1
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The upcycled roles of pseudoenzymes in two-component signal transduction. Curr Opin Microbiol 2021; 61:82-90. [PMID: 33872991 DOI: 10.1016/j.mib.2021.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/23/2022]
Abstract
Upon first glance at a bacterial genome, pseudoenzymes appear unremarkable due to their lack of critical motifs that facilitate catalysis. These pseudoenzymes exist within signal transduction enzymes including histidine kinases, response regulators, diguanylate cyclases, and phosphodiesterases. Here, we summarize recent studies of bacterial pseudo-histidine kinases and pseudo-response regulators that regulate cell division, capsule formation, and the circadian rhythm. These examples illuminate the mechanistic potential of catalytically dead signaling enzymes and their impact upon bacterial signal transduction. Moreover, proteins lacking characteristic catalytic features of two-component systems reveal the sophisticated underlying potential of canonical two-component systems.
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2
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Kim P, Kaur M, Jang HI, Kim YI. The Circadian Clock-A Molecular Tool for Survival in Cyanobacteria. Life (Basel) 2020; 10:life10120365. [PMID: 33419320 PMCID: PMC7766417 DOI: 10.3390/life10120365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth’s early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins—KaiA, KaiB, and KaiC—drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the “ticking” of the oscillator can be reconstituted inside a test tube just by mixing the three recombinant proteins with ATP and Mg2+. Along with its biochemical resilience, the post-translational rhythm of the oscillation can be reset through sensing oxidized quinone, a metabolite that becomes abundant at the onset of darkness. In addition, the output components pick up the information from the central oscillator, tuning the physiological and behavioral patterns and enabling the organism to better cope with the cyclic environmental conditions. In this review, we highlight our understanding of the cyanobacterial circadian clock and discuss how it functions as a molecular chronometer that readies the host for predictable changes in its surroundings.
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Affiliation(s)
- Pyonghwa Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
| | - Manpreet Kaur
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
| | - Hye-In Jang
- School of Cosmetic Science and Beauty Biotechnology, Semyung University, Jecheon 27136, Korea
- Correspondence: (H.-I.J.); (Y.-I.K.)
| | - Yong-Ick Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
- Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Correspondence: (H.-I.J.); (Y.-I.K.)
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3
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Partch CL. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. J Mol Biol 2020; 432:3426-3448. [DOI: 10.1016/j.jmb.2019.12.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
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4
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Kim P, Porr B, Mori T, Kim YS, Johnson CH, Diekman CO, Kim YI. CikA, an Input Pathway Component, Senses the Oxidized Quinone Signal to Generate Phase Delays in the Cyanobacterial Circadian Clock. J Biol Rhythms 2020; 35:227-234. [PMID: 31983264 DOI: 10.1177/0748730419900868] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The circadian clock is a timekeeping system in most organisms that keeps track of the time of day. The rhythm generated by the circadian oscillator must be constantly synchronized with the environmental day/night cycle to make the timekeeping system truly advantageous. In the cyanobacterial circadian clock, quinone is a biological signaling molecule used for entraining and fine-tuning the oscillator, a process in which the external signals are transduced into biological metabolites that adjust the phase of the circadian oscillation. Among the clock proteins, the pseudo-receiver domain of KaiA and CikA can sense external cues by detecting the oxidation state of quinone, a metabolite that reflects the light/dark cycle, although the molecular mechanism is not fully understood. Here, we show the antagonistic phase shifts produced by the quinone sensing of KaiA and CikA. We introduced a new cyanobacterial circadian clock mixture that includes an input component in vitro. KaiA and CikA cause phase advances and delays, respectively, in this circadian clock mixture in response to the quinone signal. In the entrainment process, oxidized quinone modulates the functions of KaiA and CikA, which dominate alternatively at day and night in the cell. This in turn changes the phosphorylation state of KaiC-the central oscillator in cyanobacteria-ensuring full synchronization of the circadian clock. Moreover, we reemphasize the mechanistic input functionality of CikA, contrary to other reports that focus only on its output action.
