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Lambert L, de Carpentier F, André P, Marchand CH, Danon A. Type II metacaspase mediates light-dependent programmed cell death in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2024; 194:2648-2662. [PMID: 37971939 PMCID: PMC10980519 DOI: 10.1093/plphys/kiad618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023]
Abstract
Among the crucial processes that preside over the destiny of cells from any type of organism are those involving their self-destruction. This process is well characterized and conceptually logical to understand in multicellular organisms; however, the levels of knowledge and comprehension of its existence are still quite enigmatic in unicellular organisms. We use Chlamydomonas (Chlamydomonas reinhardtii) to lay the foundation for understanding the mechanisms of programmed cell death (PCD) in a unicellular photosynthetic organism. In this paper, we show that while PCD induces the death of a proportion of cells, it allows the survival of the remaining population. A quantitative proteomic analysis aiming at unveiling the proteome of PCD in Chlamydomonas allowed us to identify key proteins that led to the discovery of essential mechanisms. We show that in Chlamydomonas, PCD relies on the light dependence of a photosynthetic organism to generate reactive oxygen species and induce cell death. Finally, we obtained and characterized mutants for the 2 metacaspase genes in Chlamydomonas and showed that a type II metacaspase is essential for PCD execution.
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Affiliation(s)
- Lou Lambert
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Félix de Carpentier
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin 91190, France
| | - Phuc André
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Christophe H Marchand
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique (CNRS), Paris F-75005, France
| | - Antoine Danon
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
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2
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Milito A, Aschern M, McQuillan JL, Yang JS. Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3833-3850. [PMID: 37025006 DOI: 10.1093/jxb/erad100] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Microalgae hold enormous potential to provide a safe and sustainable source of high-value compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly progressing climate change. Bioengineering microalgal strains will be key to optimizing and modifying their metabolic outputs, and to render them competitive with established industrial biotechnology hosts, such as bacteria or yeast. To achieve this, precise and tuneable control over transgene expression will be essential, which would require the development and rational design of synthetic promoters as a key strategy. Among green microalgae, Chlamydomonas reinhardtii represents the reference species for bioengineering and synthetic biology; however, the repertoire of functional synthetic promoters for this species, and for microalgae generally, is limited in comparison to other commercial chassis, emphasizing the need to expand the current microalgal gene expression toolbox. Here, we discuss state-of-the-art promoter analyses, and highlight areas of research required to advance synthetic promoter development in C. reinhardtii. In particular, we exemplify high-throughput studies performed in other model systems that could be applicable to microalgae, and propose novel approaches to interrogating algal promoters. We lastly outline the major limitations hindering microalgal promoter development, while providing novel suggestions and perspectives for how to overcome them.
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Affiliation(s)
- Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Moritz Aschern
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Josie L McQuillan
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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3
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Good News for Nuclear Transgene Expression in Chlamydomonas. Cells 2019; 8:cells8121534. [PMID: 31795196 PMCID: PMC6952782 DOI: 10.3390/cells8121534] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Chlamydomonas reinhardtii is a well-established model system for basic research questions ranging from photosynthesis and organelle biogenesis, to the biology of cilia and basal bodies, to channelrhodopsins and photoreceptors. More recently, Chlamydomonas has also been recognized as a suitable host for the production of high-value chemicals and high-value recombinant proteins. However, basic and applied research have suffered from the inefficient expression of nuclear transgenes. The combined efforts of the Chlamydomonas community over the past decades have provided insights into the mechanisms underlying this phenomenon and have resulted in mutant strains defective in some silencing mechanisms. Moreover, many insights have been gained into the parameters that affect nuclear transgene expression, like promoters, introns, codon usage, or terminators. Here I critically review these insights and try to integrate them into design suggestions for the construction of nuclear transgenes that are to be expressed at high levels.
