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Fujiwara T, Hirooka S, Yamashita S, Yagisawa F, Miyagishima SY. Development of a rapamycin-inducible protein-knockdown system in the unicellular red alga Cyanidioschyzon merolae. PLANT PHYSIOLOGY 2024; 196:77-94. [PMID: 38833589 PMCID: PMC11376382 DOI: 10.1093/plphys/kiae316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024]
Abstract
An inducible protein-knockdown system is highly effective for investigating the functions of proteins and mechanisms essential for the survival and growth of organisms. However, this technique is not available in photosynthetic eukaryotes. The unicellular red alga Cyanidioschyzon merolae possesses a very simple cellular and genomic architecture and is genetically tractable but lacks RNA interference machinery. In this study, we developed a protein-knockdown system in this alga. The constitutive system utilizes the destabilizing activity of the FK506-binding protein 12 (FKBP12)-rapamycin-binding (FRB) domain of human target of rapamycin kinase or its derivatives to knock down target proteins. In the inducible system, rapamycin treatment induces the heterodimerization of the human FRB domain fused to the target proteins with the human FKBP fused to S-phase kinase-associated protein 1 or Cullin 1, subunits of the SCF E3 ubiquitin ligase. This results in the rapid degradation of the target proteins through the ubiquitin-proteasome pathway. With this system, we successfully degraded endogenous essential proteins such as the chloroplast division protein dynamin-related protein 5B and E2 transcription factor, a regulator of the G1/S transition, within 2 to 3 h after rapamycin administration, enabling the assessment of resulting phenotypes. This rapamycin-inducible protein-knockdown system contributes to the functional analysis of genes whose disruption leads to lethality.
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Affiliation(s)
- Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka 411-8540, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Shota Yamashita
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Fumi Yagisawa
- Research Facility Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka 411-8540, Japan
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2
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Lee J, Miyagishima SY, Bhattacharya D, Yoon HS. From dusk till dawn: cell cycle progression in the red seaweed Gracilariopsis chorda (Rhodophyta). iScience 2024; 27:110190. [PMID: 38984202 PMCID: PMC11231608 DOI: 10.1016/j.isci.2024.110190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/29/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
The conserved eukaryotic functions of cell cycle genes have primarily been studied using animal/plant models and unicellular algae. Cell cycle progression and its regulatory components in red (Rhodophyta) seaweeds are poorly understood. We analyzed diurnal gene expression data to investigate the cell cycle in the red seaweed Gracilariopsis chorda. We identified cell cycle progression and transitions in G. chorda which are induced by interactions of key regulators such as E2F/DP, RBR, cyclin-dependent kinases, and cyclins from dusk to dawn. However, several typical CDK inhibitor proteins are absent in red seaweeds. Interestingly, the G1-S transition in G. chorda is controlled by delayed transcription of GINS subunit 3. We propose that the delayed S phase entry in this seaweed may have evolved to minimize DNA damage (e.g., due to UV radiation) during replication. Our results provide important insights into cell cycle-associated physiology and its molecular mechanisms in red seaweeds.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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Masuda K, Sakurai T, Hirano A. A coupled model between circadian, cell-cycle, and redox rhythms reveals their regulation of oxidative stress. Sci Rep 2024; 14:15479. [PMID: 38969743 PMCID: PMC11226698 DOI: 10.1038/s41598-024-66347-9] [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: 04/24/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024] Open
Abstract
Most organisms possess three biological oscillators, circadian clock, cell cycle, and redox rhythm, which are autonomous but interact each other. However, whether their interactions and autonomy are beneficial for organisms remains unclear. Here, we modeled a coupled oscillator system where each oscillator affected the phase of the other oscillators. We found that multiple types of coupling prevent a high H2O2 level in cells at M phase. Consequently, we hypothesized a high H2O2 sensitivity at the M phase and found that moderate coupling reduced cell damage due to oxidative stress by generating appropriate phase relationships between three rhythms, whereas strong coupling resulted in an elevated cell damage by increasing the average H2O2 level and disrupted the cell cycle. Furthermore, the multicellularity model revealed that phase variations among cells confer flexibility in synchronization with environments at the expense of adaptability to the optimal environment. Thus, both autonomy and synchrony among the oscillators are important for coordinating their phase relationships to minimize oxidative stress, and couplings balance them depending on environments.
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Affiliation(s)
- Kosaku Masuda
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan.
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Takeshi Sakurai
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- Life Science Center for Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Arisa Hirano
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan.
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan.
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Lee J, Yang JH, Weber APM, Bhattacharya D, Kim WY, Yoon HS. Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism. Mol Biol Evol 2024; 41:msae012. [PMID: 38267085 PMCID: PMC10853006 DOI: 10.1093/molbev/msae012] [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: 09/09/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic organisms. However, among Archaeplastida, red algae are the only taxa that lack phytochromes. Current knowledge about oscillatory rhythms is primarily derived from model species such as Arabidopsis thaliana and Chlamydomonas reinhardtii in the Viridiplantae, whereas little is known about these processes in other clades of the Archaeplastida, such as the red algae (Rhodophyta). We used genome-wide expression profiling of the red seaweed Gracilariopsis chorda and identified 3,098 rhythmic genes. Here, we characterized possible cryptochrome-based regulation and photosynthetic/cytosolic carbon metabolism in this species. We found a large family of cryptochrome genes in G. chorda that display rhythmic expression over the diurnal cycle and may compensate for the lack of phytochromes in this species. The input pathway gates regulatory networks of carbon metabolism which results in a compact and efficient energy metabolism during daylight hours. The system in G. chorda is distinct from energy metabolism in most plants, which activates in the dark. The green lineage, in particular, land plants, balance water loss and CO2 capture in terrestrial environments. In contrast, red seaweeds maintain a reduced set of photoreceptors and a compact cytosolic carbon metabolism to thrive in the harsh abiotic conditions typical of intertidal zones.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 four), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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Krupnik T. Factors affecting light harvesting in the red alga Cyanidioschyzon merolae. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111854. [PMID: 37659734 DOI: 10.1016/j.plantsci.2023.111854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
The phycobilisome antennas, which contain phycobilin pigments instead of chlorophyll, are crucial for the photosynthetic activity of Cyanidioschyzon merolae cells, which thrive in an acidic and hot water environment. The accessible light intensity and quality, temperature, acidity, and other factors in this environment are quite different from those in the air available for terrestrial plants. Under these conditions, adaptation to the intensity and quality of light, as well as temperature, which are key factors in photosynthesis of higher plants, also affects this process in Cyanidioschyzon merolae cells. Adaptation to varying light conditions requires fast remodeling and re-tuning of their light-harvesting antennas (phycobilisomes) at multiple levels, from regulation of gene expression to structural reorganization of protein-pigment complexes. This review presents selected data on the structure of phycobilisomes, the genetic engineering of the constituent proteins, and the latest results and opinions on the adaptation of phycobilisomes to light intensity and quality, and temperature to photosynthetic activities. We pay special attention to the latest results of the C. merolae research.
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Affiliation(s)
- Tomasz Krupnik
- Department of Molecular Plant Physiology, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02096, Poland.
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Siqueira JA, Batista-Silva W, Zsögön A, Fernie AR, Araújo WL, Nunes-Nesi A. Plant domestication: setting biological clocks. TRENDS IN PLANT SCIENCE 2023; 28:597-608. [PMID: 36822959 DOI: 10.1016/j.tplants.2023.01.009] [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: 09/23/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 05/22/2023]
Abstract
Through domestication of wild species, humans have induced large changes in the developmental and circadian clocks of plants. As a result of these changes, modern crops are more productive and adaptive to contrasting environments from the center of origin of their wild ancestors, albeit with low genetic variability and abiotic stress tolerance. Likewise, a complete restructuring of plant metabolic timekeeping probably occurred during crop domestication. Here, we highlight that contrasting timings among organs in wild relatives of crops allowed them to recognize environmental adversities faster. We further propose that connections among biological clocks, which were established during plant domestication, may represent a fundamental source of genetic variation to improve crop resilience and yield.
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Affiliation(s)
- João Antonio Siqueira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Willian Batista-Silva
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Agustin Zsögön
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
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Häfker NS, Andreatta G, Manzotti A, Falciatore A, Raible F, Tessmar-Raible K. Rhythms and Clocks in Marine Organisms. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:509-538. [PMID: 36028229 DOI: 10.1146/annurev-marine-030422-113038] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.
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Affiliation(s)
- N Sören Häfker
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Gabriele Andreatta
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Alessandro Manzotti
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Angela Falciatore
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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Pokora W, Tułodziecki S, Dettlaff-Pokora A, Aksmann A. Cross Talk between Hydrogen Peroxide and Nitric Oxide in the Unicellular Green Algae Cell Cycle: How Does It Work? Cells 2022; 11:cells11152425. [PMID: 35954269 PMCID: PMC9368121 DOI: 10.3390/cells11152425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/22/2022] Open
Abstract
The regulatory role of some reactive oxygen species (ROS) and reactive nitrogen species (RNS), such as hydrogen peroxide or nitric oxide, has been demonstrated in some higher plants and algae. Their involvement in regulation of the organism, tissue and single cell development can also be seen in many animals. In green cells, the redox potential is an important photosynthesis regulatory factor that may lead to an increase or decrease in growth rate. ROS and RNS are important signals involved in the regulation of photoautotrophic growth that, in turn, allow the cell to attain the commitment competence. Both hydrogen peroxide and nitric oxide are directly involved in algal cell development as the signals that regulate expression of proteins required for completing the cell cycle, such as cyclins and cyclin-dependent kinases, or histone proteins and E2F complex proteins. Such regulation seems to relate to the direct interaction of these signaling molecules with the redox-sensitive transcription factors, but also with regulation of signaling pathways including MAPK, G-protein and calmodulin-dependent pathways. In this paper, we aim to elucidate the involvement of hydrogen peroxide and nitric oxide in algal cell cycle regulation, considering the role of these molecules in higher plants. We also evaluate the commercial applicability of this knowledge. The creation of a simple tool, such as a precisely established modification of hydrogen peroxide and/or nitric oxide at the cellular level, leading to changes in the ROS-RNS cross-talk network, can be used for the optimization of the efficiency of algal cell growth and may be especially important in the context of increasing the role of algal biomass in science and industry. It could be a part of an important scientific challenge that biotechnology is currently focused on.