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Affiliation(s)
- Pyonghwa Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Brianna Porr
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Yong-Sung Kim
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - Carl H Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Casey O Diekman
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey.,Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, New Jersey
| | - Yong-Ick Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey.,Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, New Jersey
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5
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Abstract
Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components. Posttranslational modifications and protein–protein interactions have become a recent focus, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. This review covers the structural aspects of circadian oscillators, and serves as a primer for this exciting realm of structural biology.
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Affiliation(s)
- Reena Saini
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Seth J Davis
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany. .,Department of Biology, University of York, York, UK.
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6
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Swan JA, Golden SS, LiWang A, Partch CL. Structure, function, and mechanism of the core circadian clock in cyanobacteria. J Biol Chem 2018; 293:5026-5034. [PMID: 29440392 DOI: 10.1074/jbc.tm117.001433] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/09/2018] [Indexed: 01/09/2023] Open
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 Minireview summarizes the current structural, functional and mechanistic insights into the cyanobacterial circadian clock.
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Affiliation(s)
- Jeffrey A Swan
- From the Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Susan S Golden
- the Department of Molecular Biology and.,Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and
| | - Andy LiWang
- Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and.,the Department of Chemistry and Chemical Biology, University of California Merced, Merced, California 95343
| | - Carrie L Partch
- From the Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, .,Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and
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7
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Hung YL, Jiang I, Lee YZ, Wen CK, Sue SC. NMR Study Reveals the Receiver Domain of Arabidopsis ETHYLENE RESPONSE1 Ethylene Receptor as an Atypical Type Response Regulator. PLoS One 2016; 11:e0160598. [PMID: 27486797 PMCID: PMC4972365 DOI: 10.1371/journal.pone.0160598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/21/2016] [Indexed: 11/26/2022] Open
Abstract
The gaseous plant hormone ethylene, recognized by plant ethylene receptors, plays a pivotal role in various aspects of plant growth and development. ETHYLENE RESPONSE1 (ETR1) is an ethylene receptor isolated from Arabidopsis and has a structure characteristic of prokaryotic two-component histidine kinase (HK) and receiver domain (RD), where the RD structurally resembles bacteria response regulators (RRs). The ETR1 HK domain has autophosphorylation activity, and little is known if the HK can transfer the phosphoryl group to the RD for receptor signaling. Unveiling the correlation of the receptor structure and phosphorylation status would advance the studies towards the underlying mechanisms of ETR1 receptor signaling. In this study, using the nuclear magnetic resonance technique, our data suggested that the ETR1-RD is monomeric in solution and the rigid structure of the RD prevents the conserved aspartate residue phosphorylation. Comparing the backbone dynamics with other RRs, we propose that backbone flexibility is critical to the RR phosphorylation. Besides the limited flexibility, ETR1-RD has a unique γ loop conformation of opposite orientation, which makes ETR1-RD unfavorable for phosphorylation. These two features explain why ETR1-RD cannot be phosphorylated and is classified as an atypical type RR. As a control, phosphorylation of the ETR1-RD was also impaired when the sequence was swapped to the fragment of the bacterial typical type RR, CheY. Here, we suggest a molecule insight that the ETR1-RD already exists as an active formation and executes its function through binding with the downstream factors without phosphorylation.
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Affiliation(s)
- Yi-Lin Hung
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Instrumentation Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ingjye Jiang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Kuang Wen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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8
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Chang YG, Cohen SE, Phong C, Myers WK, Kim YI, Tseng R, Lin J, Zhang L, Boyd JS, Lee Y, Kang S, Lee D, Li S, Britt RD, Rust MJ, Golden SS, LiWang A. Circadian rhythms. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria. Science 2015; 349:324-8. [PMID: 26113641 PMCID: PMC4506712 DOI: 10.1126/science.1260031] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 05/08/2015] [Indexed: 12/26/2022]
Abstract
Organisms are adapted to the relentless cycles of day and night, because they evolved timekeeping systems called circadian clocks, which regulate biological activities with ~24-hour rhythms. The clock of cyanobacteria is driven by a three-protein oscillator composed of KaiA, KaiB, and KaiC, which together generate a circadian rhythm of KaiC phosphorylation. We show that KaiB flips between two distinct three-dimensional folds, and its rare transition to an active state provides a time delay that is required to match the timing of the oscillator to that of Earth's rotation. Once KaiB switches folds, it binds phosphorylated KaiC and captures KaiA, which initiates a phase transition of the circadian cycle, and it regulates components of the clock-output pathway, which provides the link that joins the timekeeping and signaling functions of the oscillator.
