1
|
Boodaghian N, Park H, Cohen SE. Investigating the Roles for Essential Genes in the Regulation of the Circadian Clock in Synechococcus elongatus Using CRISPR Interference. J Biol Rhythms 2024; 39:308-317. [PMID: 38357890 DOI: 10.1177/07487304241228333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Circadian rhythms are found widely throughout nature where cyanobacteria are the simplest organisms, in which the molecular details of the clock have been elucidated. Circadian rhythmicity in cyanobacteria is carried out via the KaiA, KaiB, and KaiC core oscillator proteins that keep ~24 h time. A series of input and output proteins-CikA, SasA, and RpaA-regulate the clock by sensing environmental changes and timing rhythmic activities, including global rhythms of gene expression. Our previous work identified a novel set of KaiC-interacting proteins, some of which are encoded by genes that are essential for viability. To understand the relationship of these essential genes to the clock, we applied CRISPR interference (CRISPRi) which utilizes a deactivated Cas9 protein and single-guide RNA (sgRNA) to reduce the expression of target genes but not fully abolish their expression to allow for survival. Eight candidate genes were targeted, and strains were analyzed by quantitative real-time PCR (qRT-PCR) for reduction of gene expression, and rhythms of gene expression were monitored to analyze circadian phenotypes. Strains with reduced expression of SynPCC7942_0001, dnaN, which encodes for the β-clamp of the replicative DNA polymerase, or SynPCC7942_1081, which likely encodes for a KtrA homolog involved in K+ transport, displayed longer circadian rhythms of gene expression than the wild type. As neither of these proteins have been previously implicated in the circadian clock, these data suggest that diverse cellular processes, DNA replication and K+ transport, can influence the circadian clock and represent new avenues to understand clock function.
Collapse
Affiliation(s)
- Nouneh Boodaghian
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, California
| | - Hyunsook Park
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, California
| | - Susan E Cohen
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, California
- Center for Circadian Biology, University of California, San Diego, San Diego, California
| |
Collapse
|
2
|
Chavan A, Heisler J, Chang YG, Golden SS, Partch CL, LiWang A. Protocols for in vitro reconstitution of the cyanobacterial circadian clock. Biopolymers 2024; 115:e23559. [PMID: 37421636 PMCID: PMC10772220 DOI: 10.1002/bip.23559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/26/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023]
Abstract
Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produce are important to health across diverse life forms there is growing interest in their mechanisms. However, mechanistic studies are challenging in vivo due to the complex, that is, poorly defined, milieu of live cells. Recently, we reconstituted the intact circadian clock of cyanobacteria in vitro. It oscillates autonomously and remains phase coherent for many days with a fluorescence-based readout that enables real-time observation of individual clock proteins and promoter DNA simultaneously under defined conditions without user intervention. We found that reproducibility of the reactions required strict adherence to the quality of each recombinant clock protein purified from Escherichia coli. Here, we provide protocols for preparing in vitro clock samples so that other labs can ask questions about how changing environments, like temperature, metabolites, and protein levels are reflected in the core oscillator and propagated to regulation of transcription, providing deeper mechanistic insights into clock biology.
Collapse
Affiliation(s)
- Archana Chavan
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Joel Heisler
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Yong-Gang Chang
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Susan S. Golden
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- Department of Molecular Biology, University of California – San Diego, La Jolla, CA 92093
| | - Carrie L. Partch
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- Department of Chemistry & Biochemistry, University of California – Santa Cruz, Santa Cruz, CA 95064
| | - Andy LiWang
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
- Department of Chemistry & Biochemistry, University of California – Merced, Merced, CA 95343
- Center for Cellular and Biomolecular Machines, University of California – Merced, Merced, CA 95343
| |
Collapse
|
3
|
Arbel-Goren R, Dassa B, Zhitnitsky A, Valladares A, Herrero A, Flores E, Stavans J. Spatio-temporal coherence of circadian clocks and temporal control of differentiation in Anabaena filaments. mSystems 2024; 9:e0070023. [PMID: 38079111 PMCID: PMC10805033 DOI: 10.1128/msystems.00700-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/18/2023] [Indexed: 01/24/2024] Open
Abstract
Circadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle, that gene expression in different vegetative intervals along a developed filament was discoordinated, and that the circadian clock was active in individual heterocysts. Furthermore, Anabaena mutants lacking the kaiABC genes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs in Anabaena, the temporal control of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen-deficient conditions, the clock coherent unit in Anabaena is reduced from a full filament under nitrogen-rich conditions to the vegetative cell interval between heterocysts.IMPORTANCECircadian clocks, from unicellular organisms to animals, temporally align biological processes to day and night cycles. We study the dynamics of a circadian clock-controlled gene at the individual cell level in the multicellular filamentous cyanobacterium Anabaena, under nitrogen-stress conditions. Under these conditions, some cells along filaments differentiate to carry out atmospheric nitrogen fixation and lose their capability for oxygenic photosynthesis. We found that clock synchronization is limited to organismic units of contiguous photosynthetic cells, contrary to nitrogen-replete conditions in which clocks are synchronized over a whole filament. We provided evidence that the circadian clock regulates the process of differentiation, allowing it to occur preferentially within a limited time window during the circadian clock period. Lastly, we present evidence that the signal from the core clock to clock-regulated genes is conveyed in Anabaena as in unicellular cyanobacteria.
Collapse
Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Zhitnitsky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
4
|
Santos-Merino M, Sakkos JK, Singh AK, Ducat DC. Coordination of carbon partitioning and photosynthesis by a two-component signaling network in Synechococcus elongatus PCC 7942. Metab Eng 2024; 81:38-52. [PMID: 37925065 DOI: 10.1016/j.ymben.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Photosynthetic organisms need to balance the rate of photosynthesis with the utilization of photosynthetic products by downstream reactions. While such "source/sink" pathways are well-interrogated in plants, analogous regulatory systems are unknown or poorly studied in single-celled algal and cyanobacterial species. Towards the identification of energy/sugar sensors in cyanobacteria, we utilized an engineered strain of Synechococcus elongatus PCC 7942 that allows experimental manipulation of carbon status. We conducted a screening of all two-component systems (TCS) and serine/threonine kinases (STKs) encoded in S. elongatus PCC 7942 by analyzing phenotypes consistent with sucrose-induced relaxation of sink inhibition. We narrowed the candidate sensor proteins by analyzing changes observed after sucrose feeding. We show that a clustered TCS network containing RpaA, CikB, ManS and NblS are involved in the regulation of genes related to photosynthesis, pigment synthesis, and Rubisco concentration in response to sucrose. Altogether, these results highlight a regulatory TCS group that may play under-appreciated functions in carbon partitioning and energy balancing in cyanobacteria.
Collapse
Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Jonathan K Sakkos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Amit K Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, United States.
| |
Collapse
|
5
|
Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
Collapse
Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| |
Collapse
|
6
|
McKnight BM, Kang S, Le TH, Fang M, Carbonel G, Rodriguez E, Govindarajan S, Albocher-Kedem N, Tran AL, Duncan NR, Amster-Choder O, Golden SS, Cohen SE. Roles for the Synechococcus elongatus RNA-Binding Protein Rbp2 in Regulating the Circadian Clock. J Biol Rhythms 2023; 38:447-460. [PMID: 37515350 PMCID: PMC10528358 DOI: 10.1177/07487304231188761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The cyanobacterial circadian oscillator, consisting of KaiA, KaiB, and KaiC proteins, drives global rhythms of gene expression and compaction of the chromosome and regulates the timing of cell division and natural transformation. While the KaiABC posttranslational oscillator can be reconstituted in vitro, the Kai-based oscillator is subject to several layers of regulation in vivo. Specifically, the oscillator proteins undergo changes in their subcellular localization patterns, where KaiA and KaiC are diffuse throughout the cell during the day and localized as a focus at or near the pole of the cell at night. Here, we report that the CI domain of KaiC, when in a hexameric state, is sufficient to target KaiC to the pole. Moreover, increased ATPase activity of KaiC correlates with enhanced polar localization. We identified proteins associated with KaiC in either a localized or diffuse state. We found that loss of Rbp2, found to be associated with localized KaiC, results in decreased incidence of KaiC localization and long-period circadian phenotypes. Rbp2 is an RNA-binding protein, and it appears that RNA-binding activity of Rbp2 is required to execute clock functions. These findings uncover previously unrecognized roles for Rbp2 in regulating the circadian clock and suggest that the proper localization of KaiC is required for a fully functional clock in vivo.
