1
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Géron A, Werner J, Wattiez R, Matallana-Surget S. Towards the discovery of novel molecular clocks in Prokaryotes. Crit Rev Microbiol 2024; 50:491-503. [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] [MESH Headings] [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.
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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
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2
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Neira JL, López-Redondo ML, Cámara-Artigas A, Marina A, Contreras A. Structure and dynamics of the cyanobacterial regulator SipA. Arch Biochem Biophys 2024; 754:109943. [PMID: 38395125 DOI: 10.1016/j.abb.2024.109943] [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: 10/31/2023] [Revised: 02/09/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The small, 78-residue long, regulator SipA interacts with the non-bleaching sensor histidine kinase (NblS). We have solved the solution structure of SipA on the basis of 990 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the twenty best structures for the backbone residues, obtained by CYANA, was 1.35 ± 0.21 Å, and 1.90 ± 0.16 Å when all heavy atoms were considered (the target function of CYANA was 0.540 ± 0.08). The structure is that of a β-II class protein, basically formed by a five-stranded β-sheet composed of antiparallel strands following the arrangement: Gly6-Leu11 (β-strand 1), which packs against Leu66-Val69 (β-strand 5) on one side, and against Gly36-Thr42 (β-strand 2) on the other side; Trp50-Phe54 (β-strand 3); and Gly57-Leu60 (β-strand 4). The protein is highly mobile, as shown by measurements of R1, R2, NOE and ηxy relaxation parameters, with an average order parameter () of 0.70; this mobility encompasses movements in different time scales. We hypothesize that this high flexibility allows the interaction with other proteins (among them NblS), and it explains the large conformational stability of SipA.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018, Zaragoza, Spain.
| | - María Luisa López-Redondo
- Unidad Regulación de La Síntesis de Proteínas, Instituto de Biomedicina de Valencia (CSIC), 46010, Valencia, Spain
| | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- CeiA3, 04120, Almería, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (CSIC) and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 46010, Valencia, Spain
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3
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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.
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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
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4
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Hasegawa H, Kobayashi I, Bairagi N, Watanabe S, Tanaka K. DnaK2 Mediates a Negative Feedback Regulation of the Heat Shock Responsive Hik2-Rre1 Two-Component System in the Cyanobacterium Synechococcus Elongatus PCC 7942. PLANT & CELL PHYSIOLOGY 2024; 65:120-127. [PMID: 37856257 DOI: 10.1093/pcp/pcad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
The two-component system (TCS) is a conserved signal transduction module in bacteria. The Hik2-Rre1 system is responsible for transcriptional activation upon high-temperature shift as well as plastoquinone-related redox stress in the cyanobacterium Synechococcus elongatus PCC 7942. As heat-induced de novo protein synthesis was previously shown to be required to quench the heat-activated response, we investigated the underlying mechanism in this study. We found that the heat-inducible transcription activation was alleviated by the overexpression of dnaK2, which is an essential homolog of the highly conserved HSP70 chaperone and whose expression is induced under the control of the Hik2-Rre1 TCS. Phosphorylation of Rre1 correlated with transcription of the regulatory target hspA. The redox stress response was found to be similarly repressed by dnaK2 overexpression. Considered together with the previous information, we propose a negative feedback mechanism of the Hik2-Rre1-dependent stress response that maintains the cellular homeostasis mediated by DnaK2.
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Affiliation(s)
- Hazuki Hasegawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Ikki Kobayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Nachiketa Bairagi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
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5
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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.
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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.
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6
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Alonso-Sáez L, Palacio AS, Cabello AM, Robaina-Estévez S, González JM, Garczarek L, López-Urrutia Á. Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus. mBio 2023:e0342522. [PMID: 37052490 DOI: 10.1128/mbio.03425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO2 fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.
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Affiliation(s)
- Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Antonio S Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana M Cabello
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, IEO-CSIC, Gijón, Asturias, Spain
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7
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Kato N, Iwata K, Kadowaki T, Sonoike K, Hihara Y. Dual Redox Regulation of the DNA-Binding Activity of the Response Regulator RpaB in the Cyanobacterium Synechocystis sp. PCC 6803. PLANT & CELL PHYSIOLOGY 2022; 63:1078-1090. [PMID: 35660918 DOI: 10.1093/pcp/pcac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
The response regulator RpaB plays a central role in transcriptional regulation of photosynthesis-related genes in cyanobacteria. RpaB is phosphorylated by its cognate histidine kinase Hik33 and functions as both an activator and a repressor under low-light conditions, whereas its phosphorylation level and DNA-binding activity promptly decrease upon the upshift of photon flux density, causing changes in the gene expression profile. In this study, we assessed the possibility of redox regulation of the DNA-binding activity of RpaB in Synechocystis sp. PCC 6803 by the addition of inhibitors of photosynthetic electron transport, 3-(3,4-dichlorophenyl)-1,1-dimethylurea and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, or the reducing agent dithiothreitol under different photon flux densities. Analysis of the phosphorylation level of RpaB revealed that reduction of QA and increase in the availability of reducing equivalents at the acceptor side of photosystem I (PSI) can independently trigger dephosphorylation. The redox-state-dependent regulation by an unidentified thiol other than Cys59 of RpaB is prerequisite for the phosphorylation-dependent regulation of the DNA-binding activity. Environmental signals, recognized by Hik33, and metabolic signals recognized as the availability of reducing equivalents, must be integrated at the master regulator RpaB, in order to attain the flexible regulation of acclimatory responses.