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Affiliation(s)
- Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Susan E Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Connie Phong
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - William K Myers
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Yong-Ick Kim
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Roger Tseng
- School of Natural Sciences, University of California, Merced, CA 95343, USA. Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Jenny Lin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Li Zhang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Joseph S Boyd
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yvonne Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shannon Kang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Lee
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA. Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, CA 95343, USA. Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA. Quantitative and Systems Biology, University of California, Merced, CA 95343, USA. Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA. Health Sciences Research Institute, University of California, Merced, CA 95343, USA.
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9
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Tseng R, Chang YG, Bravo I, Latham R, Chaudhary A, Kuo NW, Liwang A. Cooperative KaiA-KaiB-KaiC interactions affect KaiB/SasA competition in the circadian clock of cyanobacteria. J Mol Biol 2013; 426:389-402. [PMID: 24112939 DOI: 10.1016/j.jmb.2013.09.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/22/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
The circadian oscillator of cyanobacteria is composed of only three proteins, KaiA, KaiB, and KaiC. Together, they generate an autonomous ~24-h biochemical rhythm of phosphorylation of KaiC. KaiA stimulates KaiC phosphorylation by binding to the so-called A-loops of KaiC, whereas KaiB sequesters KaiA in a KaiABC complex far away from the A-loops, thereby inducing KaiC dephosphorylation. The switch from KaiC phosphorylation to dephosphorylation is initiated by the formation of the KaiB-KaiC complex, which occurs upon phosphorylation of the S431 residues of KaiC. We show here that formation of the KaiB-KaiC complex is promoted by KaiA, suggesting cooperativity in the initiation of the dephosphorylation complex. In the KaiA-KaiB interaction, one monomeric subunit of KaiB likely binds to one face of a KaiA dimer, leaving the other face unoccupied. We also show that the A-loops of KaiC exist in a dynamic equilibrium between KaiA-accessible exposed and KaiA-inaccessible buried positions. Phosphorylation at the S431 residues of KaiC shift the A-loops toward the buried position, thereby weakening the KaiA-KaiC interaction, which is expected to be an additional mechanism promoting formation of the KaiABC complex. We also show that KaiB and the clock-output protein SasA compete for overlapping binding sites, which include the B-loops on the CI ring of KaiC. KaiA strongly shifts the competition in KaiB's favor. Thus, in addition to stimulating KaiC phosphorylation, it is likely that KaiA plays roles in switching KaiC from phosphorylation to dephosphorylation, as well as regulating clock output.
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Affiliation(s)
- Roger Tseng
- School of Natural Sciences, University of California, Merced, CA 95343, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343, USA
| | - Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Ian Bravo
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Robert Latham
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | | | - Nai-Wei Kuo
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Andy Liwang
- School of Natural Sciences, University of California, Merced, CA 95343, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343, USA; Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA; Center for Chronobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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10
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Profile of Susan S. Golden. Proc Natl Acad Sci U S A 2013; 110:8758-60. [DOI: 10.1073/pnas.1305064110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Oxidized quinones signal onset of darkness directly to the cyanobacterial circadian oscillator. Proc Natl Acad Sci U S A 2012; 109:17765-9. [PMID: 23071342 DOI: 10.1073/pnas.1216401109] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synchronization of the circadian clock in cyanobacteria with the day/night cycle proceeds without an obvious photoreceptor, leaving open the question of its specific mechanism. The circadian oscillator can be reconstituted in vitro, where the activities of two of its proteins, KaiA and KaiC, are affected by metabolites that reflect photosynthetic activity: KaiC phosphorylation is directly influenced by the ATP/ADP ratio, and KaiA stimulation of KaiC phosphorylation is blocked by oxidized, but not reduced, quinones. Manipulation of the ATP/ADP ratio can reset the timing of KaiC phosphorylation peaks in the reconstituted in vitro oscillator. Here, we show that pulses of oxidized quinones reset the cyanobacterial circadian clock both in vitro and in vivo. Onset of darkness causes an abrupt oxidation of the plastoquinone pool in vivo, which is in contrast to a gradual decrease in the ATP/ADP ratio that falls over the course of hours until the onset of light. Thus, these two metabolic measures of photosynthetic activity act in concert to signal both the onset and duration of darkness to the cyanobacterial clock.
