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Lihanova Y, Nagel R, Jakob T, Sasso S. Characterization of activating cis-regulatory elements from the histone genes of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:525-539. [PMID: 38693717 DOI: 10.1111/tpj.16781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Regulation of gene expression in eukaryotes is controlled by cis-regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis-regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii. To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii, and their activity was quantified by flow cytometry. Two tested candidates, Eupstr and Ehist cons, significantly upregulated gene expression and were characterized in detail. Eupstr, which originates from highly expressed genes of C. reinhardtii, is an orientation-independent CRE capable of activating both the RBCS2 and β2-tubulin promoters. Ehist cons, which is a CRM from histone genes of angiosperms, upregulates the β2-tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in Ehist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta, Chlamydomonas schloesseri, and Edaphochlamys debaryana, demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
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Affiliation(s)
- Yuliia Lihanova
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Torsten Jakob
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Severin Sasso
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
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2
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Fan S, Li Y, Wang Q, Jin M, Yu M, Zhao H, Zhou C, Xu J, Li B, Li X. The role of cis-zeatin in enhancing high-temperature resistance and fucoxanthin biosynthesis in Phaeodactylum tricornutum. Appl Environ Microbiol 2024; 90:e0206823. [PMID: 38786362 PMCID: PMC11218622 DOI: 10.1128/aem.02068-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Phaeodactylum tricornutum a prominent source of industrial fucoxanthin production, faces challenges in its application due to its tolerance to high-temperature environments. This study investigates the physiological responses of P. tricornutum to high-temperature stress and its impact on fucoxanthin content, with a specific focus on the role of cis-zeatin. The results reveal that high-temperature stress inhibits P. tricornutum's growth and photosynthetic activity, leading to a decrease in fucoxanthin content. Transcriptome analysis shows that high temperature suppresses the expression of genes related to photosynthesis (e.g., psbO, psbQ, and OEC) and fucoxanthin biosynthesis (e.g., PYS, PDS1, and PSD2), underscoring the negative effects of high temperature on P. tricornutum. Interestingly, genes associated with cis-zeatin biosynthesis and cytokinesis signaling pathways exhibited increased expression under high-temperature conditions, indicating a potential role of cis-zeatin signaling in response to elevated temperatures. Content measurements confirm that high temperature enhances cis-zeatin content. Furthermore, the exogenous addition of cytokinesis mimetics or inhibitors significantly affected P. tricornutum's high-temperature resistance. Overexpression of the cis-zeatin biosynthetic enzyme gene tRNA DMATase enhanced P. tricornutum's resistance to high-temperature stress, while genetic knockout of tRNA DMATase reduced its resistance to high temperatures. Therefore, this research not only uncovers a novel mechanism for high-temperature resistance in P. tricornutum but also offers a possible alga species that can withstand high temperatures for the industrial production of fucoxanthin, offering valuable insights for practical utilization.IMPORTANCEThis study delves into Phaeodactylum tricornutum's response to high-temperature stress, specifically focusing on cis-zeatin. We uncover inhibited growth, reduced fucoxanthin, and significant cis-zeatin-related gene expression under high temperatures, highlighting potential signaling mechanisms. Crucially, genetic engineering and exogenous addition experiments confirm that the change in cis-zeatin levels could influence P. tricornutum's resistance to high-temperature stress. This breakthrough deepens our understanding of microalgae adaptation to high temperatures and offers an innovative angle for industrial fucoxanthin production. This research is a pivotal step toward developing heat-resistant microalgae for industrial use.
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Affiliation(s)
- Sizhe Fan
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yixuan Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Qi Wang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Mengjie Jin
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Mange Yu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Hejing Zhao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jilin Xu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Bing Li
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China, Ningbo, China
| | - Xiaohui Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
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3
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Beauchemin R, Merindol N, Fantino E, Lavoie P, Nouemssi SB, Meddeb-Mouelhi F, Desgagné-Penix I. Successful reversal of transgene silencing in Chlamydomonas reinhardtii. Biotechnol J 2024; 19:e2300232. [PMID: 37975165 DOI: 10.1002/biot.202300232] [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: 05/23/2023] [Revised: 09/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Chlamydomonas reinhardtii has been successfully engineered to produce compounds of interest following transgene integration and heterologous protein expression. The advantages of this model include the availability of validated tools for bioengineering, its photosynthetic ability, and its potential use as biofuel. Despite this, breakthroughs have been hindered by its ability to silence transgene expression through epigenetic changes. Histone deacetylases (HDAC) are main players in gene expression. We hypothesized that transgene silencing can be reverted with chemical treatments using HDAC inhibitors. To analyze this, we transformed C. reinhardtii, integrating into its genome the mVenus reporter gene under the HSP70-rbcs2 promoter. From 384 transformed clones, 88 (22.9%) displayed mVenus positive (mVenus+ ) cells upon flow-cytometry analysis. Five clones with different fluorescence intensities were selected. The number of integrated copies was measured by qPCR. Transgene expression levels were followed over the growth cycle and upon SAHA treatment, using a microplate reader, flow cytometry, RT-qPCR, and western blot analysis. First, we observed that expression varies with the cell cycle, reaching a maximum level just before the stationary phase in all clones. Second, we uncovered that supplementation with HDAC inhibitors of the hydroxamate family, such as vorinostat (suberoylanilide-hydroxamic-acid, SAHA) at the initiation of culture increases the frequency (% of mVenus+ cells) and the level of transgene expression per cell over the whole growth cycle, through histone deacetylase inhibition. Thus, we propose a new tool to successfully trigger the expression of heterologous proteins in the green algae C. reinhardtii, overcoming its main obstacle as an expression platform.
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Affiliation(s)
- Rémy Beauchemin
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Natacha Merindol
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Elisa Fantino
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Pamela Lavoie
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Serge Basile Nouemssi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Fatma Meddeb-Mouelhi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
- Plant Biology Research Group, Trois-Rivières, Québec, Canada
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4
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Molecular and epigenetic basis of heat stress responses and acclimatization in plants. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00400-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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5
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PDGFD switches on stem cell endothelial commitment. Angiogenesis 2022; 25:517-533. [PMID: 35859222 PMCID: PMC9519648 DOI: 10.1007/s10456-022-09847-4] [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: 02/06/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022]
Abstract
The critical factors regulating stem cell endothelial commitment and renewal remain not well understood. Here, using loss- and gain-of-function assays together with bioinformatic analysis and multiple model systems, we show that PDGFD is an essential factor that switches on endothelial commitment of embryonic stem cells (ESCs). PDGFD genetic deletion or knockdown inhibits ESC differentiation into EC lineage and increases ESC self-renewal, and PDGFD overexpression activates ESC differentiation towards ECs. RNA sequencing reveals a critical requirement of PDGFD for the expression of vascular-differentiation related genes in ESCs. Importantly, PDGFD genetic deletion or knockdown increases ESC self-renewal and decreases blood vessel densities in both embryonic and neonatal mice and in teratomas. Mechanistically, we reveal that PDGFD fulfills this function via the MAPK/ERK pathway. Our findings provide new insight of PDGFD as a novel regulator of ESC fate determination, and suggest therapeutic implications of modulating PDGFD activity in stem cell therapy.
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Zhang N, Mattoon EM, McHargue W, Venn B, Zimmer D, Pecani K, Jeong J, Anderson CM, Chen C, Berry JC, Xia M, Tzeng SC, Becker E, Pazouki L, Evans B, Cross F, Cheng J, Czymmek KJ, Schroda M, Mühlhaus T, Zhang R. Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. Commun Biol 2022; 5:460. [PMID: 35562408 PMCID: PMC9106746 DOI: 10.1038/s42003-022-03359-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under highly controlled photobioreactor conditions and revealed systems-wide shared and unique responses to 24-hour moderate (35°C) and acute (40°C) high temperatures and subsequent recovery at 25°C. We identified previously overlooked unique elements in response to moderate high temperature. Heat at 35°C transiently arrested the cell cycle followed by partial synchronization, up-regulated transcripts/proteins involved in gluconeogenesis/glyoxylate-cycle for carbon uptake and promoted growth. But 40°C disrupted cell division and growth. Both high temperatures induced photoprotection, while 40°C distorted thylakoid/pyrenoid ultrastructure, affected the carbon concentrating mechanism, and decreased photosynthetic efficiency. We demonstrated increased transcript/protein correlation during both heat treatments and hypothesize reduced post-transcriptional regulation during heat may help efficiently coordinate thermotolerance mechanisms. During recovery after both heat treatments, especially 40°C, transcripts/proteins related to DNA synthesis increased while those involved in photosynthetic light reactions decreased. We propose down-regulating photosynthetic light reactions during DNA replication benefits cell cycle resumption by reducing ROS production. Our results provide potential targets to increase thermotolerance in algae and crops. A systems-wide analysis of the single-cell green alga Chlamydomonas reinhardti reveals shared and unique responses to moderate and acute high temperatures using multiple-level investigation of transcriptomics, proteomics, cell physiology, photosynthetic parameters, and cellular ultrastructure.
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Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Erin M Mattoon
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.,Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri, 63130, USA
| | - Will McHargue
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.,Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri, 63130, USA
| | | | - David Zimmer
- TU Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Kresti Pecani
- The Rockefeller University, New York, New York, 10065, USA
| | - Jooyeon Jeong
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Cheyenne M Anderson
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.,Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri, 63130, USA
| | - Chen Chen
- University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Jeffrey C Berry
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Shin-Cheng Tzeng
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Eric Becker
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Leila Pazouki
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Bradley Evans
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Fred Cross
- The Rockefeller University, New York, New York, 10065, USA
| | - Jianlin Cheng
- University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | | | | | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.
