1
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Gupta A, Kang K, Pathania R, Saxton L, Saucedo B, Malik A, Torres-Tiji Y, Diaz CJ, Dutra Molino JV, Mayfield SP. Harnessing genetic engineering to drive economic bioproduct production in algae. Front Bioeng Biotechnol 2024; 12:1350722. [PMID: 38347913 PMCID: PMC10859422 DOI: 10.3389/fbioe.2024.1350722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.
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Affiliation(s)
- Abhishek Gupta
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Kalisa Kang
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ruchi Pathania
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Lisa Saxton
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Barbara Saucedo
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ashleyn Malik
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Yasin Torres-Tiji
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Crisandra J. Diaz
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - João Vitor Dutra Molino
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Stephen P. Mayfield
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
- California Center for Algae Biotechnology, University of California San Diego, San Diego, CA, United States
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2
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Chaumier T, Yang F, Manirakiza E, Ait-Mohamed O, Wu Y, Chandola U, Jesus B, Piganeau G, Groisillier A, Tirichine L. Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum. ISME COMMUNICATIONS 2024; 4:ycad008. [PMID: 38304080 PMCID: PMC10833087 DOI: 10.1093/ismeco/ycad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.
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Affiliation(s)
| | - Feng Yang
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Eric Manirakiza
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Ouardia Ait-Mohamed
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, Paris 75005, France
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Udita Chandola
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Bruno Jesus
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes F-44000, France
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | | | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
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3
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Grypioti E, Richard H, Kryovrysanaki N, Jaubert M, Falciatore A, Verret F, Kalantidis K. Dicer-dependent heterochromatic small RNAs in the model diatom species Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2024; 241:811-826. [PMID: 38044751 DOI: 10.1111/nph.19429] [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: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023]
Abstract
Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown. We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression-associated histone marks, and acclimatory response to nitrogen starvation. Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26-31-nt-long double-stranded sRNAs originating mostly from transposons covered by repression-associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression-associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR-KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress. Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species.
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Affiliation(s)
- Emilia Grypioti
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
- Institute of Marine Biology and Aquaculture, Hellenic Center for Marine Research, 71500, Gournes, Crete, Greece
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
| | - Hugues Richard
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
- Bioinformatics Unit, Genome Competence Center (MF1), Robert Koch Institute, 13353, Berlin, Germany
| | - Nikoleta Kryovrysanaki
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
| | - Marianne Jaubert
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005, Paris, France
| | - Angela Falciatore
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005, Paris, France
| | - Frédéric Verret
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
- Institute of Marine Biology and Aquaculture, Hellenic Center for Marine Research, 71500, Gournes, Crete, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
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4
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Hamzelou S, Belobrajdic D, Broadbent JA, Juhász A, Lee Chang K, Jameson I, Ralph P, Colgrave ML. Utilizing proteomics to identify and optimize microalgae strains for high-quality dietary protein: a review. Crit Rev Biotechnol 2023:1-16. [PMID: 38035669 DOI: 10.1080/07388551.2023.2283376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Algae-derived protein has immense potential to provide high-quality protein foods for the expanding human population. To meet its potential, a broad range of scientific tools are required to identify optimal algal strains from the hundreds of thousands available and identify ideal growing conditions for strains that produce high-quality protein with functional benefits. A research pipeline that includes proteomics can provide a deeper interpretation of microalgal composition and biochemistry in the pursuit of these goals. To date, proteomic investigations have largely focused on pathways that involve lipid production in selected microalgae species. Herein, we report the current state of microalgal proteome measurement and discuss promising approaches for the development of protein-containing food products derived from algae.
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Affiliation(s)
| | | | | | - Angéla Juhász
- School of Science, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, Joondalup, Australia
| | | | - Ian Jameson
- CSIRO Ocean and Atmosphere, Hobart, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, St Lucia, Australia
- School of Science, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, Joondalup, Australia
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5
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Liu D, Wei L. Epigenetic Regulation in Response to CO 2 Fluctuation in Marine Microalga Nannochloropsis oceanica. MICROBIAL ECOLOGY 2023; 87:4. [PMID: 38015286 DOI: 10.1007/s00248-023-02322-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/22/2023] [Indexed: 11/29/2023]
Abstract
Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.
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Affiliation(s)
- Danmei Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Li Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571129, China.
- International Science and Technology Cooperation Laboratory for Marine Microalgae Ecological Carbon Sinks, Hainan Normal University, Haikou, 571158, China.
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6
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Jiang Y, Cao T, Yang Y, Zhang H, Zhang J, Li X. A chlorophyll c synthase widely co-opted by phytoplankton. Science 2023; 382:92-98. [PMID: 37797009 DOI: 10.1126/science.adg7921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
Marine and terrestrial photosynthesis exhibit a schism in the accessory chlorophyll (Chl) that complements the function of Chl a: Chl b for green plants versus Chl c for most eukaryotic phytoplankton. The enzymes that mediate Chl c biosynthesis have long remained elusive. In this work, we identified the CHLC dioxygenase (Phatr3_J43737) from the marine diatom Phaeodactylum tricornutum as the Chl c synthase. The chlc mutants lacked Chl c, instead accumulating its precursors, and exhibited growth defects. In vitro, recombinant CHLC protein converted these precursors into Chl c, thereby confirming its identity. Phylogenetic evidence demonstrates conserved use of CHLC across phyla but also the existence of distinct Chl c synthases in different algal groups. Our study addresses a long-outstanding question with implications for both contemporary and ancient marine photosynthesis.
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Affiliation(s)
- Yanyou Jiang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Tianjun Cao
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuqing Yang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Huan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jingyu Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaobo Li
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
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7
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Lin X, Tirichine L, Zhang X. The dynamic duo: how DNA methylation and gene transcription help diatoms thrive in modern oceans. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3879-3882. [PMID: 37536061 PMCID: PMC10400112 DOI: 10.1093/jxb/erad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
This article comments on:
Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao J, Dai X, Xia J, Jin P. 2023. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. Journal of Experimental Botany74, 4259–4276.
