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Aviram R, Dandavate V, Manella G, Golik M, Asher G. Ultradian rhythms of AKT phosphorylation and gene expression emerge in the absence of the circadian clock components Per1 and Per2. PLoS Biol 2021; 19:e3001492. [PMID: 34968386 PMCID: PMC8718012 DOI: 10.1371/journal.pbio.3001492] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Rhythmicity of biological processes can be elicited either in response to environmental cycles or driven by endogenous oscillators. In mammals, the circadian clock drives about 24-hour rhythms of multitude metabolic and physiological processes in anticipation to environmental daily oscillations. Also at the intersection of environment and metabolism is the protein kinase—AKT. It conveys extracellular signals, primarily feeding-related signals, to regulate various key cellular functions. Previous studies in mice identified rhythmicity in AKT activation (pAKT) with elevated levels in the fed state. However, it is still unknown whether rhythmic AKT activation can be driven through intrinsic mechanisms. Here, we inspected temporal changes in pAKT levels both in cultured cells and animal models. In cultured cells, pAKT levels showed circadian oscillations similar to those observed in livers of wild-type mice under free-running conditions. Unexpectedly, in livers of Per1,2−/− but not of Bmal1−/− mice we detected ultradian (about 16 hours) oscillations of pAKT levels. Importantly, the liver transcriptome of Per1,2−/− mice also showed ultradian rhythms, corresponding to pAKT rhythmicity and consisting of AKT-related genes and regulators. Overall, our findings reveal ultradian rhythms in liver gene expression and AKT phosphorylation that emerge in the absence of environmental rhythms and Per1,2−/− genes. This study reveals ultradian (16-hour) rhythms in the activation of the protein kinase AKT in the livers of mice, accompanied by corresponding downstream changes in gene expression. Intriguingly, these oscillations emerge in the absence of rhythmic environmental cues and in mice lacking the circadian clock proteins Per1 and Per2.
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Affiliation(s)
- Rona Aviram
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Vaishnavi Dandavate
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Manella
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Marina Golik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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2
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Barik S. Molecular Interactions between Pathogens and the Circadian Clock. Int J Mol Sci 2019; 20:ijms20235824. [PMID: 31756974 PMCID: PMC6928883 DOI: 10.3390/ijms20235824] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/17/2019] [Accepted: 11/17/2019] [Indexed: 12/12/2022] Open
Abstract
The daily periodicity of the Earth's rotation around the Sun, referred to as circadian (Latin "circa" = about, and "diem" = day), is also mirrored in the behavior and metabolism of living beings. The discovery that dedicated cellular genes control various aspects of this periodicity has led to studies of the molecular mechanism of the circadian response at the cellular level. It is now established that the circadian genes impact on a large network of hormonal, metabolic, and immunological pathways, affecting multiple aspects of biology. Recent studies have extended the role of the circadian system to the regulation of infection, host-pathogen interaction, and the resultant disease outcome. This critical review summarizes our current knowledge of circadian-pathogen interaction at both systemic and cellular levels, but with emphasis on the molecular aspects of the regulation. Wherever applicable, the potential of a direct interaction between circadian factors and pathogenic macromolecules is also explored. Finally, this review offers new directions and guidelines for future research in this area, which should facilitate progress.
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3
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Shi SQ, Johnson CH. Circadian biology and sleep in monogenic neurological disorders and its potential application in drug discovery. Curr Opin Behav Sci 2019; 25:23-30. [PMID: 31289731 PMCID: PMC6615557 DOI: 10.1016/j.cobeha.2018.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Sleep disturbances are common in people with monogenic neurological disorders and they dramatically affect the life of individuals with the disorders and their families. The associated sleep problems are probably caused by multiple factors that have not been elucidated. Study of the underlying molecular cause, behavioral phenotypes, and reciprocal interactions in several single-gene disorders (Angelman Syndrome, Fragile X Syndrome, Rett Syndrome, and Huntington's Disease) leads to the suggestion that sleep disruption and other symptoms may directly result from abnormal operation of circadian systems due to genetic alteration and/or conflicting environmental cues for clock entrainment. Therefore, because circadian patterns modify the symptoms of neurological disorders, treatments that modulate our daily rhythms may identify heretofore unappreciated therapies for the underlying disorders.