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Affiliation(s)
- Wojciech Pokora
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdańsk Wita, Stwosza 59, 83-308 Gdańsk, Poland
- Correspondence:
| | - Szymon Tułodziecki
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdańsk Wita, Stwosza 59, 83-308 Gdańsk, Poland
| | | | - Anna Aksmann
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdańsk Wita, Stwosza 59, 83-308 Gdańsk, Poland
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Sanders CK, Hanschen ER, Biondi TC, Hovde BT, Kunde YA, Eng WL, Kwon T, Dale T. Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. "desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata, supported by a high-quality genome assembly. JOURNAL OF PHYCOLOGY 2022; 58:436-448. [PMID: 35262191 DOI: 10.1111/jpy.13242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Microalgae are diverse, with many gaps remaining in phylogenetic and physiological understanding. Thus, studying new microalgae species increases our broader comprehension of biological diversity, and evaluation of new candidates as algal production platforms can lead to improved productivity under a variety of cultivation conditions. Chlorella is a genus of fast-growing species often isolated from freshwater habitats and cultivated as a source of nutritional supplements. However, the use of freshwater increases competition with other freshwater needs. We identified Chlorella desiccata to be worthy of further investigation as a potential algae production strain, due to its isolation from a marine environment and its promising growth and biochemical composition properties. Long-read genomic sequencing was conducted for C. desiccata UTEX 2526, resulting in a high-quality, near chromosome level, diploid genome with an assembly length of 21.55 Mbp in only 18 contigs. We also report complete circular mitochondrial and chloroplast genomes. Phylogenomic and phylogenetic analyses using nuclear, chloroplast, 18S rRNA, and actin sequences revealed that this species clades within strains currently identified as Nannochloris (Trebouxiophyceae, Chlorophyta), leading to its reclassification as Nannochloris sp. "desiccata" UTEX 2526. The mode of cell division for this species is autosporulation, differing from the type species N. bacillaris. As has occurred across multiple microalgae genera, there are repeated examples of Nannochloris species reclassification in the literature. This high-quality genome assembly and phylogenetic analysis of the potential algal production strain Nannochloris sp. "desiccata" UTEX 2526 provides an important reference and useful tool for further studying this region of the phylogenetic tree.
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Affiliation(s)
- Claire K Sanders
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Erik R Hanschen
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Thomas C Biondi
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Blake T Hovde
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Yuliya A Kunde
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Wyatt L Eng
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Taehyung Kwon
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Taraka Dale
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
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Fujiwara T, Hirooka S, Miyagishima SY. A cotransformation system of the unicellular red alga Cyanidioschyzon merolae with blasticidin S deaminase and chloramphenicol acetyltransferase selectable markers. BMC PLANT BIOLOGY 2021; 21:573. [PMID: 34863100 PMCID: PMC8642924 DOI: 10.1186/s12870-021-03365-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/24/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND The unicellular red alga Cyanidioschyzon merolae exhibits a very simple cellular and genomic architecture. In addition, procedures for genetic modifications, such as gene targeting by homologous recombination and inducible/repressible gene expression, have been developed. However, only two markers for selecting transformants, uracil synthase (URA) and chloramphenicol acetyltransferase (CAT), are available in this alga. Therefore, manipulation of two or more different chromosomal loci in the same strain in C. merolae is limited. RESULTS This study developed a nuclear targeting and transformant selection system using an antibiotics blasticidin S (BS) and the BS deaminase (BSD) selectable marker by homologous recombination in C. merolae. In addition, this study has succeeded in simultaneously modifying two different chromosomal loci by a single-step cotransformation based on the combination of BSD and CAT selectable markers. A C. merolae strain that expresses mitochondrion-targeted mSCARLET (with the BSD marker) and mVENUS (with the CAT marker) from different chromosomal loci was generated with this procedure. CONCLUSIONS The newly developed BSD selectable marker enables an additional genetic modification to the already generated C. merolae transformants based on the URA or CAT system. Furthermore, the cotransformation system facilitates multiple genetic modifications. These methods and the simple nature of the C. merolae cellular and genomic architecture will facilitate studies on several phenomena common to photosynthetic eukaryotes.
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Affiliation(s)
- Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
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Cai YD, Chiu JC. Timeless in animal circadian clocks and beyond. FEBS J 2021; 289:6559-6575. [PMID: 34699674 PMCID: PMC9038958 DOI: 10.1111/febs.16253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/09/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
TIMELESS (TIM) was first identified as a molecular cog in the Drosophila circadian clock. Almost three decades of investigations have resulted in an insightful model describing the critical role of Drosophila TIM (dTIM) in circadian timekeeping in insects, including its function in mediating light entrainment and temperature compensation of the molecular clock. Furthermore, exciting discoveries on its sequence polymorphism and thermosensitive alternative RNA splicing have also established its role in regulating seasonal biology. Although mammalian TIM (mTIM), its mammalian paralog, was first identified as a potential circadian clock component in 1990s due to sequence similarity to dTIM, its role in clock regulation has been more controversial. Mammalian TIM has now been characterized as a DNA replication fork component and has been shown to promote fork progression and participate in cell cycle checkpoint signaling in response to DNA damage. Despite defective circadian rhythms displayed by mtim mutants, it remains controversial whether the regulation of circadian clocks by mTIM is direct, especially given the interconnection between the cell cycle and circadian clocks. In this review, we provide a historical perspective on the identification of animal tim genes, summarize the roles of TIM proteins in biological timing and genomic stability, and draw parallels between dTIM and mTIM despite apparent functional divergence.
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Affiliation(s)
- Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
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Miyagishima SY, Tanaka K. The Unicellular Red Alga Cyanidioschyzon merolae-The Simplest Model of a Photosynthetic Eukaryote. PLANT & CELL PHYSIOLOGY 2021; 62:926-941. [PMID: 33836072 PMCID: PMC8504449 DOI: 10.1093/pcp/pcab052] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 05/13/2023]
Abstract
Several species of unicellular eukaryotic algae exhibit relatively simple genomic and cellular architecture. Laboratory cultures of these algae grow faster than plants and often provide homogeneous cellular populations exposed to an almost equal environment. These characteristics are ideal for conducting experiments at the cellular and subcellular levels. Many microalgal lineages have recently become genetically tractable, which have started to evoke new streams of studies. Among such algae, the unicellular red alga Cyanidioschyzon merolae is the simplest organism; it possesses the minimum number of membranous organelles, only 4,775 protein-coding genes in the nucleus, and its cell cycle progression can be highly synchronized with the diel cycle. These properties facilitate diverse omics analyses of cellular proliferation and structural analyses of the intracellular relationship among organelles. C. merolae cells lack a rigid cell wall and are thus relatively easily disrupted, facilitating biochemical analyses. Multiple chromosomal loci can be edited by highly efficient homologous recombination. The procedures for the inducible/repressive expression of a transgene or an endogenous gene in the nucleus and for chloroplast genome modification have also been developed. Here, we summarize the features and experimental techniques of C. merolae and provide examples of studies using this alga. From these studies, it is clear that C. merolae-either alone or in comparative and combinatory studies with other photosynthetic organisms-can provide significant insights into the biology of photosynthetic eukaryotes.
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Affiliation(s)
- Shin-Ya Miyagishima
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
| | - Kan Tanaka
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
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Jong LW, Fujiwara T, Hirooka S, Miyagishima SY. Cell size for commitment to cell division and number of successive cell divisions in cyanidialean red algae. PROTOPLASMA 2021; 258:1103-1118. [PMID: 33675395 DOI: 10.1007/s00709-021-01628-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Several eukaryotic cell lineages proliferate by multiple fission cell cycles, during which cells grow to manyfold of their original size, then undergo several rounds of cell division without intervening growth. A previous study on volvocine green algae, including both unicellular and multicellular (colonial) species, showed a correlation between the minimum number of successive cell divisions without intervening cellular growth, and the threshold cell size for commitment to the first round of successive cell divisions: two times the average newly born daughter cell volume for unicellular Chlamydomonas reinhardtii, four times for four-celled Tetrabaena socialis, in which each cell in the colony produces a daughter colony by two successive cell divisions, and eight times for the eight-celled Gonium pectorale, in which each cell produces a daughter colony by three successive cell divisions. To assess whether this phenomenon is also applicable to other lineages, we have characterized cyanidialean red algae, namely, Cyanidioschyzon merolae, which proliferates by binary fission, as well as Cyanidium caldarium and Galdieria sulphuraria, which form up to four and 32 daughter cells (autospores), respectively, in a mother cell before hatching out. The result shows that there is also a correlation between the number of successive cell divisions and the threshold cell size for cell division or the first round of the successive cell divisions. In both C. merolae and C. caldarium, the cell size checkpoint for cell division(s) exists in the G1-phase, as previously shown in volvocine green algae. When C. merolae cells were arrested in the G1-phase and abnormally enlarged by conditional depletion of CDKA, the cells underwent two or more successive cell divisions without intervening cellular growth after recovery of CDKA, similarly to C. caldarium and G. sulphuraria. These results suggest that the threshold size for cell division is a major factor in determining the number of successive cell divisions and that evolutionary changes in the mechanism of cell size monitoring resulted in a variation of multiple fission cell cycle in eukaryotic algae.
