Autonomous clocks: cellular mechanisms, design and function
Classic paradigms of biological time control have so far centered on several major temporal programs, including the CDK-Cyclins that regulate the cell cycle. Our lab’s work has led to the discovery of an organelle clock that initiates and times centriole biogenesis — one that is normally entrained by CDK-Cyclin complexes to run in synchrony with nuclear divisions, but can also operate autonomously when the cell cycle is halted. Along with the recent discovery of a number of other such autonomous cycles, these findings now challenge the textbook view of how the cell cycle works, sparking an emerging community working on autonomous clocks – timing mechanisms that are normally coupled to the cell cycle to achieve successful mitoses, but can run autonomously to execute a variety of physiological roles when the cell cycle is halted erroneously or silenced naturally in post-mitosis.
Our lab’s core mission is to advance this budding field forward, which includes our recent discovery that cytoplasmic divisions can occur in autonomous cycles without the nucleus and mitotic CDK-Cyclin complexes. Building up on this discovery, we are currently pursuing three major questions of biology as described below. Collectively, our efforts promise a fundamental understanding of the very mechanisms that govern time in our cells, organs and bodies.
Towards a paradigm shift in biological time control: A brief introduction to autonomous clocks
How do cells perceive time and use this information in their life cycle? Our understanding of this question has centered around several mechanisms that relay the passage of time, including the CDK/Cyclin complex that times cell divisions. Decades of work helped reveal the mechanism of this complex, with the notion that it acts as a ‘master’ clock for the cell cycle, in which a gradual rise in CDK activity and/or substrate affinity triggers the cell-cycle events. Recent advances, however, have called this textbook view into question, as they reveal ‘autonomous clocks’: timing mechanisms or cycles that are entrained by the cell cycle to run with nuclear divisions, but can also run autonomously to execute specific cellular phenomena.
Autonomous clocks appear to play vital roles in physiology, such as quality control mechanisms to maintain concordant timekeeping, as fail-safe operators when the cell cycle is halted erroneously, or as sub-cellular pacemakers when the cell cycle is silenced in post-mitotic cells. For example, cellular metabolism (e.g. ATP and NADPH production) can undergo autonomous oscillations in proliferating cells. Their coupling with the CDK/Cyclin complexes appears to gate entry into the cell cycle at energetically “right” times. However, such metabolic oscillations can also run autonomously to serve as pacemakers in post mitosis (e.g., in cardiac cells for electrical excitability, or in liver for periodic insulin secretion). As such, decoding principles of autonomous clocks is critical beyond their basic biology, promising impact in physiology or medicine.
Big picture questions that define the state of the field: Our lab’s goals and long-term interests on autonomous clocks
Owing to its nascent state, our knowledge on autonomous clocks is still in its infancy. The design principles of how these clocks operate autonomously remain largely unknown. Similarly, how they can couple to run in synchrony with the cell cycle is unclear. It is also mysterious whether there are designated signaling pathways or mechanisms that help leverage the autonomy of these clocks, to maintain tissue homeostasis in development and adulthood. Guided by these major questions, our research aims to provide potentially generalizable answers to how autonomous clocks operate in cellular physiology.
Research direction #1: What are the molecular mechanisms that underlie autonomous clocks?
Even just the past few years have revealed several major discoveries on autonomous clocks, ranging from one that regulates an autonomous proteostasis cycle, to an organelle clock that controls centriole biogenesis as we were fortunate to discover. These mechanistic works have been largely limited to the insight and fortune of individual groups, in part thanks to the collective knowledge on a defined set of molecules essential to these processes. But how could one tackle the molecular clock that times a specific process, if the process itself is as complex as involving hundreds of gene products? As there are no crystallized guidelines on the biochemical and biophysical principles that govern autonomous clocks, this averts community effort on autonomous clocks and their uncharted roles in physiology and disease. Following up on recent discoveries in our laboratory, we are ambitious to unravelling the autonomous clock that regulates cytoplasmic division cycles independently of the nucleus and CDK/Cyclin complexes.
Research direction #2: How do autonomous cycles couple to run in synchrony with each other and the cell cycle?
Autonomous clocks are somehow coupled with the CDK/Cyclin complexes to run at the pace of nuclear divisions. Our knowledge on how this coupling occurs remains controversial and largely at a theoretical level. Are autonomous clocks peripheral oscillators that are forced to run with a master phase-locker (e.g. the CDK/Cyclin system) via unidirectional interactions? Or alternatively, do autonomous clocks synchronize with the CDKs through bidirectional interactions, to ‘agree’ on a mutual frequency? Unfortunately, how such coupling can be investigated reliably, or what the outcomes would even look like, is not obvious. Similarly, whether the coupling between CDKs and autonomous clocks occur directly, or whether there is a dedicated set of molecules that could act as “cogs” in between remain unclear. We are innovating genetic and optogenetic strategies to test physics-guided experimental frameworks on how autonomous clocks can couple with the CDK/Cyclin complexes. Inspired by this framework, we also take advantage of developmental genetics to discover the “molecular cogs” that help couple an otherwise autonomous cytoplasmic division cycle to nuclear divisions. As other autonomous cycles also couple to run together with nuclear divisions, our efforts set to inspire a new paradigm with which to dissect the cell cycle in physiology and how an erroneous mis-coupling can recapitulate signatures of several diseases in proliferating tissues.
Research direction #3: What roles do autonomous clocks play in development and physiology?
Though normally coupled to CDKs for successful cell divisions, it has become evident that not all instances of uncoupling in autonomous cycles are pathological. Indeed, an induced uncoupling of autonomous cycles can act as quality control and fail-safe operators when the CDK/Cyclin complexes are halted erroneously, or as pace-making programs in post-mitotic tissues where CDK activity is heavily weakened. Despite their physiological significance, the endogenous stressors and signalling mechanisms that induce such uncoupling and help leverage their autonomy to achieve tissue homeostasis remain largely unknown. By tackling a novel class of embryonic epithelial cells that slip mitosis and extrude by an autonomous division of the cytoplasm, we are chasing the molecular logic of how autonomous cycles can generate new types of “cell cycles” to provide cellular plasticity in blastoderm quality control. Since it is increasingly appreciated that the cell cycle is amazingly modular and can take unique forms to serve in tissue homeostasis (e.g., DNA endoreplication cycles of hepatocytes in liver regeneration, amitotic cycles of enterocytes in gut homeostasis, etc.), our endeavor to attempt revealing a molecular basis for such cell cycle plasticity promise broader impact for understanding tissue homeostasis programs more generally in physiology.