Collapse
Affiliation(s)
- Briana M. McKnight
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Shannon Kang
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Tam H. Le
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Genelyn Carbonel
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Esbeydi Rodriguez
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Sutharsan Govindarajan
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
- Department of Biological Sciences, SRM University AP, Amaravati, India
| | - Nitsan Albocher-Kedem
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Amanda L. Tran
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Nicholas R. Duncan
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Susan S. Golden
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Susan E. Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| |
Collapse
|
7
|
Géron A, Werner J, Wattiez R, Matallana-Surget S. Towards the discovery of novel molecular clocks in Prokaryotes. Crit Rev Microbiol 2023:1-13. [PMID: 37330701 DOI: 10.1080/1040841x.2023.2220789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms - circadian clocks - that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in Cyanobacteria within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in Cyanobacteria and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria.
Collapse
Affiliation(s)
- Augustin Géron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), University of Tübingen, Tübingen, Germany
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| |
Collapse
|
8
|
Kahn RE, Dayanidhi S, Lacham-Kaplan O, Hawley JA. Molecular clocks, satellite cells, and skeletal muscle regeneration. Am J Physiol Cell Physiol 2023; 324:C1332-C1340. [PMID: 37184229 DOI: 10.1152/ajpcell.00073.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Skeletal muscle comprises approximately 50% of individual body mass and plays vital roles in locomotion, heat production, and whole body metabolic homeostasis. This tissue exhibits a robust diurnal rhythm that is under control of the suprachiasmatic nucleus (SCN) region of the hypothalamus. The SCN acts as a "central" coordinator of circadian rhythms, while cell-autonomous "peripheral" clocks are located within almost all other tissues/organs in the body. Synchronization of the peripheral clocks in muscles (and other tissues) together with the central clock is crucial to ensure temporally coordinated physiology across all organ systems. By virtue of its mass, human skeletal muscle contains the largest collection of peripheral clocks, but within muscle resides a local stem cell population, satellite cells (SCs), which have their own functional molecular clock, independent of the numerous muscle clocks. Skeletal muscle has a daily turnover rate of 1%-2%, so the regenerative capacity of this tissue is important for whole body homeostasis/repair and depends on successful SC myogenic progression (i.e., proliferation, differentiation, and fusion). Emerging evidence suggests that SC-mediated muscle regeneration may, in part, be regulated by molecular clocks involved in SC-specific diurnal transcription. Here we provide insights on molecular clock regulation of muscle regeneration/repair and provide a novel perspective on the interplay between SC-specific molecular clocks, myogenic programs, and cell cycle kinetics that underpin myogenic progression.
Collapse
Affiliation(s)
- Ryan E Kahn
- Exercise and Nutrition Research Program, The Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
- Shirley Ryan AbilityLab, Chicago, Illinois, United States
| | - Sudarshan Dayanidhi
- Shirley Ryan AbilityLab, Chicago, Illinois, United States
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Orly Lacham-Kaplan
- Exercise and Nutrition Research Program, The Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - John A Hawley
- Exercise and Nutrition Research Program, The Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| |
Collapse
|
9
|
Zheng Y, Xue C, Chen H, Jia A, Zhao L, Zhang J, Zhang L, Wang Q. Reconstitution and expression of mcy gene cluster in the model cyanobacterium Synechococcus 7942 reveals a role of MC-LR in cell division. THE NEW PHYTOLOGIST 2023; 238:1101-1114. [PMID: 36683448 DOI: 10.1111/nph.18766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Cyanobacterial blooms pose a serious threat to public health due to the presence of cyanotoxins. Microcystin-LR (MC-LR) produced by Microcystis aeruginosa is the most common cyanotoxins. Due to the limitation of isolation, purification, and genetic manipulation techniques, it is difficult to study and verify in situ the biosynthetic pathways and molecular mechanisms of MC-LR. We reassembled the biosynthetic gene cluster (mcy cluster) of MC-LR in vitro by synthetic biology, designed and constructed the strong bidirectional promoter biPpsbA2 , transformed it into Synechococcus 7942, and successfully expressed MC-LR at a level of 0.006-0.018 fg cell-1 d-1 . We found the expression of MC-LR led to abnormal cell division and cellular filamentation, further using various methods proved that by irreversibly competing its GTP-binding site, MC-LR inhibits assembly of the cell division protein FtsZ. The study represents the first reconstitution and expression of the mcy cluster and the autotrophic production of MC-LR in model cyanobacterium, which lays the foundation for resolving the microcystins biosynthesis pathway. The discovered role of MC-LR in cell division reveals a mechanism of how blooming cyanobacteria gain a competitive edge over their nonblooming counterparts.
Collapse
Affiliation(s)
- Yanli Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chunling Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Anqi Jia
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, China
| |
Collapse
|
10
|
Fang M, Chavan AG, LiWang A, Golden SS. Synchronization of the circadian clock to the environment tracked in real time. Proc Natl Acad Sci U S A 2023; 120:e2221453120. [PMID: 36940340 PMCID: PMC10068778 DOI: 10.1073/pnas.2221453120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/08/2023] [Indexed: 03/22/2023] Open
Abstract
The circadian system of the cyanobacterium Synechococcus elongatus PCC 7942 relies on a three-protein nanomachine (KaiA, KaiB, and KaiC) that undergoes an oscillatory phosphorylation cycle with a period of ~24 h. This core oscillator can be reconstituted in vitro and is used to study the molecular mechanisms of circadian timekeeping and entrainment. Previous studies showed that two key metabolic changes that occur in cells during the transition into darkness, changes in the ATP/ADP ratio and redox status of the quinone pool, are cues that entrain the circadian clock. By changing the ATP/ADP ratio or adding oxidized quinone, one can shift the phase of the phosphorylation cycle of the core oscillator in vitro. However, the in vitro oscillator cannot explain gene expression patterns because the simple mixture lacks the output components that connect the clock to genes. Recently, a high-throughput in vitro system termed the in vitro clock (IVC) that contains both the core oscillator and the output components was developed. Here, we used IVC reactions and performed massively parallel experiments to study entrainment, the synchronization of the clock with the environment, in the presence of output components. Our results indicate that the IVC better explains the in vivo clock-resetting phenotypes of wild-type and mutant strains and that the output components are deeply engaged with the core oscillator, affecting the way input signals entrain the core pacemaker. These findings blur the line between input and output pathways and support our previous demonstration that key output components are fundamental parts of the clock.
Collapse
Affiliation(s)
- Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA92093
| | - Archana G. Chavan
- School of Natural Sciences, University of California, Merced, CA95343
| | - Andy LiWang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA92093
- School of Natural Sciences, University of California, Merced, CA95343
- Department of Chemistry & Biochemistry, University of California, Merced, CA95343
| | - Susan S. Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA92093
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
| |
Collapse
|
11
|
Kitaguchi Y, Tei H, Uriu K. Cell size homeostasis under the circadian regulation of cell division in cyanobacteria. J Theor Biol 2022; 553:111260. [PMID: 36057343 DOI: 10.1016/j.jtbi.2022.111260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/10/2022] [Accepted: 08/18/2022] [Indexed: 10/31/2022]
Abstract
Bacterial cells maintain their characteristic cell size over many generations. Several rod-shaped bacteria, such as Escherichia coli and the cyanobacteria Synechococcus elongatus, divide after adding a constant length to their length at birth. Through this division control known as the adder mechanism, perturbation in cell length due to physiological fluctuation decays over generations at a rate of 2-1 per cell division. However, previous experiments have shown that the circadian clock in cyanobacteria reduces cell division frequency at a specific time of day under constant light. This circadian gating should modulate the division control by the adder mechanism, but its significance remains unknown. Here we address how the circadian gating affects cell length, doubling time, and cell length stability in cyanobacteria by using mathematical models. We show that a cell subject to circadian gating grows for a long time, and gives birth to elongated daughter cells. These elongated daughter cells grow faster than the previous generation, as elongation speed is proportional to cell length and divide in a short time before the next gating. Hence, the distributions of doubling time and cell length become bimodal, as observed in experimental data. Interestingly, the average doubling time over the population of cells is independent of gating because the extension of doubling time by gating is compensated by its reduction in the subsequent generation. On the other hand, average cell length is increased by gating, suggesting that the circadian clock controls cell length. We then show that the decay rate of perturbation in cell length depends on the ratio of delay in division by the gating τG to the average doubling time τ0 as [Formula: see text] . We estimated τG≈2.5, τ0≈13.6 hours, and τG/τ0≈0.18 from experimental data, indicating that a long doubling time in cyanobacteria maintains the decay rate similar to that of the adder mechanism. Thus, our analysis suggests that the acquisition of the circadian clock during evolution did not impose a constraint on cell size homeostasis in cyanobacteria.