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Affiliation(s)
- Lin Wei Jong
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan.
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan.
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The Cell Division Cycle of Euglena gracilis Indicates That the Level of Circadian Plasticity to the External Light Regime Changes in Prolonged-Stationary Cultures. PLANTS 2021; 10:plants10071475. [PMID: 34371678 PMCID: PMC8309271 DOI: 10.3390/plants10071475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
In unicellular photosynthetic organisms, circadian rhythm is tightly linked to gating of cell cycle progression, and is entrained by light signal. As several organisms obtain a fitness advantage when the external light/dark cycle matches their endogenous period, and aging alters circadian rhythms, senescence phenotypes of the microalga Euglena gracilis of different culture ages were characterized with respect to the cell division cycle. We report here the effects of prolonged-stationary-phase conditions on the cell division cycles of E. gracilis under non-24-h light/dark cycles (T-cycles). Under T-cycles, cells established from 1-month-old and 2-month-old cultures produced lower cell concentrations after cultivation in the fresh medium than cells from 1-week-old culture. This decrease was not due to higher concentrations of dead cells in the populations, suggesting that cells of different culture ages differ in their capacity for cell division. Cells from 1-week-old cultures had a shorter circadian period of their cell division cycle under shortened T-cycles than aged cells. When algae were transferred to free-running conditions after entrainment to shortened T-cycles, the young cells showed the peak growth rate at a time corresponding to the first subjective night, but the aged cells did not. This suggests that circadian rhythms are more plastic in younger E. gracilis cells.
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Growth under Different Trophic Regimes and Synchronization of the Red Microalga Galdieria sulphuraria. Biomolecules 2021; 11:biom11070939. [PMID: 34202768 PMCID: PMC8301940 DOI: 10.3390/biom11070939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
The extremophilic unicellular red microalga Galdieria sulphuraria (Cyanidiophyceae) is able to grow autotrophically, or mixo- and heterotrophically with 1% glycerol as a carbon source. The alga divides by multiple fission into more than two cells within one cell cycle. The optimal conditions of light, temperature and pH (500 µmol photons m-2 s-1, 40 °C, and pH 3; respectively) for the strain Galdieria sulphuraria (Galdieri) Merola 002 were determined as a basis for synchronization experiments. For synchronization, the specific light/dark cycle, 16/8 h was identified as the precondition for investigating the cell cycle. The alga was successfully synchronized and the cell cycle was evaluated. G. sulphuraria attained two commitment points with midpoints at 10 and 13 h of the cell cycle, leading to two nuclear divisions, followed subsequently by division into four daughter cells. The daughter cells stayed in the mother cell wall until the beginning of the next light phase, when they were released. Accumulation of glycogen throughout the cell cycle was also described. The findings presented here bring a new contribution to our general understanding of the cell cycle in cyanidialean red algae, and specifically of the biotechnologically important species G. sulphuraria.
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Nayar S. Exploring the Role of a Cytokinin-Activating Enzyme LONELY GUY in Unicellular Microalga Chlorella variabilis. FRONTIERS IN PLANT SCIENCE 2021; 11:611871. [PMID: 33613586 PMCID: PMC7891180 DOI: 10.3389/fpls.2020.611871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/14/2020] [Indexed: 05/29/2023]
Abstract
LONELY GUY has been previously characterized in flowering plants to be involved in the direct activation of cytokinins. In this study, the function of the only LONELY GUY gene (CvarLOG1) from unicellular green microalga Chlorella variabilis NC64A has been investigated. CvarLOG1 expressed mainly in the lag and log phases of growth and was confirmed to be a cytokinin-activating enzyme. Overexpression of CvarLOG1 in Chlorella led to extended life in culture by almost 10-20 days, creating a "stay-green" phenotype. In the transformed alga, the cell cycle was lengthened due to delayed entry into the G2/M phase contrary to the known role of cytokinins in stimulating G2/M transition possibly due to excessive levels of this hormone. However, due to the sustained growth and delayed senescence, there was an increase in cell number by 11% and in biomass by 46% at the stationary phase, indicating a potential application for the biofuel industry. The total carbohydrate and lipid yield increased by approximately 30 and 20%, respectively. RNA-Seq-based transcriptomic analysis revealed that the genes associated with light and dark reactions of photosynthesis were upregulated, which may be the reason for the increased biomass. These data show that LOG plays an essential role during the cell cycle and in the functioning of the chloroplast and that the pathway leading to direct activation of cytokinins via LOG is functional in algae.
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Time-of-day-dependent responses of cyanobacterial cellular viability against oxidative stress. Sci Rep 2020; 10:20029. [PMID: 33208874 PMCID: PMC7676254 DOI: 10.1038/s41598-020-77141-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/03/2020] [Indexed: 01/05/2023] Open
Abstract
As an adaptation to periodic fluctuations of environmental light, photosynthetic organisms have evolved a circadian clock. Control by the circadian clock of many cellular physiological functions, including antioxidant enzymes, metabolism and the cell cycle, has attracted attention in the context of oxidative stress tolerance. However, since each physiological function works in an integrated manner to deal with oxidative stress, whether or not cell responses to oxidative stress are under circadian control remains an open question. In fact, circadian rhythms of oxidative stress tolerance have not yet been experimentally demonstrated. In the present work, we applied an assay using methyl viologen (MV), which generates reactive oxygen species (ROS) under light irradiation, and experimentally verified the circadian rhythms of oxidative stress tolerance in photosynthetic cells of the cyanobacterium Synechococcus elongatus PCC 7942, a standard model species for investigation of the circadian clock. Here, we report that ROS generated by MV treatment causes damage to stroma components and not to the photosynthetic electron transportation chain, leading to reduced cell viability. The degree of decrease in cell viability was dependent on the subjective time at which oxidative stress was applied. Thus, oxidative stress tolerance was shown to exhibit circadian rhythms. In addition, the rhythmic pattern of oxidative stress tolerance disappeared in mutant cells lacking the essential clock genes. Notably, ROS levels changed periodically, independent of the MV treatment. Thus, we demonstrate for the first time that in cyanobacterial cells, oxidative stress tolerance shows circadian oscillation.
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Farré EM. The brown clock: circadian rhythms in stramenopiles. PHYSIOLOGIA PLANTARUM 2020; 169:430-441. [PMID: 32274814 DOI: 10.1111/ppl.13104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Circadian clocks allow organisms to anticipate environmental changes associated with the diurnal light/dark cycle. Circadian oscillators have been described in plants and green algae, cyanobacteria, animals and fungi, however, little is known about the circadian clocks of photosynthetic eukaryotes outside the green lineage. Stramenopiles are a diverse group of secondary endosymbionts whose plastid originated from a red alga. Photosynthetic stramenopiles, which include diatoms and brown algae, play key roles in biogeochemical cycles and are important components of marine ecosystems. Genome annotation efforts indicated the presence of a novel type of oscillator in these organisms and the first circadian clock component in a stramenopile has been recently discovered. This review summarizes the phenotypic characterization of circadian rhythms in stramenopiles and current efforts to determine the mechanisms of this 'brown clock'. The elucidation of this brown clock will enable a deeper understanding of the role of self-sustained oscillations in the adaptation to life in marine environments.
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Affiliation(s)
- Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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Kizawa A, Osanai T. Overexpression of the response regulator rpaA causes an impaired cell division in the Cyanobacterium Synechocystis sp. PCC 6803. J GEN APPL MICROBIOL 2020; 66:121-128. [PMID: 32173680 DOI: 10.2323/jgam.2020.01.004] [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: 11/03/2022]
Abstract
In photosynthetic microorganisms, cell cycle progression depends on day and night cycles; however, how cell division is regulated in response to these environmental changes is poorly understood. RpaA has been implicated in the signal output from both circadian clocks and light/dark conditions in the unicellular spherical-celled cyanobacterium Synechocystis sp. PCC 6803. In the present study, we investigated the involvement of a two-component response regulator RpaA in cell division regulation. Firstly, we examined the effects of rpaA overexpression on cell morphology and the expression levels of cell division genes. We observed an increase in the volume of non-dividing cells and a high proportion of dividing cells in rpaA-overexpressing strains by light microscopy. The expression levels of selected cell division-related genes were higher in the rpaA-overexpressing strain than in the wild type, including minD of the Min system; cdv3 and zipN, which encode two divisome components; and murB, murC, and pbp2, which are involved in peptidoglycan (PG) synthesis. Moreover, in the rpaA-overexpressing strain, the outer membrane and cell wall PG layer were not smooth, and the outer membrane was not clearly visible by transmission electron microscopy. These results demonstrated that rpaA overexpression causes an impaired cell division, which is accompanied by transcriptional activation of cell division genes and morphological changes in the PG layer and outer membrane.
