Intrinsic timekeeping in Escherichia coli
Authors: A. A. Crofts, A. Bates, J. S. Takahashi, L. V. Hooper
Abstract
Circadian clocks allow organisms to anticipate predictable environmental changes across the day-night cycle. Here we show that the bacterium Escherichia coli exhibits intrinsic timekeeping that anticipates daily temperature cycles. E. coli biofilms entrained to daily temperature shifts, producing 24-hour rhythms in curli plaque formation that persisted under constant temperature. Mechanistically, genetic analyses localized the autonomous timing machinery to the Rcs phosphorelay, which exhibits structural and conceptual parallels with other circadian systems. The BluFR sensory pathway, which acts upstream of the Rcs phosphorelay, linked temperature and blue-light cycles to rhythmic curli production. Flagellar promoter activity and curli production peaked at opposite times of day, suggesting daily coordination of adhesion and motility programs. These findings identify an intrinsic timing system in E. coli that expands our understanding of biological timekeeping.
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Closest papers
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The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systemsFrancesca Sartor, Xin-Ming Xu, T. Popp et al. · 2023 · Science Advances · cited 26 times · Not summarized yet
The study characterizes blue- and red-light entrainment and clock properties in Bacillus subtilis, providing a bacterial comparison to E. coli temperature-driven timekeeping.
Abstract
Circadian clocks are pervasive throughout nature, yet only recently has this adaptive regulatory program been described in nonphotosynthetic bacteria. Here, we describe an inherent complexity in the Bacillus subtilis circadian clock. We find that B. subtilis entrains to blue and red light and that circadian entrainment is separable from masking through fluence titration and frequency demultiplication protocols. We identify circadian rhythmicity in constant light, consistent with the Aschoff’s rule, and entrainment aftereffects, both of which are properties described for eukaryotic circadian clocks. We report that circadian rhythms occur in wild isolates of this prokaryote, thus establishing …
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Structure, function, and mechanism of the core circadian clock in cyanobacteriaJ. Swan, S. Golden, A. LiWang et al. · 2018 · Journal of Biological Chemistry · cited 84 times · Not summarized yet
The review explains the cyanobacterial KaiABC clock whose proteins provide the structural comparison for E. coli Rcs signaling.
Abstract
Circadian rhythms enable cells and organisms to coordinate their physiology with the cyclic environmental changes that come as a result of Earth's light/dark cycles. Cyanobacteria make use of a post-translational oscillator to maintain circadian rhythms, and this elegant system has become an important model for circadian timekeeping mechanisms. Composed of three proteins, the KaiABC system undergoes an oscillatory biochemical cycle that provides timing cues to achieve a 24-h molecular clock. Together with the input/output proteins SasA, CikA, and RpaA, these six gene products account for the timekeeping, entrainment, and output signaling functions in cyanobacterial circadian rhythms. This Mi…
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Entrainment of the Circadian Clock of the Enteric Bacterium Klebsiella aerogenes by Temperature CyclesJ. Paulose, Charles V. Cassone, Kinga B. Graniczkowska et al. · 2019 · iScience · cited 47 times · Not summarized yet
The study tests whether temperature cycles entrain an endogenous circadian rhythm in a gut bacterium, using swarming motility rather than E. coli curli production.
Abstract
Summary The gastrointestinal bacterium Klebsiella (née Enterobacter) aerogenes expresses an endogenously generated, temperature-compensated circadian rhythm in swarming motility. We hypothesized that this rhythm may be synchronized/entrained in vivo by body temperature (TB). To determine entrainment, cultures expressing bioluminescence were exposed to temperature cycles of 1°C (35°C–36°C) or 3°C (34°C–37°C) in amplitude at periods (T-cycles) of T = 22, T = 24, or T = 28 h. Bacteria entrained to all T-cycles at both amplitudes and with stable phase relationships. A high-amplitude phase response curve (PRC) in response to 1-h pulses of 3°C temperature spike (34°C–37°C) at different circadian p…
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Transplantability of a circadian clock to a noncircadian organismAnna H. Chen, David Lubkowicz, Vivian Yeong et al. · 2015 · Science Advances · cited 34 times · Not summarized yet
The study reconstructs the KaiABC oscillator in E. coli and measures circadian reporter rhythms, applying an engineered clock rather than examining intrinsic E. coli timing.