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Affiliation(s)
- Shu-Qun Shi
- Department of Biological Sciences, Vanderbilt University, USA
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, USA
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4
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Mori T, Sugiyama S, Byrne M, Johnson CH, Uchihashi T, Ando T. Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time. Nat Commun 2018; 9:3245. [PMID: 30108211 PMCID: PMC6092398 DOI: 10.1038/s41467-018-05438-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/09/2018] [Indexed: 11/09/2022] Open
Abstract
The circadian clock proteins KaiA, KaiB, and KaiC reconstitute a remarkable circa-24 h oscillation of KaiC phosphorylation that persists for many days in vitro. Here we use high-speed atomic force microscopy (HS-AFM) to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on sub-second timescales. KaiA transiently interacts with KaiC, thereby stimulating KaiC autokinase activity. As KaiC becomes progressively more phosphorylated, KaiA's affinity for KaiC weakens, revealing a feedback of KaiC phosphostatus back onto the KaiA-binding events. These non-equilibrium interactions integrate high-frequency binding and unbinding events, thereby refining the period of the longer term oscillations. Moreover, this differential affinity phenomenon broadens the range of Kai protein stoichiometries that allow rhythmicity, explaining how the oscillation is resilient in an in vivo milieu that includes noise. Therefore, robustness of rhythmicity on a 24-h scale is explainable by molecular events occurring on a scale of sub-seconds.
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Affiliation(s)
- Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Shogo Sugiyama
- Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Mark Byrne
- Department of Chemistry, Physics, and Engineering, Spring Hill College, 4000 Dauphin St., Mobile, AL, 36608, USA
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA. .,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| | - Takayuki Uchihashi
- Department of Physics and Structural Biology Research Center, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, 920-1192, Japan.
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5
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Cordova JC, Olivares AO, Lang MJ. Mechanically Watching the ClpXP Proteolytic Machinery. Methods Mol Biol 2018; 1486:317-341. [PMID: 27844434 DOI: 10.1007/978-1-4939-6421-5_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Energy-dependent protein degradation is studied through the dual bead ClpXP motility assay. Processing of folded proteins involves recognition, unfolding, translocation, and degradation stages. A dual optical trap, in a passive force-clamp geometry, exhibits bead-to-bead displacements that directly follow subprocesses underlying protein degradation. Discrete nanometer-scale displacements of the bead position reveal steps, dwells and pauses during the unfolding and translocation substeps. With a few structural modifications to the protease machinery and an engineered substrate, the assay represents a "chassis" for the measurement of a wide range of substrates and related machinery. The methods described faithfully record our assay as implemented, including substrate design, wet assay preparation, and the motility assay experiment protocol. The strategies herein permit adaptation of the ClpXP mechanical assay to a wide range of protein degradation systems.
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Affiliation(s)
- Juan Carlos Cordova
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, 308-A Olin Hall, VU Mailbox: PMB 351604, Nashville, TN, 37235, USA
| | - Adrian O Olivares
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 308-A Olin Hall, VU Mailbox: PMB 351604, Nashville, TN, 37235, USA.
