24]

Humans

timeless homolog (Human)
Identifiers
SymbolTIMELESS
Alt. symbolshTIM
NCBI gene 8914
HGNC 11813
OMIM 603887
RefSeq NM_003920
UniProt Q9UNS1
Other data
Locus Chr. 12 q12-q13
Search for
Structures Swiss-model
Domains InterPro

The human timeless protein (hTIM) has been shown to be required for the production of electrical oscillations output by the suprachiasmatic nucleus (SCN), the major clock governing all tissue-specific circadian rhythms of the body. [25] This protein also interacts with the products of major clock genes CLOCK, BMAL, PER1, PER2 and PER3.

Sancar and colleagues investigated whether hTIM played a similar role to orthologs in C. elegans and types of yeast, which are known to play important roles in the cell cycle. [23] Their experiments suggested that hTIM plays an integral role in the G2/M and intra-S cell cycle checkpoints. [23] With respect to the G2/M checkpoint, hTIM binds to the ATRIP subunit on ATR – a protein kinase sensitive to DNA damage. This binding between hTIM and ATR then leads to the phosphorylation of Chk1, resulting in cell cycle arrest or apoptosis. [23] This process serves as an important control to stop the proliferation of cells with DNA damage prior to mitotic division. The role of hTIM in the intra-S checkpoint is less clear at the molecular level; however, down-regulation of hTIM leads to an increase in the rate of generation of replication forks – even in the presence of DNA damage and other regulatory responses. [23]

Current research

The Timeless gene has also been found to influence the development of disease in humans. Downregulation of the timeless gene in human carcinoma cells leads to shortened telomeres, indicating its role in telomere length maintenance. Telomere-associated DNA damage also increases in timeless depleted cells, along with the delay of telomere replication. Swi1 is a timeless-related protein that is required for DNA replication in the telomere region. [26] This association between timeless and telomeres is indicative of the gene's possible association with cancer. [27]

A single nucleotide polymorphism substitution that results in the transformation of glutamine to arginine in the amino acid sequence in the human timeless gene shows no association with either morningness or eveningness tendencies in humans. [28] This is consistent with other research, suggesting that htim is not important in the circadian rhythm of humans.

Timeless is now frequently found to be overexpressed in many different tumor types. In a study that used Timeless-targeting siRNA oligos, followed by a whole-genome expression microarray as well as network analysis. Further testing of Timeless down-regulation on cell proliferation rates of a cervical and breast cancer cell line. It was found that elevated expression of Timeless was significantly associated with more advanced tumor stage and poorer breast cancer prognosis. [29] Similarity in gene expression signatures has allowed for TIMELESS to be identified as Kinase Suppressor of Ras-1 (KSR1)-like and a potential target required for cancer cell survival. TIMELESS overexpression represents a vulnerability in Ras-driven tumors that offers potential insight into novel and selective targets found in Ras-driven cancers, which can be leveraged to develop selective and more effective therapeutics. [30]

See also

Related Research Articles

A circadian clock, or circadian oscillator, also known as one’s internal alarm clock is a biochemical oscillator that cycles with a stable phase and is synchronized with solar time.

<span class="mw-page-title-main">Cryptochrome</span> Class of photoreceptors in plants and animals

Cryptochromes 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 in a number of species. The name cryptochrome was proposed as a portmanteau combining the chromatic nature of the photoreceptor, and the cryptogamic organisms on which many blue-light studies were carried out.

<span class="mw-page-title-main">CLOCK</span> Human protein and coding gene

CLOCK is a gene encoding a basic helix-loop-helix-PAS transcription factor that is known to affect both the persistence and period of circadian rhythms.

Period (per) is a gene located on the X chromosome of Drosophila melanogaster. Oscillations in levels of both per transcript and its corresponding protein PER have a period of approximately 24 hours and together play a central role in the molecular mechanism of the Drosophila biological clock driving circadian rhythms in eclosion and locomotor activity. Mutations in the per gene can shorten (perS), lengthen (perL), and even abolish (per0) the period of the circadian rhythm.

<span class="mw-page-title-main">Period circadian protein homolog 1</span> Protein-coding gene in the species Homo sapiens

Period circadian protein homolog 1 is a protein in humans that is encoded by the PER1 gene.

<span class="mw-page-title-main">Basic helix-loop-helix ARNT-like protein 1</span> Human protein and coding gene

Basic helix-loop-helix ARNT-like protein 1 or aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL), or brain and muscle ARNT-like 1 is a protein that in humans is encoded by the BMAL1 gene on chromosome 11, region p15.3. It's also known as MOP3, and, less commonly, bHLHe5, BMAL, BMAL1C, JAP3, PASD3, and TIC.