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Affiliation(s)
- Ayumi Kizawa
- Department of Agricultural Chemistry, School of Agriculture, Meiji University
| | - Takashi Osanai
- Department of Agricultural Chemistry, School of Agriculture, Meiji University
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Yoshida Y, Mogi Y. How do plastids and mitochondria divide? Microscopy (Oxf) 2019; 68:45-56. [PMID: 30476140 DOI: 10.1093/jmicro/dfy132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/16/2018] [Indexed: 12/30/2022] Open
Abstract
Plastids and mitochondria are thought to have originated from free-living cyanobacterial and alpha-proteobacterial ancestors, respectively, via endosymbiosis. Their evolutionary origins dictate that these organelles do not multiply de novo but through the division of pre-existing plastids and mitochondria. Over the past three decades, studies have shown that plastid and mitochondrial division are performed by contractile ring-shaped structures, broadly termed the plastid and mitochondrial-division machineries. Interestingly, the division machineries are hybrid forms of the bacterial cell division system and eukaryotic membrane fission system. The structure and function of the plastid and mitochondrial-division machineries are similar to each other, implying that the division machineries evolved in parallel since their establishment in primitive eukaryotes. Compared with our knowledge of their structures, our understanding of the mechanical details of how these division machineries function is still quite limited. Here, we review and compare the structural frameworks of the plastid and mitochondrial-division machineries in both lower and higher eukaryotes. Then, we highlight fundamental issues that need to be resolved to reveal the underlying mechanisms of plastid and mitochondrial division. Finally, we highlight related studies that point to an exciting future for the field.
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Affiliation(s)
- Yamato Yoshida
- Department of Science, College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki, Japan
| | - Yuko Mogi
- Department of Science, College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki, Japan
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Miyagishima SY, Era A, Hasunuma T, Matsuda M, Hirooka S, Sumiya N, Kondo A, Fujiwara T. Day/Night Separation of Oxygenic Energy Metabolism and Nuclear DNA Replication in the Unicellular Red Alga Cyanidioschyzon merolae. mBio 2019; 10:e00833-19. [PMID: 31266864 PMCID: PMC6606799 DOI: 10.1128/mbio.00833-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
The transition from G1 to S phase and subsequent nuclear DNA replication in the cells of many species of eukaryotic algae occur predominantly during the evening and night in the absence of photosynthesis; however, little is known about how day/night changes in energy metabolism and cell cycle progression are coordinated and about the advantage conferred by the restriction of S phase to the night. Using a synchronous culture of the unicellular red alga Cyanidioschyzon merolae, we found that the levels of photosynthetic and respiratory activities peak during the morning and then decrease toward the evening and night, whereas the pathways for anaerobic consumption of pyruvate, produced by glycolysis, are upregulated during the evening and night as reported recently in the green alga Chlamydomonas reinhardtii Inhibition of photosynthesis by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) largely reduced respiratory activity and the amplitude of the day/night rhythm of respiration, suggesting that the respiratory rhythm depends largely on photosynthetic activity. Even when the timing of G1/S-phase transition was uncoupled from the day/night rhythm by depletion of retinoblastoma-related (RBR) protein, the same patterns of photosynthesis and respiration were observed, suggesting that cell cycle progression and energy metabolism are regulated independently. Progression of the S phase under conditions of photosynthesis elevated the frequency of nuclear DNA double-strand breaks (DSB). These results suggest that the temporal separation of oxygenic energy metabolism, which causes oxidative stress, from nuclear DNA replication reduces the risk of DSB during cell proliferation in C. merolaeIMPORTANCE Eukaryotes acquired chloroplasts through an endosymbiotic event in which a cyanobacterium or a unicellular eukaryotic alga was integrated into a previously nonphotosynthetic eukaryotic cell. Photosynthesis by chloroplasts enabled algae to expand their habitats and led to further evolution of land plants. However, photosynthesis causes greater oxidative stress than mitochondrion-based respiration. In seed plants, cell division is restricted to nonphotosynthetic meristematic tissues and populations of photosynthetic cells expand without cell division. Thus, seemingly, photosynthesis is spatially sequestrated from cell proliferation. In contrast, eukaryotic algae possess photosynthetic chloroplasts throughout their life cycle. Here we show that oxygenic energy conversion (daytime) and nuclear DNA replication (night time) are temporally sequestrated in C. merolae This sequestration enables "safe" proliferation of cells and allows coexistence of chloroplasts and the eukaryotic host cell, as shown in yeast, where mitochondrial respiration and nuclear DNA replication are temporally sequestrated to reduce the mutation rate.
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Affiliation(s)
- Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Atsuko Era
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Nada, Kobe, Japan
- Engineering Biology Research Center, Kobe University, Nada, Kobe, Japan
| | - Mami Matsuda
- Engineering Biology Research Center, Kobe University, Nada, Kobe, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Nobuko Sumiya
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Nada, Kobe, Japan
- Engineering Biology Research Center, Kobe University, Nada, Kobe, Japan
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
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Millius A, Ode KL, Ueda HR. A period without PER: understanding 24-hour rhythms without classic transcription and translation feedback loops. F1000Res 2019; 8. [PMID: 31031966 PMCID: PMC6468715 DOI: 10.12688/f1000research.18158.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 01/08/2023] Open
Abstract
Since Ronald Konopka and Seymour Benzer's discovery of the gene Period in the 1970s, the circadian rhythm field has diligently investigated regulatory mechanisms and intracellular transcriptional and translation feedback loops involving Period, and these investigations culminated in a 2017 Nobel Prize in Physiology or Medicine for Michael W. Young, Michael Rosbash, and Jeffrey C. Hall. Although research on 24-hour behavior rhythms started with Period, a series of discoveries in the past decade have shown us that post-transcriptional regulation and protein modification, such as phosphorylation and oxidation, are alternatives ways to building a ticking clock.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Laboratory of Systems Immunology and Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Fujiwara T, Hirooka S, Mukai M, Ohbayashi R, kanesaki Y, Watanabe S, Miyagishima S. Integration of a Galdieria plasma membrane sugar transporter enables heterotrophic growth of the obligate photoautotrophic red alga Cynanidioschyzon merolae. PLANT DIRECT 2019; 3:e00134. [PMID: 31245772 PMCID: PMC6589524 DOI: 10.1002/pld3.134] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/11/2019] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
The unicellular thermoacidophilic red alga Cyanidioschyzon merolae is an emerging model organism of photosynthetic eukaryotes. Its relatively simple genome (16.5 Mbp) with very low-genetic redundancy and its cellular structure possessing one chloroplast, mitochondrion, peroxisome, and other organelles have facilitated studies. In addition, this alga is genetically tractable, and the nuclear and chloroplast genomes can be modified by integration of transgenes via homologous recombination. Recent studies have attempted to clarify the structure and function of the photosystems of this alga. However, it is difficult to obtain photosynthesis-defective mutants for molecular genetic studies because this organism is an obligate autotroph. To overcome this issue in C. merolae, we expressed a plasma membrane sugar transporter, GsSPT1, from Galdieria sulphuraria, which is an evolutionary relative of C. merolae and capable of heterotrophic growth. The heterologously expressed GsSPT1 localized at the plasma membrane. GsSPT1 enabled C. merolae to grow mixotrophically and heterotrophically, in which cells grew in the dark with glucose or in the light with a photosynthetic inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and glucose. When the GsSPT1 transgene multiplied on the C. merolae chromosome via the URA Cm-Gs selection marker, which can multiply itself and its flanking transgene, GsSPT1 protein level increased and the heterotrophic and mixotrophic growth of the transformant accelerated. We also found that GsSPT1 overexpressing C. merolae efficiently formed colonies on solidified medium under light with glucose and DCMU. Thus, GsSPT1 overexpresser will facilitate single colony isolation and analyses of photosynthesis-deficient mutants produced either by random or site-directed mutagenesis. In addition, our results yielded evidence supporting that the presence or absence of plasma membrane sugar transporters is a major cause of difference in trophic properties between C. merolae and G. sulphuraria.
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Affiliation(s)
- Takayuki Fujiwara
- Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
- JST‐Mirai ProgramJapan Science and Technology AgencyKawaguchiSaitamaJapan
- Department of GeneticsGraduate University for Advanced Studies (SOKENDAI)MishimaShizuokaJapan
| | - Shunsuke Hirooka
- Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
- JST‐Mirai ProgramJapan Science and Technology AgencyKawaguchiSaitamaJapan
| | - Mizuna Mukai
- Department of BioscienceTokyo University of AgricultureTokyoJapan
| | - Ryudo Ohbayashi
- Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
| | - Yu kanesaki
- NODAI Genome Research CenterTokyoJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityShizuokaJapan
| | - Satoru Watanabe
- Department of BioscienceTokyo University of AgricultureTokyoJapan
| | - Shin‐ya Miyagishima
- Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
- JST‐Mirai ProgramJapan Science and Technology AgencyKawaguchiSaitamaJapan
- Department of GeneticsGraduate University for Advanced Studies (SOKENDAI)MishimaShizuokaJapan
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Nagano S, Moriyuki S, Wakamori K, Mineno H, Fukuda H. Leaf-Movement-Based Growth Prediction Model Using Optical Flow Analysis and Machine Learning in Plant Factory. FRONTIERS IN PLANT SCIENCE 2019; 10:227. [PMID: 30967880 PMCID: PMC6439531 DOI: 10.3389/fpls.2019.00227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/11/2019] [Indexed: 05/10/2023]
Abstract
Productivity stabilization is a critical issue facing plant factories. As such, researchers have been investigating growth prediction with the overall goal of improving productivity. The projected area of a plant (PA) is usually used for growth prediction, by which the growth of a plant is estimated by observing the overall approximate movement of the plant. To overcome this problem, this study focused on the time-series movement of plant leaves, using optical flow (OF) analysis to acquire this information for a lettuce. OF analysis is an image processing method that extracts the difference between two consecutive frames caused by the movement of the subject. Experiments were carried out at a commercial large-scale plant factory. By using a microcomputer with a camera module placed above the lettuce seedlings, images of 338 seedlings were taken every 20 min over 9 days (from the 6th to the 15th day after sowing). Then, the features of the leaf movement were extracted from the image by calculating the normal-vector in the OF analysis, and these features were applied to machine learning to predict the fresh weight of the lettuce at harvest time (38 days after sowing). The growth prediction model using the features extracted from the OF analysis was found to perform well with a correlation ratio of 0.743. Furthermore, this study also considered a phenotyping system that was capable of automatically analyzing a plant image, which would allow this growth prediction model to be widely used in commercial plant factories.