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6
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Abstract
All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks. Here we propose a role for KaiC family ATPases, known to be key components of the circadian clock in cyanobacteria, in archaeal signal transduction. The KaiC family is notably expanded in most archaeal genomes, and although most of these ATPases remain poorly characterized, members of the KaiC family have been shown to control archaellum assembly and have been found to be a stable component of the gas vesicle system in Halobacteria Computational analyses described here suggest that KaiC-like ATPases and their homologues with inactivated ATPase domains are involved in many other archaeal signal transduction pathways and comprise major hubs of complex regulatory networks. We predict numerous input and output domains that are linked to KaiC-like proteins, including putative homologues of eukaryotic DEATH domains that could function as adapters in archaeal signaling networks. We further address the relationships of the archaeal family of KaiC homologues to the bona fide KaiC of cyanobacteria and implications for the existence of a KaiC-based circadian clock apparatus in archaea.IMPORTANCE Little is currently known about signal transduction pathways in Archaea Recent studies indicate that KaiC-like ATPases, known as key components of the circadian clock apparatus in cyanobacteria, are involved in the regulation of archaellum assembly and, likely, type IV pili and the gas vesicle system in Archaea We performed comprehensive comparative genomic analyses of the KaiC family. A vast protein interaction network was revealed, with KaiC family proteins as hubs for numerous input and output components, many of which are shared with two-component signal transduction systems. Putative KaiC-based signal transduction systems are predicted to regulate the activities of membrane-associated complexes and individual proteins, such as signal recognition particle and membrane transporters, and also could be important for oxidative stress response regulation. KaiC-centered signal transduction networks are predicted to play major roles in archaeal physiology, and this work is expected to stimulate their experimental characterization.
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7
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Egli M. Architecture and mechanism of the central gear in an ancient molecular timer. J R Soc Interface 2017; 14:rsif.2016.1065. [PMID: 28330987 DOI: 10.1098/rsif.2016.1065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/27/2017] [Indexed: 12/16/2022] Open
Abstract
Molecular clocks are the product of natural selection in organisms from bacteria to human and their appearance early in evolution such as in the prokaryotic cyanobacterium Synechococcus elongatus suggests that these timers served a crucial role in genetic fitness. Thus, a clock allows cyanobacteria relying on photosynthesis and nitrogen fixation to temporally space the two processes and avoid exposure of nitrogenase carrying out fixation to high levels of oxygen produced during photosynthesis. Fascinating properties of molecular clocks are the long time constant, their precision and temperature compensation. Although these are hallmarks of all circadian oscillators, the actual cogs and gears that control clocks vary widely between organisms, indicating that circadian timers evolved convergently multiple times, owing to the selective pressure of an environment with a daily light/dark cycle. In S. elongatus, the three proteins KaiA, KaiB and KaiC in the presence of ATP constitute a so-called post-translational oscillator (PTO). The KaiABC PTO can be reconstituted in an Eppendorf tube and keeps time in a temperature-compensated manner. The ease by which the KaiABC clock can be studied in vitro has made it the best-investigated molecular clock system. Over the last decade, structures of all three Kai proteins and some of their complexes have emerged and mechanistic aspects have been analysed in considerable detail. This review focuses on the central gear of the S. elongatus clock and only enzyme among the three proteins: KaiC. Our determination of the three-dimensional structure of KaiC early in the quest for a better understanding of the inner workings of the cyanobacterial timer revealed its unusual architecture and conformational differences and unique features of the two RecA-like domains constituting KaiC. The structure also pinpointed phosphorylation sites and differential interactions with ATP molecules at subunit interfaces, and helped guide experiments to ferret out mechanistic aspects of the ATPase, auto-phosphorylation and auto-dephosphorylation reactions catalysed by the homo-hexamer. Comparisons between the structure of KaiC and those of nanomachines such as F1-ATPase and CaMKII also exposed shared architectural features (KaiC/ATPase), mechanistic principles (KaiC/CaMKII) and phenomena, such as subunit exchange between hexameric particles critical for function (clock synchronization, KaiABC; memory-storage, CaMKII).
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
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8
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Snijder J, Schuller JM, Wiegard A, Lössl P, Schmelling N, Axmann IM, Plitzko JM, Förster F, Heck AJR. Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Science 2017; 355:1181-1184. [PMID: 28302852 DOI: 10.1126/science.aag3218] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 02/13/2017] [Indexed: 01/18/2023]
Abstract
Cyanobacteria have a robust circadian oscillator, known as the Kai system. Reconstituted from the purified protein components KaiC, KaiB, and KaiA, it can tick autonomously in the presence of adenosine 5'-triphosphate (ATP). The KaiC hexamers enter a natural 24-hour reaction cycle of autophosphorylation and assembly with KaiB and KaiA in numerous diverse forms. We describe the preparation of stoichiometrically well-defined assemblies of KaiCB and KaiCBA, as monitored by native mass spectrometry, allowing for a structural characterization by single-particle cryo-electron microscopy and mass spectrometry. Our data reveal details of the interactions between the Kai proteins and provide a structural basis to understand periodic assembly of the protein oscillator.