In molecular biology, an oscillating gene is a gene that is expressed in a rhythmic pattern or in periodic cycles. Oscillating genes are usually circadian and can be identified by periodic changes in the state of an organism. Circadian rhythms, controlled by oscillating genes, have a period of approximately 24 hours. For example, plant leaves opening and closing at different times of the day or the sleep-wake schedule of animals can all include circadian rhythms. Other periods are also possible, such as 29.5 days resulting from circalunar rhythms or 12.4 hours resulting from circatidal rhythms. Oscillating genes include both core clock component genes and output genes. A core clock component gene is a gene necessary for to the pacemaker. However, an output oscillating gene, such as the AVP gene, is rhythmic but not necessary to the pacemaker.

<i>Cycle</i> (gene)

Cycle (cyc) is a gene in Drosophila melanogaster that encodes the CYCLE protein (CYC). The Cycle gene (cyc) is expressed in a variety of cell types in a circadian manner. It is involved in controlling both the sleep-wake cycle and circadian regulation of gene expression by promoting transcription in a negative feedback mechanism. The cyc gene is located on the left arm of chromosome 3 and codes for a transcription factor containing a basic helix-loop-helix (bHLH) domain and a PAS domain. The 2.17 kb cyc gene is divided into 5 coding exons totaling 1,625 base pairs which code for 413 aminos acid residues. Currently 19 alleles are known for cyc. Orthologs performing the same function in other species include ARNTL and ARNTL2.

Doubletime (DBT), also known as discs overgrown (DCO), is a gene that encodes the doubletime protein in fruit flies. Michael Young and his team at Rockefeller University first identified and characterized the gene in 1998.

<span class="mw-page-title-main">Michael Rosbash</span> American geneticist and chronobiologist (born 1944)

Michael Morris Rosbash is an American geneticist and chronobiologist. Rosbash is a professor and researcher at Brandeis University and investigator at the Howard Hughes Medical Institute. Rosbash's research group cloned the Drosophila period gene in 1984 and proposed the Transcription Translation Negative Feedback Loop for circadian clocks in 1990. In 1998, they discovered the cycle gene, clock gene, and cryptochrome photoreceptor in Drosophila through the use of forward genetics, by first identifying the phenotype of a mutant and then determining the genetics behind the mutation. Rosbash was elected to the National Academy of Sciences in 2003. Along with Michael W. Young and Jeffrey C. Hall, he was awarded the 2017 Nobel Prize in Physiology or Medicine "for their discoveries of molecular mechanisms controlling the circadian rhythm".

<span class="mw-page-title-main">Michael W. Young</span> American biologist and geneticist (born 1949)

Michael Warren Young is an American biologist and geneticist. He has dedicated over three decades to research studying genetically controlled patterns of sleep and wakefulness within Drosophila melanogaster.

Amita Sehgal is a molecular biologist and chronobiologist in the Department of Neuroscience at the Perelman School of Medicine at the University of Pennsylvania. Sehgal was involved in the discovery of Drosophila TIM and many other important components of the Drosophila clock mechanism. Sehgal also played a pivotal role in the development of Drosophila as a model for the study of sleep. Her research continues to be focused on understanding the genetic basis of sleep and also how circadian systems relate to other aspects of physiology.

Hitoshi Okamura is a Japanese scientist who specializes in chronobiology. He is currently a professor of Systems Biology at Kyoto University Graduate School of Pharmaceutical Sciences and the Research Director of the Japan Science Technology Institute, CREST. Okamura's research group cloned mammalian Period genes, visualized clock oscillation at the single cell level in the central clock of the SCN, and proposed a time-signal neuronal pathway to the adrenal gland. He received a Medal of Honor with Purple Ribbon in 2007 for his research and was awarded Aschoff's Ruler for his work on circadian rhythms in rodents. His lab recently revealed the effects of m6A mRNA methylation on the circadian clock, neuronal communications in jet lag, and the role of dysregulated clocks in salt-induced hypertension.

Jeffrey L. Price is an American researcher and author in the fields of circadian rhythms and molecular biology. His chronobiology work with Drosophila melanogaster has led to the discoveries of the circadian genes timeless (tim) and doubletime (dbt), and the doubletime regulators spaghetti (SPAG) and bride of doubletime (BDBT).

Paul Hardin is an American scientist in the field of chronobiology and a pioneering researcher in the understanding of circadian clocks in flies and mammals. Hardin currently serves as a distinguished professor in the biology department at Texas A&M University. He is best known for his discovery of circadian oscillations in the mRNA of the clock gene Period (per), the importance of the E-Box in per activation, the interlocked feedback loops that control rhythms in activator gene transcription, and the circadian regulation of olfaction in Drosophila melanogaster. Born in a suburb of Chicago, Matteson, Illinois, Hardin currently resides in College Station, Texas, with his wife and three children.

<i>Drosophila</i> circadian rhythm

Drosophila circadian rhythm is a daily 24-hour cycle of rest and activity in the fruit flies of the genus Drosophila. The biological process was discovered and is best understood in the species Drosophila melanogaster. Many behaviors are under circadian control including eclosion, locomotor activity, feeding, and mating. Locomotor activity is maximum at dawn and dusk, while eclosion is at dawn.