Collapse
Affiliation(s)
- Yuta Kitaguchi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1129, Japan.
| | - Hajime Tei
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1129, Japan
| | - Koichiro Uriu
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1129, Japan
| |
Collapse
|
12
|
Swan JA, Sandate CR, Chavan AG, Freeberg AM, Etwaru D, Ernst DC, Palacios JG, Golden SS, LiWang A, Lander GC, Partch CL. Coupling of distant ATPase domains in the circadian clock protein KaiC. Nat Struct Mol Biol 2022; 29:759-766. [PMID: 35864165 DOI: 10.1038/s41594-022-00803-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
The AAA+ family member KaiC is the central pacemaker for circadian rhythms in the cyanobacterium Synechococcus elongatus. Composed of two hexameric rings of adenosine triphosphatase (ATPase) domains with tightly coupled activities, KaiC undergoes a cycle of autophosphorylation and autodephosphorylation on its C-terminal (CII) domain that restricts binding of clock proteins on its N-terminal (CI) domain to the evening. Here, we use cryogenic-electron microscopy to investigate how daytime and nighttime states of CII regulate KaiB binding on CI. We find that the CII hexamer is destabilized during the day but takes on a rigidified C2-symmetric state at night, concomitant with ring-ring compression. Residues at the CI-CII interface are required for phospho-dependent KaiB association, coupling ATPase activity on CI to cooperative KaiB recruitment. Together, these studies clarify a key step in the regulation of cyanobacterial circadian rhythms by KaiC phosphorylation.
Collapse
Affiliation(s)
- Jeffrey A Swan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Colby R Sandate
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Archana G Chavan
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA
| | - Alfred M Freeberg
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Diana Etwaru
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Dustin C Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA
| | - Joseph G Palacios
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andy LiWang
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, CA, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA. .,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
13
|
Abstract
KaiC, a core clock protein in the cyanobacterial circadian clock system, hydrolyzes adenosine triphosphate (ATP) at two distinct sites in a slow but ordered manner to measure the circadian timescale. We used biochemical and structural biology techniques to characterize the properties and interplay of dual-adenosine triphosphatase (ATPase) active sites. Our results show that the N-terminal and C-terminal ATPases communicate with each other through an interface between the N-terminal and C-terminal domains in KaiC. The dual-ATPase sites are regulated rhythmically in a concerted or opposing manner dependent on the phase of the circadian clock system, controlling the affinities of KaiC for other clock proteins, KaiA and KaiB. KaiC is a dual adenosine triphosphatase (ATPase), with one active site in its N-terminal domain and another in its C-terminal domain, that drives the circadian clock system of cyanobacteria through sophisticated coordination of the two sites. To elucidate the coordination mechanism, we studied the contribution of the dual-ATPase activities in the ring-shaped KaiC hexamer and these structural bases for activation and inactivation. At the N-terminal active site, a lytic water molecule is sequestered between the N-terminal domains, and its reactivity to adenosine triphosphate (ATP) is controlled by the quaternary structure of the N-terminal ring. The C-terminal ATPase activity is regulated mostly by water-incorporating voids between the C-terminal domains, and the size of these voids is sensitive to phosphoryl modification of S431. The up-regulatory effect on the N-terminal ATPase activity inversely correlates with the affinity of KaiC for KaiB, a clock protein constitutes the circadian oscillator together with KaiC and KaiA, and the complete dissociation of KaiB from KaiC requires KaiA-assisted activation of the dual ATPase. Delicate interactions between the N-terminal and C-terminal rings make it possible for the components of the dual ATPase to work together, thereby driving the assembly and disassembly cycle of KaiA and KaiB.
Collapse
|
14
|
Abstract
Disruption of circadian rhythms causes decreased health and fitness, and evidence from multiple organisms links clock disruption to dysregulation of the cell cycle. However, the function of circadian regulation for the essential process of DNA replication remains elusive. Here, we demonstrate that in the cyanobacterium Synechococcus elongatus, a model organism with the simplest known circadian oscillator, the clock generates rhythms in DNA replication to minimize the number of open replication forks near dusk that would have to complete after sunset. Metabolic rhythms generated by the clock ensure that resources are available early at night to support any remaining replication forks. Combining mathematical modeling and experiments, we show that metabolic defects caused by clock-environment misalignment result in premature replisome disassembly and replicative abortion in the dark, leaving cells with incomplete chromosomes that persist through the night. Our study thus demonstrates that a major function of this ancient clock in cyanobacteria is to ensure successful completion of genome replication in a cycling environment.
Collapse
|
15
|
Arbel-Goren R, Buonfiglio V, Di Patti F, Camargo S, Zhitnitsky A, Valladares A, Flores E, Herrero A, Fanelli D, Stavans J. Robust, coherent, and synchronized circadian clock-controlled oscillations along Anabaena filaments. eLife 2021; 10:64348. [PMID: 33749592 PMCID: PMC8064755 DOI: 10.7554/elife.64348] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/20/2021] [Indexed: 02/01/2023] Open
Abstract
Circadian clocks display remarkable reliability despite significant stochasticity in biomolecular reactions. We study the dynamics of a circadian clock-controlled gene at the individual cell level in Anabaena sp. PCC 7120, a multicellular filamentous cyanobacterium. We found significant synchronization and spatial coherence along filaments, clock coupling due to cell-cell communication, and gating of the cell cycle. Furthermore, we observed low-amplitude circadian oscillatory transcription of kai genes encoding the post-transcriptional core oscillatory circuit and high-amplitude oscillations of rpaA coding for the master regulator transducing the core clock output. Transcriptional oscillations of rpaA suggest an additional level of regulation. A stochastic one-dimensional toy model of coupled clock cores and their phosphorylation states shows that demographic noise can seed stochastic oscillations outside the region where deterministic limit cycles with circadian periods occur. The model reproduces the observed spatio-temporal coherence along filaments and provides a robust description of coupled circadian clocks in a multicellular organism.
Collapse
Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Valentina Buonfiglio
- Dipartimento di Fisica e Astronomia, Università di Firenze, INFN and CSDC, Sesto Fiorentino, Italy
| | - Francesca Di Patti
- Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, Sesto Fiorentino, Italy
| | - Sergio Camargo
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Zhitnitsky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Duccio Fanelli
- Dipartimento di Fisica e Astronomia, Università di Firenze, INFN and CSDC, Sesto Fiorentino, Italy
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
16
|
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.
Collapse
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.)
| |
Collapse
|
17
|
Lee M, Woo HM. A Logic NAND Gate for Controlling Gene Expression in a Circadian Rhythm in Cyanobacteria. ACS Synth Biol 2020; 9:3210-3216. [PMID: 33263998 DOI: 10.1021/acssynbio.0c00455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To enable circadian control of gene expression in cyanobacteria, we constructed a genetic logic gate (NAND) using orthogonal promoters via modular CRISPR interference. The NAND gates were tested in Synechococcus elongatus PCC 7942 using a fluorescent reporter. The NAND gate dynamics were characterized based on the affinity of the dCas9 complex to the output element. Upon connecting tight gene repressions with the circadian promoter (the purF gene; peak expression at dawn), inversed peak expressions were obtained as an output of the NAND gate although the retroactivities were shown in the ON and OFF states. A dark-responsive genetic element of the NAND gate was also expanded to an AND gate in S. elongatus PCC 7942. These cyanobacterial NAND and AND gates could facilitate the control of gene expressions in dynamic metabolic engineering technologies, thereby enabling the cyanobacteria to serve as biosolar cell factories.