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7
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Santhanagopalan I, Wong R, Mathur T, Griffiths H. Orchestral manoeuvres in the light: crosstalk needed for regulation of the Chlamydomonas carbon concentration mechanism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4604-4624. [PMID: 33893473 PMCID: PMC8320531 DOI: 10.1093/jxb/erab169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 05/19/2023]
Abstract
The inducible carbon concentration mechanism (CCM) in Chlamydomonas reinhardtii has been well defined from a molecular and ultrastructural perspective. Inorganic carbon transport proteins, and strategically located carbonic anhydrases deliver CO2 within the chloroplast pyrenoid matrix where Rubisco is packaged. However, there is little understanding of the fundamental signalling and sensing processes leading to CCM induction. While external CO2 limitation has been believed to be the primary cue, the coupling between energetic supply and inorganic carbon demand through regulatory feedback from light harvesting and photorespiration signals could provide the original CCM trigger. Key questions regarding the integration of these processes are addressed in this review. We consider how the chloroplast functions as a crucible for photosynthesis, importing and integrating nuclear-encoded components from the cytoplasm, and sending retrograde signals to the nucleus to regulate CCM induction. We hypothesize that induction of the CCM is associated with retrograde signals associated with photorespiration and/or light stress. We have also examined the significance of common evolutionary pressures for origins of two co-regulated processes, namely the CCM and photorespiration, in addition to identifying genes of interest involved in transcription, protein folding, and regulatory processes which are needed to fully understand the processes leading to CCM induction.
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Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Rachel Wong
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Tanya Mathur
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
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8
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Plant Responses to Heat Stress: Physiology, Transcription, Noncoding RNAs, and Epigenetics. Int J Mol Sci 2020; 22:ijms22010117. [PMID: 33374376 PMCID: PMC7795586 DOI: 10.3390/ijms22010117] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/20/2020] [Indexed: 01/05/2023] Open
Abstract
Global warming has increased the frequency of extreme high temperature events. High temperature is a major abiotic stress that limits the growth and production of plants. Therefore, the plant response to heat stress (HS) has been a focus of research. However, the plant response to HS involves complex physiological traits and molecular or gene networks that are not fully understood. Here, we review recent progress in the physiological (photosynthesis, cell membrane thermostability, oxidative damage, and others), transcriptional, and post-transcriptional (noncoding RNAs) regulation of the plant response to HS. We also summarize advances in understanding of the epigenetic regulation (DNA methylation, histone modification, and chromatin remodeling) and epigenetic memory underlying plant–heat interactions. Finally, we discuss the challenges and opportunities of future research in the plant response to HS.
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9
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An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas. Nat Commun 2020; 11:6269. [PMID: 33293544 PMCID: PMC7722844 DOI: 10.1038/s41467-020-19983-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/05/2020] [Indexed: 01/08/2023] Open
Abstract
Silencing of exogenous DNA can make transgene expression very inefficient. Genetic screens in the model alga Chlamydomonas have demonstrated that transgene silencing can be overcome by mutations in unknown gene(s), thus producing algal strains that stably express foreign genes to high levels. Here, we show that the silencing mechanism specifically acts on transgenic DNA. Once a permissive chromatin structure has assembled, transgene expression can persist even in the absence of mutations disrupting the silencing pathway. We have identified the gene conferring the silencing and show it to encode a sirtuin-type histone deacetylase. Loss of gene function does not appreciably affect endogenous gene expression. Our data suggest that transgenic DNA is recognized and then quickly inactivated by the assembly of a repressive chromatin structure composed of deacetylated histones. We propose that this mechanism may have evolved to provide protection from potentially harmful types of environmental DNA. Strong transgene suppression has been observed in Chlamydomonas reinhardtii, but the underlying mechanism is unknown. Here, the authors identify a sirtuin-type histone deacetylase that selectively acts on transgenic DNA to repress gene expression by assembling a repressive chromatin structure composed of deacetylated histones.
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10
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Bacova R, Kolackova M, Klejdus B, Adam V, Huska D. Epigenetic mechanisms leading to genetic flexibility during abiotic stress responses in microalgae: A review. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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11
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From economy to luxury: Copper homeostasis in Chlamydomonas and other algae. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118822. [PMID: 32800924 DOI: 10.1016/j.bbamcr.2020.118822] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
Plastocyanin and cytochrome c6, abundant proteins in photosynthesis, are readouts for cellular copper status in Chlamydomonas and other algae. Their accumulation is controlled by a transcription factor copper response regulator (CRR1). The replacement of copper-containing plastocyanin with heme-containing cytochrome c6 spares copper and permits preferential copper (re)-allocation to cytochrome oxidase. Under copper-replete situations, the quota depends on abundance of various cuproproteins and is tightly regulated, except under zinc-deficiency where acidocalcisomes over-accumulate Cu(I). CRR1 has a transcriptional activation domain, a Zn-dependent DNA binding SBP-domain with a nuclear localization signal, and a C-terminal Cys-rich region that represses the zinc regulon. CRR1 activates >60 genes in Chlamydomonas through GTAC-containing CuREs; transcriptome differences are recapitulated in the proteome. The differentially-expressed genes encode assimilatory copper transporters of the CTR/SLC31 family including a novel soluble molecule, redox enzymes in the tetrapyrrole pathway that promote chlorophyll biosynthesis and photosystem 1 accumulation, and other oxygen-dependent enzymes, which may influence thylakoid membrane lipids, specifically polyunsaturated galactolipids and γ-tocopherol. CRR1 also down-regulates 2 proteins in Chlamydomonas: for plastocyanin, by activation of proteolysis, while for the di‑iron subunit of the cyclase in chlorophyll biosynthesis, through activation of an upstream promoter that generates a poorly-translated 5' extended transcript containing multiple short ORFs that inhibit translation. The functions of many CRR1-target genes are unknown, and the copper protein inventory in Chlamydomonas includes several whose functions are unexplored. The comprehensive picture of cuproproteins and copper homeostasis in this system is well-suited for reverse genetic analyses of these under-investigated components in copper biology.
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12
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Theis J, Niemeyer J, Schmollinger S, Ries F, Rütgers M, Gupta TK, Sommer F, Muranaka LS, Venn B, Schulz-Raffelt M, Willmund F, Engel BD, Schroda M. VIPP2 interacts with VIPP1 and HSP22E/F at chloroplast membranes and modulates a retrograde signal for HSP22E/F gene expression. PLANT, CELL & ENVIRONMENT 2020; 43:1212-1229. [PMID: 31994740 DOI: 10.1111/pce.13732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
VIPP proteins aid thylakoid biogenesis and membrane maintenance in cyanobacteria, algae, and plants. Some members of the Chlorophyceae contain two VIPP paralogs termed VIPP1 and VIPP2, which originate from an early gene duplication event during the evolution of green algae. VIPP2 is barely expressed under nonstress conditions but accumulates in cells exposed to high light intensities or H2 O2 , during recovery from heat stress, and in mutants with defective integration (alb3.1) or translocation (secA) of thylakoid membrane proteins. Recombinant VIPP2 forms rod-like structures in vitro and shows a strong affinity for phosphatidylinositol phosphate. Under stress conditions, >70% of VIPP2 is present in membrane fractions and localizes to chloroplast membranes. A vipp2 knock-out mutant displays no growth phenotypes and no defects in the biogenesis or repair of photosystem II. However, after exposure to high light intensities, the vipp2 mutant accumulates less HSP22E/F and more LHCSR3 protein and transcript. This suggests that VIPP2 modulates a retrograde signal for the expression of nuclear genes HSP22E/F and LHCSR3. Immunoprecipitation of VIPP2 from solubilized cells and membrane-enriched fractions revealed major interactions with VIPP1 and minor interactions with HSP22E/F. Our data support a distinct role of VIPP2 in sensing and coping with chloroplast membrane stress.
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Affiliation(s)
- Jasmine Theis
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
| | - Justus Niemeyer
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
| | - Stefan Schmollinger
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, TU Kaiserslautern, Kaiserslautern, Germany
| | - Mark Rütgers
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
| | - Tilak Kumar Gupta
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Frederik Sommer
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
| | | | - Benedikt Venn
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
| | - Miriam Schulz-Raffelt
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, TU Kaiserslautern, Kaiserslautern, Germany
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Michael Schroda
- Molekulare Biotechnologie & Systembiologie, TU Kaiserslautern, Kaiserslautern, Germany
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Formaldehyde-assisted isolation of regulatory DNA elements from Arabidopsis leaves. Nat Protoc 2020; 15:713-733. [PMID: 32042178 DOI: 10.1038/s41596-019-0277-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
Eukaryotic gene transcription is associated with the eviction of nucleosomes and the formation of open chromatin, which enables the recruitment of transcriptional coactivators and other regulatory factors. Open chromatin is thus a hallmark of functional regulatory DNA elements in genomes. In recent years, formaldehyde-assisted isolation of regulatory elements (FAIRE) has proven powerful in identifying open chromatin in the genome of various eukaryotes, particularly yeast, human, and mouse. However, it has proven challenging to adapt the FAIRE protocol for use on plant material, and the few available protocols all have their drawbacks (e.g., applicability only to specific developmental stages). In this Protocol Extension, we describe a reliable FAIRE protocol for mature Arabidopsis (Arabidopsis thaliana) leaves that adapts the original protocol for use on plants. The main differences between this protocol extension and the earlier FAIRE protocol are an increased formaldehyde concentration in the chromatin crosslinking buffer, application of a repeated vacuum to increase crosslinking efficiency, and altered composition of the DNA extraction buffer. The protocol is applicable to leaf chromatin of unstressed and stressed plants and can be completed within 1 week. Here, we also describe downstream analysis using qPCR and next-generation sequencing. However, this Protocol Extension should also be compatible with downstream hybridization to a DNA microarray. In addition, it is likely that only minor adaptations will be necessary to apply this protocol to other Arabidopsis organs or plant species.