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Affiliation(s)
- Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics and Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Jan M Schuller
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany
| | - Anika Wiegard
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics and Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Nicolas Schmelling
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Ilka M Axmann
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany
| | - Friedrich Förster
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany. .,Cryo-electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics and Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, Netherlands.
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9
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Chen Q, Yu L, Tan X, Liu S. Expression and Purification of Cyanobacterial Circadian Clock Protein KaiC and Determination of Its Auto-phosphatase Activity. Bio Protoc 2017; 7:e2140. [PMID: 34458460 DOI: 10.21769/bioprotoc.2140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/22/2016] [Accepted: 01/21/2017] [Indexed: 11/02/2022] Open
Abstract
Circadian rhythms are biological processes displaying an endogenous oscillation with a period of ~24 h. They allow organisms to anticipate and get prepared for the environmental changes caused mainly by the rotation of Earth. Circadian rhythms are driven by circadian clocks that consist of proteins, DNA, and/or RNA. Circadian clocks of cyanobacteria are the simplest and one of the best studied models. They contain the three clock proteins KaiA, KaiB, and KaiC which can be used for in vitro reconstitution experiments and determination of the auto-phosphatase activity of KaiC as described in this protocol.
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Affiliation(s)
- Qiang Chen
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.,College of Medical Science, China Three Gorges University, Yichang, China
| | - Lingling Yu
- College of Medical Science, China Three Gorges University, Yichang, China
| | - Xiao Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.,College of Medical Science, China Three Gorges University, Yichang, China
| | - Sen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.,College of Medical Science, China Three Gorges University, Yichang, China
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10
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Abstract
Chronobiological studies of prokaryotic organisms have generally lagged far behind the study of endogenous circadian clocks in eukaryotes, in which such systems are essentially ubiquitous. However, despite only being studied during the past 25 years, cyanobacteria have become important model organisms for the study of circadian rhythms and, presently, their timekeeping mechanism is the best understood of any system in terms of biochemistry, structural biology, biophysics and adaptive importance. Nevertheless, intrinsic daily rhythmicity among bacteria other than cyanobacteria is essentially unknown; some tantalizing information suggests widespread daily timekeeping among Eubacteria and Archaea through mechanisms that share common elements with the cyanobacterial clock but are distinct. Moreover, the recent surge of information about microbiome-host interactions has largely neglected the temporal dimension and yet daily cycles control important aspects of their relationship.
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11
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Makarova KS, Koonin EV, Albers SV. Diversity and Evolution of Type IV pili Systems in Archaea. Front Microbiol 2016; 7:667. [PMID: 27199977 PMCID: PMC4858521 DOI: 10.3389/fmicb.2016.00667] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/21/2016] [Indexed: 12/25/2022] Open
Abstract
Many surface structures in archaea including various types of pili and the archaellum (archaeal flagellum) are homologous to bacterial type IV pili systems (T4P). The T4P consist of multiple proteins, often with poorly conserved sequences, complicating their identification in sequenced genomes. Here we report a comprehensive census of T4P encoded in archaeal genomes using sensitive methods for protein sequence comparison. This analysis confidently identifies as T4P components about 5000 archaeal gene products, 56% of which are currently annotated as hypothetical in public databases. Combining results of this analysis with a comprehensive comparison of genomic neighborhoods of the T4P, we present models of organization of 10 most abundant variants of archaeal T4P. In addition to the differentiation between major and minor pilins, these models include extra components, such as S-layer proteins, adhesins and other membrane and intracellular proteins. For most of these systems, dedicated major pilin families are identified including numerous stand alone major pilin genes of the PilA family. Evidence is presented that secretion ATPases of the T4P and cognate TadC proteins can interact with different pilin sets. Modular evolution of T4P results in combinatorial variability of these systems. Potential regulatory or modulating proteins for the T4P are identified including KaiC family ATPases, vWA domain-containing proteins and the associated MoxR/GvpN ATPase, TFIIB homologs and multiple unrelated transcription regulators some of which are associated specific T4P. Phylogenomic analysis suggests that at least one T4P system was present in the last common ancestor of the extant archaea. Multiple cases of horizontal transfer and lineage-specific duplication of T4P loci were detected. Generally, the T4P of the archaeal TACK superphylum are more diverse and evolve notably faster than those of euryarchaea. The abundance and enormous diversity of T4P in hyperthermophilic archaea present a major enigma. Apparently, fundamental aspects of the biology of hyperthermophiles remain to be elucidated.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine - National Institutes of Health Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine - National Institutes of Health Bethesda, MD, USA