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4
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Eberhard S, Valuchova S, Ravat J, Fulneček J, Jolivet P, Bujaldon S, Lemaire SD, Wollman FA, Teixeira MT, Riha K, Xu Z. Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants. Life Sci Alliance 2019; 2:2/3/e201900315. [PMID: 31160377 PMCID: PMC6549138 DOI: 10.26508/lsa.201900315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance. Telomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. Expression of the reverse-transcriptase telomerase allows for extension of telomeric repeats to counteract natural telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)n telomeric repeats are mostly nondegenerate and that the telomeres form a protective structure, with a subset ending with a 3′ overhang and another subset presenting a blunt end. Although telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that telomeres shorten progressively in mutants of this gene. Telomerase mutants eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.
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Affiliation(s)
- Stephan Eberhard
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Sona Valuchova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Julie Ravat
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Jaroslav Fulneček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pascale Jolivet
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Sandrine Bujaldon
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Stéphane D Lemaire
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Francis-André Wollman
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Maria Teresa Teixeira
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zhou Xu
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France .,Sorbonne Université, CNRS, UMR 7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
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5
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Potdar P, Pinto P, D’Souza N, Joshi P, Malwade A, Sen S. A Novel Method to Generate MNase Ladders Reveal Rapid Chromatin Remodeling upon Gametogenesis and Mating in Chlamydomonas. Protist 2018; 169:632-644. [DOI: 10.1016/j.protis.2018.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/22/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023]
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6
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Rütgers M, Muranaka LS, Schulz-Raffelt M, Thoms S, Schurig J, Willmund F, Schroda M. Not changes in membrane fluidity but proteotoxic stress triggers heat shock protein expression in Chlamydomonas reinhardtii. PLANT, CELL & ENVIRONMENT 2017; 40:2987-3001. [PMID: 28875560 DOI: 10.1111/pce.13060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 05/06/2023]
Abstract
A conserved reaction of all organisms exposed to heat stress is an increased expression of heat shock proteins (HSPs). Several studies have proposed that HSP expression in heat-stressed plant cells is triggered by an increased fluidity of the plasma membrane. Among the main lines of evidence in support of this model are as follows: (a) the degree of membrane lipid saturation was higher in cells grown at elevated temperatures and correlated with a lower amplitude of HSP expression upon a temperature upshift, (b) membrane fluidizers induce HSP expression at physiological temperatures, and (c) membrane rigidifier dimethylsulfoxide dampens heat-induced HSP expression. Here, we tested whether this holds also for Chlamydomonas reinhardtii. We show that heat-induced HSP expression in cells grown at elevated temperatures was reduced because they already contained elevated levels of cytosolic HSP70A/90A that apparently act as negative regulators of heat shock factor 1. We find that membrane rigidifier dimethylsulfoxide impaired translation under heat stress conditions and that membrane fluidizer benzyl alcohol not only induced HSP expression but also caused protein aggregation. These findings support the classical model for the cytosolic unfolded protein response, according to which HSP expression is induced by the accumulation of unfolded proteins. Hence, the membrane fluidity model should be reconsidered.
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Affiliation(s)
- Mark Rütgers
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
| | - Ligia Segatto Muranaka
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
| | - Miriam Schulz-Raffelt
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
| | - Sylvia Thoms
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
| | - Juliane Schurig
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
| | - Felix Willmund
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
| | - Michael Schroda
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
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7
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Zhang W, Fan X, Gao Y, Liu L, Sun L, Su Q, Han J, Zhang N, Cui F, Ji J, Tong Y, Li J. Chromatin modification contributes to the expression divergence of three TaGS2 homoeologs in hexaploid wheat. Sci Rep 2017; 7:44677. [PMID: 28300215 PMCID: PMC5353557 DOI: 10.1038/srep44677] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 01/05/2023] Open
Abstract
Plastic glutamine synthetase (GS2) is responsible for ammonium assimilation. The reason that TaGS2 homoeologs in hexaploid wheat experience different selection pressures in the breeding process remains unclear. TaGS2 were minimally expressed in roots but predominantly expressed in leaves, and TaGS2-B had higher expression than TaGS2-A and TaGS2-D. ChIP assays revealed that the activation of TaGS2-B expression in leaves was correlated with increased H3K4 trimethylation. The transcriptional silencing of TaGS2 in roots was correlated with greater cytosine methylation and less H3K4 trimethylation. Micrococcal nuclease and DNase I accessibility experiments indicated that the promoter region was more resistant to digestion in roots than leaves, which indicated that the closed nucleosome conformation of the promoter region was important to the transcription initiation for the spatial-temporal expression of TaGS2. In contrast, the transcribed regions possess different nuclease accessibilities of three TaGS2 homoeologs in the same tissue, suggesting that nucleosome conformation of the transcribed region was part of the fine adjustment of TaGS2 homoeologs. This study provides evidence that histone modification, DNA methylation and nuclease accessibility coordinated the control of the transcription of TaGS2 homoeologs. Our results provided important evidence that TaGS2-B experienced the strongest selection pressures during the breeding process.