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14
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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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15
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Wang AW, Wang YJ, Zahm AM, Morgan AR, Wangensteen KJ, Kaestner KH. The Dynamic Chromatin Architecture of the Regenerating Liver. Cell Mol Gastroenterol Hepatol 2019; 9:121-143. [PMID: 31629814 PMCID: PMC6909351 DOI: 10.1016/j.jcmgh.2019.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The adult liver is the main detoxification organ and routinely is exposed to environmental insults but retains the ability to restore its mass and function upon tissue damage. However, extensive injury can lead to liver failure, and chronic injury causes fibrosis, cirrhosis, and hepatocellular carcinoma. Currently, the transcriptional regulation of organ repair in the adult liver is incompletely understood. METHODS We isolated nuclei from quiescent as well as repopulating hepatocytes in a mouse model of hereditary tyrosinemia, which recapitulates the injury and repopulation seen in toxic liver injury in human beings. We then performed the assay for transposase accessible chromatin with high-throughput sequencing specifically in repopulating hepatocytes to identify differentially accessible chromatin regions and nucleosome positioning. In addition, we used motif analysis to predict differential transcription factor occupancy and validated the in silico results with chromatin immunoprecipitation followed by sequencing for hepatocyte nuclear factor 4α (HNF4α) and CCCTC-binding factor (CTCF). RESULTS Chromatin accessibility in repopulating hepatocytes was increased in the regulatory regions of genes promoting proliferation and decreased in the regulatory regions of genes involved in metabolism. The epigenetic changes at promoters and liver enhancers correspond with the regulation of gene expression, with enhancers of many liver function genes showing a less accessible state during the regenerative process. Moreover, increased CTCF occupancy at promoters and decreased HNF4α binding at enhancers implicate these factors as key drivers of the transcriptomic changes in replicating hepatocytes that enable liver repopulation. CONCLUSIONS Our analysis of hepatocyte-specific epigenomic changes during liver repopulation identified CTCF and HNF4α as key regulators of hepatocyte proliferation and regulation of metabolic programs. Thus, liver repopulation in the setting of toxic injury makes use of both general transcription factors (CTCF) for promoter activation, and reduced binding by a hepatocyte-enriched factor (HNF4α) to temporarily limit enhancer activity. All sequencing data in this study were deposited to the Gene Expression Omnibus database and can be downloaded with accession number GSE109466.
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Affiliation(s)
- Amber W Wang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yue J Wang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida
| | - Adam M Zahm
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ashleigh R Morgan
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kirk J Wangensteen
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania.
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16
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Darkness-induced effects on gene expression in Cosmarium crenatum (Zygnematophyceae) from a polar habitat. Sci Rep 2019; 9:10559. [PMID: 31332253 PMCID: PMC6646379 DOI: 10.1038/s41598-019-47041-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
Light is a key environmental regulator in all photosynthetic organisms. Many studies focused on the physiologic response to changes in light availability of species from the Zygnematophyceae, but the impact of the absence of light and the molecular acclimation process on the other side have been poorly understood. Here we present transcriptomic analyses of Cosmarium crenatum from a polar habitat exposed to darkness. The algae were cultured in dark for one week; cell number and quantum yield of photosystem II (Fv/Fm) were monitored. Cell number was stable, but the Fv/Fm decreased in both groups, darkness-treated and control. Gene expression analysis revealed a strong repression of transcripts associated with photosynthesis, photorespiration and cell wall development. General carbohydrate and lipid metabolism were differentially regulated, but starch is shown to be the primary energy source in these conditions. Additionally, C. crenatum induced mRNA responsible for epigenetic modifications which may be a specific response to an adaption and acclimation to polar conditions. Our study sheds light on the molecular acclimation process to darkness and provides ecological implications for new perspectives in this specialized group of green algae.
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Yin Z, Chen C, Yang J, Feng W, Liu X, Zuo R, Wang J, Yang L, Zhong K, Gao C, Zhang H, Zheng X, Wang P, Zhang Z. Histone acetyltransferase MoHat1 acetylates autophagy-related proteins MoAtg3 and MoAtg9 to orchestrate functional appressorium formation and pathogenicity in Magnaporthe oryzae. Autophagy 2019; 15:1234-1257. [PMID: 30776962 DOI: 10.1080/15548627.2019.1580104] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macroautophagy/autophagy is critical for normal appressorium formation and pathogenicity of the rice blast fungus Magnaporthe oryzae, but the molecular base of autophagy linked to pathogenicity remains elusive in this or other pathogenic fungi. We found that MoHat1, a histone acetyltransferase (HAT) homolog, had a role in the regulation of autophagy through the acetylation of autophagy related proteins MoAtg3 and MoAtg9. We also found that MoHat1 was subject to regulation by the protein kinase MoGsk1 that modulated the translocation of MoHat1 from the nucleus to the cytoplasm with the assistance of MoSsb1, a protein chaperone. The alternation of intracellular location affected MoHat1 in the modification of cytosolic autophagy proteins that maintained normal autophagy. Furthermore, we provided evidence linking acetylation of MoAtg3 and MoAtg9 by MoHat1 to functional appressorium development and pathogenicity. Together with the first report of MoAtg9 being subject to acetylation regulation by MoHat1, our studies depicted how MoHat1 regulated autophagy in conjunction with MoGsk1 and how normal autophagy was linked to appressorium formation and function and pathogenicity of M. oryzae. Abbreviations: A/Ala: alanine; AP: autophagosome; Atg genes/proteins: autophagy-related genes/proteins; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; DAPI: 4', 6-diamidino-2-phenylindole; D/Asp: aspartic acid; GFP: green fluorescent protein; GSK3: glycogen synthase kinase 3; HAT: histone acetyltransferase; Hsp70: heat-shock protein 70; IH: invasive hyphae; K/Lys: lysine; MMS: methyl methanesulfonate; Mo: Magnaporthe oryzae; PAS: phagophore assembly site; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; R/Arg: arginine; S/Ser: serine; T/Thr: threonine; TOR: target of rapamycin; WT: wild type; YFP: yellow fluorescent protein.
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Affiliation(s)
- Ziyi Yin
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Chen Chen
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Jie Yang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Wanzhen Feng
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Xinyu Liu
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Rongfang Zuo
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Jingzhen Wang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Lina Yang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Kaili Zhong
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Chuyun Gao
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Haifeng Zhang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Xiaobo Zheng
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Ping Wang
- c Departments of Pediatrics, and Microbiology, Immunology, and Parasitology , Louisiana State University Health Sciences Center , New Orleans , LA , USA
| | - Zhengguang Zhang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
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Multiomics resolution of molecular events during a day in the life of Chlamydomonas. Proc Natl Acad Sci U S A 2019; 116:2374-2383. [PMID: 30659148 PMCID: PMC6369806 DOI: 10.1073/pnas.1815238116] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light-dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of the day to coordinate cellular growth before undergoing cell division. Parallel measurements of select metabolites and pigments, physiological parameters, and a subset of proteins allow us to infer metabolic events and to evaluate the impact of the transcriptome on the proteome. Among the findings are the observations that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; we propose that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases. The light stress-responsive genes PSBS, LHCSR1, and LHCSR3 show an acute response to lights-on at dawn under abrupt dark-to-light transitions, while LHCSR3 genes also exhibit a later, second burst in expression in the middle of the day dependent on light intensity. Each response to light (acute and sustained) can be selectively activated under specific conditions. Our expression dataset, complemented with coexpression networks and metabolite profiling, should constitute an excellent resource for the algal and plant communities.
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Takesue H, Hirota T, Tachimura M, Tokashiki A, Ieiri I. Nucleosome Positioning and Gene Regulation of the SGLT2 Gene in the Renal Proximal Tubular Epithelial Cells. Mol Pharmacol 2018; 94:953-962. [DOI: 10.1124/mol.118.111807] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/27/2018] [Indexed: 11/22/2022] Open
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Lai YH, Kuo C, Kuo MT, Chen HHW. Modulating Chemosensitivity of Tumors to Platinum-Based Antitumor Drugs by Transcriptional Regulation of Copper Homeostasis. Int J Mol Sci 2018; 19:ijms19051486. [PMID: 29772714 PMCID: PMC5983780 DOI: 10.3390/ijms19051486] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/10/2018] [Accepted: 05/12/2018] [Indexed: 12/21/2022] Open
Abstract
Platinum (Pt)-based antitumor agents have been effective in treating many human malignancies. Drug importing, intracellular shuffling, and exporting—carried out by the high-affinity copper (Cu) transporter (hCtr1), Cu chaperone (Ato x1), and Cu exporters (ATP7A and ATP7B), respectively—cumulatively contribute to the chemosensitivity of Pt drugs including cisplatin and carboplatin, but not oxaliplatin. This entire system can also handle Pt drugs via interactions between Pt and the thiol-containing amino acid residues in these proteins; the interactions are strongly influenced by cellular redox regulators such as glutathione. hCtr1 expression is induced by acute Cu deprivation, and the induction is regulated by the transcription factor specific protein 1 (Sp1) which by itself is also regulated by Cu concentration variations. Copper displaces zinc (Zn) coordination at the zinc finger (ZF) domains of Sp1 and inactivates its DNA binding, whereas Cu deprivation enhances Sp1-DNA interactions and increases Sp1 expression, which in turn upregulates hCtr1. Because of the shared transport system, chemosensitivity of Pt drugs can be modulated by targeting Cu transporters. A Cu-lowering agent (trientine) in combination with a Pt drug (carboplatin) has been used in clinical studies for overcoming Pt-resistance. Future research should aim at further developing effective Pt drug retention strategies for improving the treatment efficacy.