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg Freiburg, Germany
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12
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Dong P, Fan Y, Sun J, Lv M, Yi M, Tan X, Liu S. A dynamic interaction process between KaiA and KaiC is critical to the cyanobacterial circadian oscillator. Sci Rep 2016; 6:25129. [PMID: 27113386 PMCID: PMC4844972 DOI: 10.1038/srep25129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/12/2016] [Indexed: 11/09/2022] Open
Abstract
The core circadian oscillator of cyanobacteria consists of three proteins, KaiA, KaiB, and KaiC. This circadian oscillator could be functionally reconstituted in vitro with these three proteins, and therefore has been a very important model in circadian rhythm research. KaiA can bind to KaiC and then stimulate its phosphorylation, but their interaction mechanism remains elusive. In this study, we followed the "second-site suppressor" strategy to investigate the interaction mechanism of KaiA and KaiC. Using protein sequence analyses, we showed that there exist co-varying residues in the binding interface of KaiA and KaiC. The followed mutagenesis study verified that these residues are important to the functions of KaiA and KaiC, but their roles could not be fully explained by the reported complex structures of KaiA and KaiC derived peptides. Combining our data with previous reports, we suggested a dynamic interaction mechanism in KaiA-KaiC interaction, in which both KaiA and the intrinsically disordered tail of KaiC undergo significant structural changes through conformational selection and induced fit during the binding process. At last, we presented a mathematic model to support this hypothesis and explained the importance of this interaction mechanism for the KaiABC circadian oscillator.
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Affiliation(s)
- Pei Dong
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China.,College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Ying Fan
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Jianqiang Sun
- School of Statistics, Shandong Institute of Business and Technology, Yantai, 264005, China
| | - Mengting Lv
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Ming Yi
- Department of Physics, College of Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China.,College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Sen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China.,College of Medical Science, China Three Gorges University, Yichang 443002, China
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13
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Ma P, Mori T, Zhao C, Thiel T, Johnson CH. Evolution of KaiC-Dependent Timekeepers: A Proto-circadian Timing Mechanism Confers Adaptive Fitness in the Purple Bacterium Rhodopseudomonas palustris. PLoS Genet 2016; 12:e1005922. [PMID: 26982486 PMCID: PMC4794148 DOI: 10.1371/journal.pgen.1005922] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 02/16/2016] [Indexed: 11/18/2022] Open
Abstract
Circadian (daily) rhythms are a fundamental and ubiquitous property of eukaryotic organisms. However, cyanobacteria are the only prokaryotic group for which bona fide circadian properties have been persuasively documented, even though homologs of the cyanobacterial kaiABC central clock genes are distributed widely among Eubacteria and Archaea. We report the purple non-sulfur bacterium Rhodopseudomonas palustris (that harbors homologs of kaiB and kaiC) only poorly sustains rhythmicity in constant conditions-a defining characteristic of circadian rhythms. Moreover, the biochemical characteristics of the Rhodopseudomonas homolog of the KaiC protein in vivo and in vitro are different from those of cyanobacterial KaiC. Nevertheless, R. palustris cells exhibit adaptive kaiC-dependent growth enhancement in 24-h cyclic environments, but not under non-natural constant conditions. Therefore, our data indicate that Rhodopseudomonas does not have a classical circadian rhythm, but a novel timekeeping mechanism that does not sustain itself in constant conditions. These results question the adaptive value of self-sustained oscillatory capability for daily timekeepers and establish new criteria for circadian-like systems that are based on adaptive properties (i.e., fitness enhancement in rhythmic environments), rather than upon observations of persisting rhythms in constant conditions. We propose that the Rhodopseudomonas system is a "proto" circadian timekeeper, as in an ancestral system that is based on KaiC and KaiB proteins and includes some, but not necessarily all, of the canonical properties of circadian clocks. These data indicate reasonable intermediate steps by which bona fide circadian systems evolved in simple organisms.