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Affiliation(s)
- Naoki Kato
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570 Japan
| | - Kazuki Iwata
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570 Japan
| | - Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570 Japan
| | - Kintake Sonoike
- Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570 Japan
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8
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Decomposing biophotovoltaic current density profiles using the Hilbert-Huang transform reveals influences of circadian clock on cyanobacteria exoelectrogenesis. Sci Rep 2022; 12:10962. [PMID: 35768500 PMCID: PMC9243294 DOI: 10.1038/s41598-022-15111-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 04/14/2022] [Indexed: 11/21/2022] Open
Abstract
Electrons from cyanobacteria photosynthetic and respiratory systems are implicated in current generated in biophotovoltaic (BPV) devices. However, the pathway that electrons follow to electrodes remains largely unknown, limiting progress of applied research. Here we use Hilbert–Huang Transforms to decompose Synechococcus elongatus sp. PCC7942 BPV current density profiles into physically meaningful oscillatory components, and compute their instantaneous frequencies. We develop hypotheses for the genesis of the oscillations via repeat experiments with iron-depleted and 20% CO\documentclass[12pt]{minimal}
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\begin{document}$${_2}$$\end{document}2 enriched biofilms. The oscillations exhibit rhythms that are consistent with the state of the art cyanobacteria circadian model, and putative exoelectrogenic pathways. In particular, we observe oscillations consistent with: rhythmic D1:1 (photosystem II core) expression; circadian-controlled glycogen accumulation; circadian phase shifts under modified intracellular %ATP; and circadian period shortening in the absence of the iron-sulphur protein LdpA. We suggest that the extracted oscillations may be used to reverse-identify proteins and/or metabolites responsible for cyanobacteria exoelectrogenesis.
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9
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Zhu Y, Jung J, Anilkumar S, Ethiraj S, Madira S, Tran NA, Mullis DM, Casey KM, Walsh SK, Stark CJ, Venkatesh A, Boakye A, Wang H, Woo YJ. A novel photosynthetic biologic topical gel for enhanced localized hyperoxygenation augments wound healing in peripheral artery disease. Sci Rep 2022; 12:10028. [PMID: 35705660 PMCID: PMC9200759 DOI: 10.1038/s41598-022-14085-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 02/15/2022] [Indexed: 11/26/2022] Open
Abstract
Peripheral artery disease and the associated ischemic wounds are substantial causes of global morbidity and mortality, affecting over 200 million people worldwide. Although advancements have been made in preventive, pharmacologic, and surgical strategies to treat this disease, ischemic wounds, a consequence of end-stage peripheral artery disease, remain a significant clinical and economic challenge. Synechococcus elongatus is a cyanobacterium that grows photoautotrophically and converts carbon dioxide and water into oxygen. We present a novel topical biologic gel containing S. elongatus that provides oxygen via photosynthesis to augment wound healing by rescuing ischemic tissues caused by peripheral artery disease. By using light rather than blood as a source of energy, our novel topical therapy significantly accelerated wound healing in two rodent ischemic wound models. This novel topical gel can be directly translated to clinical practice by using a localized, portable light source without interfering with patients' daily activities, demonstrating potential to generate a paradigm shift in treating ischemic wounds from peripheral artery disease. Its novelty, low production cost, and ease of clinical translatability can potentially impact the clinical care for millions of patients suffering from peripheral arterial disease.
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Affiliation(s)
- Yuanjia Zhu
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jinsuh Jung
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Shreya Anilkumar
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Sidarth Ethiraj
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Sarah Madira
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Nicholas A Tran
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Danielle M Mullis
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | - Sabrina K Walsh
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Charles J Stark
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Akshay Venkatesh
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Alexander Boakye
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Hanjay Wang
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Y Joseph Woo
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Cardiothoracic Surgery, Falk Cardiovascular Research Center, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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10
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Ibrahim IM, Rowden SJL, Cramer WA, Howe CJ, Puthiyaveetil S. Thiol redox switches regulate the oligomeric state of cyanobacterial Rre1, RpaA, and RpaB response regulators. FEBS Lett 2022; 596:1533-1543. [PMID: 35353903 PMCID: PMC9321951 DOI: 10.1002/1873-3468.14340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/18/2022]
Abstract
Cyanobacteria employ two‐component sensor‐response regulator systems to monitor and respond to environmental challenges. The response regulators RpaA, RpaB, Rre1 and RppA are integral to circadian clock function and abiotic stress acclimation in cyanobacteria. RpaA, RpaB and Rre1 are known to interact with ferredoxin or thioredoxin, raising the possibility of their thiol regulation. Here, we report that Synechocystis sp. PCC 6803 Rre1, RpaA and RpaB exist as higher‐order oligomers under oxidising conditions and that reduced thioredoxin A converts them to monomers. We further show that these response regulators contain redox‐responsive cysteine residues with an Em7 around −300 mV. These findings suggest a direct thiol modulation of the activity of these response regulators, independent of their cognate sensor kinases.
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Affiliation(s)
- Iskander M Ibrahim
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Stephen J L Rowden
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Sujith Puthiyaveetil
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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11
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Kim P, Kaur M, Jang HI, Kim YI. The Circadian Clock-A Molecular Tool for Survival in Cyanobacteria. Life (Basel) 2020; 10:life10120365. [PMID: 33419320 PMCID: PMC7766417 DOI: 10.3390/life10120365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth’s early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins—KaiA, KaiB, and KaiC—drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the “ticking” of the oscillator can be reconstituted inside a test tube just by mixing the three recombinant proteins with ATP and Mg2+. Along with its biochemical resilience, the post-translational rhythm of the oscillation can be reset through sensing oxidized quinone, a metabolite that becomes abundant at the onset of darkness. In addition, the output components pick up the information from the central oscillator, tuning the physiological and behavioral patterns and enabling the organism to better cope with the cyclic environmental conditions. In this review, we highlight our understanding of the cyanobacterial circadian clock and discuss how it functions as a molecular chronometer that readies the host for predictable changes in its surroundings.
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Affiliation(s)
- Pyonghwa Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
| | - Manpreet Kaur
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
| | - Hye-In Jang
- School of Cosmetic Science and Beauty Biotechnology, Semyung University, Jecheon 27136, Korea
- Correspondence: (H.-I.J.); (Y.-I.K.)
| | - Yong-Ick Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
- Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Correspondence: (H.-I.J.); (Y.-I.K.)