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Affiliation(s)
- Shogo Nagano
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Shogo Moriyuki
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan
| | - Kazumasa Wakamori
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hiroshi Mineno
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Hirokazu Fukuda
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
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25
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Pancha I, Shima H, Higashitani N, Igarashi K, Higashitani A, Tanaka K, Imamura S. Target of rapamycin-signaling modulates starch accumulation via glycogenin phosphorylation status in the unicellular red alga Cyanidioschyzon merolae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:485-499. [PMID: 30351485 DOI: 10.1111/tpj.14136] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/23/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
The target of rapamycin (TOR) signaling pathway is involved in starch accumulation in various eukaryotic organisms; however, the molecular mechanism behind this phenomenon in eukaryotes has not been elucidated. We report a regulatory mechanism of starch accumulation by TOR in the unicellular red alga, Cyanidioschyzon merolae. The starch content in C. merolae after TOR-inactivation by rapamycin, a TOR-specific inhibitor, was increased by approximately 10-fold in comparison with its drug vehicle, dimethyl sulfoxide. However, our previous transcriptome analysis showed that the expression level of genes related to carbohydrate metabolism was unaffected by rapamycin, indicating that starch accumulation is regulated at post-transcriptional levels. In this study, we performed a phosphoproteome analysis using liquid chromatography-tandem mass spectrometry to investigate potential post-transcriptional modifications, and identified 52 proteins as candidate TOR substrates. Among the possible substrates, we focused on the function of CmGLG1, because its phosphorylation at the Ser613 residue was decreased after rapamycin treatment, and overexpression of CmGLG1 resulted in a 4.7-fold higher starch content. CmGLG1 is similar to the priming protein, glycogenin, which is required for the initiation of starch/glycogen synthesis, and a budding yeast complementation assay demonstrated that CmGLG1 can functionally substitute for glycogenin. We found an approximately 60% reduction in the starch content in a phospho-mimicking CmGLG1 overexpression strain, in which Ser613 was substituted with aspartic acid, in comparison with the wild-type CmGLG1 overexpression cells. Our results indicate that TOR modulates starch accumulation by changing the phosphorylation status of the CmGLG1 Ser613 residue in C. merolae.
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Affiliation(s)
- Imran Pancha
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575, Japan
| | - Nahoko Higashitani
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575, Japan
| | - Atsushi Higashitani
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
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26
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Wong DCS, O’Neill JS. Non-transcriptional processes in circadian rhythm generation. CURRENT OPINION IN PHYSIOLOGY 2018; 5:117-132. [PMID: 30596188 PMCID: PMC6302373 DOI: 10.1016/j.cophys.2018.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
'Biological clocks' orchestrate mammalian biology to a daily rhythm. Whilst 'clock gene' transcriptional circuits impart rhythmic regulation to myriad cellular systems, our picture of the biochemical mechanisms that determine their circadian (∼24 hour) period is incomplete. Here we consider the evidence supporting different models for circadian rhythm generation in mammalian cells in light of evolutionary factors. We find it plausible that the circadian timekeeping mechanism in mammalian cells is primarily protein-based, signalling biological timing information to the nucleus by the post-translational regulation of transcription factor activity, with transcriptional feedback imparting robustness to the oscillation via hysteresis. We conclude by suggesting experiments that might distinguish this model from competing paradigms.
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27
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Gaucher J, Montellier E, Sassone-Corsi P. Molecular Cogs: Interplay between Circadian Clock and Cell Cycle. Trends Cell Biol 2018; 28:368-379. [DOI: 10.1016/j.tcb.2018.01.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/21/2018] [Accepted: 01/22/2018] [Indexed: 12/29/2022]
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28
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Poliner E, Takeuchi T, Du ZY, Benning C, Farré EM. Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779. ACS Synth Biol 2018; 99:112-127. [PMID: 29518315 PMCID: PMC6616531 DOI: 10.1111/tpj.14314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 04/25/2023]
Abstract
Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, Nannochloropsis oceanica CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for N. oceanica that enables the generation of marker-free mutant lines. The CEN/ARS6 region from Saccharomyces cerevisiae was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene ( NR) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO).
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Affiliation(s)
- Eric Poliner
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
| | - Tomomi Takeuchi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Zhi-Yan Du
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Christoph Benning
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
- Plant Biology Department, Michigan State University, East Lansing, Michigan
| | - Eva M. Farré
- Plant Biology Department, Michigan State University, East Lansing, Michigan
- Corresponding Author: Eva M. Farré (), Phone: +1-517-353-5215
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29
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Yoshida Y. Insights into the Mechanisms of Chloroplast Division. Int J Mol Sci 2018; 19:ijms19030733. [PMID: 29510533 PMCID: PMC5877594 DOI: 10.3390/ijms19030733] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 02/08/2023] Open
Abstract
The endosymbiosis of a free-living cyanobacterium into an ancestral eukaryote led to the evolution of the chloroplast (plastid) more than one billion years ago. Given their independent origins, plastid proliferation is restricted to the binary fission of pre-existing plastids within a cell. In the last 25 years, the structure of the supramolecular machinery regulating plastid division has been discovered, and some of its component proteins identified. More recently, isolated plastid-division machineries have been examined to elucidate their structural and mechanistic details. Furthermore, complex studies have revealed how the plastid-division machinery morphologically transforms during plastid division, and which of its component proteins play a critical role in generating the contractile force. Identifying the three-dimensional structures and putative functional domains of the component proteins has given us hints about the mechanisms driving the machinery. Surprisingly, the mechanisms driving plastid division resemble those of mitochondrial division, indicating that these division machineries likely developed from the same evolutionary origin, providing a key insight into how endosymbiotic organelles were established. These findings have opened new avenues of research into organelle proliferation mechanisms and the evolution of organelles.
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Affiliation(s)
- Yamato Yoshida
- Department of Science, College of Science, Ibaraki University, Ibaraki 310-8512, Japan.
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30
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Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W. Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol 2018; 14:e7962. [PMID: 29496885 PMCID: PMC5830654 DOI: 10.15252/msb.20177962] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/22/2018] [Accepted: 01/30/2018] [Indexed: 12/28/2022] Open
Abstract
Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in proteins of photosynthesis, primary and secondary metabolism, including pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates in the day than the night likely contribute to these changes, via an interaction with rhythmic changes in RNA abundance. Photoperiodic control of protein levels might be greatest only if high translation rates coincide with high transcript levels in some photoperiods. We term this proposed mechanism "translational coincidence", mathematically model its components, and demonstrate its effect on the Arabidopsis proteome. Datasets from a green alga and a cyanobacterium suggest that translational coincidence contributes to seasonal control of the proteome in many phototrophic organisms. This may explain why many transcripts but not their cognate proteins exhibit diurnal rhythms.
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Affiliation(s)
- Daniel D Seaton
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alexander Graf
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland
| | - Katja Baerenfaller
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland
| | - Mark Stitt
- System Regulation Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Wilhelm Gruissem
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland
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31
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Inoue K, Araki T, Endo M. Circadian clock during plant development. JOURNAL OF PLANT RESEARCH 2018; 131:59-66. [PMID: 29134443 PMCID: PMC5897470 DOI: 10.1007/s10265-017-0991-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/06/2017] [Indexed: 05/14/2023]
Abstract
Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season. Recent genomic studies have demonstrated that polymorphism in circadian clock genes may contribute to local adaptations over a wide range of latitudes in many plant species. In the present review, we summarize the circadian regulation of biological processes throughout the life cycle of plants, and describe the contribution of the circadian clock to local adaptation.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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32
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Henslee EA, Crosby P, Kitcatt SJ, Parry JSW, Bernardini A, Abdallat RG, Braun G, Fatoyinbo HO, Harrison EJ, Edgar RS, Hoettges KF, Reddy AB, Jabr RI, von Schantz M, O'Neill JS, Labeed FH. Rhythmic potassium transport regulates the circadian clock in human red blood cells. Nat Commun 2017; 8:1978. [PMID: 29215003 PMCID: PMC5719349 DOI: 10.1038/s41467-017-02161-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 11/10/2017] [Indexed: 12/18/2022] Open
Abstract
Circadian rhythms organize many aspects of cell biology and physiology to a daily temporal program that depends on clock gene expression cycles in most mammalian cell types. However, circadian rhythms are also observed in isolated mammalian red blood cells (RBCs), which lack nuclei, suggesting the existence of post-translational cellular clock mechanisms in these cells. Here we show using electrophysiological and pharmacological approaches that human RBCs display circadian regulation of membrane conductance and cytoplasmic conductivity that depends on the cycling of cytoplasmic K+ levels. Using pharmacological intervention and ion replacement, we show that inhibition of K+ transport abolishes RBC electrophysiological rhythms. Our results suggest that in the absence of conventional transcription cycles, RBCs maintain a circadian rhythm in membrane electrophysiology through dynamic regulation of K+ transport. Circadian rhythms usually rely on cyclic variations in gene expression. Red blood cells, however, display circadian rhythms while being devoid of nuclear DNA. Here, Henslee and colleagues show that circadian rhythms in isolated human red blood cells are dependent on rhythmic transport of K+ ions.