Abstract
Researchers have reconstructed a circadian clock that can function by itself in a living, non-circadian bacteria. Circadian oscillators are posttranslationally regulated and affect gene expression in autotrophic cyanobacteria. Oscillations are controlled by phosphorylation of the KaiC protein, which is modulated by the KaiA and KaiB proteins. However, it remains unclear how time information is transmitted to transcriptional output. We show reconstruction of the KaiABC oscillator in the noncircadian bacterium Escherichia coli. This orthogonal system shows circadian oscillations in KaiC phosphorylation and in a synthetic transcriptional reporter. Coexpression of KaiABC with additional native c…
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Rhythmic Timekeeping in Rice: Emerging Mechanisms and Regulatory Networks.Samantha J. Cordingley, Dawn H. Nagel · 2026 · Plant and Cell Physiology · Not summarized yet
The review surveys rice circadian mechanisms and regulatory networks, rather than bacterial timekeeping.
Abstract
The circadian clock is an endogenous time-keeping mechanism found in most eukaryotes that integrates external signals to synchronize biological processes with the environment. Circadian and diel rhythms across multiple regulatory layers help coordinate gene expression underlying plant processes such as metabolism, stress responses, and agronomic traits. In the context of a changing environment, a comprehensive understanding of how circadian-mediated regulatory mechanisms can contribute to plant resilient strategies continues to be a priority. In this mini review, we highlight the pleiotropic functions of the rice circadian clock in coordinating diverse processes.
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The critical human pathogen Acinetobacter baumannii exhibits light-regulated circadian rhythmsValentín Permingeat, Bárbara Edith Perez Mora, M. Migliori et al. · 2025 · Communications Biology · cited 4 times · Not summarized yet
The study tests endogenous circadian rhythms and light regulation in Acinetobacter baumannii, another bacterium whose rhythms respond to environmental cues.
Abstract
Acinetobacter baumannii is recognized as the paradigm of multidrug-resistant superbug, topping the WHO priority list of critical human pathogens. Interestingly, it senses and responds to blue light, which modulates global aspects of its physiology, including pathogenicity. We hypothesized that light could serve as a signal to synchronize the bacterial physiology to the host’s behavior and/or to the environment. At environmental temperatures, light regulation is mainly governed by the photoreceptor BlsA. In this work, we identified the existence of daily rhythms in blsA promoter activity displaying a robust response to light, as well as endogenous circadian rhythms in A. baumannii. In fact, w…
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From phenomenon to mechanism in the circadian clock of Synechococcus elongatusSusan S. Golden · 2026 · npj Biological Timing and Sleep · Not summarized yet
The account describes the KaiABC oscillator and its structural dynamics, providing context for the paper’s comparison of Rcs proteins with cyanobacterial clock proteins.
Abstract
Creative and collaborative research in the early 21st century revealed the mechanistic secrets of the cyanobacterial circadian clock, a nanomachine whose function can be studied in vitro. The structural dynamics of the Synechococcus elongatus circadian oscillator, comprising KaiA, KaiB, and KaiC, establish a near 24 h cycle of activity of the global transcription regulator RpaA by rhythmically changing the interaction platform of kinases that control RpaA phosphorylation.
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Endogenous clock-mediated regulation of intracellular oxygen dynamics is essential for diazotrophic growth of unicellular cyanobacteriaA. Bandyopadhyay, Annesha Sengupta, T. Elvitigala et al. · 2024 · Nature Communications · cited 16 times · Not summarized yet
The study links a cyanobacterial circadian clock to intracellular oxygen rhythms and nitrogen-fixing growth, addressing clock-controlled physiology in another bacterium.