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12
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Morphological plasticity of hyperelongated cells caused by overexpression of translation elongation factor P in Synechococcus elongatus PCC7942. Appl Microbiol Biotechnol 2020; 104:8801-8812. [PMID: 32915258 DOI: 10.1007/s00253-020-10874-8] [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: 06/16/2020] [Revised: 08/17/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
Translation elongation factors (EFs) are proteins that play important roles during the elongation stage of protein synthesis. In prokaryotes, at least four EFs function in repetitive reactions (EF-Tu, EF-Ts, EF-G, and EF-P). EF-P plays a vital role in the specialized translation of consecutive proline amino acid motifs. It was also recently recognized that EF-P acts throughout translation elongation. Here, we demonstrated for the first time that cell division and morphology are intimately linked to the control of EF-P in the model cyanobacterium Synechococcus elongatus PCC7942. We constructed the overexpression of a wild-type gene product for EF-P (Synpcc7942_2565) as a tool to identify EF-P functionality. The overexpression of EF-P resulted in the morphological plasticity of hyperelongated cells. During the stationary phase, EF-P overexpressors displayed cell lengths of 150 μm or longer, approximately 35 times longer than the control. Total cellular protein and amino acid content were also increased in overexpressors. To explore the molecular mechanisms underlying hyperelongation, gene expression analysis was performed. The results revealed that cell division genes, including ftn6, minD, mreB, mreC, and ftsZ, were modulated in overexpressors. Strikingly, ftn6 was severely down-regulated. Little is known regarding EF-P in prokaryotic photosynthetic organisms. Our results suggest that cyanobacterial EF-P participates in the acceleration of protein synthesis and also regulates cell division processes. These findings suggest new ways to modify translation and metabolism in cyanobacteria. Phenotypic and metabolic alterations caused by overexpressing EF-P may also be beneficial for applications such as low-cost, green molecular factories. KEY POINTS: • Cell division and cell morphology in the cyanobacterium Synechococcus elongatus PCC7942 are closely linked with the control of translation elongation factor P (EF-P). • Overexpression of EF-P leads to morphological plasticity in hyperelongated cells. • Cyanobacterial EF-P is involved in the acceleration of protein synthesis and the regulation of cell division processes.
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13
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Yasuda A, Inami D, Hanaoka M. RpaB, an essential response regulator for high-light stress, is extensively involved in transcriptional regulation under light-intensity upshift conditions in Synechococcus elongatus PCC 7942. J GEN APPL MICROBIOL 2020; 66:73-79. [PMID: 32269205 DOI: 10.2323/jgam.2020.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In cyanobacteria, transcription of a set of genes is specifically induced by high-light-stress conditions. In previous studies, RpaB, a response regulator of the two-component system, was shown to be involved in this regulation in vitro and in vivo. In this study, we examined whether RpaB-dependent transcriptional regulation was extensively observed, not only under high-light-stress conditions but also under various light intensities. Transcription of high-light-dependent genes hliA, nblA and rpoD3 was transiently and drastically induced during a dark-to-light shift in a manner similar to high-light-stress responses. Moreover, expression of these genes was activated under various light-intensity upshift conditions. Phos-tag SDS-PAGE experiments showed that the phosphorylation level of RpaB was decreased along with transcriptional induction of target genes in all of the light environments examined herein. These results suggest that RpaB may be widely involved in transcriptional regulation under dark-to-light and light-intensity upshift conditions and that high-light-responsive genes may be required in various light conditions other than high-light condition. Furthermore, it is hypothesised that RpaB is regulated by redox-dependent signals rather than by high-light-stress-dependent signals.
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Affiliation(s)
- Akira Yasuda
- Division of Applied Biological Chemistry, Graduate School of Horticulture, Chiba University
| | - Daichi Inami
- Division of Applied Biological Chemistry, Graduate School of Horticulture, Chiba University
| | - Mitsumasa Hanaoka
- Division of Applied Biological Chemistry, Graduate School of Horticulture, Chiba University.,Plant Molecular Science Center, Chiba University
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14
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Chen H, Cheng Y, Tian J, Yang P, Zhang X, Chen Y, Hu Y, Wu J. Dissolved oxygen from microalgae-gel patch promotes chronic wound healing in diabetes. SCIENCE ADVANCES 2020; 6:eaba4311. [PMID: 32440554 PMCID: PMC7228761 DOI: 10.1126/sciadv.aba4311] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/02/2020] [Indexed: 05/05/2023]
Abstract
Chronic wounds in diabetes undergo a lifetime risk of developing into diabetic foot ulcers. Oxygen is crucial to wound healing by regulating cell proliferation, migration, and neovascularization. However, current oxygen therapies, including hyperbaric oxygen (HBO) and topical gaseous oxygen (TGO), mainly employ gaseous oxygen delivery, which is much less effective in penetrating the skin. Here, we introduce an oxygen-producing patch, made of living microalgae hydrogel, which can produce dissolved oxygen. The superior performance of the patch that results from its dissolved oxygen delivery is >100-fold much more efficient than TGO penetrating the skin. Further experiments indicate that the patch could promote cell proliferation, migration, and tube formation in vitro, and improve chronic wound healing and the survival of skin grafts in diabetic mice. We believe that the microalgae-gel patch can provide continuous dissolved oxygen to improve chronic wound healing.
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Affiliation(s)
- Huanhuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yuhao Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Jingrun Tian
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Peizheng Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Xuerao Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yunhao Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yiqiao Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing 210093, China
| | - Jinhui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
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15
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Labella JI, Llop A, Contreras A. The default cyanobacterial linked genome: an interactive platform based on cyanobacterial linkage networks to assist functional genomics. FEBS Lett 2020; 594:1661-1674. [PMID: 32233038 DOI: 10.1002/1873-3468.13775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/14/2020] [Accepted: 03/12/2020] [Indexed: 01/01/2023]
Abstract
A database of cyanobacterial linked genomes that can be accessed through an interactive platform (https://dfgm.ua.es/genetica/investigacion/cyanobacterial_genetics/Resources.html) was generated on the bases of conservation of gene neighborhood across 124 cyanobacterial species. It allows flexible generation of gene networks at different threshold values. The default cyanobacterial linked genome, whose global properties are analyzed here, connects most of the cyanobacterial core genes. The potential of the web tool is discussed in relation to other bioinformatics approaches based on guilty-by-association principles, with selected examples of networks illustrating its usefulness for genes found exclusively in cyanobacteria or in cyanobacteria and chloroplasts. We believe that this tool will provide useful predictions that are readily testable in Synechococcus elongatus PCC7942 and other model organisms performing oxygenic photosynthesis.
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Affiliation(s)
- Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Antonio Llop
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Asuncion Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
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16
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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.