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Affiliation(s)
- Yu-Hsuan Lai
- Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
| | - Chin Kuo
- Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
| | - Macus Tien Kuo
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
| | - Helen H W Chen
- Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan.
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan 70101, Taiwan.
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Ling Y, Serrano N, Gao G, Atia M, Mokhtar M, Woo YH, Bazin J, Veluchamy A, Benhamed M, Crespi M, Gehring C, Reddy ASN, Mahfouz MM. Thermopriming triggers splicing memory in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2659-2675. [PMID: 29474581 PMCID: PMC5920379 DOI: 10.1093/jxb/ery062] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/13/2018] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stresses limit crop productivity. Exposure to a non-lethal stress, referred to as priming, can allow plants to survive subsequent and otherwise lethal conditions; the priming effect persists even after a prolonged stress-free period. However, the molecular mechanisms underlying priming are not fully understood. Here, we investigated the molecular basis of heat-shock memory and the role of priming in Arabidopsis thaliana. Comprehensive analysis of transcriptome-wide changes in gene expression and alternative splicing in primed and non-primed plants revealed that alternative splicing functions as a novel component of heat-shock memory. We show that priming of plants with a non-lethal heat stress results in de-repression of splicing after a second exposure to heat stress. By contrast, non-primed plants showed significant repression of splicing. These observations link 'splicing memory' to the ability of plants to survive subsequent and otherwise lethal heat stress. This newly discovered priming-induced splicing memory may represent a general feature of heat-stress responses in plants and other organisms as many of the key components are conserved among eukaryotes. Furthermore, this finding could facilitate the development of novel approaches to improve plant survival under extreme heat stress.
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Affiliation(s)
- Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Natalia Serrano
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ge Gao
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohamed Atia
- Agricultural Genetic Engineering Research Institute (AGERI), Giza Egypt
| | - Morad Mokhtar
- Agricultural Genetic Engineering Research Institute (AGERI), Giza Egypt
| | - Yong H Woo
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jeremie Bazin
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, Gif-sur-Yvette Cedex, France
| | - Alaguraj Veluchamy
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Moussa Benhamed
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Martin Crespi
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, Gif-sur-Yvette Cedex, France
| | - Christoph Gehring
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - A S N Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Correspondence:
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Gallaher SD, Fitz-Gibbon ST, Strenkert D, Purvine SO, Pellegrini M, Merchant SS. High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:545-565. [PMID: 29172250 PMCID: PMC5775909 DOI: 10.1111/tpj.13788] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 05/18/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal-based platform for producing biofuels and bio-products. Its highly repetitive, ~205-kbp circular chloroplast genome and ~15.8-kbp linear mitochondrial genome were sequenced prior to the advent of high-throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA-Seq was used to quantify their relative abundances across 12 different growth conditions. Forty-six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA-Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine-rich polynucleotide tails were observed at the 3'-end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.
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Affiliation(s)
- Sean D. Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Corresponding author:
| | - Sorel T. Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
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Huang Q, Ma C, Chen L, Luo D, Chen R, Liang F. Mechanistic Insights Into the Interaction Between Transcription Factors and Epigenetic Modifications and the Contribution to the Development of Obesity. Front Endocrinol (Lausanne) 2018; 9:370. [PMID: 30034368 PMCID: PMC6043677 DOI: 10.3389/fendo.2018.00370] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
Objective: The development of obesity is inseparable from genetic and epigenetic factors, and transcription factors (TFs) play an essential role in these two mechanisms. This review analyzes the interaction of TFs with epigenetic modifications and the epigenetic mechanisms underlying peroxisome proliferator-activated receptor (PPAR)γ, an important transcription factor, in the development of obesity. Methods: We describe the relationship between TFs and different epigenetic modifications and illustrate the several mechanisms described. Next, we summarize the epigenetic mechanisms of PPARs, an important class of transcription factors involved in obesity, that induce obesity with different triggering factors. Finally, we discuss the mechanisms of epigenetic modification of PPAR-related ligands in lipid metabolism and propose future avenues of research. Results: TFs participate in epigenetic modifications in different forms, causing changes in gene expression. The interactions between the different epigenetic modifications and PPARs are important biological developments that affect fat tissue differentiation, lipogenesis, and lipid metabolism, thereby inducing or inhibiting the development of obesity. We then highlight the need for more research to understand the role of epigenetic modifications and PPARs. Conclusions: Epigenetic mechanisms involved in the regulation of PPARs may be excellent therapeutic targets for obesity treatment. However, there is a need for a deeper understanding of how PPARs and other obesity-related transcription factors interact with epigenetic modifications.
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Affiliation(s)
- Qi Huang
- Department of Acupuncture and Moxibustion, Hubei University of Chinese Medicine, Wuhan, China
| | - Chaoyang Ma
- Department of Rehabilitation, The Central Hospital of Wuhan, Tongji Medical College of Huazhong Science and Technology University, Wuhan, China
| | - Li Chen
- Department of Acupuncture and Moxibustion, Hubei University of Chinese Medicine, Wuhan, China
| | - Dan Luo
- Department of Traditional Chinese Medicine, Huazhong University of Science and Technology Tongji Medical College, Wuhan, China
| | - Rui Chen
- Department of Integrated TCM and Western Medicine, Union Hospital, Tongji Medical College of Huazhong Science and Technology University, Wuhan, China
- *Correspondence: Rui Chen
| | - Fengxia Liang
- Department of Acupuncture and Moxibustion, Hubei University of Chinese Medicine, Wuhan, China
- Fengxia Liang
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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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López-Paz C, Liu D, Geng S, Umen JG. Identification of Chlamydomonas reinhardtii endogenous genic flanking sequences for improved transgene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1232-1244. [PMID: 28980350 PMCID: PMC5718938 DOI: 10.1111/tpj.13731] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 09/17/2017] [Accepted: 09/22/2017] [Indexed: 05/03/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular green alga that has attracted interest due to its potential biotechnological applications, and as a model for algal biofuel and energy metabolism. Despite all the advantages that this unicellular alga offers, poor and inconsistent expression of nuclear transgenes remains an obstacle for basic and applied research. We used a data-mining strategy to identify highly expressed genes in Chlamydomonas whose flanking sequences were tested for the ability to drive heterologous nuclear transgene expression. Candidates identified in this search included two ribosomal protein genes, RPL35a and RPL23, and ferredoxin, FDX1, whose flanking regions including promoters, terminators and untranslated sequences could drive stable luciferase transgene expression to significantly higher levels than the commonly used Hsp70A-RBCS2 (AR) hybrid promoter/terminator sequences. The RPL23 flanking sequences were further tested using the zeocin resistance gene sh-ble as a reporter in monocistronic and dicistronic constructs, and consistently yielded higher numbers of zeocin-resistant transformants and higher levels of resistance than AR- or PSAD-based vectors. Chlamydomonas RPL23 sequences also enabled transgene expression in Volvox carteri. Our study provides an additional benchmark for strong constitutive expression of transgenes in Chlamydomonas, and develops a general approach for identifying flanking sequences that can be used to drive transgene expression for any organism where transcriptome data are available.
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Affiliation(s)
- Cristina López-Paz
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - Dianyi Liu
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
- Department of Biology, University of Missouri, One University Boulevard, St. Louis, MO 63121, USA
| | - Sa Geng
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - James G. Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
- Corresponding author: James G. Umen, Donald Danforth Plant Science Center 975 N. Warson Rd., St. Louis, MO 63132, Tel: (314) 587-1689,
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Zhang S, Liang M, Naqvi NI, Lin C, Qian W, Zhang LH, Deng YZ. Phototrophy and starvation-based induction of autophagy upon removal of Gcn5-catalyzed acetylation of Atg7 in Magnaporthe oryzae. Autophagy 2017; 13:1318-1330. [PMID: 28594263 PMCID: PMC5584857 DOI: 10.1080/15548627.2017.1327103] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Magnaporthe oryzae, the ascomycete fungus that causes rice blast disease, initiates conidiation in response to light when grown on Prune-Agar medium containing both carbon and nitrogen sources. Macroautophagy/autophagy was shown to be essential for M. oryzae conidiation and induced specifically upon exposure to light but is undetectable in the dark. Therefore, it is inferred that autophagy is naturally induced by light, rather than by starvation during M. oryzae conidiation. However, the signaling pathway(s) involved in such phototropic induction of autophagy remains unknown. We identified an M. oryzae ortholog of GCN5 (MGG_03677), encoding a histone acetyltransferase (HAT) that negatively regulates light- and nitrogen-starvation-induced autophagy, by acetylating the autophagy protein Atg7. Furthermore, we unveiled novel regulatory mechanisms on Gcn5 at both transcriptional and post-translational levels, governing its function associated with the unique phototropic response of autophagy in this pathogenic fungus. Thus, our study depicts a signaling network and regulatory mechanism underlying the autophagy induction by important environmental clues such as light and nutrients.