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Affiliation(s)
- Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yingjie Gao
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang 050024, China
| | - Lei Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijing Sun
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China
| | - Qiannan Su
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fa Cui
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
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8
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Scranton MA, Ostrand JT, Georgianna DR, Lofgren SM, Li D, Ellis RC, Carruthers DN, Dräger A, Masica DL, Mayfield SP. Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.02.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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9
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Fu Y, Luo GZ, Chen K, Deng X, Yu M, Han D, Hao Z, Liu J, Lu X, Dore LC, Weng X, Ji Q, Mets L, He C. N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell 2015; 161:879-892. [PMID: 25936837 DOI: 10.1016/j.cell.2015.04.010] [Citation(s) in RCA: 357] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/16/2015] [Accepted: 03/27/2015] [Indexed: 01/08/2023]
Abstract
N(6)-methyldeoxyadenosine (6mA or m(6)A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here, we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms.
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Affiliation(s)
- Ye Fu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Guan-Zheng Luo
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Kai Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Xin Deng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Dali Han
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Ziyang Hao
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Jianzhao Liu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Xingyu Lu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Louis C Dore
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Xiaocheng Weng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Quanjiang Ji
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Laurens Mets
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th St, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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10
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Roy D, Paul A, Roy A, Ghosh R, Ganguly P, Chaudhuri S. Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress. PLoS One 2014; 9:e100343. [PMID: 24940877 PMCID: PMC4062490 DOI: 10.1371/journal.pone.0100343] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 05/25/2014] [Indexed: 11/26/2022] Open
Abstract
The rice ortholog of DREB1, OsDREB1b, is transcriptionally induced by cold stress and over-expression of OsDREB1b results in increase tolerance towards high salt and freezing stress. This spatio-temporal expression of OsDREB1b is preceded by the change in chromatin structure at the promoter and the upstream region for gene activation. The promoter and the upstream region of OsDREB1b genes appear to be arranged into a nucleosome array. Nucleosome mapping of ∼700bp upstream region of OsDREB1b shows two positioned nucleosomes between −610 to −258 and a weakly positioned nucleosome at the core promoter and the TSS. Upon cold stress, there is a significant change in the nucleosome arrangement at the upstream region with increase in DNaseI hypersensitivity or MNase digestion in the vicinity of cis elements and TATA box at the core promoter. ChIP assays shows hyper-acetylation of histone H3K9 throughout the locus whereas region specific increase was observed in H3K14ac and H3K27ac. Moreover, there is an enrichment of RNA PolII occupancy at the promoter region during transcription activation. There is no significant change in the H3 occupancy in OsDREB1b locus negating the possibility of nucleosome loss during cold stress. Interestingly, cold induced enhanced transcript level of OsDREB1b as well as histone H3 acetylation at the upstream region was found to diminish when stressed plants were returned to normal temperature. The result indicates absolute necessity of changes in chromatin conformation for the transcription up-regulation of OsDREB1b gene in response to cold stress. The combined results show the existence of closed chromatin conformation at the upstream and promoter region of OsDREB1b in the transcription “off” state. During cold stress, changes in region specific histone modification marks promote the alteration of chromatin structure to facilitate the binding of transcription machinery for proper gene expression.