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17
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Riediger M, Kadowaki T, Nagayama R, Georg J, Hihara Y, Hess WR. Biocomputational Analyses and Experimental Validation Identify the Regulon Controlled by the Redox-Responsive Transcription Factor RpaB. iScience 2019; 15:316-331. [PMID: 31103851 PMCID: PMC6525291 DOI: 10.1016/j.isci.2019.04.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 11/24/2022] Open
Abstract
Oxygenic photosynthesis requires the coordination of environmental stimuli with the regulation of transcription. The transcription factor RpaB is conserved from the simplest unicellular cyanobacteria to complex eukaryotic algae, representing more than 1 billion years of evolution. To predict the RpaB-controlled regulon in the cyanobacterium Synechocystis, we analyzed the positional distribution of binding sites together with high-resolution mapping data of transcriptional start sites (TSSs). We describe more than 150 target promoters whose activity responds to fluctuating light conditions. Binding sites close to the TSS mediate repression, whereas sites centered ∼50 nt upstream mediate activation. Using complementary experimental approaches, we found that RpaB controls genes involved in photoprotection, cyclic electron flow and state transitions, photorespiration, and nirA and isiA for which we suggest cross-regulation with the transcription factors NtcA or FurA. The deep integration of RpaB with diverse photosynthetic gene functions makes it one of the most important and versatile transcriptional regulators. RpaB controls a complex regulon, widely beyond the photosynthetic machinery The expression of the RNA regulators IsrR, PsrR1, and others depends on RpaB RpaB exhibits cross-regulations with other transcription factors, NtcA and Fur RpaB is a crucial transcriptional regulator in a photosynthetic microorganism
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Affiliation(s)
- Matthias Riediger
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Ryuta Nagayama
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Jens Georg
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany.
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18
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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.
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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.
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19
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Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria. mSystems 2019; 4:mSystems00317-18. [PMID: 30746496 PMCID: PMC6365647 DOI: 10.1128/msystems.00317-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/11/2019] [Indexed: 12/20/2022] Open
Abstract
Marine microbes must manage variation in their chemical, physical, and biological surroundings. Because they directly link bacterial physiology to environmental changes, TCS systems are crucial to the bacterial cell. This study surveyed TCS systems in a large number of marine bacteria and identified key phylogenetic and lifestyle patterns in environmental sensing. We found evidence that, in comparison with bacteria as a whole, marine organisms have irregular TCS system constructs which might represent an adaptation specific to the marine environment. Additionally, we demonstrate the biogeochemical relevance of TCS systems by correlating the presence of the PMT9312_0717 response regulator protein to phosphate concentrations in the South Pacific. We highlight that despite their potential ecological and biogeochemical relevance, TCS systems have been understudied in the marine ecosystem. This report expands our understanding of the breadth of bacterial TCS systems and how marine bacteria have adapted to survive in their unique environment. Two-component sensory (TCS) systems link microbial physiology to the environment and thus may play key roles in biogeochemical cycles. In this study, we surveyed the TCS systems of 328 diverse marine bacterial species. We identified lifestyle traits such as copiotrophy and diazotrophy that are associated with larger numbers of TCS system genes within the genome. We compared marine bacterial species with 1,152 reference bacterial species from a variety of habitats and found evidence of extra response regulators in marine genomes. Examining the location of TCS genes along the circular bacterial genome, we also found that marine bacteria have a large number of “orphan” genes, as well as many hybrid histidine kinases. The prevalence of “extra” response regulators, orphan genes, and hybrid TCS systems suggests that marine bacteria break with traditional understanding of how TCS systems operate. These trends suggest prevalent regulatory networking, which may allow coordinated physiological responses to multiple environmental signals and may represent a specific adaptation to the marine environment. We examine phylogenetic and lifestyle traits that influence the number and structure of two-component systems in the genome, finding, for example, that a lack of two-component systems is a hallmark of oligotrophy. Finally, in an effort to demonstrate the importance of TCS systems to marine biogeochemistry, we examined the distribution of Prochlorococcus/Synechococcus response regulator PMT9312_0717 in metaproteomes of the tropical South Pacific. We found that this protein’s abundance is related to phosphate concentrations, consistent with a putative role in phosphate regulation. IMPORTANCE Marine microbes must manage variation in their chemical, physical, and biological surroundings. Because they directly link bacterial physiology to environmental changes, TCS systems are crucial to the bacterial cell. This study surveyed TCS systems in a large number of marine bacteria and identified key phylogenetic and lifestyle patterns in environmental sensing. We found evidence that, in comparison with bacteria as a whole, marine organisms have irregular TCS system constructs which might represent an adaptation specific to the marine environment. Additionally, we demonstrate the biogeochemical relevance of TCS systems by correlating the presence of the PMT9312_0717 response regulator protein to phosphate concentrations in the South Pacific. We highlight that despite their potential ecological and biogeochemical relevance, TCS systems have been understudied in the marine ecosystem. This report expands our understanding of the breadth of bacterial TCS systems and how marine bacteria have adapted to survive in their unique environment.
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20
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Fleming KE, O’Shea EK. An RpaA-Dependent Sigma Factor Cascade Sets the Timing of Circadian Transcriptional Rhythms in Synechococcus elongatus. Cell Rep 2018; 25:2937-2945.e3. [DOI: 10.1016/j.celrep.2018.11.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/31/2018] [Accepted: 11/12/2018] [Indexed: 10/27/2022] Open
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21
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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.
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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
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22
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Abramson BW, Lensmire J, Lin YT, Jennings E, Ducat DC. Redirecting carbon to bioproduction via a growth arrest switch in a sucrose-secreting cyanobacterium. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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23
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Espinosa J, Labella JI, Cantos R, Contreras A. Energy drives the dynamic localization of cyanobacterial nitrogen regulators during diurnal cycles. Environ Microbiol 2018; 20:1240-1252. [PMID: 29441670 DOI: 10.1111/1462-2920.14071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to the challenges imposed by the succession of days and nights. Two conserved cyanobacterial proteins, PII and PipX, function as hubs of the nitrogen interaction network, forming complexes with a variety of diverse targets. While PII proteins are found in all three domains of life as integrators of signals of the nitrogen and carbon balance, PipX proteins are unique to cyanobacteria, where they provide a mechanistic link between PII signalling and the control of gene expression by the global nitrogen regulator NtcA. Here we demonstrate that PII and PipX display distinct localization patterns during diurnal cycles, co-localizing into the same foci at the periphery and poles of the cells during dark periods, a circadian-independent process requiring a low ATP/ADP ratio. Genetic, cellular biology and biochemical approaches used here provide new insights into the nitrogen regulatory network, calling attention to the roles of PII as energy sensors and its interactions with PipX in the context of essential signalling pathways. This study expands the contribution of the nitrogen regulators PII and PipX to integrate and transduce key environmental signals that allow cyanobacteria to thrive in our planet.