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Affiliation(s)
- Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, PR China
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, F-44000 Nantes, France
| | - Xu Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, PR China
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Wu Y, Tirichine L. Chromosome-Wide Distribution and Characterization of H3K36me3 and H3K27Ac in the Marine Model Diatom Phaeodactylum tricornutum. PLANTS (BASEL, SWITZERLAND) 2023; 12:2852. [PMID: 37571007 PMCID: PMC10421102 DOI: 10.3390/plants12152852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Histone methylation and acetylation play a crucial role in response to developmental cues and environmental changes. Previously, we employed mass spectrometry to identify histone modifications such as H3K27ac and H3K36me3 in the model diatom Phaeodactylum tricornutum, which have been shown to be important for transcriptional activation in animal and plant species. To further investigate their evolutionary implications, we utilized chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) and explored their genome-wide distribution in P. tricornutum. Our study aimed to determine their role in transcriptional regulation of genes and transposable elements (TEs) and their co-occurrence with other histone marks. Our results revealed that H3K27ac and H3K36me3 were predominantly localized in promoters and genic regions indicating a high conservation pattern with studies of the same marks in plants and animals. Furthermore, we report the diversity of genes encoding H3 lysine 36 (H3K36) trimethylation-specific methyltransferase in microalgae leveraging diverse sequencing resources including the Marine Microbial Eukaryote Transcriptome Sequencing Project database (MMETSP). Our study expands the repertoire of epigenetic marks in a model microalga and provides valuable insights into the evolutionary context of epigenetic-mediated gene regulation. These findings shed light on the intricate interplay between histone modifications and gene expression in microalgae, contributing to our understanding of the broader epigenetic landscape in eukaryotic organisms.
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Affiliation(s)
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, F-44000 Nantes, France;
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9
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Han J, Yu G, Zhang X, Dai Y, Zhang H, Zhang B, Wang K. Histone Maps in Gossypium darwinii Reveal Epigenetic Regulation Drives Subgenome Divergence and Cotton Domestication. Int J Mol Sci 2023; 24:10607. [PMID: 37445787 DOI: 10.3390/ijms241310607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The functional annotation of genomes, including chromatin modifications, is essential to understand the intricate architecture of chromatin and the consequential gene regulation. However, such an annotation remains limited for cotton genomes. Here, we conducted chromatin profiling in a wild allotetraploid cotton Gossypium darwinii (AD genome) by integrating the data of histone modification, transcriptome, and chromatin accessibility. We revealed that the A subgenome showed a higher level of active histone marks and lower level of repressive histone marks than the D subgenome, which was consistent with the expression bias between the two subgenomes. We show that the bias in transcription and histone modification between the A and D subgenomes may be caused by genes unique to the subgenome but not by homoeologous genes. Moreover, we integrate histone marks and open chromatin to define six chromatin states (S1-S6) across the cotton genome, which index different genomic elements including genes, promoters, and transposons, implying distinct biological functions. In comparison to the domesticated cotton species, we observed that 23.2% of genes in the genome exhibit a transition from one chromatin state to another at their promoter. Strikingly, the S2 (devoid of epigenetic marks) to S3 (enriched for the mark of open chromatin) was the largest transition group. These transitions occurred simultaneously with changes in gene expression, which were significantly associated with several domesticated traits in cotton. Collectively, our study provides a useful epigenetic resource for research on allopolyploid plants. The domestication-induced chromatin dynamics and associated genes identified here will aid epigenetic engineering, improving polyploid crops.
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Affiliation(s)
- Jinlei Han
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Guangrun Yu
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Xin Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Yan Dai
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
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10
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Wu Y, Chaumier T, Manirakiza E, Veluchamy A, Tirichine L. PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum. Sci Rep 2023; 13:8320. [PMID: 37221245 DOI: 10.1038/s41598-023-35403-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/17/2023] [Indexed: 05/25/2023] Open
Abstract
Recent advances in DNA sequencing technologies particularly long-read sequencing, greatly improved genomes assembly. However, this has created discrepancies between published annotations and epigenome tracks, which have not been updated to keep pace with the new assemblies. Here, we used the latest improved telomere-to-telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genes annotation and newly published transposable elements to map the epigenome landscape, namely DNA methylation and post-translational modifications of histones. This provides the community with PhaeoEpiView, a browser that allows the visualization of epigenome data and transcripts on an updated and contiguous reference genome, to better understand the biological significance of the mapped data. We updated previously published histone marks with a more accurate peak calling using mono instead of poly(clonal) antibodies and deeper sequencing. PhaeoEpiView ( https://PhaeoEpiView.univ-nantes.fr ) will be continuously updated with the newly published epigenomic data, making it the largest and richest epigenome browser of any stramenopile. In the upcoming era of molecular environmental studies, where epigenetics plays a significant role, we anticipate that PhaeoEpiView will become a widely used tool.
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Affiliation(s)
- Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, 44000, Nantes, France
| | | | - Eric Manirakiza
- Nantes Université, CNRS, US2B, UMR 6286, 44000, Nantes, France
| | | | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, 44000, Nantes, France.
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11
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Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao JY, Dai X, Xia J, Jin P. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad150. [PMID: 37100754 DOI: 10.1093/jxb/erad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 06/19/2023]
Abstract
Genetic changes together with epigenetic modifications such as DNA methylation have been demonstrated to regulate many biological processes and thereby govern the response of organisms to environmental changes. However, how DNA methylation might act cooperatively with gene transcription and thereby mediate the long-term adaptive responses of marine microalgae to global change is virtually unknown. Here we performed a transcriptomic analysis, and a whole-genome bisulfite sequencing, along with phenotypic analysis of a model marine diatom Phaeodactylum tricornutum adapted for two years to high CO2 and/or warming conditions. Our results show that the methylated islands (peaks of methylation) mCHH were positively correlated with expression of genes in the sub-region of the gene body when the populations were grown under high CO2 or its combination with warming for ~2 years. We further identified the differentially expressed genes (DEGs) and hence the metabolic pathways in which they function, at the transcriptomics level in differentially methylated regions (DMRs). Although DEGs in DMRs contributed only 18-24% of the total DEGs, we found that those DEGs acted cooperatively with DNA methylation and then regulated key processes such as central carbon metabolism, amino acid metabolism, ribosome biogenesis, terpenoid backbone biosynthesis, and degradation of misfolded proteins. Taken together, by integrating transcriptomic, epigenetic and phenotypic analysis, our study provides evidence for DNA methylation acting cooperatively with gene transcription to contribute to the adaptation of microalgae to global changes.