Abstract
The discovery of nitrogen fixation in unicellular cyanobacteria provided the first clues for the existence of a circadian clock in prokaryotes. However, recalcitrance to genetic manipulation barred their use as model systems for deciphering the clock function. Here, we explore the circadian clock in the now genetically amenable Cyanothece 51142, a unicellular, nitrogen-fixing cyanobacterium. Unlike non-diazotrophic clock models, Cyanothece 51142 exhibits conspicuous self-sustained rhythms in various discernable phenotypes, offering a platform to directly study the effects of the clock on the physiology of an organism. Deletion of kaiA, an essential clock component in the cyanobacterial syste…
Prior work it builds on
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Physiology of circadian entrainment.D. Golombek, R. Rosenstein · 2010 · Physiological Reviews · cited 1,057 times · Not summarized yet
The review covers mechanisms of photic entrainment in mammalian circadian rhythms, a broader account of how environmental cues synchronize clocks.
Abstract
Mammalian circadian rhythms are controlled by endogenous biological oscillators, including a master clock located in the hypothalamic suprachiasmatic nuclei (SCN). Since the period of this oscillation is of approximately 24 h, to keep synchrony with the environment, circadian rhythms need to be entrained daily by means of Zeitgeber ("time giver") signals, such as the light-dark cycle. Recent advances in the neurophysiology and molecular biology of circadian rhythmicity allow a better understanding of synchronization. In this review we cover several aspects of the mechanisms for photic entrainment of mammalian circadian rhythms, including retinal sensitivity to light by means of novel photopi…
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PAS dimerization at the nexus of the mammalian circadian clockDiksha Sharma, C. Partch · 2023 · Journal of Molecular Biology · cited 19 times · Not summarized yet
The study examines structural interactions among mammalian clock proteins, a different system for molecular circadian timekeeping.
Abstract
Circadian rhythms are genetically encoded molecular clocks for internal biological timekeeping. Organisms from single-cell bacteria to humans use these clocks to adapt to the external environment and synchronize their physiology and behavior to solar light/dark cycles. Although the proteins that constitute the molecular ‘cogs’ and give rise to circadian rhythms are now known, we still lack a detailed understanding of how these proteins interact to generate and sustain the ~24-hour circadian clock. Structural studies have helped to expand the architecture of clock proteins and have revealed the abundance of the only well-defined structured regions in the mammalian clock called Per-ARNT-Sim (P…
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Temperature as a universal resetting cue for mammalian circadian oscillatorsEthan D. Buhr, Seung-Hee Yoo, J. Takahashi · 2010 · Science · cited 885 times · Not summarized yet
The study reports that temperature cycles reset peripheral mammalian clocks but not the SCN, providing a comparison for temperature entrainment in E. coli.
Abstract
Time and Temperature Daily cycles in environmental temperature are an important cue for many organisms to synchronize their endogenous circadian clock. However, mammals do not respond to this cue. Studying mouse tissue, Buhr et al. (p. 379; see the Perspective by Edery) find that this resistance to temperature is a feature specific to the suprachiasmatic nucleus (SCN), a region of the mammalian brain that functions as the body's master clock. In contrast, the clocks in peripheral tissues (for example, lung, liver) are fully capable of resetting in response to temperature changes and do so by a mechanism involving the heat shock pathway. The SCN drives daily rhythms in body temperature, and S…
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CikA, a bacteriophytochrome that resets the cyanobacterial circadian clock.O. Schmitz, Mitsunori Katayama, S. Williams et al. · 2000 · Science · cited 291 times · Not summarized yet
The study identifies cyanobacterial CikA as a clock-resetting bacteriophytochrome, relevant background on sensory input to bacterial clocks.
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Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria.M. Ishiura, Shinsuke Kutsuna, S. Aoki et al. · 1998 · Science · cited 808 times · Not summarized yet
The study describes kaiABC expression as a cyanobacterial circadian feedback process, providing foundational work on bacterial clock mechanisms.
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