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Affiliation(s)
- Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - José I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Raquel Cantos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
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24
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Khara P, Mohapatra SS, Biswas I. Role of CovR phosphorylation in gene transcription in Streptococcus mutans. MICROBIOLOGY-SGM 2018; 164:704-715. [PMID: 29504927 DOI: 10.1099/mic.0.000641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptococcus mutans, the primary aetiological agent of dental caries, is one of the major bacteria of the human oral cavity. The pathogenicity of this bacterium is attributed not only to the expression of virulence factors, but also to its ability to respond and adapt rapidly to the ever-changing conditions of the oral cavity. The two-component signal transduction system (TCS) CovR/S plays a crucial role in virulence and stress response in many streptococci. Surprisingly, in S. mutans the response regulator CovR appears to be an orphan, as the cognate sensor kinase, CovS, is absent in all the strains. We found that acetyl phosphate, an intracellular phosphodonor molecule known to act in signalling, might play a role in CovR phosphorylation in vivo. We also found that in vitro, upon phosphorylation by potassium phosphoramide (a high-energy phophodonor) CovR formed a dimer and showed altered electrophoretic mobility. As expected, we found that the conserved aspartic acid residue at position 53 (D53) was the site of phosphorylation, since neither phosphorylation nor dimerization was seen when an alanine-substituted CovR mutant (D53A) was used. Surprisingly, we found that the ability of CovR to act as a transcriptional regulator does not depend upon its phosphorylation status, since the D53A mutant behaved similarly to the wild-type protein in both in vivo and in vitro DNA-binding assays. This unique phosphorylation-mediated inhibition of CovR function in S. mutans sheds light on an unconventional mechanism of the signal transduction pathway.
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Affiliation(s)
- Pratick Khara
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Saswat Sourav Mohapatra
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.,Present address: Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, TN 603203, India
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
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25
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Swan JA, Golden SS, LiWang A, Partch CL. Structure, function, and mechanism of the core circadian clock in cyanobacteria. J Biol Chem 2018; 293:5026-5034. [PMID: 29440392 DOI: 10.1074/jbc.tm117.001433] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/09/2018] [Indexed: 01/09/2023] Open
Abstract
Circadian rhythms enable cells and organisms to coordinate their physiology with the cyclic environmental changes that come as a result of Earth's light/dark cycles. Cyanobacteria make use of a post-translational oscillator to maintain circadian rhythms, and this elegant system has become an important model for circadian timekeeping mechanisms. Composed of three proteins, the KaiABC system undergoes an oscillatory biochemical cycle that provides timing cues to achieve a 24-h molecular clock. Together with the input/output proteins SasA, CikA, and RpaA, these six gene products account for the timekeeping, entrainment, and output signaling functions in cyanobacterial circadian rhythms. This Minireview summarizes the current structural, functional and mechanistic insights into the cyanobacterial circadian clock.
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Affiliation(s)
- Jeffrey A Swan
- From the Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Susan S Golden
- the Department of Molecular Biology and.,Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and
| | - Andy LiWang
- Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and.,the Department of Chemistry and Chemical Biology, University of California Merced, Merced, California 95343
| | - Carrie L Partch
- From the Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, .,Center for Circadian Biology and Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, and
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Piechura JR, Amarnath K, O'Shea EK. Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria. eLife 2017; 6:32032. [PMID: 29239721 PMCID: PMC5785211 DOI: 10.7554/elife.32032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/13/2017] [Indexed: 12/31/2022] Open
Abstract
The circadian clock interacts with other regulatory pathways to tune physiology to predictable daily changes and unexpected environmental fluctuations. However, the complexity of circadian clocks in higher organisms has prevented a clear understanding of how natural environmental conditions affect circadian clocks and their physiological outputs. Here, we dissect the interaction between circadian regulation and responses to fluctuating light in the cyanobacterium Synechococcus elongatus. We demonstrate that natural changes in light intensity substantially affect the expression of hundreds of circadian-clock-controlled genes, many of which are involved in key steps of metabolism. These changes in expression arise from circadian and light-responsive control of RNA polymerase recruitment to promoters by a network of transcription factors including RpaA and RpaB. Using phenomenological modeling constrained by our data, we reveal simple principles that underlie the small number of stereotyped responses of dusk circadian genes to changes in light. Living things face daily, predictable challenges due to the regular day and night cycle imposed by the Earth’s rotation. Many of them have evolved an internal ‘circadian’ clock to anticipate daily changes in the environment. However, nature can also change in unpredictable ways, and in order to survive, organisms must account for both the time of day stipulated by their clocks and changes in their present environment. For example, cyanobacteria depend on the sun for survival and must cope with light variations throughout the day and the absence of light at nighttime. Circadian clocks are made up of specific genes and their proteins. Most of what we know about how these clocks control the behavior of an organism comes from experiments performed under constant conditions. Previous research has shown that under such circumstances, the circadian clock of cyanobacteria periodically turns on a set of genes every 24 hours via a protein called RpaA. However, to understand how cyanobacteria use this clock, we must know how it works in a fluctuating environment. To test this, Piechura, Amarnath and O’Shea measured the activation of genes in cyanobacteria that had been exposed to changes in light mimicking those in nature. Compared to constant conditions, fluctuating light drastically changed the timing of activation of circadian genes. When light decreased – as it would in nature during sunset or if a cloud blocks the sun – the circadian genes were activated. Changes in light did not change the ‘ticking’ of the clock, but did affect the ability of RpaA to turn on circadian genes. Moreover, the activity of a second protein called RpaB increased when light decreased and the genes were activated. Thus, cyanobacteria switch on circadian genes as the sun is setting or during unexpected shade, likely through RpaA and RpaB, to help them survive without light. This study shows that circadian clocks activate genes differently in the real world compared to unnatural, constant conditions. This may prompt scientists to think carefully about how an organism’s natural environment can affect its inner workings. A next step will be to see how else light affects circadian gene levels. A deeper understanding of how cyanobacteria control their genes in a natural environment will be useful for scientists who engineer these organisms to produce biofuels from sunlight.