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Affiliation(s)
- Jiaofeng Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yunyue Zhou
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Climate Change Cluster, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - Jiamin Lin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiali Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yucong Lu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shiman Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengcheng Ye
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengting Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jing Yuan Zhao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoying Dai
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
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12
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Hoguin A, Yang F, Groisillier A, Bowler C, Genovesio A, Ait-Mohamed O, Vieira FRJ, Tirichine L. The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases. Commun Biol 2023; 6:253. [PMID: 36894681 PMCID: PMC9998398 DOI: 10.1038/s42003-023-04629-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.
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Affiliation(s)
- Antoine Hoguin
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Feng Yang
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | | | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Auguste Genovesio
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Ouardia Ait-Mohamed
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
- Laboratory of Computational and Quantitative Biology-LCQB - UMR 7238 CNRS-Sorbonne Université. Institut de Biologie Paris Seine, 75005, Paris, France.
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France.
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13
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Nef C, Madoui MA, Pelletier É, Bowler C. Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. PLoS Biol 2022; 20:e3001893. [PMID: 36441816 PMCID: PMC9731442 DOI: 10.1371/journal.pbio.3001893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/08/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.
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Affiliation(s)
- Charlotte Nef
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Mohammed-Amin Madoui
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Éric Pelletier
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Metabolic Genomics, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Université Evry, Université Paris Saclay, Evry, France
| | - Chris Bowler
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- * E-mail:
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14
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Liu S, Storti M, Finazzi G, Bowler C, Dorrell RG. A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum. FRONTIERS IN PLANT SCIENCE 2022; 13:950467. [PMID: 36212359 PMCID: PMC9546453 DOI: 10.3389/fpls.2022.950467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.
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Affiliation(s)
- Shun Liu
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Mattia Storti
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
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15
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Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol 2022; 6:1007-1023. [PMID: 35680998 PMCID: PMC7613034 DOI: 10.1038/s41559-022-01771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Bernd Franz Lang
- Robert Cedergren Centre in Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-Garcia
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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16
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Paramecium Polycomb repressive complex 2 physically interacts with the small RNA-binding PIWI protein to repress transposable elements. Dev Cell 2022; 57:1037-1052.e8. [DOI: 10.1016/j.devcel.2022.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/10/2022] [Accepted: 03/21/2022] [Indexed: 12/30/2022]
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17
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Vijayanathan M, Trejo-Arellano MG, Mozgová I. Polycomb Repressive Complex 2 in Eukaryotes-An Evolutionary Perspective. EPIGENOMES 2022; 6:3. [PMID: 35076495 PMCID: PMC8788455 DOI: 10.3390/epigenomes6010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
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Affiliation(s)
- Mallika Vijayanathan
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - María Guadalupe Trejo-Arellano
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - Iva Mozgová
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
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18
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Xia L, Kong X, Song H, Han Q, Zhang S. Advances in proteome-wide analysis of plant lysine acetylation. PLANT COMMUNICATIONS 2022; 3:100266. [PMID: 35059632 PMCID: PMC8760137 DOI: 10.1016/j.xplc.2021.100266] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Lysine acetylation (LysAc) is a conserved and important post-translational modification (PTM) that plays a key role in plant physiological and metabolic processes. Based on advances in Lys-acetylated protein immunoenrichment and mass-spectrometric technology, LysAc proteomics studies have been performed in many species. Such studies have made substantial contributions to our understanding of plant LysAc, revealing that Lys-acetylated histones and nonhistones are involved in a broad spectrum of plant cellular processes. Here, we present an extensive overview of recent research on plant Lys-acetylproteomes. We provide in-depth insights into the characteristics of plant LysAc modifications and the mechanisms by which LysAc participates in cellular processes and regulates metabolism and physiology during plant growth and development. First, we summarize the characteristics of LysAc, including the properties of Lys-acetylated sites, the motifs that flank Lys-acetylated lysines, and the dynamic alterations in LysAc among different tissues and developmental stages. We also outline a map of Lys-acetylated proteins in the Calvin-Benson cycle and central carbon metabolism-related pathways. We then introduce some examples of the regulation of plant growth, development, and biotic and abiotic stress responses by LysAc. We discuss the interaction between LysAc and Nα-terminal acetylation and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we propose recommendations for future studies in the field. We conclude that LysAc of proteins plays an important role in the regulation of the plant life cycle.
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Affiliation(s)
- Linchao Xia
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xiangge Kong
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haifeng Song
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Qingquan Han
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Sheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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19
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Erlendson AA, Freitag M. Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases. Methods Mol Biol 2022; 2529:3-40. [PMID: 35733008 DOI: 10.1007/978-1-0716-2481-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.
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Affiliation(s)
- Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
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20
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Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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21
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Inagaki S. Silencing and anti-silencing mechanisms that shape the epigenome in plants. Genes Genet Syst 2021; 96:217-228. [PMID: 34719532 DOI: 10.1266/ggs.21-00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Epigenome information mediates genome function and maintenance by regulating gene expression and chromatin organization. Because the epigenome pattern can change in response to internal and external environments, it may underlie an adaptive genome response that modulates phenotypes during development and in changing environments. Here I summarize recent progress in our understanding of how epigenome patterns are shaped and modulated by concerted actions of silencing and anti-silencing factors mainly in Arabidopsis thaliana. I discuss the dynamic nature of epigenome regulation, which is realized by cooperation and counteraction among silencing and anti-silencing factors, and how the dynamic epigenome mediates robust and plastic responses of plants to fluctuating environments.