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12
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Pattanayek R, Sidiqi SK, Egli M. Crystal structure of the redox-active cofactor dibromothymoquinone bound to circadian clock protein KaiA and structural basis for dibromothymoquinone's ability to prevent stimulation of KaiC phosphorylation by KaiA. Biochemistry 2012; 51:8050-2. [PMID: 23020633 DOI: 10.1021/bi301222t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
KaiA protein that stimulates KaiC phosphorylation in the cyanobacterial circadian clock was recently shown to be destabilized by dibromothymoquinone (DBMIB), thus revealing KaiA as a sensor of the plastoquinone (PQ) redox state and suggesting an indirect control of the clock by light through PQ redox changes. Here we show using X-ray crystallography that several DBMIBs are bound to KaiA dimer. Some binding modes are consistent with oligomerization of N-terminal KaiA pseudoreceiver domains and/or reduced interdomain flexibility. DBMIB bound to the C-terminal KaiA (C-KaiA) domain and limited stimulation of KaiC kinase activity by C-KaiA in the presence of DBMIB demonstrate that the cofactor may weakly inhibit KaiA-KaiC binding.
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Affiliation(s)
- Rekha Pattanayek
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
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13
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Xu Q, Christen B, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Figurski DH, Shapiro L, Wilson IA. Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization. Mol Microbiol 2012; 83:712-27. [PMID: 22211578 DOI: 10.1111/j.1365-2958.2011.07954.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type IV pili. The pilus assembly protein TadZ (called CpaE in Caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type IV pilus biogenesis systems. The crystal structure of TadZ from Eubacterium rectale (ErTadZ), in complex with ATP and Mg(2+) , was determined to 2.1 Å resolution. ErTadZ contains an atypical ATPase domain with a variant of a deviant Walker-A motif that retains ATP binding capacity while displaying only low intrinsic ATPase activity. The bound ATP plays an important role in dimerization of ErTadZ. The N-terminal atypical receiver domain resembles the canonical receiver domain of response regulators, but has a degenerate, stripped-down 'active site'. Homology modelling of the N-terminal atypical receiver domain of CpaE indicates that it has a conserved protein-protein binding surface similar to that of the polar localization module of the social mobility protein FrzS, suggesting a similar function. Our structural results also suggest that TadZ localizes to the pole through the atypical receiver domain during an early stage of pili biogenesis, and functions as a hub for recruiting other pili components, thus providing insights into the Tad pilus assembly process.
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14
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Mackey SR, Golden SS, Ditty JL. The itty-bitty time machine genetics of the cyanobacterial circadian clock. ADVANCES IN GENETICS 2011; 74:13-53. [PMID: 21924974 DOI: 10.1016/b978-0-12-387690-4.00002-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cyanobacterium Synechococcus elongatus PCC 7942 has been used as the prokaryotic model system for the study of circadian rhythms for the past two decades. Its genetic malleability has been instrumental in the discovery of key input, oscillator, and output components and has also provided monumental insights into the mechanism by which proteins function to maintain and dictate 24-h time. In addition, basic research into the prokaryotic system has led to interesting advances in eukaryotic circadian mechanisms. Undoubtedly, continued genetic and mutational analyses of this single-celled cyanobacterium will aid in teasing out the intricacies of the Kai-based circadian clock to advance our understanding of this system as well as other more "complex" systems.