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Affiliation(s)
- Shulin Zhang
- a Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture , South China Agricultural University , Guangzhou , China.,b Guangdong Province Key Laboratory of Microbial Signals and Disease Control, and Integrative Microbiology Research Centre , South China Agricultural University , Guangzhou , China
| | - Meiling Liang
- a Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture , South China Agricultural University , Guangzhou , China.,b Guangdong Province Key Laboratory of Microbial Signals and Disease Control, and Integrative Microbiology Research Centre , South China Agricultural University , Guangzhou , China
| | - Naweed I Naqvi
- c Temasek Life Sciences Laboratory, and Department of Biological Sciences , National University of Singapore , Singapore
| | - Chaoxiang Lin
- a Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture , South China Agricultural University , Guangzhou , China.,b Guangdong Province Key Laboratory of Microbial Signals and Disease Control, and Integrative Microbiology Research Centre , South China Agricultural University , Guangzhou , China
| | - Wanqiang Qian
- d The New Countryside Development Institute of South China Agricultural University , Guangzhou , China
| | - Lian-Hui Zhang
- a Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture , South China Agricultural University , Guangzhou , China.,b Guangdong Province Key Laboratory of Microbial Signals and Disease Control, and Integrative Microbiology Research Centre , South China Agricultural University , Guangzhou , China
| | - Yi Zhen Deng
- a Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture , South China Agricultural University , Guangzhou , China.,b Guangdong Province Key Laboratory of Microbial Signals and Disease Control, and Integrative Microbiology Research Centre , South China Agricultural University , Guangzhou , China
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Kumar D, Strenkert D, Patel-King RS, Leonard MT, Merchant SS, Mains RE, King SM, Eipper BA. A bioactive peptide amidating enzyme is required for ciliogenesis. eLife 2017; 6. [PMID: 28513435 PMCID: PMC5461114 DOI: 10.7554/elife.25728] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/15/2017] [Indexed: 02/06/2023] Open
Abstract
The pathways controlling cilium biogenesis in different cell types have not been fully elucidated. We recently identified peptidylglycine α-amidating monooxygenase (PAM), an enzyme required for generating amidated bioactive signaling peptides, in Chlamydomonas and mammalian cilia. Here, we show that PAM is required for the normal assembly of motile and primary cilia in Chlamydomonas, planaria and mice. Chlamydomonas PAM knockdown lines failed to assemble cilia beyond the transition zone, had abnormal Golgi architecture and altered levels of cilia assembly components. Decreased PAM gene expression reduced motile ciliary density on the ventral surface of planaria and resulted in the appearance of cytosolic axonemes lacking a ciliary membrane. The architecture of primary cilia on neuroepithelial cells in Pam-/- mouse embryos was also aberrant. Our data suggest that PAM activity and alterations in post-Golgi trafficking contribute to the observed ciliogenesis defects and provide an unanticipated, highly conserved link between PAM, amidation and ciliary assembly.
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Affiliation(s)
- Dhivya Kumar
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, United States
| | - Ramila S Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States
| | - Michael T Leonard
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, United States
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, United States.,Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, United States
| | - Richard E Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, United States
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States
| | - Betty A Eipper
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States.,Department of Neuroscience, University of Connecticut Health Center, Farmington, United States
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Kurniasih SD, Yamasaki T, Kong F, Okada S, Widyaningrum D, Ohama T. UV-mediated Chlamydomonas mutants with enhanced nuclear transgene expression by disruption of DNA methylation-dependent and independent silencing systems. PLANT MOLECULAR BIOLOGY 2016; 92:629-641. [PMID: 27761764 DOI: 10.1007/s11103-016-0529-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/10/2016] [Indexed: 06/06/2023]
Abstract
In this investigation, we succeeded to generate Chlamydomonas mutants that bear dramatically enhanced ability for transgene expression. To yield these mutants, we utilized DNA methyltransferase deficient strain. These mutants must be useful as a plant cell factory. Chlamydomonas reinhardtii (hereafter Chlamydomonas) is a green freshwater microalga. It is a promising cell factory for the production of recombinant proteins because it rapidly grows in simple salt-based media. However, expression of transgenes integrated into the nuclear genome of Chlamydomonas is very poor, probably because of severe transcriptional silencing irrespective of the genomic position. In this study, we generated Chlamydomonas mutants by ultraviolet (UV)-mediated mutagenesis of maintenance-type DNA methyltransferase gene (MET1)-null mutants to overcome this disadvantage. We obtained several mutants with an enhanced ability to overexpress various transgenes irrespective of their integrated genomic positions. In addition, transformation efficiencies were significantly elevated. Our findings indicate that in addition to mechanisms involving MET1, transgene expression is regulated by a DNA methylation-independent transgene silencing system in Chlamydomonas. This is in agreement with the fact that DNA methylation occurs rarely in this organism. The generated mutants may be useful for the low-cost production of therapeutic proteins and eukaryotic enzymes based on their rapid growth in simple salt-based media.
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Affiliation(s)
- Sari Dewi Kurniasih
- School of Environmental Science and Engineering, Kochi University of Technology, Tosayamada, Kochi, 782-8502, Japan
| | - Tomohito Yamasaki
- School of Environmental Science and Engineering, Kochi University of Technology, Tosayamada, Kochi, 782-8502, Japan
| | - Fantao Kong
- School of Environmental Science and Engineering, Kochi University of Technology, Tosayamada, Kochi, 782-8502, Japan
| | - Sigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural & Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Dwiyantari Widyaningrum
- School of Environmental Science and Engineering, Kochi University of Technology, Tosayamada, Kochi, 782-8502, Japan
| | - Takeshi Ohama
- School of Environmental Science and Engineering, Kochi University of Technology, Tosayamada, Kochi, 782-8502, Japan.
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Strenkert D, Limso CA, Fatihi A, Schmollinger S, Basset GJ, Merchant SS. Genetically Programmed Changes in Photosynthetic Cofactor Metabolism in Copper-deficient Chlamydomonas. J Biol Chem 2016; 291:19118-31. [PMID: 27440043 DOI: 10.1074/jbc.m116.717413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 01/08/2023] Open
Abstract
Genetic and genomic studies indicate that copper deficiency triggers changes in the expression of genes encoding key enzymes in various chloroplast-localized lipid/pigment biosynthetic pathways. Among these are CGL78 involved in chlorophyll biosynthesis and HPPD1, encoding 4-hydroxyphenylpyruvate dioxygenase catalyzing the committed step of plastoquinone and tocopherol biosyntheses. Copper deficiency in wild-type cells does not change the chlorophyll content, but a survey of chlorophyll protein accumulation in this situation revealed increased accumulation of LHCSR3, which is blocked at the level of mRNA accumulation when either CGL78 expression is reduced or in the crd1 mutant, which has a copper-nutrition conditional defect at the same step in chlorophyll biosynthesis. Again, like copper-deficient crd1 strains, cgl78 knock-down lines also have reduced chlorophyll content concomitant with loss of PSI-LHCI super-complexes and reduced abundance of a chlorophyll binding subunit of PSI, PSAK, which connects LHCI to PSI. For HPPD1, increased mRNA results in increased abundance of the corresponding protein in copper-deficient cells concomitant with CRR1-dependent increased accumulation of γ-tocopherols, but not plastoquinone-9 nor total tocopherols. In crr1 mutants, where increased HPPD1 expression is blocked, plastochromanol-8, derived from plastoquinone-9 and purported to also have an antioxidant function, is found instead. Although not previously found in algae, this metabolite may occur only in stress conditions.
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Affiliation(s)
- Daniela Strenkert
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Clariss Ann Limso
- the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Abdelhak Fatihi
- the Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, 78026 Versailles Cedex, France, and
| | - Stefan Schmollinger
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Gilles J Basset
- the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Sabeeha S Merchant
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095,
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30
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Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S. Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:387-99. [DOI: 10.1089/omi.2016.0065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Debasish Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
| | - Santosh Noronha
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P. Wangikar
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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31
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Zahid KR, Ali F, Shah F, Younas M, Shah T, Shahwar D, Hassan W, Ahmad Z, Qi C, Lu Y, Iqbal A, Wu W. Response and Tolerance Mechanism of Cotton Gossypium hirsutum L. to Elevated Temperature Stress: A Review. FRONTIERS IN PLANT SCIENCE 2016; 7:937. [PMID: 27446165 PMCID: PMC4927942 DOI: 10.3389/fpls.2016.00937] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/13/2016] [Indexed: 05/23/2023]
Abstract
Cotton is an important multipurpose crop which is highly sensitive to both biotic and abiotic stresses. Proper management of this cash crop requires systematic understanding of various environmental conditions that are vital to yield and quality. High temperature stress can severely affect the viability of pollens and anther indehiscence, which leads to significant yield losses. Cotton can respond to withstand adverse environmental condition in several phases among which the accumulation of chemicals is extremely vital. Calcium, kinases, reactive oxygen species, carbohydrate, transcription factors, gene expression regulation, and plant hormones signaling pathways are playing a handy role in activating the major genes responsible to encounter and defend elevated temperature stress. The production of heat shock proteins is up-regulated when crops are unleashed to high temperature stress. Molecular breeding can play a functional role to identify superior genes for all the important attributes as well as provide breeder ready markers for developing ideotypes. The development of high-temperature resistant transgenic cultivars of cotton can grant a stability benefit and can also ameliorate the production capacity in response to elevated temperature.