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Affiliation(s)
- Peijun Ma
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Chi Zhao
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Teresa Thiel
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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14
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Abstract
A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ∼ 24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes.
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Affiliation(s)
- Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Hassane Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA.
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15
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Pattanayek R, Egli M. Protein-Protein Interactions in the Cyanobacterial Circadian Clock: Structure of KaiA Dimer in Complex with C-Terminal KaiC Peptides at 2.8 Å Resolution. Biochemistry 2015. [PMID: 26200123 DOI: 10.1021/acs.biochem.5b00694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the cyanobacterial circadian clock, the KaiA, -B, and -C proteins with ATP constitute a post-translational oscillator. KaiA stimulates the KaiC autokinase, and KaiB antagonizes KaiA action. KaiA contacts the intrinsically disordered C-terminal regions of KaiC hexamer to promote phosphorylation across subunit interfaces. The crystal structure of KaiA dimer from Synechococcus elongatus with two KaiC C-terminal 20mer peptides bound reveals that the latter adopt an α-helical conformation and contact KaiA α-helical bundles via mostly hydrophobic interactions. This complex and the crystal structure of KaiC hexamer with truncated C-terminal tails can be fit into the electron microscopy (EM) density of the KaiA:KaiC complex. The hybrid model helps rationalize clock phenotypes of KaiA and KaiC mutants.
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Affiliation(s)
- Rekha Pattanayek
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
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16
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Gurevich L, Cohen-Luria R, Wagner N, Ashkenasy G. Robustness of synthetic circadian clocks to multiple environmental changes. Chem Commun (Camb) 2015; 51:5672-5. [PMID: 25714790 DOI: 10.1039/c5cc00098j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A molecular network that mimics circadian clocks from cyanobacteria is constructed in silico. Simulating its oscillatory behaviour under variable conditions reveals its robustness relative to networks of alternative topologies. The principles for synthetic chemical circadian networks to work properly are consequently highlighted.
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Affiliation(s)
- Lilia Gurevich
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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17
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Abstract
For a biological oscillator to function as a circadian pacemaker that confers a fitness advantage, its timing functions must be stable in response to environmental and metabolic fluctuations. One such stability enhancer, temperature compensation, has long been a defining characteristic of these timekeepers. However, an accurate biological timekeeper must also resist changes in metabolism, and this review suggests that temperature compensation is actually a subset of a larger phenomenon, namely metabolic compensation, which maintains the frequency of circadian oscillators in response to a host of factors that impinge on metabolism and would otherwise destabilize these clocks. The circadian system of prokaryotic cyanobacteria is an illustrative model because it is composed of transcriptional and nontranscriptional oscillators that are coupled to promote resilience. Moreover, the cyanobacterial circadian program regulates gene activity and metabolic pathways, and it can be manipulated to improve the expression of bioproducts that have practical value.
