1
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Ando T, Fukuda S, Ngo KX, Flechsig H. High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action. Annu Rev Biophys 2024; 53:19-39. [PMID: 38060998 DOI: 10.1146/annurev-biophys-030722-113353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Structural biology is currently undergoing a transformation into dynamic structural biology, which reveals the dynamic structure of proteins during their functional activity to better elucidate how they function. Among the various approaches in dynamic structural biology, high-speed atomic force microscopy (HS-AFM) is unique in the ability to film individual molecules in dynamic action, although only topographical information is acquirable. This review provides a guide to the use of HS-AFM for biomolecular imaging and showcases several examples, as well as providing information on up-to-date progress in HS-AFM technology. Finally, we discuss the future prospects of HS-AFM in the context of dynamic structural biology in the upcoming era.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Kien X Ngo
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan;
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2
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Liu Y, Zhan J, Li J, Lian M, Li J, Xia C, Zhou F, Xie W. Characterization of the DNA accessibility of chloroplast genomes in grasses. Commun Biol 2024; 7:760. [PMID: 38909165 PMCID: PMC11193712 DOI: 10.1038/s42003-024-06374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/23/2024] [Indexed: 06/24/2024] Open
Abstract
Although the chloroplast genome (cpDNA) of higher plants is known to exist as a large protein-DNA complex called 'plastid nucleoid', researches on its DNA state and regulatory elements are limited. In this study, we performed the assay for transposase-accessible chromatin sequencing (ATAC-seq) on five common tissues across five grasses, and found that the accessibility of different regions in cpDNA varied widely, with the transcribed regions being highly accessible and accessibility patterns around gene start and end sites varying depending on the level of gene expression. Further analysis identified a total of 3970 putative protein binding footprints on cpDNAs of five grasses. These footprints were enriched in intergenic regions and co-localized with known functional elements. Footprints and their flanking accessibility varied dynamically among tissues. Cross-species analysis showed that footprints in coding regions tended to overlap non-degenerate sites and contain a high proportion of highly conserved sites, indicating that they are subject to evolutionary constraints. Taken together, our results suggest that the accessibility of cpDNA has biological implications and provide new insights into the transcriptional regulation of chloroplasts.
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Affiliation(s)
- Yinmeng Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430000, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China
| | - Jinling Zhan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430000, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China
| | - Junjie Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430000, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China
| | - Mengjie Lian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430000, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China
| | - Jiacheng Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430000, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China
| | - Chunjiao Xia
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430000, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430000, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430000, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430000, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430000, China.
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3
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Zhang D, Xu S, Luo Z, Lin Z. MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions. Nat Commun 2024; 15:5140. [PMID: 38886375 PMCID: PMC11183143 DOI: 10.1038/s41467-024-49490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Holliday junction resolution is a crucial process in homologous recombination and DNA double-strand break repair. Complete Holliday junction resolution requires two stepwise incisions across the center of the junction, but the precise mechanism of metal ion-catalyzed Holliday junction cleavage remains elusive. Here, we perform a metal ion-triggered catalysis in crystals to investigate the mechanism of Holliday junction cleavage by MOC1. We capture the structures of MOC1 in complex with a nicked Holliday junction at various catalytic states, including the ground state, the one-metal ion binding state, and the two-metal ion binding state. Moreover, we also identify a third metal ion that may aid in the nucleophilic attack on the scissile phosphate. Further structural and biochemical analyses reveal a metal ion-mediated allosteric regulation between the two active sites, contributing to the enhancement of the second strand cleavage following the first strand cleavage, as well as the precise symmetric cleavage across the Holliday junction. Our work provides insights into the mechanism of metal ion-catalyzed Holliday junction resolution by MOC1, with implications for understanding how cells preserve genome integrity during the Holliday junction resolution phase.
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Affiliation(s)
- Danping Zhang
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Shenjie Xu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, 215123, China
| | - Zhipu Luo
- MOE Key Laboratory of Geriatric Diseases and Immunology, Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, 215123, China.
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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4
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Nishimura Y. Plastid Nucleoids: Insights into Their Shape and Dynamics. PLANT & CELL PHYSIOLOGY 2024; 65:551-559. [PMID: 37542434 DOI: 10.1093/pcp/pcad090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/07/2023]
Abstract
Chloroplasts/plastids are unique organelles found in plant cells and some algae and are responsible for performing essential functions such as photosynthesis. The plastid genome, consisting of circular and linear DNA molecules, is packaged and organized into specialized structures called nucleoids. The composition and dynamics of these nucleoids have been the subject of intense research, as they are critical for proper plastid functions and development. In this mini-review, recent advances in understanding the organization and regulation of plastid nucleoids are overviewed, with a focus on the various proteins and factors that regulate the shape and dynamics of nucleoids, including DNA-binding proteins and membrane anchorage proteins. The dynamic nature of nucleoid organization, which is influenced by a variety of developmental cues and the cell cycle, is also examined.