Collapse
Affiliation(s)
- Mieun Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| |
Collapse
|
18
|
Springstein BL, Nürnberg DJ, Weiss GL, Pilhofer M, Stucken K. Structural Determinants and Their Role in Cyanobacterial Morphogenesis. Life (Basel) 2020; 10:E355. [PMID: 33348886 PMCID: PMC7766704 DOI: 10.3390/life10120355] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Cells have to erect and sustain an organized and dynamically adaptable structure for an efficient mode of operation that allows drastic morphological changes during cell growth and cell division. These manifold tasks are complied by the so-called cytoskeleton and its associated proteins. In bacteria, FtsZ and MreB, the bacterial homologs to tubulin and actin, respectively, as well as coiled-coil-rich proteins of intermediate filament (IF)-like function to fulfil these tasks. Despite generally being characterized as Gram-negative, cyanobacteria have a remarkably thick peptidoglycan layer and possess Gram-positive-specific cell division proteins such as SepF and DivIVA-like proteins, besides Gram-negative and cyanobacterial-specific cell division proteins like MinE, SepI, ZipN (Ftn2) and ZipS (Ftn6). The diversity of cellular morphologies and cell growth strategies in cyanobacteria could therefore be the result of additional unidentified structural determinants such as cytoskeletal proteins. In this article, we review the current advances in the understanding of the cyanobacterial cell shape, cell division and cell growth.
Collapse
Affiliation(s)
- Benjamin L. Springstein
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis J. Nürnberg
- Department of Physics, Biophysics and Biochemistry of Photosynthetic Organisms, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Gregor L. Weiss
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Karina Stucken
- Department of Food Engineering, Universidad de La Serena, La Serena 1720010, Chile;
| |
Collapse
|
19
|
Involvement of glycogen metabolism in circadian control of UV resistance in cyanobacteria. PLoS Genet 2020; 16:e1009230. [PMID: 33253146 PMCID: PMC7728383 DOI: 10.1371/journal.pgen.1009230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/10/2020] [Accepted: 10/28/2020] [Indexed: 11/30/2022] Open
Abstract
Most organisms harbor circadian clocks as endogenous timing systems in order to adapt to daily environmental changes, such as exposure to ultraviolet (UV) light. It has been hypothesized that the circadian clock evolved to prevent UV-sensitive activities, such as DNA replication and cell division, during the daytime. Indeed, circadian control of UV resistance has been reported in several eukaryotic organisms, from algae to higher organisms, although the underlying mechanisms remain unknown. Here, we demonstrate that the unicellular cyanobacterium Synechococcus elongatus PCC 7942 exhibits a circadian rhythm in resistance to UV-C and UV-B light, which is higher during subjective dawn and lower during subjective dusk. Nullification of the clock gene cluster kaiABC or the DNA-photolyase phr abolished rhythmicity with constitutively lower resistance to UV-C light, and amino acid substitutions of KaiC altered the period lengths of the UV-C resistance rhythm. In order to elucidate the molecular mechanism underlying the circadian regulation of UV-C resistance, transposon insertion mutants that alter UV-C resistance were isolated. Mutations to the master circadian output mediator genes sasA and rpaA and the glycogen degradation enzyme gene glgP abolished circadian rhythms of UV-C resistance with constitutively high UV-C resistance. Combining these results with further experiments using ATP synthesis inhibitor and strains with modified metabolic pathways, we showed that UV-C resistance is weakened by directing more metabolic flux from the glycogen degradation to catabolic pathway such as oxidative pentose phosphate pathway and glycolysis. We suggest glycogen-related metabolism in the dark affects circadian control in UV sensitivity, while the light masks this effect through the photolyase function. Most organisms harbor circadian clocks to adapt to daily environmental changes. It has been hypothesized that adaptation to UV radiation during the day was a driving force of the evolution of the circadian clock (known as “the flight from light” hypothesis). Thus, understanding the relationship with UV resistance is important to consider the physiological relevance and an evolutionary origin of the circadian clock. We here demonstrate that the unicellular cyanobacterium, Synechococcus elongatus exhibits a circadian rhythm in resistance to UV-C light, which is higher and lower during subjective dawn and dusk, respectively. This rhythm was abolished by nullification of the clock gene cluster kaiABC, and the period length was changed consistently by period mutations on kaiC. Genetic screening revealed that nullification of clock-associating genes sasA, cikA and rpaA, and of a glycogen degradation enzyme gene glgP abolished or attenuated the UV-resistance rhythm. Combining these results with further experiments using an ATP synthesis inhibitor and strains with modified metabolic pathways, we suggest a that the circadian clock confers adaptive fitness by balancing a trade-off between glycogen-related energy metabolism and the UV-resistance property.
Collapse
|
20
|
Springstein BL, Weissenbach J, Koch R, Stücker F, Stucken K. The role of the cytoskeletal proteins MreB and FtsZ in multicellular cyanobacteria. FEBS Open Bio 2020; 10:2510-2531. [PMID: 33112491 PMCID: PMC7714070 DOI: 10.1002/2211-5463.13016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/17/2020] [Accepted: 10/26/2020] [Indexed: 01/28/2023] Open
Abstract
Multiseriate and true‐branching cyanobacteria are at the peak of prokaryotic morphological complexity. However, little is known about the mechanisms governing multiplanar cell division and morphogenesis. Here, we study the function of the prokaryotic cytoskeletal proteins, MreB and FtsZ in Fischerella muscicola PCC 7414 and Chlorogloeopsis fritschii PCC 6912. Vancomycin and HADA labeling revealed a mixed apical, septal, and lateral trichome growth mode in F. muscicola, whereas C. fritschii exhibits septal growth. In all morphotypes from both species, MreB forms either linear filaments or filamentous strings and can interact with FtsZ. Furthermore, multiplanar cell division in F. muscicola likely depends on FtsZ dosage. Our results lay the groundwork for future studies on cytoskeletal proteins in morphologically complex cyanobacteria.
Collapse
Affiliation(s)
| | - Julia Weissenbach
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
| | - Robin Koch
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
| | - Fenna Stücker
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
| | - Karina Stucken
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Germany
| |
Collapse
|
21
|
Ho PY, Martins BMC, Amir A. A Mechanistic Model of the Regulation of Division Timing by the Circadian Clock in Cyanobacteria. Biophys J 2020; 118:2905-2913. [PMID: 32497517 DOI: 10.1016/j.bpj.2020.04.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/02/2020] [Accepted: 04/30/2020] [Indexed: 11/15/2022] Open
Abstract
The cyanobacterium Synechococcus elongatus possesses a circadian clock in the form of a group of proteins whose concentrations and phosphorylation states oscillate with daily periodicity under constant conditions. The circadian clock regulates the cell cycle such that the timing of the cell divisions is biased toward certain times during the circadian period, but the mechanism underlying this phenomenon remains unclear. Here, we propose a mechanism in which a protein limiting for division accumulates at a rate proportional to the cell volume growth and is modulated by the clock. This "modulated rate" model, in which the clock signal is integrated over time to affect division timing, differs fundamentally from the previously proposed "gating" concept, in which the clock is assumed to suppress divisions during a specific time window. We found that although both models can capture the single-cell statistics of division timing in S. elongatus, only the modulated rate model robustly places divisions away from darkness during changes in the environment. Moreover, within the framework of the modulated rate model, existing experiments on S. elongatus are consistent with the simple mechanism that division timing is regulated by the accumulation of a division limiting protein in a phase with genes whose activity peaks at dusk.
Collapse
Affiliation(s)
- Po-Yi Ho
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - Bruno M C Martins
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts.
| |
Collapse
|
22
|
Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms. Nat Commun 2020; 11:2763. [PMID: 32488076 PMCID: PMC7265539 DOI: 10.1038/s41467-020-16593-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 05/04/2020] [Indexed: 01/23/2023] Open
Abstract
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit daily rhythms in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 6% of Plasmodium falciparum genes show 24 h rhythms in expression under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a 24 h transcriptional rhythm and disrupting it in rodent malaria parasites shortens the IDC by 2-3 h; (v) Multiple processes including DNA replication, and the ubiquitin and proteasome pathways, are affected by loss of coordination with host rhythms and by disruption of SR10. Our results reveal malaria parasites are at least partly responsible for scheduling the IDC and coordinating their development with host daily rhythms. The mechanism underlying periodicity of Plasmodium’s intra-erythrocytic developmental cycle (IDC) is unclear. Here, Subudhi et al. show that serpentine receptor 10 (SR10) plays a role in regulating the schedule of the IDC in line with the timing of host daily rhythms.