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Affiliation(s)
- Kashif Rafiq Zahid
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal UniversityWuhan, China
| | - Farhan Ali
- Cereal Crops Research InstitutePirsabak, Nowshera, Pakistan
| | - Farooq Shah
- Department of Agriculture, Abdul Wali Khan University MardanKhyber Pakhtunkhwa, Pakistan
| | - Muhammad Younas
- Department of Biotechnology, Mohi-ud-Din Islamic UniversityAzad Jammu and Kashmir, Pakistan
| | - Tariq Shah
- Department of Agricultural Economics and Management, Huazhong Agricultural UniversityWuhan, China
| | - Durri Shahwar
- Department of Plant Breeding and Genetics, University of SwabiKhyber Pakhtunkhwa, Pakistan
| | - Waseem Hassan
- Department of Soil and Environmental Sciences, Muhammad Nawaz Shareef University of AgricultureMultan, Pakistan
| | - Zahoor Ahmad
- Key Lab of Crop Disease Monitoring and Safety Control, Huazhong Agricultural UniversityWuhan, China
| | - Chao Qi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal UniversityWuhan, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural UniversityWenjian Sichuan, China
| | - Amjad Iqbal
- Department of Agriculture, Abdul Wali Khan University MardanKhyber Pakhtunkhwa, Pakistan
| | - Wei Wu
- College of Agronomy, Northwest A&F UniversityYangling, China
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32
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Muranaka LS, Rütgers M, Bujaldon S, Heublein A, Geimer S, Wollman FA, Schroda M. TEF30 Interacts with Photosystem II Monomers and Is Involved in the Repair of Photodamaged Photosystem II in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2016; 170:821-40. [PMID: 26644506 PMCID: PMC4734564 DOI: 10.1104/pp.15.01458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/04/2015] [Indexed: 05/03/2023]
Abstract
The remarkable capability of photosystem II (PSII) to oxidize water comes along with its vulnerability to oxidative damage. Accordingly, organisms harboring PSII have developed strategies to protect PSII from oxidative damage and to repair damaged PSII. Here, we report on the characterization of the THYLAKOID ENRICHED FRACTION30 (TEF30) protein in Chlamydomonas reinhardtii, which is conserved in the green lineage and induced by high light. Fractionation studies revealed that TEF30 is associated with the stromal side of thylakoid membranes. By using blue native/Deriphat-polyacrylamide gel electrophoresis, sucrose density gradients, and isolated PSII particles, we found TEF30 to quantitatively interact with monomeric PSII complexes. Electron microscopy images revealed significantly reduced thylakoid membrane stacking in TEF30-underexpressing cells when compared with control cells. Biophysical and immunological data point to an impaired PSII repair cycle in TEF30-underexpressing cells and a reduced ability to form PSII supercomplexes after high-light exposure. Taken together, our data suggest potential roles for TEF30 in facilitating the incorporation of a new D1 protein and/or the reintegration of CP43 into repaired PSII monomers, protecting repaired PSII monomers from undergoing repeated repair cycles or facilitating the migration of repaired PSII monomers back to stacked regions for supercomplex reassembly.
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Affiliation(s)
- Ligia Segatto Muranaka
- Molekulare Biotechnologie und Systembiologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany (L.S.M., M.R., M.S.);Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, 7141 Paris, France (S.B., F.-A.W.); andZellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany (A.H., S.G.)
| | - Mark Rütgers
- Molekulare Biotechnologie und Systembiologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany (L.S.M., M.R., M.S.);Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, 7141 Paris, France (S.B., F.-A.W.); andZellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany (A.H., S.G.)
| | - Sandrine Bujaldon
- Molekulare Biotechnologie und Systembiologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany (L.S.M., M.R., M.S.);Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, 7141 Paris, France (S.B., F.-A.W.); andZellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany (A.H., S.G.)
| | - Anja Heublein
- Molekulare Biotechnologie und Systembiologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany (L.S.M., M.R., M.S.);Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, 7141 Paris, France (S.B., F.-A.W.); andZellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany (A.H., S.G.)
| | - Stefan Geimer
- Molekulare Biotechnologie und Systembiologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany (L.S.M., M.R., M.S.);Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, 7141 Paris, France (S.B., F.-A.W.); andZellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany (A.H., S.G.)
| | - Francis-André Wollman
- Molekulare Biotechnologie und Systembiologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany (L.S.M., M.R., M.S.);Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, 7141 Paris, France (S.B., F.-A.W.); andZellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany (A.H., S.G.)
| | - Michael Schroda
- Molekulare Biotechnologie und Systembiologie, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany (L.S.M., M.R., M.S.);Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, 7141 Paris, France (S.B., F.-A.W.); andZellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany (A.H., S.G.)
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Zalutskaya Z, Lapina T, Ermilova E. The Chlamydomonas reinhardtii alternative oxidase 1 is regulated by heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:229-34. [PMID: 26492131 DOI: 10.1016/j.plaphy.2015.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/03/2015] [Accepted: 10/09/2015] [Indexed: 05/27/2023]
Abstract
The alternative oxidase (AOX) is a non-energy conserving terminal oxidase that has emerged as an important mitochondrial component of the cell stress responses. Although the most studied abiotic condition in relation to Chlamydomonas reinhardtii is high temperature, changes in AOX capacity of the alga were studied only under oxidative stress and cold. To examine whether elevated temperatures affected AOX1 expression, we applied quantitative real-time PCR and pharmaceutical approaches. In this work, we demonstrated a sharp increase in AOX1 transcript and protein abundance under heat stress. Furthermore, C. reinhardtii cells displayed a large increase in alternative respiration in response to high temperature. Feeding with the protein kinase inhibitor staurosporine strongly retarded the AOX1 transcription. Finally, the addition of the calcium chelator EGTA prevented heat-induced AOX1 expression. Together, our results imply that heat-inducible Ca(2+) influx and protein kinase(s) may mediate AOX1 expression at elevated temperatures. Characterization of heat-induced AOX1 regulation in the green alga C. reinhardtii provides a framework for a more complete understanding of the function of this conserved protein.
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Affiliation(s)
- Zhanneta Zalutskaya
- Lab Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Tatiana Lapina
- Lab Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Elena Ermilova
- Lab Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Saint-Petersburg, Russia.
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34
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Barahimipour R, Strenkert D, Neupert J, Schroda M, Merchant SS, Bock R. Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:704-17. [PMID: 26402748 PMCID: PMC4715772 DOI: 10.1111/tpj.13033] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/24/2015] [Accepted: 09/14/2015] [Indexed: 05/17/2023]
Abstract
The efficiency of gene expression in all organisms depends on the nucleotide composition of the coding region. GC content and codon usage are the two key sequence features known to influence gene expression, but the underlying molecular mechanisms are not entirely clear. Here we have determined the relative contributions of GC content and codon usage to the efficiency of nuclear gene expression in the unicellular green alga Chlamydomonas reinhardtii. By comparing gene variants that encode an identical amino acid sequence but differ in their GC content and/or codon usage, we show that codon usage is the key factor determining translational efficiency and, surprisingly, also mRNA stability. By contrast, unfavorable GC content affects gene expression at the level of the chromatin structure by triggering heterochromatinization. We further show that mutant algal strains that permit high-level transgene expression are less susceptible to epigenetic transgene suppression and do not establish a repressive chromatin structure at the transgenic locus. Our data disentangle the relationship between GC content and codon usage, and suggest simple strategies to overcome the transgene expression problem in Chlamydomonas.
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Affiliation(s)
- Rouhollah Barahimipour
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniela Strenkert
- University of California Los Angeles, Department of Chemistry and Biochemistry, and Institute for Genomics and Proteomics, 607 Charles E. Young Dr. East, Los Angeles, California 90095, USA
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Michael Schroda
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sabeeha S. Merchant
- University of California Los Angeles, Department of Chemistry and Biochemistry, and Institute for Genomics and Proteomics, 607 Charles E. Young Dr. East, Los Angeles, California 90095, USA
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- For correspondence (Fax: +49-331-567-8701; )
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Zhang SD, Ling LZ, Yi TS. Evolution and divergence of SBP-box genes in land plants. BMC Genomics 2015; 16:787. [PMID: 26467431 PMCID: PMC4606839 DOI: 10.1186/s12864-015-1998-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/03/2015] [Indexed: 01/24/2023] Open
Abstract
Background Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood. Methods 104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants. Results We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants. Conclusions Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1998-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany of the Chinese Academy of Sciences, Kunming, 650201, China.
| | - Li-Zhen Ling
- BGI-Yunnan, BGI-Shenzhen, Kunming, 650106, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany of the Chinese Academy of Sciences, Kunming, 650201, China.
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Mussgnug JH. Genetic tools and techniques for Chlamydomonas reinhardtii. Appl Microbiol Biotechnol 2015; 99:5407-18. [PMID: 26025017 DOI: 10.1007/s00253-015-6698-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/10/2015] [Accepted: 05/15/2015] [Indexed: 11/29/2022]
Abstract
The development of tools has always been a major driving force for the advancement of science. Optical microscopes were the first instruments that allowed discovery and descriptive studies of the subcellular features of microorganisms. Although optical and electron microscopes remained at the forefront of microbiological research tools since their inventions, the advent of molecular genetics brought about questions which had to be addressed with new "genetic tools". The unicellular green microalgal genus Chlamydomonas, especially the most prominent species C. reinhardtii, has become a frequently used model organism for many diverse fields of research and molecular genetic analyses of C. reinhardtii, as well as the available genetic tools and techniques, have become increasingly sophisticated throughout the last decades. The aim of this review is to provide an overview of the molecular key features of C. reinhardtii and summarize the progress related to the development of tools and techniques for genetic engineering of this organism, from pioneering DNA transformation experiments to state-of-the-art techniques for targeted nuclear genome editing and high-throughput screening approaches.