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Affiliation(s)
- Dipan Roy
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Amit Paul
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Adrita Roy
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Ritesh Ghosh
- School of Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Payel Ganguly
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
- * E-mail:
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11
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Zhang W, Zhang T, Wu Y, Jiang J. Open Chromatin in Plant Genomes. Cytogenet Genome Res 2014; 143:18-27. [DOI: 10.1159/000362827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Valledor L, Furuhashi T, Recuenco-Muñoz L, Wienkoop S, Weckwerth W. System-level network analysis of nitrogen starvation and recovery in Chlamydomonas reinhardtii reveals potential new targets for increased lipid accumulation. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:171. [PMID: 25663847 PMCID: PMC4320484 DOI: 10.1186/s13068-014-0171-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/17/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen starvation is known to cause drastic alterations in physiology and metabolism leading to the accumulation of lipid bodies in many microalgae, and it thus presents an important alternative for biofuel production. However, despite the importance of this process, the molecular mechanisms that mediate the metabolic remodeling induced by N starvation and especially by stress recovery are still poorly understood, and new candidates for bioengineering are needed to make this process useful for biofuel production. RESULTS We have studied the molecular changes involved in the adaptive mechanisms to N starvation and full recovery of the vegetative cells in the microalga Chlamydomonas reinhardtii during a four-day time course. High throughput mass spectrometry was employed to integrate the proteome and the metabolome with physiological changes. N starvation led to an accumulation of oil bodies and reduced Fv/Fm.. Distinct enzymes potentially participating in the carbon-concentrating mechanism (CAH7, CAH8, PEPC1) are strongly accumulated. The membrane composition is changed, as indicated by quantitative lipid profiles. A reprogramming of protein biosynthesis was observed by increased levels of cytosolic ribosomes, while chloroplastidic were dramatically reduced. Readdition of N led to, the identification of early responsive proteins mediating stress recovery, indicating their key role in regaining and sustaining normal vegetative growth. Analysis of the data with multivariate correlation analysis, Granger causality, and sparse partial least square (sPLS) provided a functional network perspective of the molecular processes. Cell growth and N metabolism were clearly linked by the branched chain amino acids, suggesting an important role in this stress. Lipid accumulation was also tightly correlated to the COP II protein, involved in vesicle and lysosome coating, and a major lipid droplet protein. This protein, together with other key proteins mediating signal transduction and adaption (BRI1, snRKs), constitute a series of new metabolic and regulatory targets. CONCLUSIONS This work not only provides new insights and corrects previous models by analyzing a complex dataset, but also increases our biochemical understanding of the adaptive mechanisms to N starvation in Chlamydomonas, pointing to new bioengineering targets for increased lipid accumulation, a key step for a sustainable and profitable microalgae-based biofuel production.
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Affiliation(s)
- Luis Valledor
- />Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
- />Cyanoteam, Global Change Research Center-Czechglobe, Academy of Sciences of the Czech Republic, Belidla 4, 603 00 Brno, Czech Republic
- />Present address: Plant Physiology, University of Oviedo, Catedrático Rodrígo Uría s/n, E-33006 Oviedo, Spain
| | - Takeshi Furuhashi
- />Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Luis Recuenco-Muñoz
- />Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Stefanie Wienkoop
- />Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Wolfram Weckwerth
- />Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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Strenkert D, Schmollinger S, Schroda M. Heat shock factor 1 counteracts epigenetic silencing of nuclear transgenes in Chlamydomonas reinhardtii. Nucleic Acids Res 2013; 41:5273-89. [PMID: 23585280 PMCID: PMC3664811 DOI: 10.1093/nar/gkt224] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We found previously that the Chlamydomonas HSP70A promoter counteracts transcriptional silencing of downstream promoters in a transgene setting. To elucidate the underlying mechanisms, we analyzed chromatin state and transgene expression in transformants containing HSP70A-RBCS2-ble (AR-ble) constructs harboring deletions/mutations in the A promoter. We identified histone modifications at transgenic R promoters indicative for repressive chromatin, i.e. low levels of histone H3/4 acetylation and H3-lysine 4 trimethylation and high levels of H3-lysine 9 monomethylation. Transgenic A promoters also harbor lower levels of active chromatin marks than the native A promoter, but levels were higher than those at transgenic R promoters. Strikingly, in AR promoter fusions, the chromatin state at the A promoter was transferred to R. This effect required intact HSE4, HSE1/2 and TATA-box in the A promoter and was mediated by heat shock factor (HSF1). However, time-course analyses in strains inducibly depleted of HSF1 revealed that a transcriptionally competent chromatin state alone was not sufficient for activating the R promoter, but required constitutive HSF1 occupancy at transgenic A. We propose that HSF1 constitutively forms a scaffold at the transgenic A promoter, presumably containing mediator and TFIID, from which local chromatin remodeling and polymerase II recruitment to downstream promoters is realized.