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Affiliation(s)
- Soichi Inagaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo.,PRESTO, Japan Science and Technology Agency
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22
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Miyagishima SY, Tanaka K. The Unicellular Red Alga Cyanidioschyzon merolae-The Simplest Model of a Photosynthetic Eukaryote. PLANT & CELL PHYSIOLOGY 2021; 62:926-941. [PMID: 33836072 PMCID: PMC8504449 DOI: 10.1093/pcp/pcab052] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 05/13/2023]
Abstract
Several species of unicellular eukaryotic algae exhibit relatively simple genomic and cellular architecture. Laboratory cultures of these algae grow faster than plants and often provide homogeneous cellular populations exposed to an almost equal environment. These characteristics are ideal for conducting experiments at the cellular and subcellular levels. Many microalgal lineages have recently become genetically tractable, which have started to evoke new streams of studies. Among such algae, the unicellular red alga Cyanidioschyzon merolae is the simplest organism; it possesses the minimum number of membranous organelles, only 4,775 protein-coding genes in the nucleus, and its cell cycle progression can be highly synchronized with the diel cycle. These properties facilitate diverse omics analyses of cellular proliferation and structural analyses of the intracellular relationship among organelles. C. merolae cells lack a rigid cell wall and are thus relatively easily disrupted, facilitating biochemical analyses. Multiple chromosomal loci can be edited by highly efficient homologous recombination. The procedures for the inducible/repressive expression of a transgene or an endogenous gene in the nucleus and for chloroplast genome modification have also been developed. Here, we summarize the features and experimental techniques of C. merolae and provide examples of studies using this alga. From these studies, it is clear that C. merolae-either alone or in comparative and combinatory studies with other photosynthetic organisms-can provide significant insights into the biology of photosynthetic eukaryotes.
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Affiliation(s)
- Shin-Ya Miyagishima
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
| | - Kan Tanaka
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
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23
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Rommelfanger S, Zhou M, Shaghasi H, Tzeng SC, Evans BS, Paša-Tolić L, Umen JG, Pesavento JJ. An Improved Top-Down Mass Spectrometry Characterization of Chlamydomonas reinhardtii Histones and Their Post-translational Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1671-1688. [PMID: 34165968 PMCID: PMC9236284 DOI: 10.1021/jasms.1c00029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/01/2023]
Abstract
We present an updated analysis of the linker and core histone proteins and their proteoforms in the green microalga Chlamydomonas reinhardtii by top-down mass spectrometry (TDMS). The combination of high-resolution liquid chromatographic separation, robust fragmentation, high mass spectral resolution, the application of a custom search algorithm, and extensive manual analysis enabled the characterization of 86 proteoforms across all four core histones H2A, H2B, H3, and H4 and the linker histone H1. All canonical H2A paralogs, which vary in their C-termini, were identified, along with the previously unreported noncanonical variant H2A.Z that had high levels of acetylation and C-terminal truncations. Similarly, a majority of the canonical H2B paralogs were identified, along with a smaller noncanonical variant, H2B.v1, that was highly acetylated. Histone H4 exhibited a novel acetylation profile that differs significantly from that found in other organisms. A majority of H3 was monomethylated at K4 with low levels of co-occuring acetylation, while a small fraction of H3 was trimethylated at K4 with high levels of co-occuring acetylation.
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Affiliation(s)
- Sarah
R. Rommelfanger
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
- Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Henna Shaghasi
- Saint
Mary’s College of California, Moraga, California 94575, United States
| | - Shin-Cheng Tzeng
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
| | - Bradley S. Evans
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
| | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - James G. Umen
- Donald
Danforth Plant Science Center, St. Louis, Missouri 63132, United States
- Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - James J. Pesavento
- Saint
Mary’s College of California, Moraga, California 94575, United States
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Déléris A, Berger F, Duharcourt S. Role of Polycomb in the control of transposable elements. Trends Genet 2021; 37:882-889. [PMID: 34210514 DOI: 10.1016/j.tig.2021.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 01/12/2023]
Abstract
It is generally considered that Polycomb Repressive Complex (PRC)2 deposits the histone mark H3K27me3 on silent protein-coding genes, while transposable elements are repressed by DNA and/or H3K9 methylation. Yet, there is increasing evidence that PRC2 also targets and even silences transposable elements in representatives of several distantly related eukaryotic lineages. In plants and animals, H3K27me3 is present on transposable elements in mutants and specific cell types devoid of DNA methylation. In this Opinion, we summarize the experimental evidence for this phenomenon across the eukaryotic kingdom, and discuss its functional and evolutionary significance. We hypothesize that an ancestral role of Polycomb group (PcG) proteins was to silence transposable elements.
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Affiliation(s)
- Angélique Déléris
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Sandra Duharcourt
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
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25
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Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. Proc Natl Acad Sci U S A 2021; 118:2009974118. [PMID: 33419955 DOI: 10.1073/pnas.2009974118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.
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26
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Rastogi A, Lin X, Lombard B, Loew D, Tirichine L. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms. AIMS GENETICS 2021. [DOI: 10.3934/genet.2015.3.173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractRecent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epigenetic features found in mammals and plants suggesting their ancient origin. Phaeodactylum tricornutum and Thalassiosira pseudonana, pennate and centric diatoms, respectively, emerged as model species to address questions on the evolution of epigenetic phenomena such as what has been lost, retained or has evolved in contemporary species. In the present work, we will discuss how the study of non-model or emerging model organisms, such as diatoms, helps understand the evolutionary history of epigenetic mechanisms with a particular focus on DNA methylation and histone modifications.
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Affiliation(s)
- Achal Rastogi
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
| | - Xin Lin
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Leïla Tirichine
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
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27
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Carlier F, Li M, Maroc L, Debuchy R, Souaid C, Noordermeer D, Grognet P, Malagnac F. Loss of EZH2-like or SU(VAR)3-9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina. Epigenetics Chromatin 2021; 14:22. [PMID: 33962663 PMCID: PMC8105982 DOI: 10.1186/s13072-021-00395-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Selective gene silencing is key to development. It is generally accepted that H3K27me3-enriched heterochromatin maintains transcriptional repression established during early development and regulates cell fate. Conversely, H3K9me3-enriched heterochromatin prevents differentiation but constitutes protection against transposable elements. We exploited the fungus Podospora anserina, a valuable alternative to higher eukaryote models, to question the biological relevance and functional interplay of these two distinct heterochromatin conformations. RESULTS We established genome-wide patterns of H3K27me3 and H3K9me3 modifications, and found these marks mutually exclusive within gene-rich regions but not within repeats. We generated the corresponding histone methyltransferase null mutants and showed an interdependence of H3K9me3 and H3K27me3 marks. Indeed, removal of the PaKmt6 EZH2-like enzyme resulted not only in loss of H3K27me3 but also in significant H3K9me3 reduction. Similarly, removal of PaKmt1 SU(VAR)3-9-like enzyme caused loss of H3K9me3 and substantial decrease of H3K27me3. Removal of the H3K9me binding protein PaHP1 provided further support to the notion that each type of heterochromatin requires the presence of the other. We also established that P. anserina developmental programs require H3K27me3-mediated silencing, since loss of the PaKmt6 EZH2-like enzyme caused severe defects in most aspects of the life cycle including growth, differentiation processes and sexual reproduction, whereas loss of the PaKmt1 SU(VAR)3-9-like enzyme resulted only in marginal defects, similar to loss of PaHP1. CONCLUSIONS Our findings support a conserved function of the PRC2 complex in fungal development. However, we uncovered an intriguing evolutionary fluidity in the repressive histone deposition machinery, which challenges canonical definitions of constitutive and facultative heterochromatin.