Collapse
|
23
|
The circadian clock and darkness control natural competence in cyanobacteria. Nat Commun 2020; 11:1688. [PMID: 32245943 PMCID: PMC7125226 DOI: 10.1038/s41467-020-15384-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 03/05/2020] [Indexed: 11/15/2022] Open
Abstract
The cyanobacterium Synechococcus elongatus is a model organism for the study of circadian rhythms. It is naturally competent for transformation—that is, it takes up DNA from the environment, but the underlying mechanisms are unclear. Here, we use a genome-wide screen to identify genes required for natural transformation in S. elongatus, including genes encoding a conserved Type IV pilus, genes known to be associated with competence in other bacteria, and others. Pilus biogenesis occurs daily in the morning, while natural transformation is maximal when the onset of darkness coincides with the dusk circadian peak. Thus, the competence state in cyanobacteria is regulated by the circadian clock and can adapt to seasonal changes of day length. The cyanobacterium Synechococcus elongatus is a model organism for the study of circadian rhythms, and is naturally competent for transformation. Here, Taton et al. identify genes required for natural transformation in this organism, and show that the coincidence of circadian dusk and darkness regulates the competence state in different day lengths.
Collapse
|
24
|
Synechocystis KaiC3 Displays Temperature- and KaiB-Dependent ATPase Activity and Is Important for Growth in Darkness. J Bacteriol 2020; 202:JB.00478-19. [PMID: 31767776 PMCID: PMC6989803 DOI: 10.1128/jb.00478-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/17/2019] [Indexed: 02/05/2023] Open
Abstract
Cyanobacteria form a heterogeneous bacterial group with diverse lifestyles, acclimation strategies, and differences in the presence of circadian clock proteins. In Synechococcus elongatus PCC 7942, a unique posttranslational KaiABC oscillator drives circadian rhythms. ATPase activity of KaiC correlates with the period of the clock and mediates temperature compensation. Synechocystis sp. strain PCC 6803 expresses additional Kai proteins, of which KaiB3 and KaiC3 proteins were suggested to fine-tune the standard KaiAB1C1 oscillator. In the present study, we therefore characterized the enzymatic activity of KaiC3 as a representative of nonstandard KaiC homologs in vitro KaiC3 displayed ATPase activity lower than that of the Synechococcus elongatus PCC 7942 KaiC protein. ATP hydrolysis was temperature dependent. Hence, KaiC3 is missing a defining feature of the model cyanobacterial circadian oscillator. Yeast two-hybrid analysis showed that KaiC3 interacts with KaiB3, KaiC1, and KaiB1. Further, KaiB3 and KaiB1 reduced in vitro ATP hydrolysis by KaiC3. Spot assays showed that chemoheterotrophic growth in constant darkness is completely abolished after deletion of ΔkaiAB1C1 and reduced in the absence of kaiC3 We therefore suggest a role for adaptation to darkness for KaiC3 as well as a cross talk between the KaiC1- and KaiC3-based systems.IMPORTANCE The circadian clock influences the cyanobacterial metabolism, and deeper understanding of its regulation will be important for metabolic optimizations in the context of industrial applications. Due to the heterogeneity of cyanobacteria, characterization of clock systems in organisms apart from the circadian model Synechococcus elongatus PCC 7942 is required. Synechocystis sp. strain PCC 6803 represents a major cyanobacterial model organism and harbors phylogenetically diverged homologs of the clock proteins, which are present in various other noncyanobacterial prokaryotes. By our in vitro studies we unravel the interplay of the multiple Synechocystis Kai proteins and characterize enzymatic activities of the nonstandard clock homolog KaiC3. We show that the deletion of kaiC3 affects growth in constant darkness, suggesting its involvement in the regulation of nonphotosynthetic metabolic pathways.
Collapse
|
25
|
Disruption of the Molecular Circadian Clock and Cancer: An Epigenetic Link. Biochem Genet 2019; 58:189-209. [DOI: 10.1007/s10528-019-09938-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/03/2019] [Indexed: 01/08/2023]
|
26
|
The Cancer Clock Is (Not) Ticking: Links between Circadian Rhythms and Cancer. Clocks Sleep 2019; 1:435-458. [PMID: 33089179 PMCID: PMC7445810 DOI: 10.3390/clockssleep1040034] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/10/2019] [Indexed: 12/23/2022] Open
Abstract
Circadian rhythms regulate many physiological and behavioral processes, including sleep, metabolism and cell division, which have a 24-h oscillation pattern. Rhythmicity is generated by a transcriptional–translational feedback loop in individual cells, which are synchronized by the central pacemaker in the brain and external cues. Epidemiological and clinical studies indicate that disruption of these rhythms can increase both tumorigenesis and cancer progression. Environmental changes (shift work, jet lag, exposure to light at night), mutations in circadian regulating genes, and changes to clock gene expression are recognized forms of disruption and are associated with cancer risk and/or cancer progression. Experimental data in animals and cell cultures further supports the role of the cellular circadian clock in coordinating cell division and DNA repair, and disrupted cellular clocks accelerate cancer cell growth. This review will summarize studies linking circadian disruption to cancer biology and explore how such disruptions may be further altered by common characteristics of tumors including hypoxia and acidosis. We will highlight how circadian rhythms might be exploited for cancer drug development, including how delivery of current chemotherapies may be enhanced using chronotherapy. Understanding the role of circadian rhythms in carcinogenesis and tumor progression will enable us to better understand causes of cancer and how to treat them.
Collapse
|
27
|
Welkie DG, Rubin BE, Diamond S, Hood RD, Savage DF, Golden SS. A Hard Day's Night: Cyanobacteria in Diel Cycles. Trends Microbiol 2019; 27:231-242. [PMID: 30527541 PMCID: PMC6377297 DOI: 10.1016/j.tim.2018.11.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are influential in global geochemistry and are promising candidates for industrial applications. Because the livelihood of cyanobacteria is directly dependent upon light, a comprehensive understanding of metabolism in these organisms requires taking into account the effects of day-night transitions and circadian regulation. These events synchronize intracellular processes with the solar day. Accordingly, metabolism is controlled and structured differently in cyanobacteria than in heterotrophic bacteria. Thus, the approaches applied to engineering heterotrophic bacteria will need to be revised for the cyanobacterial chassis. Here, we summarize important findings related to diurnal metabolism in cyanobacteria and present open questions in the field.
Collapse
Affiliation(s)
- David G Welkie
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA 94720, USA
| | - Rachel D Hood
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, 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.
| |
Collapse
|
28
|
Abstract
Life has adapted to Earth's day-night cycle with the evolution of endogenous biological clocks. Whereas these circadian rhythms typically involve extensive transcription-translation feedback in higher organisms, cyanobacteria have a circadian clock, which functions primarily as a protein-based post-translational oscillator. Known as the Kai system, it consists of three proteins KaiA, KaiB, and KaiC. In this chapter, we provide a detailed structural overview of the Kai components and how they interact to produce circadian rhythms of global gene expression in cyanobacterial cells. We discuss how the circadian oscillation is coupled to gene expression, intertwined with transcription-translation feedback mechanisms, and entrained by input from the environment. We discuss the use of mathematical models and summarize insights into the cyanobacterial circadian clock from theoretical studies. The molecular details of the Kai system are well documented for the model cyanobacterium Synechococcus elongatus, but many less understood varieties of the Kai system exist across the highly diverse phylum of Cyanobacteria. Several species contain multiple kai-gene copies, while others like marine Prochlorococcus strains have a reduced kaiBC-only system, lacking kaiA. We highlight recent findings on the genomic distribution of kai genes in Bacteria and Archaea and finally discuss hypotheses on the evolution of the Kai system.
Collapse
Affiliation(s)
- Joost Snijder
- Snijder Bioscience, Zevenwouden 143, 3524CN, Utrecht, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ilka Maria Axmann
- Synthetic Microbiology, Biology Department, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| |
Collapse
|
29
|
Martins BMC, Tooke AK, Thomas P, Locke JCW. Cell size control driven by the circadian clock and environment in cyanobacteria. Proc Natl Acad Sci U S A 2018; 115:E11415-E11424. [PMID: 30409801 PMCID: PMC6275512 DOI: 10.1073/pnas.1811309115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light-dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.