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Affiliation(s)
- Joseph Robert Piechura
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Kapil Amarnath
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Erin K O'Shea
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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27
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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.
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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
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28
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Bhadra U, Thakkar N, Das P, Pal Bhadra M. Evolution of circadian rhythms: from bacteria to human. Sleep Med 2017; 35:49-61. [DOI: 10.1016/j.sleep.2017.04.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/07/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
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29
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Cohen JE, Goldstone AB, Paulsen MJ, Shudo Y, Steele AN, Edwards BB, Patel JB, MacArthur JW, Hopkins MS, Burnett CE, Jaatinen KJ, Thakore AD, Farry JM, Truong VN, Bourdillon AT, Stapleton LM, Eskandari A, Fairman AS, Hiesinger W, Esipova TV, Patrick WL, Ji K, Shizuru JA, Woo YJ. An innovative biologic system for photon-powered myocardium in the ischemic heart. SCIENCE ADVANCES 2017; 3:e1603078. [PMID: 28630913 PMCID: PMC5470824 DOI: 10.1126/sciadv.1603078] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Coronary artery disease is one of the most common causes of death and disability, afflicting more than 15 million Americans. Although pharmacological advances and revascularization techniques have decreased mortality, many survivors will eventually succumb to heart failure secondary to the residual microvascular perfusion deficit that remains after revascularization. We present a novel system that rescues the myocardium from acute ischemia, using photosynthesis through intramyocardial delivery of the cyanobacterium Synechococcus elongatus. By using light rather than blood flow as a source of energy, photosynthetic therapy increases tissue oxygenation, maintains myocardial metabolism, and yields durable improvements in cardiac function during and after induction of ischemia. By circumventing blood flow entirely to provide tissue with oxygen and nutrients, this system has the potential to create a paradigm shift in the way ischemic heart disease is treated.
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Affiliation(s)
- Jeffrey E. Cohen
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew B. Goldstone
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J. Paulsen
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yasuhiro Shudo
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amanda N. Steele
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bryan B. Edwards
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jay B. Patel
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John W. MacArthur
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael S. Hopkins
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Casey E. Burnett
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin J. Jaatinen
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Akshara D. Thakore
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Justin M. Farry
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vi N. Truong
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra T. Bourdillon
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lyndsay M. Stapleton
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anahita Eskandari
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander S. Fairman
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Hiesinger
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tatiana V. Esipova
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William L. Patrick
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keven Ji
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Judith A. Shizuru
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Y. Joseph Woo
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
- Corresponding author.
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30
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He BZ, Zhou X, O'Shea EK. Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway. eLife 2017; 6:25157. [PMID: 28485712 PMCID: PMC5446240 DOI: 10.7554/elife.25157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/29/2017] [Indexed: 01/23/2023] Open
Abstract
Although combinatorial regulation is a common feature in gene regulatory networks, how it evolves and affects network structure and function is not well understood. In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are required for gene induction and survival during phosphate starvation. In the related human commensal C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate starvation and is only partially required for inducing PHO genes. Phylogenetic survey suggests that reduced dependence on Pho2 evolved in C. glabrata and closely related species. In S. cerevisiae, less Pho2-dependent Pho4 orthologs induce more genes. In C. glabrata, its Pho4 binds to more locations and induces three times as many genes as Pho4 in S. cerevisiae does. Our work shows how evolution of combinatorial regulation allows for rapid expansion of a gene regulatory network’s targets, possibly extending its physiological functions. The diversity of life on Earth has intrigued generations of scientists and nature lovers alike. Research over recent decades has revealed that much of the diversity we can see did not require the invention of new genes. Instead, living forms diversified mostly by using old genes in new ways – for example, by changing when or where an existing gene became active. This kind of change is referred to as “regulatory evolution”. A class of proteins called transcription factors are hot spots in regulatory evolution. These proteins recognize specific sequences of DNA to control the activity of other genes, and so represent the “readers” of the genetic information. Small changes to how a transcription factor is regulated, or the genes it targets, can lead to dramatic changes in an organism. Before we can understand how life on Earth evolved to be so diverse, scientists must first answer how transcription factors evolve and what consequences this has on their target genes. So far, most studies of regulatory evolution have focused on networks of transcription factors and genes that control how an organism develops. He et al. have now studied a regulatory network that is behind a different process, namely how an organism responds to stress or starvation. These two types of regulatory networks are structured differently and work in different ways. These differences made He et al. wonder if the networks evolved differently too. The chemical phosphate is an essential nutrient for all living things, and He et al. compared how two different species of yeast responded to a lack of phosphate. The key difference was how much a major transcription factor known as Pho4 depended on a so-called co-activator protein named Pho2 to carry out its role. Baker’s yeast (Saccharomyces cerevisiae), which is commonly used in laboratory experiments, requires both Pho4 and Pho2 to activate about 20 genes when inorganic phosphate is not available in its environment. However, in a related yeast species called Candida glabrata, Pho4 has evolved to depend less on Pho2. He et al. went on to show that, as well as being less dependent on Pho2, Pho4 in C. glabrata activates more than three times as many genes as Pho4 in S. cerevisiae does in the absence of phosphate. These additional gene targets for Pho4 in C. glabrata are predicted to extend the network’s activities, and allow it to regulate new process including the yeast’s responses to other types of stress and the building of the yeast’s cell wall. Together these findings show a new way that regulatory networks can evolve, that is, by reducing its dependence on the co-activator, a transcription factor can expand the number of genes it targets. This has not been seen for regulatory networks related to development, suggesting that different networks can indeed evolve in different ways. Lastly, because disease-causing microbes are often stressed inside their hosts and C. glabrata sometimes infects humans, understanding how this yeast’s response to stress has evolved may lead to new ways to prevent and treat this infection.