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Affiliation(s)
- F Carlier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
- Group Fungal Epigenomics, Department of Mycology, Institut Pasteur, Paris, France
| | - M Li
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - L Maroc
- Génétique Quantitative et Évolution-Le Moulon, INRA-Université Paris-Saclay-CNRS-AgroParisTech, Batiment 400, UFR Des Sciences, 91405, Orsay CEDEX, France
| | - R Debuchy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - C Souaid
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
- Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, Aix-Marseille University, 13288, Marseille, France
| | - D Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - P Grognet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
| | - F Malagnac
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
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28
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Zhao X, Rastogi A, Deton Cabanillas AF, Ait Mohamed O, Cantrel C, Lombard B, Murik O, Genovesio A, Bowler C, Bouyer D, Loew D, Lin X, Veluchamy A, Vieira FRJ, Tirichine L. Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2021; 229:3208-3220. [PMID: 33533496 DOI: 10.1111/nph.17129] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/24/2020] [Indexed: 05/28/2023]
Abstract
In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.
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Affiliation(s)
- Xue Zhao
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
- CNRS UMR6286, UFIP UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière 44322, Nantes Cedex 03, France
| | - Achal Rastogi
- Corteva AgriscienceTM, Ascendas IT Park, 12th floor, Atria, V, Madhapur, Telangana, 500081, India
| | - Anne Flore Deton Cabanillas
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Ouardia Ait Mohamed
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Catherine Cantrel
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Berangère Lombard
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, PSL Research University, 26 rue d'Ulm, Cedex 05 Paris, 75248, France
| | - Omer Murik
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Auguste Genovesio
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Daniel Bouyer
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, PSL Research University, 26 rue d'Ulm, Cedex 05 Paris, 75248, France
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, Centre de Recherche, College of Ocean Camp; Earth Sciences,, Xiamen University, Xiamen, 361102, China
| | - Alaguraj Veluchamy
- Laboratory of Chromatin Biochemistry, 4700 King Abdullah University of Science and Technology (KAUST), BESE Division Building 2, Level 3, Office B2-3327, Thuwal, 23955-6900, Saudi Arabia
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Leila Tirichine
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
- CNRS UMR6286, UFIP UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière 44322, Nantes Cedex 03, France
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29
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Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum. Sci Rep 2021; 11:2954. [PMID: 33536552 PMCID: PMC7859220 DOI: 10.1038/s41598-021-82529-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/15/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.
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30
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Annunziata R, Balestra C, Marotta P, Ruggiero A, Manfellotto F, Benvenuto G, Biffali E, Ferrante MI. An optimised method for intact nuclei isolation from diatoms. Sci Rep 2021; 11:1681. [PMID: 33462289 PMCID: PMC7813820 DOI: 10.1038/s41598-021-81238-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 12/22/2020] [Indexed: 01/21/2023] Open
Abstract
Due to their abundance in the oceans, their extraordinary biodiversity and the increasing use for biotech applications, the study of diatom biology is receiving more and more attention in the recent years. One of the limitations in developing molecular tools for diatoms lies in the peculiar nature of their cell wall, that is made of silica and organic molecules and that hinders the application of standard methods for cell lysis required, for example, to extract organelles. In this study we present a protocol for intact nuclei isolation from diatoms that was successfully applied to three different species: two pennates, Pseudo-nitzschia multistriata and Phaeodactylum tricornutum, and one centric diatom species, Chaetoceros diadema. Intact nuclei were extracted by treatment with acidified NH4F solution combined to low intensity sonication pulses and separated from cell debris via FAC-sorting upon incubation with SYBR Green. Microscopy observations confirmed the integrity of isolated nuclei and high sensitivity DNA electrophoresis showed that genomic DNA extracted from isolated nuclei has low degree of fragmentation. This protocol has proved to be a flexible and versatile method to obtain intact nuclei preparations from different diatom species and it has the potential to speed up applications such as epigenetic explorations as well as single cell ("single nuclei") genomics, transcriptomics and proteomics in different diatom species.
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Affiliation(s)
| | | | - Pina Marotta
- Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
| | | | | | | | - Elio Biffali
- Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
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31
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Wong JM, Hofmann GE. Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO 2 during early development. BMC Genomics 2021; 22:32. [PMID: 33413121 PMCID: PMC7792118 DOI: 10.1186/s12864-020-07327-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The red sea urchin Mesocentrotus franciscanus is an ecologically important kelp forest herbivore and an economically valuable wild fishery species. To examine how M. franciscanus responds to its environment on a molecular level, differences in gene expression patterns were observed in embryos raised under combinations of two temperatures (13 °C or 17 °C) and two pCO2 levels (475 μatm or 1050 μatm). These combinations mimic various present-day conditions measured during and between upwelling events in the highly dynamic California Current System with the exception of the 17 °C and 1050 μatm combination, which does not currently occur. However, as ocean warming and acidification continues, warmer temperatures and higher pCO2 conditions are expected to increase in frequency and to occur simultaneously. The transcriptomic responses of the embryos were assessed at two developmental stages (gastrula and prism) in light of previously described plasticity in body size and thermotolerance under these temperature and pCO2 treatments. RESULTS Although transcriptomic patterns primarily varied by developmental stage, there were pronounced differences in gene expression as a result of the treatment conditions. Temperature and pCO2 treatments led to the differential expression of genes related to the cellular stress response, transmembrane transport, metabolic processes, and the regulation of gene expression. At each developmental stage, temperature contributed significantly to the observed variance in gene expression, which was also correlated to the phenotypic attributes of the embryos. On the other hand, the transcriptomic response to pCO2 was relatively muted, particularly at the prism stage. CONCLUSIONS M. franciscanus exhibited transcriptomic plasticity under different temperatures, indicating their capacity for a molecular-level response that may facilitate red sea urchins facing ocean warming as climate change continues. In contrast, the lack of a robust transcriptomic response, in combination with observations of decreased body size, under elevated pCO2 levels suggest that this species may be negatively affected by ocean acidification. High present-day pCO2 conditions that occur due to coastal upwelling may already be influencing populations of M. franciscanus.