Collapse
Affiliation(s)
- Bruno M C Martins
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Amy K Tooke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College London, SW7 2AZ London, United Kingdom
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom;
| |
Collapse
|
30
|
Martins BMC, Tooke AK, Thomas P, Locke JCW. Cell size control driven by the circadian clock and environment in cyanobacteria. Proc Natl Acad Sci U S A 2018. [PMID: 30409801 DOI: 10.1002/(sici)1521-1878(200001)22:1¡10::aid-bies4¿3.0.co;2-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light-dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.
Collapse
Affiliation(s)
- Bruno M C Martins
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Amy K Tooke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College London, SW7 2AZ London, United Kingdom
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, CB2 1LR Cambridge, United Kingdom;
| |
Collapse
|
31
|
Köbler C, Schultz SJ, Kopp D, Voigt K, Wilde A. The role of the Synechocystis sp. PCC 6803 homolog of the circadian clock output regulator RpaA in day-night transitions. Mol Microbiol 2018; 110:847-861. [PMID: 30216574 DOI: 10.1111/mmi.14129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/07/2018] [Accepted: 07/12/2018] [Indexed: 01/20/2023]
Abstract
Cyanobacteria exhibit rhythmic gene expression with a period length of 24 hours to adapt to daily environmental changes. In the model organism Synechococcuselongatus PCC 7942, the central oscillator consists of the three proteins KaiA, KaiB and KaiC and utilizes the histidine kinase SasA and its response regulator RpaA as output-signaling pathway. Synechocystis sp. PCC 6803 contains in addition to the canonical kaiAB1C1 gene cluster two further homologs of the kaiB and kaiC genes. Here, we demonstrate that the SasA-RpaA system interacts with the KaiAB1C1 core oscillator only. Interaction with KaiC2 and KaiC3 proteins was not detected, suggesting different signal transduction components for the clock homologs. Inactivation of rpaA in Synechocystis sp. PCC 6803 leads to reduced viability of the mutant in light-dark cycles, especially under mixotrophic growth conditions. Chemoheterotrophic growth of the ∆rpaA strain in the dark was abolished completely. Transcriptomic data revealed that RpaA is mainly involved in the regulation of genes related to CO2 - acclimation in the light and to carbon metabolism in the dark. Further, our results indicate a link between the circadian clock and phototaxis.
Collapse
Affiliation(s)
- Christin Köbler
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Siri-Jasmin Schultz
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Dominik Kopp
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Karsten Voigt
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany.,BIOSS Centre of Biological Signalling Studies, University of Freiburg, 79106, Freiburg, Germany
| |
Collapse
|
32
|
Honda T, Morimoto D, Sako Y, Yoshida T. LexA Binds to Transcription Regulatory Site of Cell Division Gene ftsZ in Toxic Cyanobacterium Microcystis aeruginosa. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:549-556. [PMID: 29774437 DOI: 10.1007/s10126-018-9826-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Previously, we showed that DNA replication and cell division in toxic cyanobacterium Microcystis aeruginosa are coordinated by transcriptional regulation of cell division gene ftsZ and that an unknown protein specifically bound upstream of ftsZ (BpFz; DNA-binding protein to an upstream site of ftsZ) during successful DNA replication and cell division. Here, we purified BpFz from M. aeruginosa strain NIES-298 using DNA-affinity chromatography and gel-slicing combined with gel electrophoresis mobility shift assay (EMSA). The N-terminal amino acid sequence of BpFz was identified as TNLESLTQ, which was identical to that of transcription repressor LexA from NIES-843. EMSA analysis using mutant probes showed that the sequence GTACTAN3GTGTTC was important in LexA binding. Comparison of the upstream regions of lexA in the genomes of closely related cyanobacteria suggested that the sequence TASTRNNNNTGTWC could be a putative LexA recognition sequence (LexA box). Searches for TASTRNNNNTGTWC as a transcriptional regulatory site (TRS) in the genome of M. aeruginosa NIES-843 showed that it was present in genes involved in cell division, photosynthesis, and extracellular polysaccharide biosynthesis. Considering that BpFz binds to the TRS of ftsZ during normal cell division, LexA may function as a transcriptional activator of genes related to cell reproduction in M. aeruginosa, including ftsZ. This may be an example of informality in the control of bacterial cell division.
Collapse
Affiliation(s)
- Takashi Honda
- Graduate school of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Daichi Morimoto
- Graduate school of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiko Sako
- Graduate school of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Graduate school of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan.
| |
Collapse
|
33
|
Roles for ClpXP in regulating the circadian clock in Synechococcus elongatus. Proc Natl Acad Sci U S A 2018; 115:E7805-E7813. [PMID: 30061418 DOI: 10.1073/pnas.1800828115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In cyanobacteria, the KaiABC posttranslational oscillator drives circadian rhythms of gene expression and controls the timing of cell division. The Kai-based oscillator can be reconstituted in vitro, demonstrating that the clock can run without protein synthesis and degradation; however, protein degradation is known to be important for clock function in vivo. Here, we report that strains deficient in the ClpXP1P2 protease have, in addition to known long-period circadian rhythms, an exaggerated ability to synchronize with the external environment (reduced "jetlag") compared with WT strains. Deletion of the ClpX chaperone, but not the protease subunits ClpP1 or ClpP2, results in cell division defects in a manner that is dependent on the expression of a dusk-peaking factor. We propose that chaperone activities of ClpX are required to coordinate clock control of cell division whereas the protease activities of the ClpXP1P2 complex are required to maintain appropriate periodicity of the clock and its synchronization with the external environment.
Collapse
|
34
|
Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA. Proc Natl Acad Sci U S A 2018; 115:E7174-E7183. [PMID: 29991601 DOI: 10.1073/pnas.1802940115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recurrent pattern of light and darkness generated by Earth's axial rotation has profoundly influenced the evolution of organisms, selecting for both biological mechanisms that respond acutely to environmental changes and circadian clocks that program physiology in anticipation of daily variations. The necessity to integrate environmental responsiveness and circadian programming is exemplified in photosynthetic organisms such as cyanobacteria, which depend on light-driven photochemical processes. The cyanobacterium Synechococcus elongatus PCC 7942 is an excellent model system for dissecting these entwined mechanisms. Its core circadian oscillator, consisting of three proteins, KaiA, KaiB, and KaiC, transmits time-of-day signals to clock-output proteins, which reciprocally regulate global transcription. Research performed under constant light facilitates analysis of intrinsic cycles separately from direct environmental responses but does not provide insight into how these regulatory systems are integrated during light-dark cycles. Thus, we sought to identify genes that are specifically necessary in a day-night environment. We screened a dense bar-coded transposon library in both continuous light and daily cycling conditions and compared the fitness consequences of loss of each nonessential gene in the genome. Although the clock itself is not essential for viability in light-dark cycles, the most detrimental mutations revealed by the screen were those that disrupt KaiA. The screen broadened our understanding of light-dark survival in photosynthetic organisms, identified unforeseen clock-protein interaction dynamics, and reinforced the role of the clock as a negative regulator of a nighttime metabolic program that is essential for S. elongatus to survive in the dark.
Collapse
|
35
|
Jun S, Si F, Pugatch R, Scott M. Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:056601. [PMID: 29313526 PMCID: PMC5897229 DOI: 10.1088/1361-6633/aaa628] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1-3), we review the first 'golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4-7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the 'adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome 'sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.
Collapse
Affiliation(s)
- Suckjoon Jun
- Department of Physics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America. Section of Molecular Biology, Division of Biology, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America
| | | | | | | |
Collapse
|
36
|
Santos TMA, Lammers MG, Zhou M, Sparks IL, Rajendran M, Fang D, De Jesus CLY, Carneiro GFR, Cui Q, Weibel DB. Small Molecule Chelators Reveal That Iron Starvation Inhibits Late Stages of Bacterial Cytokinesis. ACS Chem Biol 2018; 13:235-246. [PMID: 29227619 DOI: 10.1021/acschembio.7b00560] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial cell division requires identification of the division site, assembly of the division machinery, and constriction of the cell envelope. These processes are regulated in response to several cellular and environmental signals. Here, we use small molecule iron chelators to characterize the surprising connections between bacterial iron homeostasis and cell division. We demonstrate that iron starvation downregulates the transcription of genes encoding proteins involved in cell division, reduces protein biosynthesis, and prevents correct positioning of the division machinery at the division site. These combined events arrest the constriction of the cell during late stages of cytokinesis in a manner distinct from known mechanisms of inhibiting cell division. Overexpression of genes encoding cell division proteins or iron transporters partially suppresses the biological activity of iron chelators and restores growth and division. We propose a model demonstrating the effect of iron availability on the regulatory mechanisms coordinating division in response to the nutritional state of the cell.
