Transcription translation feedback loop

Widely conserved across species, the TTFL is auto-regulatory, in which transcription of clock genes is regulated by their own protein products.

For example, French astronomer Jean-Jacques d’Ortous de Mairan noted the periodic 24-hour movement of Mimosa plant leaves as early as 1729.

However, science has only recently begun to uncover the cellular mechanisms responsible for driving observed circadian rhythms.

The cellular basis of circadian rhythms is supported by the fact that rhythms have been observed in single-celled organisms[1] Beginning in the 1970s, experiments conducted by Ron Konopka and colleagues, in which forward genetic methods were used to induce mutation, revealed that Drosophila melanogaster specimens with altered period (Per) genes also demonstrated altered periodicity.

Subsequent major discoveries confirmed this model; notably experiments led by Thomas K. Darlington and Nicholas Gekakis in the late 1990s that identified clock proteins and characterized their methods in Drosophila and mice, respectively.

These experiments gave rise to the transcription-translation feedback loop (TTFL) model that has now become the dominant paradigm for explaining circadian behavior in a wide array of species.

[4] Once enough modified protein products accumulate in the cytoplasm, they are transported into the nucleus where they inhibit the positive element from the promoter to stop transcription of clock genes.

The clock gene is thus transcribed at low levels until its protein products are degraded, allowing for positive regulatory elements to bind to the promoter and restart transcription.

[7] During the night, TIM and PER are able to form heterodimers and accumulate slowly in the cytoplasm, where PER is phosphorylated by the kinase DOUBLETIME (DBT).

The post-transcriptional modification of multiple phosphate groups both targets the complex for degradation and facilitates nuclear localization.

Once PER and TIM degrade, CYC-CLK dimers are able to bind the E-boxes again to initiate transcription, closing the negative feedback loop.

CLOCKWORK ORANGE (CWO) binds the E-boxes to act as a direct competitor of CYC-CLK, therefore inhibiting transcription.

[8] Cryptochrome in Drosophila is a blue-light photoreceptor that triggers degradation of TIM, indirectly leading to the clock phase being reset and the renewed promotion of per expression.

The way the mammalian system works is that BMAL1 forms a heterodimer with CLOCK to initiate transcription of mPer and cryptochrome (cry).

In the nucleus, PER-CRY negatively regulates the transcription of their cognate genes by binding BMAL1-CLOCK and causing their release from the E-box promoter.

[9] The first TTFL model was proposed for Arabidopsis thaliana in 2001 and included two MYB transcription factors, LATE ELONGATED HYPOCOTYL (LHY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), and TIMING OF CAB EXPRESSION 1 (TOC1).

[12] Post-translational feedback loops (PTFLs) involved in clock gene regulation have also been uncovered, often working in tandem with the TTFL model.

In both mammals and plants, post-translational modifications such as phosphorylation and acetylation regulate the abundance and/or activity of clock genes and proteins.

This three-protein post-translational system is widely accepted to be the core oscillator, both necessary and sufficient to drive daily rhythms.

Figure shows the Drosophila melanogaster TTFL and their general interactions between the main players. In this case we can see how CLK and CYC are the positive regulators (yellow and green) and PER and TIM are the negative (red and blue) regulators that each play a role in the circadian clock.
Figure shows the mammalian TTFL and the general interactions between the main players. This shows how PER and CRY both are negative regulators (red arrows) for BMAL1 and CLOCK, since they cause inhibition of BMAL1 and CLOCK by preventing transcription. BMAL1 and CLOCK (green arrows) are positive regulators since they encourage the transcription, and later the translation of PER and CRY.
Overview of the Neurospora TTFL and the general interactions between the regulators. In this case WC-1 and WC-2 (red) are seen as the positive elements where they come together to encourage transcription of FRQ. FRQ (green) is the negative regulator which after translation, comes back as negative feedback.
Figure shows the TTFL of plants ( Arabidopsis ). This shows how the different regulators function and how this still qualifies to be a TTFL because of the feedback loops that occur.