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Affiliation(s)
- Juliet M Wong
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
- Present address: Department of Biological Sciences, Florida International University, North Miami, FL, 33181, USA.
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
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32
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Bourdareau S, Tirichine L, Lombard B, Loew D, Scornet D, Wu Y, Coelho SM, Cock JM. Histone modifications during the life cycle of the brown alga Ectocarpus. Genome Biol 2021; 22:12. [PMID: 33397407 PMCID: PMC7784034 DOI: 10.1186/s13059-020-02216-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 12/02/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. RESULTS A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. CONCLUSIONS The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.
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Affiliation(s)
- Simon Bourdareau
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Leila Tirichine
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Paris, Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Paris, Cedex 05, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Yue Wu
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
- Current address: Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
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33
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Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M, Bouzayen M. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. THE NEW PHYTOLOGIST 2021; 229:902-919. [PMID: 32875585 PMCID: PMC7821339 DOI: 10.1111/nph.16902] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 05/10/2023]
Abstract
Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower-to-fruit transition remains poor. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.
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Affiliation(s)
- Guojian Hu
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Baowen Huang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Keke Wang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Pierre Frasse
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Elie Maza
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Anis Djari
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐SaclayCNRSINRAUniversity Paris‐SudUniversity of EvryUniversity Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayBatiment 630Orsay91405France
| | - Philippe Gallusci
- UMR EGFVBordeaux Sciences AgroINRAUniversité de Bordeaux210 Chemin de Leysotte, CS 50008Villenave d’Ornon33882France
| | - Zhengguo Li
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
| | - Mohamed Zouine
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Mondher Bouzayen
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
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Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
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Genome-wide identification and transcriptional modulation of histone variants and modification related genes in the low pH-exposed marine rotifer Brachionus koreanus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100748. [PMID: 33032078 DOI: 10.1016/j.cbd.2020.100748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/05/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Histone modification is considered to be a major epigenetic control mechanism. These modifications (e.g. acetylation, phosphorylation, and methylation) may affect the interaction of histones with DNA and/or regulate DNA-based processes (e.g., recombination, repair, replication, and transcription) and chromatin remodeling complexes. Despite their significance in metazoan life and evolution, few studies have been conducted to identify genes undergoing epigenetic control modification in aquatic invertebrates. In this study, we identified whole core histones (70 total genes) and post-translational modification (PTM) histone genes (63 total genes) in the marine rotifer Brachionus koreanus through whole-genome analysis, and annotated them according to the human nomenclature. Notably, upon comparative analysis of cis-regulatory motif sequences, we found that B. koreanus core histone protein structures were similar to those of mammals. Furthermore, to examine the effect of parental low pH stress on the offspring's epigenetic regulation, we investigated the expression of PTM genes in two generations of B. koreanus exposed to low pH conditions. Given that the B. koreanus genome does not possess DNA methyltransferase 1 and 3 genes, we concluded that histone genes could be involved as an important epigenetic mechanism in B. koreanus. Therefore, the histone-associated genes identified in this study could be useful for ecotoxicological studies and facilitate the application of chromatin immunoprecipitation sequencing using high-throughput DNA sequencing based on the genome-wide identification of transcription factor binding sites in rotifers.
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Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. THE PLANT CELL 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
Abstract
Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
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Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, Akimcheva S, Bowman JL, Cognat V, Maréchal-Drouard L, Ekker H, Hong SF, Kohchi T, Lin SS, Liu LYD, Nakamura Y, Valeeva LR, Shakirov EV, Shippen DE, Wei WL, Yagura M, Yamaoka S, Yamato KT, Liu C, Berger F. Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Curr Biol 2020; 30:573-588.e7. [PMID: 32004456 PMCID: PMC7209395 DOI: 10.1016/j.cub.2019.12.015] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Genome packaging by nucleosomes is a hallmark of eukaryotes. Histones and the pathways that deposit, remove, and read histone modifications are deeply conserved. Yet, we lack information regarding chromatin landscapes in extant representatives of ancestors of the main groups of eukaryotes, and our knowledge of the evolution of chromatin-related processes is limited. We used the bryophyte Marchantia polymorpha, which diverged from vascular plants circa 400 mya, to obtain a whole chromosome genome assembly and explore the chromatin landscape and three-dimensional genome organization in an early diverging land plant lineage. Based on genomic profiles of ten chromatin marks, we conclude that the relationship between active marks and gene expression is conserved across land plants. In contrast, we observed distinctive features of transposons and other repetitive sequences in Marchantia compared with flowering plants. Silenced transposons and repeats did not accumulate around centromeres. Although a large fraction of constitutive heterochromatin was marked by H3K9 methylation as in flowering plants, a significant proportion of transposons were marked by H3K27me3, which is otherwise dedicated to the transcriptional repression of protein-coding genes in flowering plants. Chromatin compartmentalization analyses of Hi-C data revealed that repressed B compartments were densely decorated with H3K27me3 but not H3K9 or DNA methylation as reported in flowering plants. We conclude that, in early plants, H3K27me3 played an essential role in heterochromatin function, suggesting an ancestral role of this mark in transposon silencing.
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Affiliation(s)
- Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Bence Galik
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Tasuku Ito
- John Innes Centre, Colney lane, Norwich NR4 7UH, UK
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Svetlana Akimcheva
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, 3800 VIC, Australia
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Laurence Maréchal-Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Heinz Ekker
- Vienna BioCenter Core Facilities (VBCF), Next Generation Sequencing facility, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Li-Yu Daisy Liu
- Department of Agronomy, National Taiwan University, Taipei 106, Taiwan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Lia R Valeeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Republic of Tatarstan 420008, Russia
| | - Eugene V Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Republic of Tatarstan 420008, Russia; Department of Biological Sciences, Marshall University, Huntington, WV 25701, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Wei-Lun Wei
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Masaru Yagura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria.