Collapse
Affiliation(s)
- Thiago M. A. Santos
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Matthew G. Lammers
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Maoquan Zhou
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Ian L. Sparks
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Madhusudan Rajendran
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Dong Fang
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Crystal L. Y. De Jesus
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Gabriel F. R. Carneiro
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Douglas B. Weibel
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department
of Biomedical Engineering, University of Wisconsin—Madison, 1550 Engineering Drive, Madison, Wisconsin 53706, United States
| |
Collapse
|
37
|
Inoue K, Araki T, Endo M. Circadian clock during plant development. JOURNAL OF PLANT RESEARCH 2018; 131:59-66. [PMID: 29134443 PMCID: PMC5897470 DOI: 10.1007/s10265-017-0991-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/06/2017] [Indexed: 05/14/2023]
Abstract
Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season. Recent genomic studies have demonstrated that polymorphism in circadian clock genes may contribute to local adaptations over a wide range of latitudes in many plant species. In the present review, we summarize the circadian regulation of biological processes throughout the life cycle of plants, and describe the contribution of the circadian clock to local adaptation.
Collapse
Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| |
Collapse
|
38
|
Three-Dimensional Superresolution Imaging of the FtsZ Ring during Cell Division of the Cyanobacterium Prochlorococcus. mBio 2017; 8:mBio.00657-17. [PMID: 29162705 PMCID: PMC5698547 DOI: 10.1128/mbio.00657-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Superresolution imaging has revealed subcellular structures and protein interactions in many organisms. However, superresolution microscopy with lateral resolution better than 100 nm has not been achieved in photosynthetic cells due to the interference of a high-autofluorescence background. Here, we developed a photobleaching method to effectively reduce the autofluorescence of cyanobacterial and plant cells. We achieved lateral resolution of ~10 nm with stochastic optical reconstruction microscopy (STORM) in the sphere-shaped cyanobacterium Prochlorococcus and the flowering plant Arabidopsis thaliana. During the cell cycle of Prochlorococcus, we characterized the three-dimensional (3D) organization of the cell division protein FtsZ, which forms a ring structure at the division site and is important for cytokinesis of bacteria and chloroplasts. Although the FtsZ ring assembly process in rod-shaped bacteria has been studied extensively, it has rarely been studied in sphere-shaped bacteria. Similarly to rod-shaped bacteria, our results with Prochlorococcus also showed the assembly of FtsZ clusters into incomplete rings and then complete rings during cell division. Differently from rod-shaped bacteria, the FtsZ ring diameter was not found to decrease during Prochlorococcus cell division. We also discovered a novel double-Z-ring structure, which may be the Z rings of two daughter cells in a predivisional mother cell. Our results showed a quantitative picture of the in vivo Z ring organization of sphere-shaped bacteria. Superresolution microscopy has not been widely used to study photosynthetic cells due to their high-autofluorescence background. Here, we developed a photobleaching method to reduce the autofluorescence of cyanobacteria and plant cells. After photobleaching, we performed superresolution imaging in the cyanobacterium Prochlorococcus and the flowering plant Arabidopsis thaliana with ~10-nm resolution, which is the highest resolution in a photosynthetic cell. With this method, we characterized the 3D organization of the cell division protein FtsZ in Prochlorococcus. We found that the morphological variation of the FtsZ ring during cell division of the sphere-shaped cyanobacterium Prochlorococcus is similar but not identical to that of rod-shaped bacteria. Our method might also be applicable to other photosynthetic organisms.
Collapse
|
39
|
Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers SV, Axmann IM, Wiegard A. Minimal tool set for a prokaryotic circadian clock. BMC Evol Biol 2017; 17:169. [PMID: 28732467 PMCID: PMC5520375 DOI: 10.1186/s12862-017-0999-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear. RESULTS Using a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs. CONCLUSION Our analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.
Collapse
Affiliation(s)
- Nicolas M. Schmelling
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
| | - Robert Lehmann
- Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, 10115 Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea, Albert-Ludwigs-University Freiburg, Institute of Biology II, Schaenzlestrasse 1, Freiburg, 79104 Germany
| | - Christian Beck
- Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, 10115 Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Albert-Ludwigs-University Freiburg, Institute of Biology II, Schaenzlestrasse 1, Freiburg, 79104 Germany
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
| | - Anika Wiegard
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
| |
Collapse
|
40
|
Lambert G, Chew J, Rust MJ. Costs of Clock-Environment Misalignment in Individual Cyanobacterial Cells. Biophys J 2017; 111:883-891. [PMID: 27558731 DOI: 10.1016/j.bpj.2016.07.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/11/2016] [Accepted: 07/01/2016] [Indexed: 11/29/2022] Open
Abstract
Circadian rhythms are endogenously generated daily oscillations in physiology that are found in all kingdoms of life. Experimental studies have shown that the fitness of Synechococcus elongatus, a photosynthetic microorganism, is severely affected in non-24-h environments. However, it has been difficult to study the effects of clock-environment mismatch on cellular physiology because such measurements require a precise determination of both clock state and growth rate in the same cell. Here, we designed a microscopy platform that allows us to expose cyanobacterial cells to pulses of light and dark while quantitatively measuring their growth, division rate, and circadian clock state over many days. Our measurements reveal that decreased fitness can result from a catastrophic growth arrest caused by unexpected darkness in a small subset of cells with incorrect clock times corresponding to the subjective morning. We find that the clock generates rhythms in the instantaneous growth rate of the cell, and that the time of darkness vulnerability coincides with the time of most rapid growth. Thus, the clock mediates a fundamental trade-off between growth and starvation tolerance in cycling environments. By measuring the response of the circadian rhythm to dark pulses of varying lengths, we constrain a mathematical model of a population's fitness under arbitrary light/dark schedules. This model predicts that the circadian clock is only advantageous in highly regular cycling environments with frequencies sufficiently close to the natural frequency of the clock.
Collapse
Affiliation(s)
- Guillaume Lambert
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois
| | - Justin Chew
- Medical Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, Illinois
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois.
| |
Collapse
|
41
|
Liu X, Dang Y, Matsu-Ura T, He Y, He Q, Hong CI, Liu Y. DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition. Mol Cell 2017. [PMID: 28648778 DOI: 10.1016/j.molcel.2017.05.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle. Here, we show that DNA replication is required for circadian clock function in Neurospora. Genetic and pharmacological inhibition of DNA replication abolished both overt and molecular rhythmicities by repressing frequency (frq) gene transcription. DNA replication is essential for the rhythmic changes of nucleosome composition at the frq promoter. The FACT complex, known to be involved in histone disassembly/reassembly, is required for clock function and is recruited to the frq promoter in a replication-dependent manner to promote replacement of histone H2A.Z by H2A. Finally, deletion of H2A.Z uncoupled the dependence of the circadian clock on DNA replication. Together, these results establish circadian clock and cell cycle as interdependent coupled oscillators and identify DNA replication as a critical process in the circadian mechanism.
Collapse
Affiliation(s)
- Xiao Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Toru Matsu-Ura
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yubo He
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA; Department of Biochemistry and Cell Biology, McMurtry College, Rice University, Houston, TX 77005, USA
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Christian I Hong
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.
| |
Collapse
|
42
|
Shostak A. Circadian Clock, Cell Division, and Cancer: From Molecules to Organism. Int J Mol Sci 2017; 18:E873. [PMID: 28425940 PMCID: PMC5412454 DOI: 10.3390/ijms18040873] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022] Open
Abstract
As a response to environmental changes driven by the Earth's axial rotation, most organisms evolved an internal biological timer-the so called circadian clock-which regulates physiology and behavior in a rhythmic fashion. Emerging evidence suggests an intimate interplay between the circadian clock and another fundamental rhythmic process, the cell cycle. However, the precise mechanisms of this connection are not fully understood. Disruption of circadian rhythms has a profound impact on cell division and cancer development and, vice versa, malignant transformation causes disturbances of the circadian clock. Conventional knowledge attributes tumor suppressor properties to the circadian clock. However, this implication might be context-dependent, since, under certain conditions, the clock can also promote tumorigenesis. Therefore, a better understanding of the molecular links regulating the physiological balance between the two cycles will have potential significance for the treatment of cancer and associated disorders.