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Affiliation(s)
- Jan H Mussgnug
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615, Bielefeld, Germany,
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Schroda M, Hemme D, Mühlhaus T. The Chlamydomonas heat stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:466-480. [PMID: 25754362 DOI: 10.1111/tpj.12816] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 05/18/2023]
Abstract
Heat waves occurring at increased frequency as a consequence of global warming jeopardize crop yield safety. One way to encounter this problem is to genetically engineer crop plants toward increased thermotolerance. To identify entry points for genetic engineering, a thorough understanding of how plant cells perceive heat stress and respond to it is required. Using the unicellular green alga Chlamydomonas reinhardtii as a model system to study the fundamental mechanisms of the plant heat stress response has several advantages. Most prominent among them is the suitability of Chlamydomonas for studying stress responses system-wide and in a time-resolved manner under controlled conditions. Here we review current knowledge on how heat is sensed and signaled to trigger temporally and functionally grouped sub-responses termed response elements to prevent damage and to maintain cellular homeostasis in plant cells.
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Affiliation(s)
- Michael Schroda
- Molecular Biotechnology & Systems Biology, TU Kaiserslautern, Paul-Ehrlich-Straße 23, 67663, Kaiserslautern, Germany
| | - Dorothea Hemme
- Molecular Biotechnology & Systems Biology, TU Kaiserslautern, Paul-Ehrlich-Straße 23, 67663, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Molecular Biotechnology & Systems Biology, TU Kaiserslautern, Paul-Ehrlich-Straße 23, 67663, Kaiserslautern, Germany
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Damodaran SP, Eberhard S, Boitard L, Rodriguez JG, Wang Y, Bremond N, Baudry J, Bibette J, Wollman FA. A millifluidic study of cell-to-cell heterogeneity in growth-rate and cell-division capability in populations of isogenic cells of Chlamydomonas reinhardtii. PLoS One 2015; 10:e0118987. [PMID: 25760649 PMCID: PMC4356620 DOI: 10.1371/journal.pone.0118987] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022] Open
Abstract
To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers) and a significant subpopulation of slowly dividing cells (slow-growers). These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes.
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Affiliation(s)
- Shima P. Damodaran
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Stephan Eberhard
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC 7141, Paris, France
| | - Laurent Boitard
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jairo Garnica Rodriguez
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Yuxing Wang
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
- Optical Science & Engineering Research Center, Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - Nicolas Bremond
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jean Baudry
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jérôme Bibette
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
- * E-mail: (JB); (FAW)
| | - Francis-André Wollman
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC 7141, Paris, France
- * E-mail: (JB); (FAW)
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Ryu JY, Kim JY, Park CM. Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2015; 10:e1093715. [PMID: 26452406 PMCID: PMC4883874 DOI: 10.1080/15592324.2015.1093715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/07/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
Gravitropism is an important growth movement in response to gravity in virtually all higher plants: the roots showing positive gravitropism and the shoots showing negative gravitropism. The gravitropic orientation of plant organs is also influenced by environmental factors, such as light and temperature. It is known that a zinc finger (ZF)-containing transcription factor SHOOT GRAVITROPISM 5/INDETERMINATE DOMAIN 15 (SGR5/IDD15) mediates the early events of gravitropic responses occurring in inflorescence stems. We have recently found that SGR5 gene undergoes alternative splicing to produce 2 protein variants, the full-size SGR5α transcription factor and the truncated SGR5β form lacking functional ZF motifs. The SGR5β form inhibits SGR5α function possibly by forming nonfunctional heterodimers that are excluded from DNA binding. Notably, SGR5 alternative splicing is accelerated at high temperatures, resulting in a high-level accumulation of SGR5β proteins. Accordingly, transgenic plants overexpressing SGR5β exhibit a reduction in the negative gravitropism of inflorescence stems, as observed in the SGR5-defective mutant. It is proposed that the thermos-responsive alternative splicing of SGR5 gene provides an adaptation strategy by which plants protect the shoots from aerial heat frequently occurring in natural habitats.
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Affiliation(s)
- Jae Yong Ryu
- Department of Chemistry; Seoul National University; Seoul, Korea
| | - Joo-Young Kim
- Department of Chemistry; Seoul National University; Seoul, Korea
| | - Chung-Mo Park
- Department of Chemistry; Seoul National University; Seoul, Korea
- Plant Genomics and Breeding Institute; Seoul National University; Seoul, Korea
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Liu J, Feng L, Li J, He Z. Genetic and epigenetic control of plant heat responses. FRONTIERS IN PLANT SCIENCE 2015; 6:267. [PMID: 25964789 PMCID: PMC4408840 DOI: 10.3389/fpls.2015.00267] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/03/2015] [Indexed: 05/18/2023]
Abstract
Plants have evolved sophisticated genetic and epigenetic regulatory systems to respond quickly to unfavorable environmental conditions such as heat, cold, drought, and pathogen infections. In particular, heat greatly affects plant growth and development, immunity and circadian rhythm, and poses a serious threat to the global food supply. According to temperatures exposing, heat can be usually classified as warm ambient temperature (about 22-27°C), high temperature (27-30°C) and extremely high temperature (37-42°C, also known as heat stress) for the model plant Arabidopsis thaliana. The genetic mechanisms of plant responses to heat have been well studied, mainly focusing on elevated ambient temperature-mediated morphological acclimation and acceleration of flowering, modulation of circadian clock and plant immunity by high temperatures, and thermotolerance to heat stress. Recently, great progress has been achieved on epigenetic regulation of heat responses, including DNA methylation, histone modifications, histone variants, ATP-dependent chromatin remodeling, histone chaperones, small RNAs, long non-coding RNAs and other undefined epigenetic mechanisms. These epigenetic modifications regulate the expression of heat-responsive genes and function to prevent heat-related damages. This review focuses on recent progresses regarding the genetic and epigenetic control of heat responses in plants, and pays more attention to the role of the major epigenetic mechanisms in plant heat responses. Further research perspectives are also discussed.
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Affiliation(s)
- Junzhong Liu
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences – Chinese Academy of SciencesShanghai, China
| | - Lili Feng
- School of Life Science and Technology, ShanghaiTech UniversityShanghai, China
| | - Jianming Li
- Plant Signaling Laboratory, The Plant Stress Biology Center, Shanghai Institutes for Biological Sciences – Chinese Academy of SciencesShanghai, China
- *Correspondence: Zuhua He, National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China ; Jianming Li, Plant Signaling Laboratory, The Plant Stress Biology Center, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang District, Shanghai 201602, China
| | - Zuhua He
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences – Chinese Academy of SciencesShanghai, China
- *Correspondence: Zuhua He, National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China ; Jianming Li, Plant Signaling Laboratory, The Plant Stress Biology Center, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang District, Shanghai 201602, China
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Chang CY, Lin WD, Tu SL. Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens. PLANT PHYSIOLOGY 2014; 165:826-840. [PMID: 24777346 PMCID: PMC4044832 DOI: 10.1104/pp.113.230540] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plant growth and development are constantly influenced by temperature fluctuations. To respond to temperature changes, different levels of gene regulation are modulated in the cell. Alternative splicing (AS) is a widespread mechanism increasing transcriptome complexity and proteome diversity. Although genome-wide studies have revealed complex AS patterns in plants, whether AS impacts the stress defense of plants is not known. We used heat shock (HS) treatments at nondamaging temperature and messenger RNA sequencing to obtain HS transcriptomes in the moss Physcomitrella patens. Data analysis identified a significant number of novel AS events in the moss protonema. Nearly 50% of genes are alternatively spliced. Intron retention (IR) is markedly repressed under elevated temperature but alternative donor/acceptor site and exon skipping are mainly induced, indicating differential regulation of AS in response to heat stress. Transcripts undergoing heat-sensitive IR are mostly involved in specific functions, which suggests that plants regulate AS with transcript specificity under elevated temperature. An exonic GAG-repeat motif in these IR regions may function as a regulatory cis-element in heat-mediated AS regulation. A conserved AS pattern for HS transcription factors in P. patens and Arabidopsis (Arabidopsis thaliana) reveals that heat regulation for AS evolved early during land colonization of green plants. Our results support that AS of specific genes, including key HS regulators, is fine-tuned under elevated temperature to modulate gene regulation and reorganize metabolic processes.