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18
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Affiliation(s)
- Martin Egli
- Department
of Biochemistry, Vanderbilt University,
School of Medicine, Nashville, Tennessee 37232, United States
| | - Carl H. Johnson
- Department
of Biological Sciences, College of Arts and Science, Vanderbilt University, Nashville, Tennessee 37235, United States
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19
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Wagner N, Alasibi S, Peacock-Lopez E, Ashkenasy G. Coupled Oscillations and Circadian Rhythms in Molecular Replication Networks. J Phys Chem Lett 2015; 6:60-65. [PMID: 26263092 DOI: 10.1021/jz502350u] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Living organisms often display rhythmic and oscillatory behavior. We investigate here a challenge in contemporary Systems Chemistry, that is, to construct "bottom-up" molecular networks that display such complex behavior. We first describe oscillations during self-replication by applying kinetic parameters relevant to peptide replication in an open environment. Small networks of coupled oscillators are then constructed in silico, producing various functions such as logic gates, integrators, counters, triggers, and detectors. These networks are finally utilized to simulate the connectivity and network topology of the Kai proteins circadian clocks from the S. elongatus cyanobacteria, thus producing rhythms whose constant frequency is independent of the input intake rate and robust toward concentration fluctuations. We suggest that this study helps further reveal the underlying principles of biological clocks and may provide clues into their emergence in early molecular evolution.
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Affiliation(s)
- Nathaniel Wagner
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
| | - Samaa Alasibi
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
| | - Enrique Peacock-Lopez
- ‡Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
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20
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Abstract
Structural approaches have provided insight into the mechanisms of circadian clock oscillators. This review focuses upon the myriad structural methods that have been applied to the molecular architecture of cyanobacterial circadian proteins, their interactions with each other, and the mechanism of the KaiABC posttranslational oscillator. X-ray crystallography and solution NMR were deployed to gain an understanding of the three-dimensional structures of the three proteins KaiA, KaiB, and KaiC that make up the inner timer in cyanobacteria. A hybrid structural biology approach including crystallography, electron microscopy, and solution scattering has shed light on the shapes of binary and ternary Kai protein complexes. Structural studies of the cyanobacterial oscillator demonstrate both the strengths and the limitations of the divide-and-conquer strategy. Thus, investigations of complexes involving domains and/or peptides have afforded valuable information into Kai protein interactions. However, high-resolution structural data are still needed at the level of complexes between the 360-kDa KaiC hexamer that forms the heart of the clock and its KaiA and KaiB partners.
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21
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Egli M. Intricate protein-protein interactions in the cyanobacterial circadian clock. J Biol Chem 2014; 289:21267-75. [PMID: 24936066 DOI: 10.1074/jbc.r114.579607] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyanobacterial circadian clock consists of a post-translational oscillator (PTO) and a PTO-dependent transcription-translation feedback loop (TTFL). The PTO can be reconstituted in vitro with the KaiA, KaiB, and KaiC proteins, enabling detailed biochemical and biophysical investigations. Both the CI and the CII halves of the KaiC hexamer harbor ATPases, but only the C-terminal CII ring exhibits kinase and phospho-transferase activities. KaiA stimulates the kinase and KaiB associates with KaiC during the dephosphorylation phase and sequesters KaiA. Recent research has led to conflicting models of the KaiB-KaiC interaction, precluding a clear understanding of KaiB function and KaiABC clock mechanism.
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Affiliation(s)
- Martin Egli
- From the Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232-0146
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22
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Pattanayek R, Xu Y, Lamichhane A, Johnson CH, Egli M. An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1375-90. [PMID: 24816106 PMCID: PMC4722857 DOI: 10.1107/s1399004714003228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/12/2014] [Indexed: 11/10/2022]
Abstract
A post-translational oscillator (PTO) composed of the proteins KaiA, KaiB and KaiC is at the heart of the cyanobacterial circadian clock. KaiC interacts with KaiA and KaiB over the daily cycle, and CII domains undergo rhythmic phosphorylation/dephosphorylation with a 24 h period. Both the N-terminal (CI) and C-terminal (CII) rings of KaiC exhibit ATPase activity. The CI ATPase proceeds in an input-independent fashion, but the CII ATPase is subject to metabolic input signals. The crystal structure of KaiC from Thermosynechococcus elongatus allows insight into the different anatomies of the CI and CII ATPases. Four consecutive arginines in CI (Arg linker) that connect the P-loop, CI subunits and CI and CII at the ring interface are primary candidates for the coordination of the CI and CII activities. The mutation of linker residues alters the period or triggers arhythmic behavior. Comparison between the CI and CII structures also reveals differences in loop regions that are key to KaiA and KaiB binding and activation of CII ATPase and kinase. Common packing features in KaiC crystals shed light on the KaiB-KaiC interaction.