Collapse
Affiliation(s)
- Anton Shostak
- Circadian Rhythms and Molecular Clocks Group, Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany.
| |
Collapse
|
43
|
Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang YG, Heisler J, Li S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. Structural basis of the day-night transition in a bacterial circadian clock. Science 2017; 355:1174-1180. [PMID: 28302851 DOI: 10.1126/science.aag2516] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 02/13/2017] [Indexed: 12/14/2022]
Abstract
Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post-adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA.
Collapse
Affiliation(s)
- Roger Tseng
- Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Nicolette F Goularte
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Archana Chavan
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jansen Luu
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Susan E Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Joel Heisler
- Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alicia K Michael
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, 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
- Quantitative and Systems Biology, University of California, Merced, CA 95343, USA. .,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.,Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA.,Health Sciences Research Institute, University of California, Merced, CA 95343, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA. .,Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
44
|
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.
Collapse
|
45
|
Westermark S, Steuer R. Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach. Front Bioeng Biotechnol 2016; 4:95. [PMID: 28083530 PMCID: PMC5183639 DOI: 10.3389/fbioe.2016.00095] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 12/09/2016] [Indexed: 11/29/2022] Open
Abstract
Oxygenic photosynthesis dominates global primary productivity ever since its evolution more than three billion years ago. While many aspects of phototrophic growth are well understood, it remains a considerable challenge to elucidate the manifold dependencies and interconnections between the diverse cellular processes that together facilitate the synthesis of new cells. Phototrophic growth involves the coordinated action of several layers of cellular functioning, ranging from the photosynthetic light reactions and the electron transport chain, to carbon-concentrating mechanisms and the assimilation of inorganic carbon. It requires the synthesis of new building blocks by cellular metabolism, protection against excessive light, as well as diurnal regulation by a circadian clock and the orchestration of gene expression and cell division. Computational modeling allows us to quantitatively describe these cellular functions and processes relevant for phototrophic growth. As yet, however, computational models are mostly confined to the inner workings of individual cellular processes, rather than describing the manifold interactions between them in the context of a living cell. Using cyanobacteria as model organisms, this contribution seeks to summarize existing computational models that are relevant to describe phototrophic growth and seeks to outline their interactions and dependencies. Our ultimate aim is to understand cellular functioning and growth as the outcome of a coordinated operation of diverse yet interconnected cellular processes.
Collapse
Affiliation(s)
- Stefanie Westermark
- Fachinstitut für Theoretische Biologie (ITB), Institut für Biologie, Humboldt-Universität zu Berlin , Berlin , Germany
| | - Ralf Steuer
- Fachinstitut für Theoretische Biologie (ITB), Institut für Biologie, Humboldt-Universität zu Berlin , Berlin , Germany
| |
Collapse
|
46
|
Abstract
Organisms use circadian clocks to generate 24‐h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these different frequencies are generated. Here, we examine this problem by studying the coupling of the clock to the alternative sigma factor sigC in the cyanobacterium Synechococcus elongatus. Using single‐cell microscopy, we find that psbAI, a key photosynthesis gene regulated by both sigC and the clock, is activated with two peaks of gene expression every circadian cycle under constant low light. This two‐peak oscillation is dependent on sigC, without which psbAI rhythms revert to one oscillatory peak per day. We also observe two circadian peaks of elongation rate, which are dependent on sigC, suggesting a role for the frequency doubling in modulating growth. We propose that the two‐peak rhythm in psbAI expression is generated by an incoherent feedforward loop between the clock, sigC and psbAI. Modelling and experiments suggest that this could be a general network motif to allow frequency doubling of outputs.
Collapse
Affiliation(s)
| | - Arijit K Das
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Liliana Antunes
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - James Cw Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK .,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Microsoft Research, Cambridge, UK
| |
Collapse
|
47
|
MacCready JS, Schossau J, Osteryoung KW, Ducat DC. Robust Min-system oscillation in the presence of internal photosynthetic membranes in cyanobacteria. Mol Microbiol 2016; 103:483-503. [PMID: 27891682 DOI: 10.1111/mmi.13571] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2016] [Indexed: 11/29/2022]
Abstract
The oscillatory Min system of Escherichia coli defines the cell division plane by regulating the site of FtsZ-ring formation and represents one of the best-understood examples of emergent protein self-organization in nature. The oscillatory patterns of the Min-system proteins MinC, MinD and MinE (MinCDE) are strongly dependent on the geometry of membranes they bind. Complex internal membranes within cyanobacteria could disrupt this self-organization by sterically occluding or sequestering MinCDE from the plasma membrane. Here, it was shown that the Min system in the cyanobacterium Synechococcus elongatus PCC 7942 oscillates from pole-to-pole despite the potential spatial constraints imposed by their extensive thylakoid network. Moreover, reaction-diffusion simulations predict robust oscillations in modeled cyanobacterial cells provided that thylakoid network permeability is maintained to facilitate diffusion, and suggest that Min proteins require preferential affinity for the plasma membrane over thylakoids to correctly position the FtsZ ring. Interestingly, in addition to oscillating, MinC exhibits a midcell localization dependent on MinD and the DivIVA-like protein Cdv3, indicating that two distinct pools of MinC are coordinated in S. elongatus. Our results provide the first direct evidence for Min oscillation outside of E. coli and have broader implications for Min-system function in bacteria and organelles with internal membrane systems.
Collapse
Affiliation(s)
- Joshua S MacCready
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Jory Schossau
- Department of Computer Science, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Daniel C Ducat
- Department of Biochemistry, MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
48
|
|
49
|
Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers SV, Axmann IM, Wiegard A. Minimal Tool Set for a Prokaryotic Circadian Clock.. [DOI: 10.1101/075291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
AbstractBackgroundCircadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacteriumSynechococcus elongatusPCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.ResultsUsing a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous toSynechococcus elongatusPCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.ConclusionOur analysis of 11,264 genomes clearly demonstrates that components of theSynechococcus elongatusPCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.
Collapse
|
50
|
A Combined Computational and Genetic Approach Uncovers Network Interactions of the Cyanobacterial Circadian Clock. J Bacteriol 2016; 198:2439-47. [PMID: 27381914 DOI: 10.1128/jb.00235-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/27/2016] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED Two-component systems (TCS) that employ histidine kinases (HK) and response regulators (RR) are critical mediators of cellular signaling in bacteria. In the model cyanobacterium Synechococcus elongatus PCC 7942, TCSs control global rhythms of transcription that reflect an integration of time information from the circadian clock with a variety of cellular and environmental inputs. The HK CikA and the SasA/RpaA TCS transduce time information from the circadian oscillator to modulate downstream cellular processes. Despite immense progress in understanding of the circadian clock itself, many of the connections between the clock and other cellular signaling systems have remained enigmatic. To narrow the search for additional TCS components that connect to the clock, we utilized direct-coupling analysis (DCA), a statistical analysis of covariant residues among related amino acid sequences, to infer coevolution of new and known clock TCS components. DCA revealed a high degree of interaction specificity between SasA and CikA with RpaA, as expected, but also with the phosphate-responsive response regulator SphR. Coevolutionary analysis also predicted strong specificity between RpaA and a previously undescribed kinase, HK0480 (herein CikB). A knockout of the gene for CikB (cikB) in a sasA cikA null background eliminated the RpaA phosphorylation and RpaA-controlled transcription that is otherwise present in that background and suppressed cell elongation, supporting the notion that CikB is an interactor with RpaA and the clock network. This study demonstrates the power of DCA to identify subnetworks and key interactions in signaling pathways and of combinatorial mutagenesis to explore the phenotypic consequences. Such a combined strategy is broadly applicable to other prokaryotic systems. IMPORTANCE Signaling networks are complex and extensive, comprising multiple integrated pathways that respond to cellular and environmental cues. A TCS interaction model, based on DCA, independently confirmed known interactions and revealed a core set of subnetworks within the larger HK-RR set. We validated high-scoring candidate proteins via combinatorial genetics, demonstrating that DCA can be utilized to reduce the search space of complex protein networks and to infer undiscovered specific interactions for signaling proteins in vivo Significantly, new interactions that link circadian response to cell division and fitness in a light/dark cycle were uncovered. The combined analysis also uncovered a more basic core clock, illustrating the synergy and applicability of a combined computational and genetic approach for investigating prokaryotic signaling networks.
Collapse
|