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Affiliation(s)
- Chiung-Yun Chang
- Institute of Plant and Microbial Biology (C.-Y.C., W.-D.L., S.-L.T.) and Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program (C.-Y.C., S.-L.T.), Academia Sinica, Taipei 11529, Taiwan; andGraduate Institute of Biotechnology (C.-Y.C.) and Biotechnology Center (S.-L.T.), National Chung-Hsing University, Taichung 402, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology (C.-Y.C., W.-D.L., S.-L.T.) and Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program (C.-Y.C., S.-L.T.), Academia Sinica, Taipei 11529, Taiwan; andGraduate Institute of Biotechnology (C.-Y.C.) and Biotechnology Center (S.-L.T.), National Chung-Hsing University, Taichung 402, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial Biology (C.-Y.C., W.-D.L., S.-L.T.) and Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program (C.-Y.C., S.-L.T.), Academia Sinica, Taipei 11529, Taiwan; andGraduate Institute of Biotechnology (C.-Y.C.) and Biotechnology Center (S.-L.T.), National Chung-Hsing University, Taichung 402, Taiwan
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Simon JM, Giresi PG, Davis IJ, Lieb JD. Addendum: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc 2014. [DOI: 10.1038/nprot.2014.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Vischi Winck F, Arvidsson S, Riaño-Pachón DM, Hempel S, Koseska A, Nikoloski Z, Urbina Gomez DA, Rupprecht J, Mueller-Roeber B. Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation. PLoS One 2013; 8:e79909. [PMID: 24224019 PMCID: PMC3816576 DOI: 10.1371/journal.pone.0079909] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 10/01/2013] [Indexed: 11/18/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO 2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
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Affiliation(s)
- Flavia Vischi Winck
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Samuel Arvidsson
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Mauricio Riaño-Pachón
- Group of Computational and Evolutionary Biology, Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | - Sabrina Hempel
- University of Potsdam, Institute of Physics, Potsdam-Golm, Germany
- Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Aneta Koseska
- University of Potsdam, Institute of Physics, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- Systems Biology and Mathematical Modeling Group, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - David Alejandro Urbina Gomez
- Group of Computational and Evolutionary Biology, Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | - Jens Rupprecht
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail:
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Schmollinger S, Schulz-Raffelt M, Strenkert D, Veyel D, Vallon O, Schroda M. Dissecting the heat stress response in Chlamydomonas by pharmaceutical and RNAi approaches reveals conserved and novel aspects. MOLECULAR PLANT 2013; 6:1795-1813. [PMID: 23713078 DOI: 10.1093/mp/sst086] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
To study how conserved fundamental concepts of the heat stress response (HSR) are in photosynthetic eukaryotes, we applied pharmaceutical and antisense/amiRNA approaches to the unicellular green alga Chlamydomonas reinhardtii. The Chlamydomonas HSR appears to be triggered by the accumulation of unfolded proteins, as it was induced at ambient temperatures by feeding cells with the arginine analog canavanine. The protein kinase inhibitor staurosporine strongly retarded the HSR, demonstrating the importance of phosphorylation during activation of the HSR also in Chlamydomonas. While the removal of extracellular calcium by the application of EGTA and BAPTA inhibited the HSR in moss and higher plants, only the addition of BAPTA, but not of EGTA, retarded the HSR and impaired thermotolerance in Chlamydomonas. The addition of cycloheximide, an inhibitor of cytosolic protein synthesis, abolished the attenuation of the HSR, indicating that protein synthesis is necessary to restore proteostasis. HSP90 inhibitors induced a stress response when added at ambient conditions and retarded attenuation of the HSR at elevated temperatures. In addition, we detected a direct physical interaction between cytosolic HSP90A/HSP70A and heat shock factor 1, but surprisingly this interaction persisted after the onset of stress. Finally, the expression of antisense constructs targeting chloroplast HSP70B resulted in a delay of the cell's entire HSR, thus suggesting the existence of a retrograde stress signaling cascade that is desensitized in HSP70B-antisense strains.
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Affiliation(s)
- Stefan Schmollinger
- Molekulare Biotechnologie und Systembiologie, TU Kaiserslautern, Paul-Ehrlich-Str. 23, D-67663 Kaiserslautern, Germany
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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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Preston JC, Hileman LC. Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family. FRONTIERS IN PLANT SCIENCE 2013; 4:80. [PMID: 23577017 PMCID: PMC3617394 DOI: 10.3389/fpls.2013.00080] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/19/2013] [Indexed: 05/18/2023]
Abstract
The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors is functionally diverse, controlling a number of fundamental aspects of plant growth and development, including vegetative phase change, flowering time, branching, and leaf initiation rate. In natural plant populations, variation in flowering time and shoot architecture have major consequences for fitness. Likewise, in crop species, variation in branching and developmental rate impact biomass and yield. Thus, studies aimed at dissecting how the various functions are partitioned among different SPL genes in diverse plant lineages are key to providing insight into the genetic basis of local adaptation and have already garnered attention by crop breeders. Here we use phylogenetic reconstruction to reveal nine major SPL gene lineages, each of which is described in terms of function and diversification. To assess evidence for ancestral and derived functions within each SPL gene lineage, we use ancestral character state reconstructions. Our analyses suggest an emerging pattern of sub-functionalization, neo-functionalization, and possible convergent evolution following both ancient and recent gene duplication. Based on these analyses we suggest future avenues of research that may prove fruitful for elucidating the importance of SPL gene evolution in plant growth and development.
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Affiliation(s)
| | - Lena C. Hileman
- Ecology and Evolutionary Biology, The University of KansasLawrence, KS, USA
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Cheaib M, Simon M. Dynamic chromatin remodelling of ciliate macronuclear DNA as determined by an optimized chromatin immunoprecipitation (ChIP) method for Paramecium tetraurelia. Appl Microbiol Biotechnol 2013; 97:2661-70. [PMID: 23385475 DOI: 10.1007/s00253-013-4708-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/04/2013] [Accepted: 01/07/2013] [Indexed: 01/08/2023]
Abstract
We report the detailed evaluation of crucial parameters for chromatin immunoprecipitation (ChIP) of macronuclear DNA in the unicellular eukaryote Paramecium tetraurelia. Optimized parameters include crosslinking conditions, chromatin sonication and antibody titration thus providing a detailed protocol for successful ChIP in P. tetraurelia. As this ciliate is bacterivorous and RNAi by feeding represents a powerful tool for analysis of gene function, we moreover determined the effects of ingested nucleic acids by food bacteria. Feasibility of our protocol is demonstrated by characterisation of chromatin remodelling at promoters of cytosolic HSP70 isoforms during transcriptional activation under heat shock conditions by analyzing RNA abundance, nucleosome occupancy and levels of H3 lysine 9 acetylation.
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Affiliation(s)
- Miriam Cheaib
- Faculty of Biology, Molecular Protistology, University of Kaiserslautern, Gottlieb-Daimler Straße Building 14, 67663 Kaiserslautern, Germany
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Gutzat R, Mittelsten Scheid O. Epigenetic responses to stress: triple defense? CURRENT OPINION IN PLANT BIOLOGY 2012; 15:568-73. [PMID: 22960026 PMCID: PMC3508409 DOI: 10.1016/j.pbi.2012.08.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/16/2012] [Indexed: 05/19/2023]
Abstract
Stressful conditions for plants can originate from numerous physical, chemical and biological factors, and plants have developed a plethora of survival strategies including developmental and morphological adaptations, specific signaling and defense pathways as well as innate and acquired immunity. While it has become clear in recent years that many stress responses involve epigenetic components, we are far from understanding the mechanisms and molecular interactions. Extending our knowledge is fundamental, not least for plant breeding and conservation biology. This review will highlight recent insights into epigenetic stress responses at the level of signaling, chromatin modification, and potentially heritable consequences.
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Yeh CH, Kaplinsky NJ, Hu C, Charng YY. Some like it hot, some like it warm: phenotyping to explore thermotolerance diversity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 195:10-23. [PMID: 22920995 PMCID: PMC3430125 DOI: 10.1016/j.plantsci.2012.06.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/07/2012] [Accepted: 06/07/2012] [Indexed: 05/18/2023]
Abstract
Plants have evolved overlapping but distinct cellular responses to different aspects of high temperature stress. These responses include basal thermotolerance, short- and long-term acquired thermotolerance, and thermotolerance to moderately high temperatures. This 'thermotolerance diversity' means that multiple phenotypic assays are essential for fully describing the functions of genes involved in heat stress responses. A large number of genes with potential roles in heat stress responses have been identified using genetic screens and genome wide expression studies. We examine the range of phenotypic assays that have been used to characterize thermotolerance phenotypes in both Arabidopsis and crop plants. Three major variables differentiate thermotolerance assays: (1) the heat stress regime used, (2) the developmental stage of the plants being studied, and (3) the actual phenotype which is scored. Consideration of these variables will be essential for deepening our understanding of the molecular genetics of plant thermotolerance.
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Affiliation(s)
- Ching-Hui Yeh
- Department of Life Sciences, National Central University, Taiwan 32001, ROC
| | | | - Catherine Hu
- Agricultural Biotechnology Research Center, Academia Sinica, Taiwan 11529, ROC
| | - Yee-yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, Taiwan 11529, ROC
- Corresponding author: ; FAX: 886-2-26515600
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Pape M, Lambertz C, Happe T, Hemschemeier A. Differential expression of the Chlamydomonas [FeFe]-hydrogenase-encoding HYDA1 gene is regulated by the copper response regulator1. PLANT PHYSIOLOGY 2012; 159:1700-12. [PMID: 22669892 PMCID: PMC3425207 DOI: 10.1104/pp.112.200162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 06/02/2012] [Indexed: 05/20/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii adapts to anaerobic or hypoxic conditions by developing a complex fermentative metabolism including the production of molecular hydrogen by [FeFe]-hydrogenase isoform1 (HYDA1). HYDA1 transcript and hydrogenase protein accumulate in the absence of oxygen or copper (Cu). Factors regulating this differential gene expression have been unknown so far. In this study, we report on the isolation of a Chlamydomonas mutant strain impaired in HYDA1 gene expression by screening an insertional mutagenesis library for HYDA1 promoter activity using the arylsulfatase-encoding ARYLSULFATASE2 gene as a selection marker. The mutant strain has a deletion of the COPPER RESPONSE REGULATOR1 (CRR1) gene encoding for CRR1, indicating that this SQUAMOSA-PROMOTER BINDING PROTEIN (SBP) domain transcription factor is involved in the regulation of HYDA1 transcription. Treating the C. reinhardtii wild type with mercuric ions, which were shown to inhibit the binding of the SBP domain to DNA, prevented or deactivated HYDA1 gene expression. Reporter gene analyses of the HYDA1 promoter revealed that two GTAC motifs, which are known to be the cores of CRR1 binding sites, are necessary for full promoter activity in hypoxic conditions or upon Cu starvation. However, mutations of the GTAC sites had a much stronger impact on reporter gene expression in Cu-deficient cells. Electrophoretic mobility shift assays showed that the CRR1 SBP domain binds to one of the GTAC cores in vitro. These combined results prove that CRR1 is involved in HYDA1 promoter activation.
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