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Affiliation(s)
- Daniela Strenkert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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14
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Strenkert D, Schmollinger S, Schroda M. Protocol: methodology for chromatin immunoprecipitation (ChIP) in Chlamydomonas reinhardtii. PLANT METHODS 2011; 7:35. [PMID: 22050920 PMCID: PMC3225300 DOI: 10.1186/1746-4811-7-35] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/03/2011] [Indexed: 05/19/2023]
Abstract
We report on a detailed chromatin immunoprecipitation (ChIP) protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example for the normalization of ChIP results as determined by real-time PCR.
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Affiliation(s)
- Daniela Strenkert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stefan Schmollinger
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Michael Schroda
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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15
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Strenkert D, Schmollinger S, Sommer F, Schulz-Raffelt M, Schroda M. Transcription factor-dependent chromatin remodeling at heat shock and copper-responsive promoters in Chlamydomonas reinhardtii. THE PLANT CELL 2011; 23:2285-301. [PMID: 21705643 PMCID: PMC3160021 DOI: 10.1105/tpc.111.085266] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/09/2011] [Accepted: 06/07/2011] [Indexed: 05/19/2023]
Abstract
How transcription factors affect chromatin structure to regulate gene expression in response to changes in environmental conditions is poorly understood in the green lineage. To shed light on this issue, we used chromatin immunoprecipitation and formaldehyde-assisted isolation of regulatory elements to investigate the chromatin structure at target genes of HSF1 and CRR1, key transcriptional regulators of the heat shock and copper starvation responses, respectively, in the unicellular green alga Chlamydomonas reinhardtii. Generally, we detected lower nucleosome occupancy, higher levels of histone H3/4 acetylation, and lower levels of histone H3 Lys 4 (H3K4) monomethylation at promoter regions of active genes compared with inactive promoters and transcribed and intergenic regions. Specifically, we find that activated HSF1 and CRR1 transcription factors mediate the acetylation of histones H3/4, nucleosome eviction, remodeling of the H3K4 mono- and dimethylation marks, and transcription initiation/elongation. By this, HSF1 and CRR1 quite individually remodel and activate target promoters that may be inactive and embedded into closed chromatin (HSP22F/CYC6) or weakly active and embedded into partially opened (CPX1) or completely opened chromatin (HSP70A/CRD1). We also observed HSF1-independent histone H3/4 deacetylation at the RBCS2 promoter after heat shock, suggesting interplay of specific and presumably more generally acting factors to adapt gene expression to the new requirements of a changing environment.
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16
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Neupert J, Karcher D, Bock R. Generation of Chlamydomonas strains that efficiently express nuclear transgenes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:1140-50. [PMID: 19036032 DOI: 10.1111/j.1365-313x.2008.03746.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is both an invaluable model organism for plant biology and an attractive biotechnological production system. Despite the availability of efficient methods for introduction of foreign genes into the nuclear genome of the alga, transgene expression levels are usually very poor. This is a serious limitation that has severely hampered both post-genomics research in Chlamydomonas and use of the alga in molecular farming. Here we report a solution to this problem. We have designed a genetic screen that facilitates isolation of algal strains that efficiently express introduced transgenes. The levels of accumulation of foreign protein in our expression strains are almost uniformly high in all transgenic clones and are little influenced by position effects. The possibility of expressing transgenes to high levels will greatly facilitate post-genomics research in Chlamydomonas, and will also boost exploitation of the alga as an inexpensive production host for biopharmaceuticals and other valuable compounds.