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Affiliation(s)
- Erin A Henslee
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Priya Crosby
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Stephen J Kitcatt
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Jack S W Parry
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Andrea Bernardini
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Rula G Abdallat
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK.,Department of Biomedical Engineering, The Hashemite University, 330127, Zarqa, 13115, Jordan
| | - Gabriella Braun
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Henry O Fatoyinbo
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Esther J Harrison
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Rachel S Edgar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Kai F Hoettges
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Akhilesh B Reddy
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Rita I Jabr
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Malcolm von Schantz
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Fatima H Labeed
- Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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33
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El-Athman R, Genov NN, Mazuch J, Zhang K, Yu Y, Fuhr L, Abreu M, Li Y, Wallach T, Kramer A, Schmitt CA, Relógio A. The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity. PLoS Biol 2017; 15:e2002940. [PMID: 29216180 PMCID: PMC5720494 DOI: 10.1371/journal.pbio.2002940] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/02/2017] [Indexed: 12/29/2022] Open
Abstract
The mammalian circadian clock and the cell cycle are two major biological oscillators whose coupling influences cell fate decisions. In the present study, we use a model-driven experimental approach to investigate the interplay between clock and cell cycle components and the dysregulatory effects of RAS on this coupled system. In particular, we focus on the Ink4a/Arf locus as one of the bridging clock-cell cycle elements. Upon perturbations by the rat sarcoma viral oncogene (RAS), differential effects on the circadian phenotype were observed in wild-type and Ink4a/Arf knock-out mouse embryonic fibroblasts (MEFs), which could be reproduced by our modelling simulations and correlated with opposing cell cycle fate decisions. Interestingly, the observed changes can be attributed to in silico phase shifts in the expression of core-clock elements. A genome-wide analysis revealed a set of differentially expressed genes that form an intricate network with the circadian system with enriched pathways involved in opposing cell cycle phenotypes. In addition, a machine learning approach complemented by cell cycle analysis classified the observed cell cycle fate decisions as dependent on Ink4a/Arf and the oncogene RAS and highlighted a putative fine-tuning role of Bmal1 as an elicitor of such processes, ultimately resulting in increased cell proliferation in the Ink4a/Arf knock-out scenario. This indicates that the dysregulation of the core-clock might work as an enhancer of RAS-mediated regulation of the cell cycle. Our combined in silico and in vitro approach highlights the important role of the circadian clock as an Ink4a/Arf-dependent modulator of oncogene-induced cell fate decisions, reinforcing its function as a tumour-suppressor and the close interplay between the clock and the cell cycle network. In mammals, the circadian clock controls the punctual regulation of biological processes, which, in turn, affect physiology and behaviour, allowing for the synchronisation of internal time to environmental light-dark cycles. Malfunctions of the circadian clock are associated with pathological phenotypes including cancer. Given the range of molecular time-dependent processes, including metabolism, DNA repair, and the cell cycle, the clock is hypothesised to act as a tumour suppressor. With the help of mathematical modelling and whole-genome analysis combined with machine learning, we investigated the RAS-dependent dysregulation of the circadian clock. We find that the tumour-suppressor Ink4a/Arf acts as a key mediator of RAS oncogene-induced changes in the circadian system, thereby mediating the interplay between the clock and the cell cycle.
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Affiliation(s)
- Rukeia El-Athman
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
| | - Nikolai N. Genov
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
| | - Jeannine Mazuch
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
| | - Kaiyang Zhang
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
| | - Yong Yu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Luise Fuhr
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
| | - Mónica Abreu
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
| | - Yin Li
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
| | - Thomas Wallach
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Achim Kramer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Clemens A. Schmitt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Angela Relógio
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology, and Tumor Immunology, and Molecular Cancer Research Center, Germany
- * E-mail:
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34
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Kawase Y, Imamura S, Tanaka K. A MYB-type transcription factor, MYB2, represses light-harvesting protein genes in Cyanidioschyzon merolae. FEBS Lett 2017; 591:2439-2448. [PMID: 28748638 DOI: 10.1002/1873-3468.12763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 11/07/2022]
Abstract
While searching for transcriptional regulators that respond to changes in light regimes, we identified a MYB domain-containing protein, MYB2, that accumulates under dark and other conditions in the unicellular red alga Cyanidioschyzon merolae. The isolation and analysis of a MYB2 mutant revealed that MYB2 represses the expression of the nuclear-encoded chloroplast RNA polymerase sigma factor gene SIG2, which results in the repression of the chloroplast-encoded phycobilisome genes that are under its control. Since nuclear-encoded phycobilisome and other light-harvesting protein genes are also repressed by MYB2, we conclude that MYB2 has a role in repressing the expression of light-harvesting genes. The MYB2 mutant is sensitive to a prolonged dark incubation, indicating the importance of MYB2 for cell viability in the dark.
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Affiliation(s)
- Yasuko Kawase
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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35
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Onuma R, Mishra N, Miyagishima SY. Regulation of chloroplast and nucleomorph replication by the cell cycle in the cryptophyte Guillardia theta. Sci Rep 2017; 7:2345. [PMID: 28539635 PMCID: PMC5443833 DOI: 10.1038/s41598-017-02668-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/13/2017] [Indexed: 01/08/2023] Open
Abstract
The chloroplasts of cryptophytes arose through a secondary endosymbiotic event in which a red algal endosymbiont was integrated into a previously nonphotosynthetic eukaryote. The cryptophytes retain a remnant of the endosymbiont nucleus (nucleomorph) that is replicated once in the cell cycle along with the chloroplast. To understand how the chloroplast, nucleomorph and host cell divide in a coordinated manner, we examined the expression of genes/proteins that are related to nucleomorph replication and chloroplast division as well as the timing of nuclear and nucleomorph DNA synthesis in the cryptophyte Guillardia theta. Nucleus-encoded nucleomorph HISTONE H2A mRNA specifically accumulated during the nuclear S phase. In contrast, nucleomorph-encoded genes/proteins that are related to nucleomorph replication and chloroplast division (FtsZ) are constantly expressed throughout the cell cycle. The results of this study and previous studies on chlorarachniophytes suggest that there was a common evolutionary pattern in which an endosymbiont lost its replication cycle-dependent transcription while cell-cycle-dependent transcriptional regulation of host nuclear genes came to restrict the timing of nucleomorph replication and chloroplast division.
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Affiliation(s)
- Ryo Onuma
- Department of Cell Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
| | - Neha Mishra
- Department of Cell Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Cell Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.
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36
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Sumiya N, Miyagishima SY. Hierarchal order in the formation of chloroplast division machinery in the red alga Cyanidioschyzon merolae. Commun Integr Biol 2017; 10:e1294298. [PMID: 28451055 PMCID: PMC5398205 DOI: 10.1080/19420889.2017.1294298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/25/2022] Open
Abstract
Chloroplasts have evolved from a cyanobacterial endosymbiont and multiply by dividing. Chloroplast division is performed by constriction of the ring-like protein complex (the PD machinery), which forms at the division site. The PD machinery is composed of cyanobacteria-descended components such as FtsZ and eukaryote-derived proteins such as the dynamin-related protein, DRP5B. In the red alga Cyanidioschyzon merolae, FtsZ ring formation on the stromal side precedes PDR1 and DRP5B ring formation on the cytosolic side. In this study, we impaired FtsZ ring formation in C. merolae by overexpressing FtsZ just before FtsZ ring formation. As a result, PDR1 and DRP5B failed to localize at the chloroplast division site, suggesting that FtsZ ring formation is required for the PDR1 and DRP5B rings. We further found, by expressing a dominant negative form of DRP5B, that DRP5B ring formation begins on the nuclear side of the chloroplast division site. These findings provide insight into how the PD machinery forms in red algae.
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Affiliation(s)
- Nobuko Sumiya
- Department of Cell Genetics, National Institute of Genetics, Shizuoka, Japan.,Core Research for Evolutional Science and Technology Program, Japan Science and Technology Agency, Saitama, Japan
| | - Shin-Ya Miyagishima
- Department of Cell Genetics, National Institute of Genetics, Shizuoka, Japan.,Core Research for Evolutional Science and Technology Program, Japan Science and Technology Agency, Saitama, Japan.,Department of Genetics, Graduate University for Advanced Studies, Shizuoka, Japan
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37
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Shostak A. Circadian Clock, Cell Division, and Cancer: From Molecules to Organism. Int J Mol Sci 2017; 18:E873. [PMID: 28425940 PMCID: PMC5412454 DOI: 10.3390/ijms18040873] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022] Open
Abstract
As a response to environmental changes driven by the Earth's axial rotation, most organisms evolved an internal biological timer-the so called circadian clock-which regulates physiology and behavior in a rhythmic fashion. Emerging evidence suggests an intimate interplay between the circadian clock and another fundamental rhythmic process, the cell cycle. However, the precise mechanisms of this connection are not fully understood. Disruption of circadian rhythms has a profound impact on cell division and cancer development and, vice versa, malignant transformation causes disturbances of the circadian clock. Conventional knowledge attributes tumor suppressor properties to the circadian clock. However, this implication might be context-dependent, since, under certain conditions, the clock can also promote tumorigenesis. Therefore, a better understanding of the molecular links regulating the physiological balance between the two cycles will have potential significance for the treatment of cancer and associated disorders.