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Rastogi A, Vieira FRJ, Deton-Cabanillas AF, Veluchamy A, Cantrel C, Wang G, Vanormelingen P, Bowler C, Piganeau G, Hu H, Tirichine L. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum. THE ISME JOURNAL 2020; 14:347-363. [PMID: 31624346 PMCID: PMC6976637 DOI: 10.1038/s41396-019-0528-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022]
Abstract
Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.
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Affiliation(s)
- Achal Rastogi
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Corteva Agriscience™, The V Ascendas, Atria Block, 12th Floor, Madhapur, Hyderabad, 500081, India
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Alaguraj Veluchamy
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Catherine Cantrel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Pieter Vanormelingen
- Department of Biology, Research Group Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281/S8 9000, Gent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gwenael Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China.
| | - Leila Tirichine
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France.
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Butler T, Kapoore RV, Vaidyanathan S. Phaeodactylum tricornutum: A Diatom Cell Factory. Trends Biotechnol 2020; 38:606-622. [PMID: 31980300 DOI: 10.1016/j.tibtech.2019.12.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
A switch from a petroleum-based to a biobased economy requires the capacity to produce both high-value low-volume and low-value high-volume products. Recent evidence supports the development of microalgae-based microbial cell factories with the objective of establishing environmentally sustainable manufacturing solutions. Diatoms display rich diversity and potential in this regard. We focus on Phaeodactylum tricornutum, a pennate diatom that is commonly found in marine ecosystems, and discuss recent trends in developing the diatom chassis for the production of a suite of natural and genetically engineered products. Both upstream and downstream developments are reviewed for the commercial development of P. tricornutum as a cell factory for a spectrum of marketable products.
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Affiliation(s)
- Thomas Butler
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK
| | - Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK; Present address: Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Seetharaman Vaidyanathan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK.
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Ait-Mohamed O, Novák Vanclová AMG, Joli N, Liang Y, Zhao X, Genovesio A, Tirichine L, Bowler C, Dorrell RG. PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:590949. [PMID: 33178253 PMCID: PMC7596299 DOI: 10.3389/fpls.2020.590949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 05/04/2023]
Abstract
Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.
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Affiliation(s)
- Ouardia Ait-Mohamed
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anna M. G. Novák Vanclová
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Nathalie Joli
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Yue Liang
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Xue Zhao
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
| | - Auguste Genovesio
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
- *Correspondence: Leila Tirichine,
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Chris Bowler,
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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41
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Ayyappan V, Sripathi VR, Kalavacharla V(K, Saha MC, Thimmapuram J, Bhide KP, Fiedler E. Genome-wide identification of histone methylation (H3K9 me2) and acetylation (H4K12 ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). BMC Genomics 2019; 20:667. [PMID: 31438854 PMCID: PMC6704705 DOI: 10.1186/s12864-019-6038-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/16/2019] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. RESULTS This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. CONCLUSIONS The genome-wide histone modifications reported here can be utilized in understanding the regulation of genes important in the phenylpropanoid-monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
| | - Venkateswara R. Sripathi
- Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL USA
| | - Venu ( Kal) Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE USA
| | | | | | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN USA
| | - Elizabeth Fiedler
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
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Abstract
As the process that silences gene expression ensues during development, the stage is set for the activity of Polycomb-repressive complex 2 (PRC2) to maintain these repressed gene profiles. PRC2 catalyzes a specific histone posttranslational modification (hPTM) that fosters chromatin compaction. PRC2 also facilitates the inheritance of this hPTM through its self-contained "write and read" activities, key to preserving cellular identity during cell division. As these changes in gene expression occur without changes in DNA sequence and are inherited, the process is epigenetic in scope. Mutants of mammalian PRC2 or of its histone substrate contribute to the cancer process and other diseases, and research into these aberrant pathways is yielding viable candidates for therapeutic targeting. The effectiveness of PRC2 hinges on its being recruited to the proper chromatin sites; however, resolving the determinants to this process in the mammalian case was not straightforward and thus piqued the interest of many in the field. Here, we chronicle the latest advances toward exposing mammalian PRC2 and its high maintenance.
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Affiliation(s)
- Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ozgur Oksuz
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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43
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Frapporti A, Miró Pina C, Arnaiz O, Holoch D, Kawaguchi T, Humbert A, Eleftheriou E, Lombard B, Loew D, Sperling L, Guitot K, Margueron R, Duharcourt S. The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium. Nat Commun 2019; 10:2710. [PMID: 31221974 PMCID: PMC6586856 DOI: 10.1038/s41467-019-10648-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/23/2019] [Indexed: 01/11/2023] Open
Abstract
In animals and plants, the H3K9me3 and H3K27me3 chromatin silencing marks are deposited by different protein machineries. H3K9me3 is catalyzed by the SET-domain SU(VAR)3-9 enzymes, while H3K27me3 is catalyzed by the SET-domain Enhancer-of-zeste enzymes, which are the catalytic subunits of Polycomb Repressive Complex 2 (PRC2). Here, we show that the Enhancer-of-zeste-like protein Ezl1 from the unicellular eukaryote Paramecium tetraurelia, which exhibits significant sequence and structural similarities with human EZH2, catalyzes methylation of histone H3 in vitro and in vivo with an apparent specificity toward K9 and K27. We find that H3K9me3 and H3K27me3 co-occur at multiple families of transposable elements in an Ezl1-dependent manner. We demonstrate that loss of these histone marks results in global transcriptional hyperactivation of transposable elements with modest effects on protein-coding gene expression. Our study suggests that although often considered functionally distinct, H3K9me3 and H3K27me3 may share a common evolutionary history as well as a common ancestral role in silencing transposable elements.
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Affiliation(s)
- Andrea Frapporti
- Institut Jacques Monod, Université de Paris, CNRS, 75013, Paris, France
- The Gurdon Institute, University of Cambridge, Cambridge, CB21QN, UK
| | - Caridad Miró Pina
- Institut Jacques Monod, Université de Paris, CNRS, 75013, Paris, France
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette CEDEX, France
| | - Daniel Holoch
- Institut Curie, Paris Sciences et Lettres Research University, INSERM, U934, CNRS, UMR3215, Paris, 75005, France
| | | | - Adeline Humbert
- Institut Jacques Monod, Université de Paris, CNRS, 75013, Paris, France
| | - Evangelia Eleftheriou
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette CEDEX, France
| | - Bérangère Lombard
- Institut Curie, Paris Sciences et Lettres Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France
| | - Damarys Loew
- Institut Curie, Paris Sciences et Lettres Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette CEDEX, France
| | - Karine Guitot
- Sorbonne Université, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Raphaël Margueron
- Institut Curie, Paris Sciences et Lettres Research University, INSERM, U934, CNRS, UMR3215, Paris, 75005, France
| | - Sandra Duharcourt
- Institut Jacques Monod, Université de Paris, CNRS, 75013, Paris, France.