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Affiliation(s)
- Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, Potsdam-Golm, Germany
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17
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A new assay for promoter analysis in Chlamydomonas reveals roles for heat shock elements and the TATA box in HSP70A promoter-mediated activation of transgene expression. EUKARYOTIC CELL 2007; 7:172-6. [PMID: 17993574 DOI: 10.1128/ec.00055-07] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The aim of this work was to identify cis-regulatory sequences within the Chlamydomonas HSP70A promoter that mediate its stimulatory effect on the expression of downstream promoters. For this, we deleted/mutated the HSP70A promoter and, using a new assay, quantified its stimulatory effect. Our results indicate that the effect is mediated largely by heat shock elements and the TATA box.
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18
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Shao N, Krieger-Liszkay A, Schroda M, Beck CF. A reporter system for the individual detection of hydrogen peroxide and singlet oxygen: its use for the assay of reactive oxygen species produced in vivo. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 50:475-87. [PMID: 17376156 DOI: 10.1111/j.1365-313x.2007.03065.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A reporter system for the assay of reactive oxygen species (ROS) was developed in Chlamydomonas reinhardtii, a plant model organism well suited for the application of inhibitors and generators of various types of ROS. This system employs various HSP70A promoter segments fused to a Renilla reniformis luciferase gene as a reporter. Transformants with the complete HSP70A promoter were inducible by both hydrogen peroxide and singlet oxygen. Constructs that lacked upstream heat-shock elements (HSEs) were inducible by hydrogen peroxide, indicating that this induction does not require such HSEs. Rather, downstream elements located between positions -81 to -149 with respect to the translation start site appear to be involved. In contrast, upstream sequences are essential for the response to singlet oxygen. Thus, activation by singlet oxygen appears to require promoter elements that are different from those used by hydrogen peroxide. ROS generated endogenously by treatment of the alga with metronidazole, protoporphyrin IX, dinoterb or high light intensities were detected by this reporter system, and distinguished as production of hydrogen peroxide (metronidazole) and singlet oxygen (protoporphyrin IX, dinoterb, high light). This system thus makes it possible to test whether, under varying environmental conditions including the application of abiotic stress, hydrogen peroxide or singlet oxygen or both are produced.
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Affiliation(s)
- Ning Shao
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
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19
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Kodama Y, Nagaya S, Shinmyo A, Kato K. Mapping and characterization of DNase I hypersensitive sites in Arabidopsis chromatin. PLANT & CELL PHYSIOLOGY 2007; 48:459-70. [PMID: 17283013 DOI: 10.1093/pcp/pcm017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Recent genome-wide analyses of yeast and human chromatin revealed the widespread prevalence of DNase I hypersensitive sites (DNase I HSs) at gene regulatory regions with possible roles in eukaryotic gene regulation. The presence of DNase I HSs in plants has been described for only a few genes, and we analyzed the chromatin structure of an 80 kb genomic region containing 30 variably expressed genes by DNase I sensitivity assay at 500 bp resolution in Arabidopsis. Distinct DNase I HSs were found at the 5' and/or 3' ends of most genes irrespective of their expression levels. Further analysis of well-characterized genes showed that the DNase I HSs occurred near cis-regulatory elements in the promoters of these genes. Upon transcriptional activation of a heat-inducible gene, the DNase I HS was extended into the vicinity of a cis-element and adjacent TATA element in the promoter. Concomitant with this change in DNase I HS, histones were acetylated, removed from the promoter, and a transcription activator bound to this cis-element. These results suggest that the DNase I HSs participate in the transcriptional regulation of Arabidopsis genes by enhancing the access of chromatin remodeling factors and/or transcription factors to their target sites as seen in yeast and human chromatin.