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Affiliation(s)
- Anton Shostak
- Circadian Rhythms and Molecular Clocks Group, Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany.
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38
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Fujiwara T, Ohnuma M, Kuroiwa T, Ohbayashi R, Hirooka S, Miyagishima SY. Development of a Double Nuclear Gene-Targeting Method by Two-Step Transformation Based on a Newly Established Chloramphenicol-Selection System in the Red Alga Cyanidioschyzon merolae. FRONTIERS IN PLANT SCIENCE 2017; 8:343. [PMID: 28352279 PMCID: PMC5348525 DOI: 10.3389/fpls.2017.00343] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/27/2017] [Indexed: 05/24/2023]
Abstract
The unicellular red alga Cyanidioschyzon merolae possesses a simple cellular architecture that consists of one mitochondrion, one chloroplast, one peroxisome, one Golgi apparatus, and several lysosomes. The nuclear genome content is also simple, with very little genetic redundancy (16.5 Mbp, 4,775 genes). In addition, molecular genetic tools such as gene targeting and inducible gene expression systems have been recently developed. These cytological features and genetic tractability have facilitated various omics analyses. However, only a single transformation selection marker URA has been made available and thus the application of genetic modification has been limited. Here, we report the development of a nuclear targeting method by using chloramphenicol and the chloramphenicol acetyltransferase (CAT) gene. In addition, we found that at least 200-bp homologous arms are required and 500-bp arms are sufficient for a targeted single-copy insertion of the CAT selection marker into the nuclear genome. By means of a combination of the URA and CAT transformation systems, we succeeded in producing a C. merolae strain that expresses HA-cyclin 1 and FLAG-CDKA from the chromosomal CYC1 and CDKA loci, respectively. These methods of multiple nuclear targeting will facilitate genetic manipulation of C. merolae.
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Affiliation(s)
- Takayuki Fujiwara
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- Department of Genetics, Graduate University for Advanced StudiesShizuoka, Japan
| | - Mio Ohnuma
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- National Institute of Technology, Hiroshima CollegeHiroshima, Japan
| | - Tsuneyoshi Kuroiwa
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- Department of Chemical and Biological Science, Faculty of Science, Japan Women’s UniversityTokyo, Japan
| | - Ryudo Ohbayashi
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
| | - Shunsuke Hirooka
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
| | - Shin-Ya Miyagishima
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- Department of Genetics, Graduate University for Advanced StudiesShizuoka, Japan
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39
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Imoto Y, Abe Y, Okumoto K, Honsho M, Kuroiwa H, Kuroiwa T, Fujiki Y. Defining the dynamin-based ring organizing center on the peroxisome-dividing machinery isolated from Cyanidioschyzon merolae. J Cell Sci 2017; 130:853-867. [PMID: 28115534 DOI: 10.1242/jcs.199182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/05/2017] [Indexed: 11/20/2022] Open
Abstract
Organelle division is executed through contraction of a ring-shaped supramolecular dividing machinery. A core component of the machinery is the dynamin-based ring conserved during the division of mitochondrion, plastid and peroxisome. Here, using isolated peroxisome-dividing (POD) machinery from a unicellular red algae, Cyanidioschyzon merolae, we identified a dynamin-based ring organizing center (DOC) that acts as an initiation point for formation of the dynamin-based ring. C. merolae contains a single peroxisome, the division of which can be highly synchronized by light-dark stimulation; thus, intact POD machinery can be isolated in bulk. Dynamin-based ring homeostasis is maintained by the turnover of the GTP-bound form of the dynamin-related protein Dnm1 between the cytosol and division machinery via the DOC. A single DOC is formed on the POD machinery with a diameter of 500-700 nm, and the dynamin-based ring is unidirectionally elongated from the DOC in a manner that is dependent on GTP concentration. During the later step of membrane fission, the second DOC is formed and constructs the double dynamin-based ring to make the machinery thicker. These findings provide new insights to define fundamental mechanisms underlying the dynamin-based membrane fission in eukaryotic cells.
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Affiliation(s)
- Yuuta Imoto
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuichi Abe
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Masanori Honsho
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Haruko Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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40
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Zienkiewicz M, Krupnik T, Drożak A, Golke A, Romanowska E. Chloramphenicol acetyltransferase-a new selectable marker in stable nuclear transformation of the red alga Cyanidioschyzon merolae. PROTOPLASMA 2017; 254:587-596. [PMID: 26715590 DOI: 10.1007/s00709-015-0936-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/21/2015] [Indexed: 05/03/2023]
Abstract
In this study, we have shown the applicability of chloramphenicol acetyltransferase as a new and convenient selectable marker for stable nuclear transformation as well as potential chloroplast transformation of Cyanidioschyzon merolae-a new model organism, which offers unique opportunities for studding the mitochondrial and plastid physiology as well as various evolutionary, structural, and functional features of the photosynthetic apparatus.
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41
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Okamura E, Sakamoto T, Sasaki T, Matsunaga S. A Plant Ancestral Polo-Like Kinase Sheds Light on the Mystery of the Evolutionary Disappearance of Polo-Like Kinases in the Plant Kingdom. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Erika Okamura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Tatsuki Sasaki
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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42
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Zienkiewicz M, Krupnik T, Drożak A, Golke A, Romanowska E. Transformation of the Cyanidioschyzon merolae chloroplast genome: prospects for understanding chloroplast function in extreme environments. PLANT MOLECULAR BIOLOGY 2017; 93:171-183. [PMID: 27796719 PMCID: PMC5243890 DOI: 10.1007/s11103-016-0554-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/22/2016] [Indexed: 05/06/2023]
Abstract
We have successfully transformed an exthemophilic red alga with the chloramphenicol acetyltransferase gene, rendering this organism insensitive to its toxicity. Our work paves the way to further work with this new modelorganism. Here we report the first successful attempt to achieve a stable, under selectable pressure, chloroplast transformation in Cyanidioschizon merolae-an extremophilic red alga of increasing importance as a new model organism. The following protocol takes advantage of a double homologous recombination phenomenon in the chloroplast, allowing to introduce an exogenous, selectable gene. For that purpose, we decided to use chloramphenicol acetyltransferase (CAT), as chloroplasts are particularly vulnerable to chloramphenicol lethal effects (Zienkiewicz et al. in Protoplasma, 2015, doi: 10.1007/s00709-015-0936-9 ). We adjusted two methods of DNA delivery: the PEG-mediated delivery and the biolistic bombardment based delivery, either of these methods work sufficiently with noticeable preference to the former. Application of a codon-optimized sequence of the cat gene and a single colony selection yielded C. merolae strains, capable of resisting up to 400 µg/mL of chloramphenicol. Our method opens new possibilities in production of site-directed mutants, recombinant proteins and exogenous protein overexpression in C. merolae-a new model organism.
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Affiliation(s)
- Maksymilian Zienkiewicz
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warsaw, Poland.
| | - Tomasz Krupnik
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Anna Drożak
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Anna Golke
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Elżbieta Romanowska
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warsaw, Poland
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43
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Abstract
Chloroplasts evolved from a cyanobacterial endosymbiont. It is believed that the synchronization of endosymbiotic and host cell division, as is commonly seen in existing algae, was a critical step in establishing the permanent organelle. Algal cells typically contain one or only a small number of chloroplasts that divide once per host cell cycle. This division is based partly on the S-phase-specific expression of nucleus-encoded proteins that constitute the chloroplast-division machinery. In this study, using the red alga Cyanidioschyzon merolae, we show that cell-cycle progression is arrested at the prophase when chloroplast division is blocked before the formation of the chloroplast-division machinery by the overexpression of Filamenting temperature-sensitive (Fts) Z2-1 (Fts72-1), but the cell cycle progresses when chloroplast division is blocked during division-site constriction by the overexpression of either FtsZ2-1 or a dominant-negative form of dynamin-related protein 5B (DRP5B). In the cells arrested in the prophase, the increase in the cyclin B level and the migration of cyclin-dependent kinase B (CDKB) were blocked. These results suggest that chloroplast division restricts host cell-cycle progression so that the cell cycle progresses to the metaphase only when chloroplast division has commenced. Thus, chloroplast division and host cell-cycle progression are synchronized by an interactive restriction that takes place between the nucleus and the chloroplast. In addition, we observed a similar pattern of cell-cycle arrest upon the blockage of chloroplast division in the glaucophyte alga Cyanophora paradoxa, raising the possibility that the chloroplast division checkpoint contributed to the establishment of the permanent organelle.
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44
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Gutierrez C. 25 Years of Cell Cycle Research: What's Ahead? TRENDS IN PLANT SCIENCE 2016; 21:823-833. [PMID: 27401252 DOI: 10.1016/j.tplants.2016.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/13/2016] [Accepted: 06/21/2016] [Indexed: 05/27/2023]
Abstract
We have reached 25 years since the first molecular approaches to plant cell cycle. Fortunately, we have witnessed an enormous advance in this field that has benefited from using complementary approaches including molecular, cellular, genetic and genomic resources. These studies have also branched and demonstrated the functional relevance of cell cycle regulators for virtually every aspect of plant life. The question is - where are we heading? I review here the latest developments in the field and briefly elaborate on how new technological advances should contribute to novel approaches that will benefit the plant cell cycle field. Understanding how the cell division cycle is integrated at the organismal level is perhaps one of the major challenges.