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Affiliation(s)
- Rekha Pattanayek
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Yao Xu
- Department of Biological Sciences, College of Arts and Science, Vanderbilt University, Nashville, TN 35235, USA
| | - Aashish Lamichhane
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Carl H. Johnson
- Department of Biological Sciences, College of Arts and Science, Vanderbilt University, Nashville, TN 35235, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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23
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Diversity of KaiC-based timing systems in marine Cyanobacteria. Mar Genomics 2014; 14:3-16. [PMID: 24388874 DOI: 10.1016/j.margen.2013.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 11/19/2013] [Accepted: 12/18/2013] [Indexed: 12/21/2022]
Abstract
The coordination of biological activities into daily cycles provides an important advantage for the fitness of diverse organisms. Most eukaryotes possess an internal clock ticking with a periodicity of about one day to anticipate sunrise and sunset. The 24-hour period of the free-running rhythm is highly robust against many changes in the natural environment. Among prokaryotes, only Cyanobacteria are known to harbor such a circadian clock. Its core oscillator consists of just three proteins, KaiA, KaiB, and KaiC that produce 24-hour oscillations of KaiC phosphorylation, even in vitro. This unique three-protein oscillator is well documented for the freshwater cyanobacterium Synechococcus elongatus PCC 7942. Several physiological studies demonstrate a circadian clock also for other Cyanobacteria including marine species. Genes for the core clock components are present in nearly all marine cyanobacterial species, though there are large differences in the specific composition of these genes. In the first section of this review we summarize data on the model circadian clock from S. elongatus PCC 7942 and compare it to the reduced clock system of the marine cyanobacterium Prochlorococcus marinus MED4. In the second part we discuss the diversity of timing mechanisms in other marine Cyanobacteria with regard to the presence or absence of different components of the clock.
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Villarreal SA, Pattanayek R, Williams DR, Mori T, Qin X, Johnson CH, Egli M, Stewart PL. CryoEM and molecular dynamics of the circadian KaiB-KaiC complex indicates that KaiB monomers interact with KaiC and block ATP binding clefts. J Mol Biol 2013; 425:3311-24. [PMID: 23796516 PMCID: PMC3940072 DOI: 10.1016/j.jmb.2013.06.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/18/2013] [Accepted: 06/11/2013] [Indexed: 01/07/2023]
Abstract
The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effect. Here, we present a crystallographic structure of the wild-type Synechococcus elongatus KaiB and a cryo-electron microscopy (cryoEM) structure of a KaiBC complex. The crystal structure shows the expected dimer core structure and significant conformational variations of the KaiB C-terminal region, which is functionally important in maintaining rhythmicity. The KaiBC sample was formed with a C-terminally truncated form of KaiC, KaiC-Δ489, which is persistently phosphorylated. The KaiB-KaiC-Δ489 structure reveals that the KaiC hexamer can bind six monomers of KaiB, which form a continuous ring of density in the KaiBC complex. We performed cryoEM-guided molecular dynamics flexible fitting simulations with crystal structures of KaiB and KaiC to probe the KaiBC protein-protein interface. This analysis indicated a favorable binding mode for the KaiB monomer on the CII end of KaiC, involving two adjacent KaiC subunits and spanning an ATP binding cleft. A KaiC mutation, R468C, which has been shown to affect the affinity of KaiB for KaiC and lengthen the period in a bioluminescence rhythm assay, is found within the middle of the predicted KaiBC interface. The proposed KaiB binding mode blocks access to the ATP binding cleft in the CII ring of KaiC, which provides insight into how KaiB might influence the phosphorylation status of KaiC.
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Affiliation(s)
- Seth A. Villarreal
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rekha Pattanayek
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Dewight R. Williams
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Ximing Qin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Carl H. Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Phoebe L. Stewart
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA
- To whom correspondence should be addressed. Tel: 216-368-4349; Fax: 216-368-1300; , 10900 Euclid Ave, Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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