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Affiliation(s)
- Yuichi Kodama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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20
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Bert AG, Johnson BV, Baxter EW, Cockerill PN. A modular enhancer is differentially regulated by GATA and NFAT elements that direct different tissue-specific patterns of nucleosome positioning and inducible chromatin remodeling. Mol Cell Biol 2007; 27:2870-85. [PMID: 17283044 PMCID: PMC1899937 DOI: 10.1128/mcb.02323-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
We investigated alternate mechanisms employed by enhancers to position and remodel nucleosomes and activate tissue-specific genes in divergent cell types. We demonstrated that the granulocyte-macrophage colony-stimulating factor (GM-CSF) gene enhancer is modular and recruits different sets of transcription factors in T cells and myeloid cells. The enhancer recruited distinct inducible tissue-specific enhanceosome-like complexes and directed nucleosomes to different positions in these cell types. In undifferentiated T cells, the enhancer was activated by inducible binding of two NFAT/AP-1 complexes which disrupted two specifically positioned nucleosomes (N1 and N2). In myeloid cells, the enhancer was remodeled by GATA factors which constitutively displaced an upstream nucleosome (N0) and cooperated with inducible AP-1 elements to activate transcription. In mast cells, which express both GATA-2 and NFAT, these two pathways combined to activate the enhancer and generate high-level gene expression. At least 5 kb of the GM-CSF locus was organized as an array of nucleosomes with fixed positions, but the enhancer adopted different nucleosome positions in T cells and mast cells. Furthermore, nucleosomes located between the enhancer and promoter were mobilized upon activation in an enhancer-dependent manner. These studies reveal that distinct tissue-specific mechanisms can be used either alternately or in combination to activate the same enhancer.
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Affiliation(s)
- Andrew G Bert
- Experimental Haematology, Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, United Kingdom
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21
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von Gromoff ED, Schroda M, Oster U, Beck CF. Identification of a plastid response element that acts as an enhancer within the Chlamydomonas HSP70A promoter. Nucleic Acids Res 2006; 34:4767-79. [PMID: 16971458 PMCID: PMC1635268 DOI: 10.1093/nar/gkl602] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chloroplast-derived signals control a subset of nuclear genes in higher plants and eukaryotic algae. Among the types of signals identified are intermediates of chlorophyll biosynthesis such as Mg-protoporphyrin IX (MgProto). In Chlamydomonas reinhardtii, it was suggested that this tetrapyrrole mediates the light induction of chaperone gene HSP70A. Here we have analyzed cis elements involved in the regulation of HSP70A by MgProto and light. We identified two promoters and between their transcription start sites two regulatory regions that each may confer inducibility by MgProto and light to both HSP70A promoters. These regulatory regions, when cloned in front of basal non-light inducible heterologous promoters, conferred inducibility by MgProto and light. The orientation and distance independent function of these cis-regulatory sequences qualifies them as enhancers that mediate the response of nuclear genes to a chloroplast signal. Mutational analysis of one of these regulatory regions and an alignment with promoters of other MgProto-inducible genes revealed the sequence motif (G/C)CGA(C/T)N(A/G)N15 (T/C/A)(A/T/G) which, as shown for HSP70A, may confer MgProto responsiveness. This cis-acting sequence element is employed for induction of HSP70A by both MgProto and light, lending support to the model that light induction of this gene is mediated via MgProto.
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Affiliation(s)
- Erika D. von Gromoff
- To whom correspondence should be addressed. Tel: +49 761 203 2713; Fax: +49 761 203 2745;
| | - Michael Schroda
- Institut für Biologie II, Lehrstuhl Biochemie der Pflanzen, Universität Freiburg, Schaenzlestrasse 1D-79104 Freiburg, Germany
| | - Ulrike Oster
- Department Biologie 1, Universität München, Botanik, Menzingerstrasse 67D-80638 München, Germany
| | - Christoph F. Beck
- To whom correspondence should be addressed. Tel: +49 761 203 2713; Fax: +49 761 203 2745;
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