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Affiliation(s)
- Bin Z He
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Xu Zhou
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Erin K O'Shea
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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31
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Puszynska AM, O'Shea EK. Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian output pathway. eLife 2017; 6. [PMID: 28430105 PMCID: PMC5400509 DOI: 10.7554/elife.23210] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022] Open
Abstract
The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect, and demonstrate that the rpaA- strain cannot maintain appropriate energy status at night, does not accumulate carbon reserves during the day, and is defective in transcription of genes crucial for utilization of carbohydrate stores at night. Reconstruction of carbon utilization pathways combined with provision of an external carbon source restores energy charge and viability of the rpaA- strain in light/dark cycling conditions. Our observations highlight how a circadian output pathway controls and temporally coordinates essential pathways in carbon metabolism to maximize fitness of cells facing periodic energy limitations. DOI:http://dx.doi.org/10.7554/eLife.23210.001 The cycle of day and night is one of the most recurrent and predictable environmental changes on our planet. Consequently, organisms have evolved mechanisms that allow them to measure time over 24 hours and prepare for the periodic changes between light and dark. These mechanisms, known as circadian clocks, alter the activity of some of the organism’s genes in a rhythmic way across the course of a day. This in turn causes certain behaviors and biological activities of the organism to follow a daily cycle. The bacterium Synechococcus elongatus needs to be able to track the daily cycle of light and dark because it performs photosynthesis and depends on sunlight to form sugars, which can later be broken down to release energy. The time information encoded in the circadian clock of S. elongatus is transmitted to the protein RpaA, which drives the regular circadian changes in gene activity in the cell. If RpaA is removed from the cell or prevented from working, S. elongatus can no longer control rhythmic gene activity and is unable to survive the night. To better understand how the circadian system schedules biological tasks to help an organism to survive, Puszynska and O'Shea studied S. elongatus cells. This revealed that the bacteria normally prepare for darkness by storing sugars during the day and activating several genes at dusk to make enzymes that are required to break down stored sugars. This provides the cells with energy that they need to survive the night. But mutant cells that lack the gene that produces RpaA do not prepare for darkness; they do not accumulate a store of sugars during the day or activate the vital genes at dusk. They have low internal energy levels in the dark and they cannot survive long periods of darkness. Providing the mutant cells with sugar and restoring the activity of the genes responsible for breaking down sugar enabled the cells to maintain energy in darkness and survive the night. It therefore appears that one role of the circadian system of S. elongatus is to coordinate building up sugar reserves during the day with breaking down sugar stores to generate energy during the night. Puszynska and O'Shea also found many other genes that are not activated at dusk in the mutant cells. It will therefore be important to study whether other pathways that help cells to survive and grow are defective in these mutant cells. DOI:http://dx.doi.org/10.7554/eLife.23210.002
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Affiliation(s)
- Anna M Puszynska
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Erin K O'Shea
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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32
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Abstract
Chronobiological studies of prokaryotic organisms have generally lagged far behind the study of endogenous circadian clocks in eukaryotes, in which such systems are essentially ubiquitous. However, despite only being studied during the past 25 years, cyanobacteria have become important model organisms for the study of circadian rhythms and, presently, their timekeeping mechanism is the best understood of any system in terms of biochemistry, structural biology, biophysics and adaptive importance. Nevertheless, intrinsic daily rhythmicity among bacteria other than cyanobacteria is essentially unknown; some tantalizing information suggests widespread daily timekeeping among Eubacteria and Archaea through mechanisms that share common elements with the cyanobacterial clock but are distinct. Moreover, the recent surge of information about microbiome-host interactions has largely neglected the temporal dimension and yet daily cycles control important aspects of their relationship.
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33
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Kobayashi I, Watanabe S, Kanesaki Y, Shimada T, Yoshikawa H, Tanaka K. Conserved two-component Hik34-Rre1 module directly activates heat-stress inducible transcription of major chaperone and other genes in Synechococcus elongatus PCC 7942. Mol Microbiol 2017; 104:260-277. [PMID: 28106321 DOI: 10.1111/mmi.13624] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 11/28/2022]
Abstract
Bacteria and other organisms, including cyanobacteria, employ two-component signal transducing modules comprising histidine kinases and response regulators to acclimate to changing environments. While the number and composition of these modules differ among cyanobacteria, two response regulators that contain DNA binding domains, RpaB and Rre1, are conserved in all sequenced cyanobacterial genomes and are essential for viability. Although RpaB negatively or positively regulates high light and other stress-responsive gene expression, little is known about the function of Rre1. Here, they investigated the direct regulatory targets of Rre1 in the cyanobacterium Synechococcus elongatus PCC 7942. Chromatin immunoprecipitation and high-density tiling array analysis were used to map Rre1 binding sites. The sites included promoter regions for chaperone genes such as dnaK2, groESL-1, groEL-2, hspA and htpG, as well as the group 2 sigma factor gene rpoD2. In vivo and in vitro analyses revealed that Rre1 phosphorylation level, DNA binding activity and adjacent gene transcription increased in response to heat stress. These responses were much diminished in a knock-out mutant of Hik34, a previously identified heat shock regulator. Based on our results, we propose Hik34-Rre1 is the heat shock-responsive signaling module that positively regulates major chaperone and other genes in cyanobacteria.
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Affiliation(s)
- Ikki Kobayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Graduate School of Interdisciplinary Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-29, Midori-ku, Yokohama, 226-8503, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Tomohiro Shimada
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
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34
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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.