Transcription-translation feedback loop (TTFL) is a cellular model for explaining circadian rhythms in behavior and physiology. Widely conserved across species, the TTFL is auto-regulatory, in which transcription of clock genes is regulated by their own protein products.

dClock (clk) is a gene located on the 3L chromosome of Drosophila melanogaster. Mapping and cloning of the gene indicates that it is the Drosophila homolog of the mouse gene CLOCK (mClock). The Jrk mutation disrupts the transcription cycling of per and tim and manifests dominant effects.

Ravi Allada is an Indian-American chronobiologist studying the circadian and homeostatic regulation of sleep primarily in the fruit fly Drosophila. He is currently the Executive Director of the Michigan Neuroscience Institute (MNI), a collective which connects neuroscience investigators across the University of Michigan to probe the mysteries of the brain on a cellular, molecular, and behavioral level. Working with Michael Rosbash, he positionally cloned the Drosophila Clock gene. In his laboratory at Northwestern, he discovered a conserved mechanism for circadian control of sleep-wake cycle, as well as circuit mechanisms that manage levels of sleep.

Charles J. Weitz is a chronobiologist and neurobiologist whose work primarily focuses on studying the molecular biology and genetics of circadian clocks.

References

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  11. 1 2 Myers MP, Wager-Smith K, Rothenfluh-Hilfiker A, Young MW (March 1996). "Light-induced degradation of TIMELESS and entrainment of the Drosophila circadian clock". Science. 271 (5256): 1736–40. Bibcode:1996Sci...271.1736M. doi:10.1126/science.271.5256.1736. PMID   8596937. S2CID   6811496.
  12. ↑ Brody TB. "Gene name - timeless". Interactive Fly, Drosophila. Society for Developmental Biology. Retrieved 9 April 2015.
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  18. ↑ Koike N, Hida A, Numano R, Hirose M, Sakaki Y, Tei H (Dec 1998). "Identification of the mammalian homologues of the Drosophila timeless gene, Timeless1". FEBS Letters. 441 (3): 427–431. doi:10.1016/S0014-5793(98)01597-X. PMID   9891984. S2CID   32212533.
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  20. ↑ Young MW, Kay SA (Sep 2001). "Time zones: a comparative genetics of circadian clocks". Nature Reviews Genetics. 2 (9): 702–715. doi:10.1038/35088576. PMID   11533719. S2CID   13286388.
  21. ↑ Benna C, Scannapieco P, Piccin A, Sandrelli F, Zordan M, Rosato E, Kyriacou CP, Valle G, Costa R (Jul 2000). "A second timeless gene in Drosophila shares greater sequence similarity with mammalian tim". Current Biology. 10 (14): R512–R513. Bibcode:2000CBio...10.R512B. doi: 10.1016/S0960-9822(00)00594-7 . PMID   10899011. S2CID   36451473.
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  24. ↑ Gustafson CL, Partch CL (January 2015). "Emerging models for the molecular basis of mammalian circadian timing". Biochemistry. 54 (2): 134–49. doi:10.1021/bi500731f. PMC   4303291 . PMID   25303119.
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  26. ↑ Gadaleta MC, González-Medina A, Noguchi E (November 2016). "Timeless protection of telomeres". Current Genetics. 62 (4): 725–730. doi:10.1007/s00294-016-0599-x. PMC   5056121 . PMID   27068713.
  27. ↑ Leman AR, Dheekollu J, Deng Z, Lee SW, Das MM, Lieberman PM, Noguchi E (June 2012). "Timeless preserves telomere length by promoting efficient DNA replication through human telomeres". Cell Cycle. 11 (12): 2337–47. doi:10.4161/cc.20810. PMC   3383593 . PMID   22672906.
  28. ↑ Pedrazzoli M, Ling L, Finn L, Kubin L, Young T, Katzenberg D, Mignot E (2000). "A polymorphism in the human timeless gene is not associated with diurnal preferences in normal adults". Sleep Research Online. 3 (2): 73–6. PMID   11382904.
  29. ↑ Mao Y, Fu A, Leaderer D, Zheng T, Chen K, Zhu Y (October 2013). "Potential cancer-related role of circadian gene TIMELESS suggested by expression profiling and in vitro analyses". BMC Cancer. 13: 498. doi: 10.1186/1471-2407-13-498 . PMC   3924353 . PMID   24161199.
  30. ↑ Clymer BK, Fisher KW, Kelly DL, White MA, Lewis RE (2016-07-22). "Abstract 1252: TIMELESS is a KSR1-like effector of Ras-driven colon tumorigenesis". Cancer Research. 76 (14 Supplement): 1252. doi:10.1158/1538-7445.am2016-1252.

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