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Affiliation(s)
- Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Nicolas Cabrera 1, 28049 Madrid, Spain.
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45
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Harashima H, Sugimoto K. Integration of developmental and environmental signals into cell proliferation and differentiation through RETINOBLASTOMA-RELATED 1. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:95-103. [PMID: 26799131 DOI: 10.1016/j.pbi.2015.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/03/2015] [Accepted: 12/06/2015] [Indexed: 05/23/2023]
Abstract
Plants continuously form new organs during post-embryonic development, thus progression of the proliferative cell cycle and subsequent transition into differentiation must be tightly controlled by developmental and environmental cues. Recent studies have begun to uncover how cell proliferation and cell differentiation are coordinated at the molecular level through tight transcriptional regulation of cell cycle and/or developmental regulators. Accumulating evidence suggests that RETINOBLASTOMA-RELATED 1 (RBR1), the Arabidopsis homolog of the human tumor suppressor Retinoblastoma (Rb), functions as a molecular hub linking cell proliferation, differentiation, and environmental response. In this review we will discuss recent findings on cell cycle regulation, highlighting the emerging roles of RBR1 as a key integrator of internal differentiation cues and external stimuli into the cell cycle machinery.
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Affiliation(s)
- Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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46
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Burnetti AJ, Aydin M, Buchler NE. Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates. Mol Biol Cell 2016; 27:64-74. [PMID: 26538026 PMCID: PMC4694762 DOI: 10.1091/mbc.e15-07-0454] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/21/2015] [Accepted: 10/27/2015] [Indexed: 01/30/2023] Open
Abstract
Cells have evolved oscillators with different frequencies to coordinate periodic processes. Here we studied the interaction of two oscillators, the cell division cycle (CDC) and the yeast metabolic cycle (YMC), in budding yeast. Previous work suggested that the CDC and YMC interact to separate high oxygen consumption (HOC) from DNA replication to prevent genetic damage. To test this hypothesis, we grew diverse strains in chemostat and measured DNA replication and oxygen consumption with high temporal resolution at different growth rates. Our data showed that HOC is not strictly separated from DNA replication; rather, cell cycle Start is coupled with the initiation of HOC and catabolism of storage carbohydrates. The logic of this YMC-CDC coupling may be to ensure that DNA replication and cell division occur only when sufficient cellular energy reserves have accumulated. Our results also uncovered a quantitative relationship between CDC period and YMC period across different strains. More generally, our approach shows how studies in genetically diverse strains efficiently identify robust phenotypes and steer the experimentalist away from strain-specific idiosyncrasies.
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Affiliation(s)
- Anthony J Burnetti
- Program in Cellular & Molecular Biology, Duke University, Durham, NC 27708 University Program in Genetics & Genomics, Duke University, Durham, NC 27708 Center for Genomic & Computational Biology, Duke University, Durham, NC 22710 Department of Biology, Duke University, Durham, NC 27708
| | - Mert Aydin
- Center for Genomic & Computational Biology, Duke University, Durham, NC 22710 Department of Biology, Duke University, Durham, NC 27708
| | - Nicolas E Buchler
- Center for Genomic & Computational Biology, Duke University, Durham, NC 22710 Department of Biology, Duke University, Durham, NC 27708
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47
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Fujiwara T, Kanesaki Y, Hirooka S, Era A, Sumiya N, Yoshikawa H, Tanaka K, Miyagishima SY. A nitrogen source-dependent inducible and repressible gene expression system in the red alga Cyanidioschyzon merolae. FRONTIERS IN PLANT SCIENCE 2015; 6:657. [PMID: 26379685 PMCID: PMC4549557 DOI: 10.3389/fpls.2015.00657] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/10/2015] [Indexed: 05/19/2023]
Abstract
The unicellular red alga Cyanidioschyzon merolae is a model organism for studying the basic biology of photosynthetic organisms. The C. merolae cell is composed of an extremely simple set of organelles. The genome is completely sequenced. Gene targeting and a heat-shock inducible gene expression system has been recently established. However, a conditional gene knockdown system has not been established, which is required for the examination of function of genes that are essential to cell viability and primary mutant defects. In the current study, we first evaluated the expression of a transgene from two chromosomal neutral loci located in the intergenic region between CMD184C and CMD185C, and a region upstream of the URA5.3 gene. There was no significant difference in expression between them and this result suggests that both may be used as neutral loci. We then designed an inducible and repressible gene expression by using promoters of nitrate-assimilation genes. The expression of nitrate-assimilation genes such as NR (nitrate reductase), NIR (nitrite reductase), and NRT (the nitrate/nitrite transporter) are reversibly regulated by their dependence on nitrogen sources. We constructed stable strains in which a cassette containing the NR, NIR, or NRT promoter and sfGFP gene was inserted in a region upstream of URA5.3 and examined the efficacy of the promoters. The NR, NIR, and NRT promoters were constitutively activated in the nitrate medium, whereas their activities were extremely low in presence of ammonium. The activation of each promoter was immediately inhibited within a period of 1 h by the addition of ammonium. Thus, a conditional knockdown system in C. merolae was successfully established. The activity varies among the promoters, and each is selectable according to the expression level of a target gene estimated by RNA-sequencing. This method is applicable to defects in genes of interest in photosynthetic organism.
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Affiliation(s)
- Takayuki Fujiwara
- Department of Cell Genetics, National Institute of GeneticsMishima, Japan
- *Correspondence: Takayuki Fujiwara and Shin-Ya Miyagishima, Department of Cell Genetics, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan, ;
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of AgricultureTokyo, Japan
| | - Shunsuke Hirooka
- Department of Cell Genetics, National Institute of GeneticsMishima, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyKawaguchi, Japan
| | - Atsuko Era
- Department of Cell Genetics, National Institute of GeneticsMishima, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyKawaguchi, Japan
| | - Nobuko Sumiya
- Department of Cell Genetics, National Institute of GeneticsMishima, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyKawaguchi, Japan
| | - Hirofumi Yoshikawa
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyKawaguchi, Japan
- Department of Bioscience, Tokyo University of AgricultureTokyo, Japan
| | - Kan Tanaka
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyKawaguchi, Japan
- Chemical Resources Laboratory, Tokyo Institute of TechnologyYokohama, Japan
| | - Shin-Ya Miyagishima
- Department of Cell Genetics, National Institute of GeneticsMishima, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyKawaguchi, Japan
- Department of Genetics, Graduate University for Advanced StudiesMishima, Japan
- *Correspondence: Takayuki Fujiwara and Shin-Ya Miyagishima, Department of Cell Genetics, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan, ;
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48
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Abstract
As major contributors to global oxygen levels and producers of fatty acids, carotenoids, sterols, and phycocolloids, algae have significant ecological and commercial roles. Early algal models have contributed much to our understanding of circadian clocks at physiological and biochemical levels. The genetic and molecular approaches that identified clock components in other taxa have not been as widely applied to algae. We review results from seven species: the chlorophytes Chlamydomonas reinhardtii, Ostreococcus tauri, and Acetabularia spp.; the dinoflagellates Lingulodinium polyedrum and Symbiodinium spp.; the euglenozoa Euglena gracilis; and the red alga Cyanidioschyzon merolae. The relative simplicity, experimental tractability, and ecological and evolutionary diversity of algal systems may now make them particularly useful in integrating quantitative data from "omic" technologies (e.g., genomics, transcriptomics, metabolomics, and proteomics) with computational and mathematical methods.
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Affiliation(s)
- Zeenat B Noordally
- SynthSys and School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom
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49
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Development of a heat-shock inducible gene expression system in the red alga Cyanidioschyzon merolae. PLoS One 2014; 9:e111261. [PMID: 25337786 PMCID: PMC4206486 DOI: 10.1371/journal.pone.0111261] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
The cell of the unicellular red alga Cyanidioschyzon merolae contains a single chloroplast and mitochondrion, the division of which is tightly synchronized by a light/dark cycle. The genome content is extremely simple, with a low level of genetic redundancy, in photosynthetic eukaryotes. In addition, transient transformation and stable transformation by homologous recombination have been reported. However, for molecular genetic analyses of phenomena that are essential for cellular growth and survival, inducible gene expression/suppression systems are needed. Here, we report the development of a heat-shock inducible gene expression system in C. merolae. CMJ101C, encoding a small heat shock protein, is transcribed only when cells are exposed to an elevated temperature. Using a superfolder GFP as a reporter protein, the 200-bp upstream region of CMJ101C orf was determined to be the optimal promoter for heat-shock induction. The optimal temperature to induce expression is 50°C, at which C. merolae cells are able to proliferate. At least a 30-min heat shock is required for the expression of a protein of interest and a 60-min heat shock yields the maximum level of protein expression. After the heat shock, the mRNA level decreases rapidly. As an example of the system, the expression of a dominant negative form of chloroplast division DRP5B protein, which has a mutation in the GTPase domain, was induced. Expression of the dominant negative DRP5B resulted in the appearance of aberrant-shaped cells in which two daughter chloroplasts and the cells are still connected by a small DRP5B positive tube-like structure. This result suggests that the dominant negative DRP5B inhibited the final scission of the chloroplast division site, but not the earlier stages of division site constriction. It is also suggested that cell cycle progression is not arrested by the impairment of chloroplast division at the final stage.
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