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Affiliation(s)
- Shannon R Mackey
- Biology Department, St. Ambrose University, Davenport, Iowa, USA
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15
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Wood TL, Bridwell-Rabb J, Kim YI, Gao T, Chang YG, LiWang A, Barondeau DP, Golden SS. The KaiA protein of the cyanobacterial circadian oscillator is modulated by a redox-active cofactor. Proc Natl Acad Sci U S A 2010; 107:5804-9. [PMID: 20231482 PMCID: PMC2851934 DOI: 10.1073/pnas.0910141107] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian rhythms exhibited in the cyanobacterium Synechococcus elongatus are generated by an oscillator comprised of the proteins KaiA, KaiB, and KaiC. An external signal that commonly affects the circadian clock is light. Previously, we reported that the bacteriophytochrome-like protein CikA passes environmental signals to the oscillator by directly binding a quinone and using cellular redox state as a measure of light in this photosynthetic organism. Here, we report that KaiA also binds the quinone analog 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), and the oxidized form of DBMIB, but not its reduced form, decreases the stability of KaiA in vivo, causes multimerization in vitro, and blocks KaiA stimulation of KaiC phosphorylation, which is central to circadian oscillation. Our data suggest that KaiA directly senses environmental signals as changes in redox state and modulates the circadian clock.
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Affiliation(s)
- Thammajun L. Wood
- The Center for Biological Clocks Research, Department of Biology, and
| | | | - Yong-Ick Kim
- Center for Chronobiology and Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093-0116; and
| | - Tiyu Gao
- The Center for Biological Clocks Research, Department of Biology, and
| | - Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, CA 95340
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, CA 95340
| | - David P. Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Susan S. Golden
- The Center for Biological Clocks Research, Department of Biology, and
- Center for Chronobiology and Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093-0116; and
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16
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Bourret RB. Receiver domain structure and function in response regulator proteins. Curr Opin Microbiol 2010; 13:142-9. [PMID: 20211578 DOI: 10.1016/j.mib.2010.01.015] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
Abstract
During signal transduction by two-component regulatory systems, sensor kinases detect and encode input information while response regulators (RRs) control output. Most receiver domains function as phosphorylation-mediated switches within RRs, but some transfer phosphoryl groups in multistep phosphorelays. Conserved features of receiver domain amino acid sequence correlate with structure and hence function. Receiver domains catalyze their own phosphorylation and dephosphorylation in reactions requiring a divalent cation. Molecular dynamics simulations are supplementing structural investigation of the conformational changes that underlie receiver domain switch function. As understanding of features shared by all receiver domains matures, factors conferring differences (e.g. in reaction rate or specificity) are receiving increased attention. Numerous examples of atypical receiver or pseudo-receiver domains that function without phosphorylation have recently been characterized.
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Affiliation(s)
- Robert B Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
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17
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Lin YH, Gao R, Binns AN, Lynn DG. Capturing the VirA/VirG TCS of Agrobacterium tumefaciens. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:161-77. [PMID: 18792688 DOI: 10.1007/978-0-387-78885-2_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two-component systems (TCS) regulate pathogenic commitment in many interactions and provide an opportunity for unique therapeutic intervention. The VirA/VirG TCS of Agrobacterium tumefaciens mediates inter-kingdom gene transfer in the development of host tumors and sets in motion the events that underlie the great success of this multi-host plant pathogen. Significant proof for the feasibility of interventions has now emerged with the discovery of a natural product that effectively "blinds" the pathogen to the host via inhibition of VirA/VirG signal transduction. Moreover, the emerging studies on the mechanism of signal perception have revealed general sites suitable for intervention of TCS signaling. Given the extensive functional homology, it should now be possible to transfer the models discovered for VirA/VirG broadly to other pathogenic interactions.
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Affiliation(s)
- Yi-Han Lin
- Center for Fundamental and Applied Molecular Evolution, Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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18
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Dong G, Golden SS. How a cyanobacterium tells time. Curr Opin Microbiol 2008; 11:541-6. [PMID: 18983934 DOI: 10.1016/j.mib.2008.10.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 10/07/2008] [Accepted: 10/08/2008] [Indexed: 11/27/2022]
Abstract
The cyanobacterium Synechococcus elongatus builds a circadian clock on an oscillator composed of three proteins, KaiA, KaiB, and KaiC, which can recapitulate a circadian rhythm of KaiC phosphorylation in vitro. The molecular structures of all three proteins are known, and the phosphorylation steps of KaiC, the interaction dynamics among the three Kai proteins, and a weak ATPase activity of KaiC have all been characterized. An input pathway of redox-sensitive proteins uses photosynthetic function to relay light/dark information to the oscillator, and signal transduction proteins of well-known families broadcast temporal information to the genome, where global changes in transcription and a compaction of the chromosome are clock regulated.