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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
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35
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Labella JI, Obrebska A, Espinosa J, Salinas P, Forcada-Nadal A, Tremiño L, Rubio V, Contreras A. Expanding the Cyanobacterial Nitrogen Regulatory Network: The GntR-Like Regulator PlmA Interacts with the PII-PipX Complex. Front Microbiol 2016; 7:1677. [PMID: 27840625 PMCID: PMC5083789 DOI: 10.3389/fmicb.2016.01677] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/06/2016] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteria, phototrophic organisms that perform oxygenic photosynthesis, perceive nitrogen status by sensing 2-oxoglutarate levels. PII, a widespread signaling protein, senses and transduces nitrogen and energy status to target proteins, regulating metabolism and gene expression. In cyanobacteria, under conditions of low 2-oxoglutarate, PII forms complexes with the enzyme N-acetyl glutamate kinase, increasing arginine biosynthesis, and with PII-interacting protein X (PipX), making PipX unavailable for binding and co-activation of the nitrogen regulator NtcA. Both the PII-PipX complex structure and in vivo functional data suggested that this complex, as such, could have regulatory functions in addition to PipX sequestration. To investigate this possibility we performed yeast three-hybrid screening of genomic libraries from Synechococcus elongatus PCC7942, searching for proteins interacting simultaneously with PII and PipX. The only prey clone found in the search expressed PlmA, a member of the GntR family of transcriptional regulators proven here by gel filtration to be homodimeric. Interactions analyses further confirmed the simultaneous requirement of PII and PipX, and showed that the PlmA contacts involve PipX elements exposed in the PII-PipX complex, specifically the C-terminal helices and one residue of the tudor-like body. In contrast, PII appears not to interact directly with PlmA, possibly being needed indirectly, to induce an extended conformation of the C-terminal helices of PipX and for modulating the surface polarity at the PII-PipX boundary, two elements that appear crucial for PlmA binding. Attempts to inactive plmA confirmed that this gene is essential in S. elongatus. Western blot assays revealed that S. elongatus PlmA, irrespective of the nitrogen regime, is a relatively abundant transcriptional regulator, suggesting the existence of a large PlmA regulon. In silico studies showed that PlmA is universally and exclusively found in cyanobacteria. Based on interaction data, on the relative amounts of the proteins involved in PII-PipX-PlmA complexes, determined in western assays, and on the restrictions imposed by the symmetries of trimeric PII and dimeric PlmA molecules, a structural and regulatory model for PlmA function is discussed in the context of the cyanobacterial nitrogen interaction network.
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Affiliation(s)
- Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Anna Obrebska
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Paloma Salinas
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | | | - Lorena Tremiño
- Instituto de Biomedicina de Valencia of the CSIC Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia of the CSICValencia, Spain; Group 739, CIBER de Enfermedades Raras (CIBERER-ISCIII)Valencia, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
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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.
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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.
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Agrawal R, Sahoo BK, Saini DK. Cross-talk and specificity in two-component signal transduction pathways. Future Microbiol 2016; 11:685-97. [PMID: 27159035 DOI: 10.2217/fmb-2016-0001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two-component signaling systems (TCSs) are composed of two proteins, sensor kinases and response regulators, which can cross-talk and integrate information between them by virtue of high-sequence conservation and modular nature, to generate concerted and diversified responses. However, TCSs have been shown to be insulated, to facilitate linear signal transmission and response generation. Here, we discuss various mechanisms that confer specificity or cross-talk among TCSs. The presented models are supported with evidence that indicate the physiological significance of the observed TCS signaling architecture. Overall, we propose that the signaling topology of any TCSs cannot be predicted using obvious sequence or structural rules, as TCS signaling is regulated by multiple factors, including spatial and temporal distribution of the participating proteins.
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Affiliation(s)
- Ruchi Agrawal
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India
| | - Bikash Kumar Sahoo
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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Abstract
Life on earth is subject to daily and predictable fluctuations in light intensity, temperature, and humidity created by rotation of the earth. Circadian rhythms, generated by a circadian clock, control temporal programs of cellular physiology to facilitate adaptation to daily environmental changes. Circadian rhythms are nearly ubiquitous and are found in both prokaryotic and eukaryotic organisms. Here we introduce the molecular mechanism of the circadian clock in the model cyanobacterium Synechococcus elongatus PCC 7942. We review the current understanding of the cyanobacterial clock, emphasizing recent work that has generated a more comprehensive understanding of how the circadian oscillator becomes synchronized with the external environment and how information from the oscillator is transmitted to generate rhythms of biological activity. These results have changed how we think about the clock, shifting away from a linear model to one in which the clock is viewed as an interactive network of multifunctional components that are integrated into the context of the cell in order to pace and reset the oscillator. We conclude with a discussion of how this basic timekeeping mechanism differs in other cyanobacterial species and how information gleaned from work in cyanobacteria can be translated to understanding rhythmic phenomena in other prokaryotic systems.
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Wilde A, Hihara Y. Transcriptional and posttranscriptional regulation of cyanobacterial photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:296-308. [PMID: 26549130 DOI: 10.1016/j.bbabio.2015.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 10/02/2015] [Accepted: 11/03/2015] [Indexed: 12/22/2022]
Abstract
Cyanobacteria are well established model organisms for the study of oxygenic photosynthesis, nitrogen metabolism, toxin biosynthesis, and salt acclimation. However, in comparison to other model bacteria little is known about regulatory networks, which allow cyanobacteria to acclimate to changing environmental conditions. The current work has begun to illuminate how transcription factors modulate expression of different photosynthetic regulons. During the past few years, the research on other regulatory principles like RNA-based regulation showed the importance of non-protein regulators for bacterial lifestyle. Investigations on modulation of photosynthetic components should elucidate the contributions of all factors within the context of a larger regulatory network. Here, we focus on regulation of photosynthetic processes including transcriptional and posttranscriptional mechanisms, citing examples from a limited number of cyanobacterial species. Though, the general idea holds true for most species, important differences exist between various organisms, illustrating diversity of acclimation strategies in the very heterogeneous cyanobacterial clade. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof Conrad Mullineaux.
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Affiliation(s)
- Annegret Wilde
- University of Freiburg, Institute of Biology III, Schänzlestr. 1, 79104 Freiburg, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Germany
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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Shultzaberger RK, Boyd JS, Diamond S, Greenspan RJ, Golden SS. Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context. Annu Rev Genet 2015; 49:485-505. [PMID: 26442846 DOI: 10.1146/annurev-genet-111212-133227] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Early research on the cyanobacterial clock focused on characterizing the genes needed to keep, entrain, and convey time within the cell. As the scope of assays used in molecular genetics has expanded to capture systems-level properties (e.g., RNA-seq, ChIP-seq, metabolomics, high-throughput screening of genetic variants), so has our understanding of how the clock fits within and influences a broader cellular context. Here we review the work that has established a global perspective of the clock, with a focus on (a) an emerging network-centric view of clock architecture, (b) mechanistic insights into how temporal and environmental cues are transmitted and integrated within this network,
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Affiliation(s)
- Ryan K Shultzaberger
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, USA, 92093
| | - Joseph S Boyd
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Division of Biological Sciences, University of California San Diego, La Jolla, USA, 92093
| | - Spencer Diamond
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Division of Biological Sciences, University of California San Diego, La Jolla, USA, 92093
| | - Ralph J Greenspan
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, USA, 92093
| | - Susan S Golden
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Division of Biological Sciences, University of California San Diego, La Jolla, USA, 92093
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