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44
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Abstract
Epigenetic gene regulation ensures the mitotically or meiotically stable heritability (or both) of gene expression or protein activity states and maintains repetitive element repression and cellular identities. The repressive Polycomb-group (PcG) proteins consist of several large complexes that control cellular memory by acting on chromatin and are antagonized by the Trithorax-group proteins. Especially, Polycomb repressive complex 2 (PRC2) is highly conserved in plants and animals but its function in unicellular eukaryotes and during land plant evolution is less understood. Additional PcG complexes and associated proteins are only partially conserved and have evolved in a lineage-specific manner. In this review, I will focus on recent advances in the understanding of PcG function in the green lineage and its contribution to land plant evolution.
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Affiliation(s)
- Daniel Schubert
- Department of Biology, Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
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45
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Huang R, Ding J, Gao K, Cruz de Carvalho MH, Tirichine L, Bowler C, Lin X. A Potential Role for Epigenetic Processes in the Acclimation Response to Elevated pCO 2 in the Model Diatom Phaeodactylum tricornutum. Front Microbiol 2019; 9:3342. [PMID: 30692981 PMCID: PMC6340190 DOI: 10.3389/fmicb.2018.03342] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/27/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.
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Affiliation(s)
- Ruiping Huang
- State Key Laboratory of Marine Environmental Science,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jiancheng Ding
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Maria Helena Cruz de Carvalho
- Ecology and Evolutionary Biology Section, Institut de Biologie de l’École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS UMR8197, Inserm U1024, PSL Research University, Paris, France
- Faculté des Sciences et Technologie, Université Paris Est-Créteil, Créteil, France
| | - Leila Tirichine
- Faculté des Sciences et Techniques, Université de Nantes, CNRS UMR6286, UFIP, Nantes, France
| | - Chris Bowler
- Ecology and Evolutionary Biology Section, Institut de Biologie de l’École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS UMR8197, Inserm U1024, PSL Research University, Paris, France
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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46
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Abstract
Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
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Affiliation(s)
- Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Center for Coastal Oceans Research, Institute for Water and Environment, Florida International University, North Miami, Florida 33181, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
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47
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Hovde BT, Hanschen ER, Steadman Tyler CR, Lo CC, Kunde Y, Davenport K, Daligault H, Msanne J, Canny S, Eyun SI, Riethoven JJM, Polle J, Starkenburg SR. Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae). ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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48
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Yang M, Lin X, Liu X, Zhang J, Ge F. Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline. MOLECULAR PLANT 2018; 11:1292-1307. [PMID: 30176371 DOI: 10.1016/j.molp.2018.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the development of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry (MS)-based proteomics data. Our proteogenomic analysis unambiguously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricornutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https://sourceforge.net/projects/gapeproteogenomic.
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Affiliation(s)
- Mingkun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xin Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jia Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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49
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Wei L, Xu J. Optimized methods of chromatin immunoprecipitation for profiling histone modifications in industrial microalgae Nannochloropsis spp. JOURNAL OF PHYCOLOGY 2018; 54:358-367. [PMID: 29444334 DOI: 10.1111/jpy.12623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
Epigenetic factors such as histone modifications play integral roles in plant development and stress response, yet their implications in algae remain poorly understood. In the industrial oleaginous microalgae Nannochloropsis spp., the lack of an efficient methodology for chromatin immunoprecipitation (ChIP), which determines the specific genomic location of various histone modifications, has hindered probing the epigenetic basis of their photosynthetic carbon conversion and storage as oil. Here, a detailed ChIP protocol was developed for Nannochloropsis oceanica, which represents a reliable approach for the analysis of histone modifications, chromatin state, and transcription factor-binding sites at the epigenetic level. Using ChIP-qPCR, genes related to photosynthetic carbon fixation in this microalga were systematically assessed. Furthermore, a ChIP-Seq protocol was established and optimized, which generated a genome-wide profile of histone modification events, using histone mark H3K9Ac as an example. These results are the first step for appreciation of the chromatin landscape in industrial oleaginous microalgae and for epigenetics-based microalgal feedstock development.
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Affiliation(s)
- Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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50
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Benoiston AS, Ibarbalz FM, Bittner L, Guidi L, Jahn O, Dutkiewicz S, Bowler C. The evolution of diatoms and their biogeochemical functions. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0397. [PMID: 28717023 DOI: 10.1098/rstb.2016.0397] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 11/12/2022] Open
Abstract
In contemporary oceans diatoms are an important group of eukaryotic phytoplankton that typically dominate in upwelling regions and at high latitudes. They also make significant contributions to sporadic blooms that often occur in springtime. Recent surveys have revealed global information about their abundance and diversity, as well as their contributions to biogeochemical cycles, both as primary producers of organic material and as conduits facilitating the export of carbon and silicon to the ocean interior. Sequencing of diatom genomes is revealing the evolutionary underpinnings of their ecological success by examination of their gene repertoires and the mechanisms they use to adapt to environmental changes. The rise of the diatoms over the last hundred million years is similarly being explored through analysis of microfossils and biomarkers that can be traced through geological time, as well as their contributions to seafloor sediments and fossil fuel reserves. The current review aims to synthesize current information about the evolution and biogeochemical functions of diatoms as they rose to prominence in the global ocean.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Anne-Sophie Benoiston
- Sorbonne Universités, UPMC Univ. Paris 06, Univ. Antilles, Univ. Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Federico M Ibarbalz
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris, France
| | - Lucie Bittner
- Sorbonne Universités, UPMC Univ. Paris 06, Univ. Antilles, Univ. Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Lionel Guidi
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV) UMR7093, Observatoire Océanologique, 06230 Villefranche-sur-Mer, France.,Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Oliver Jahn
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54-1514 MIT, Cambridge, MA 02139, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54-1514 MIT, Cambridge, MA 02139, USA
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris, France
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