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Affiliation(s)
- Guogang Dong
- Center for Biological Clocks Research and Department of Biology, Texas A&M University, College Station, TX 77843-3258, United States
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Golden SS. Integrating the circadian oscillator into the life of the cyanobacterial cell. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2008; 72:331-8. [PMID: 18419290 DOI: 10.1101/sqb.2007.72.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In two decades, the study of circadian rhythms in cyanobacteria has gone from observations of phenomena in intractable species to the development of a model organism for mechanistic study, atomic-resolution structures of components, and reconstitution of a circadian biochemical oscillation in vitro. With sophisticated biochemical, biophysical, genetic, and genomic tools in place, the circadian clock of the unicellular cyanobacterium Synechococcus elongatus is poised to be the first for which a systems-level understanding can be achieved.
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Affiliation(s)
- S S Golden
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258, USA
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Proteins found in a CikA interaction assay link the circadian clock, metabolism, and cell division in Synechococcus elongatus. J Bacteriol 2008; 190:3738-46. [PMID: 18344369 DOI: 10.1128/jb.01721-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diverse organisms time their cellular activities to occur at distinct phases of Earth's solar day, not through the direct regulation of these processes by light and darkness but rather through the use of an internal biological (circadian) clock that is synchronized with the external cycle. Input pathways serve as mechanisms to transduce external cues to a circadian oscillator to maintain synchrony between this internal oscillation and the environment. The circadian input pathway in the cyanobacterium Synechococcus elongatus PCC 7942 requires the kinase CikA. A cikA null mutant exhibits a short circadian period, the inability to reset its clock in response to pulses of darkness, and a defect in cell division. Although CikA is copurified with the Kai proteins that constitute the circadian central oscillator, no direct interaction between CikA and either KaiA, KaiB, or KaiC has been demonstrated. Here, we identify four proteins that may help connect CikA with the oscillator. Phenotypic analyses of null and overexpression alleles demonstrate that these proteins are involved in at least one of the functions--circadian period regulation, phase resetting, and cell division--attributed to CikA. Predictions based on sequence similarity suggest that these proteins function through protein phosphorylation, iron-sulfur cluster biosynthesis, and redox regulation. Collectively, these results suggest a model for circadian input that incorporates proteins that link the circadian clock, metabolism, and cell division.
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Narikawa R, Kohchi T, Ikeuchi M. Characterization of the photoactive GAF domain of the CikA homolog (SyCikA, Slr1969) of the cyanobacterium Synechocystis sp. PCC 6803. Photochem Photobiol Sci 2008; 7:1253-9. [DOI: 10.1039/b811214b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mackey SR, Golden SS. Winding up the cyanobacterial circadian clock. Trends Microbiol 2007; 15:381-8. [PMID: 17804240 DOI: 10.1016/j.tim.2007.08.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/22/2007] [Accepted: 08/22/2007] [Indexed: 11/19/2022]
Abstract
The endogenous circadian clock of the cyanobacterium Synechococcus elongatus controls many cellular processes and confers an adaptive advantage on this organism in a competitive environment. To be advantageous, this internal biological oscillator must be reset daily to remain in synchrony with its environment and to transduce temporal information to control behaviors at appropriate times of day. Recent studies have discovered new components of these input and output pathways of the clock that help to 'wind up' our understanding of the clock system as a whole. Here we review the mechanisms by which S. elongatus maintains internal time, discuss how external stimuli affect this oscillation, and evaluate the mechanisms underlying circadian controlled cellular events.
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Affiliation(s)
- Shannon R Mackey
- Department of Biology, St. Ambrose University, Davenport, IA 52803, USA
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