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Affiliation(s)
- Yoshiki Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kita-Shirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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5
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Sivakrishna
Rao G, Saleh AH, Melliti F, Muntjeeb S, Mahfouz M. Harnessing Peptide Nucleic Acids and the Eukaryotic Resolvase MOC1 for Programmable, Precise Generation of Double-Strand DNA Breaks. Anal Chem 2024; 96:2599-2609. [PMID: 38300270 PMCID: PMC10867802 DOI: 10.1021/acs.analchem.3c05133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Programmable site-specific nucleases (SSNs) hold extraordinary promise to unlock myriad gene editing applications in medicine and agriculture. However, developing small and specific SSNs is needed to overcome the delivery and specificity translational challenges of current genome engineering technologies. Structure-guided nucleases have been harnessed to generate double-strand DNA breaks but with limited success and translational potential. Here, we harnessed the power of peptide nucleic acids (PNAs) for site-specific DNA invasion and the generation of localized DNA structures that are recognized and cleaved by the eukaryotic resolvase AtMOC1 from Arabidopsis thaliana. We named this technology PNA-assisted Resolvase-mediated (PNR) editing. We tested the PNR editing concept in vitro and demonstrated its precise target specificity, examined the nucleotide requirement around the PNA invasion for the AtMOC1-mediated cleavage, mapped the AtMOC1-mediated cleavage sites, tested the role of different types and lengths of PNA molecules invasion into dsDNA for the AtMOC1-mediated cleavage, optimized the in vitro PNA invasion and AtMOC1 cleavage conditions such as temperature, buffer conditions, and cleavage time points, and demonstrated the multiplex cleavage for precise fragment release. We discuss the best design parameters for efficient, site-specific in vitro cleavage using PNR editors.
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Affiliation(s)
- Gundra Sivakrishna
Rao
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Ahmed H. Saleh
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Firdaws Melliti
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Syed Muntjeeb
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Magdy Mahfouz
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
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6
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Zhang W, Yang Z, Wang W, Sun Q. Primase promotes the competition between transcription and replication on the same template strand resulting in DNA damage. Nat Commun 2024; 15:73. [PMID: 38168108 PMCID: PMC10761990 DOI: 10.1038/s41467-023-44443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Transcription-replication conflicts (TRCs), especially Head-On TRCs (HO-TRCs) can introduce R-loops and DNA damage, however, the underlying mechanisms are still largely unclear. We previously identified a chloroplast-localized RNase H1 protein AtRNH1C that can remove R-loops and relax HO-TRCs for genome integrity. Through the mutagenesis screen, we identify a mutation in chloroplast-localized primase ATH that weakens the binding affinity of DNA template and reduces the activities of RNA primer synthesis and delivery. This slows down DNA replication, and reduces competition of transcription-replication, thus rescuing the developmental defects of atrnh1c. Strand-specific DNA damage sequencing reveals that HO-TRCs cause DNA damage at the end of the transcription unit in the lagging strand and overexpression of ATH can boost HO-TRCs and exacerbates DNA damage. Furthermore, mutation of plastid DNA polymerase Pol1A can similarly rescue the defects in atrnh1c mutants. Taken together these results illustrate a potentially conserved mechanism among organisms, of which the primase activity can promote the occurrence of transcription-replication conflicts leading to HO-TRCs and genome instability.
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Affiliation(s)
- Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Wenjie Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China.
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7
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Fernie AR, Skirycz A. Plant metabolism: A protein map of the photosynthetic organelle. Curr Biol 2023; 33:R1147-R1150. [PMID: 37935127 DOI: 10.1016/j.cub.2023.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
While chloroplasts are commonly recognized as a hub in photosynthetic metabolism, our understanding of the protein functionality and spatial organization remains fragmentary. A recent study provides insights into a number of poorly characterized proteins, including unexpected spatial distributions of enzymes.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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8
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Wang L, Patena W, Van Baalen KA, Xie Y, Singer ER, Gavrilenko S, Warren-Williams M, Han L, Harrigan HR, Hartz LD, Chen V, Ton VTNP, Kyin S, Shwe HH, Cahn MH, Wilson AT, Onishi M, Hu J, Schnell DJ, McWhite CD, Jonikas MC. A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways. Cell 2023; 186:3499-3518.e14. [PMID: 37437571 DOI: 10.1016/j.cell.2023.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/14/2023]
Abstract
Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.
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Affiliation(s)
- Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kelly A Van Baalen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihua Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Emily R Singer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Linqu Han
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Henry R Harrigan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Linnea D Hartz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vivian Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vinh T N P Ton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Saw Kyin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Henry H Shwe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Matthew H Cahn
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jianping Hu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Claire D McWhite
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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9
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Structural and Functional Characterization of the Holliday Junction Resolvase RuvC from Deinococcus radiodurans. Microorganisms 2022; 10:microorganisms10061160. [PMID: 35744678 PMCID: PMC9228767 DOI: 10.3390/microorganisms10061160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Holliday junctions (HJs) are four-way DNA structures, which are an important intermediate in the process of homologous recombination. In most bacteria, HJs are cleaved by specific nucleases called RuvC resolvases at the end of homologous recombination. Deinococcus radiodurans is an extraordinary radiation-resistant bacterium and is known as an ideal model organism for elucidating DNA repair processes. Here, we described the biochemical properties and the crystal structure of RuvC from D. radiodurans (DrRuvC). DrRuvC exhibited an RNase H fold that belonged to the retroviral integrase family. Among many DNA substrates, DrRuvC specifically bound to HJ DNA and cleaved it. In particular, Mn2+ was the preferred bivalent metal co-factor for HJ cleavage, whereas high concentrations of Mg2+ inhibited the binding of DrRuvC to HJ. In addition, DrRuvC was crystallized and the crystals diffracted to 1.6 Å. The crystal structure of DrRuvC revealed essential amino acid sites for cleavage and binding activities, indicating that DrRuvC was a typical resolvase with a characteristic choice for metal co-factor.
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10
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Mahapatra K, Banerjee S, De S, Mitra M, Roy P, Roy S. An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update. Front Cell Dev Biol 2021; 9:671698. [PMID: 34447743 PMCID: PMC8383295 DOI: 10.3389/fcell.2021.671698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022] Open
Abstract
Besides the nuclear genome, plants possess two small extra chromosomal genomes in mitochondria and chloroplast, respectively, which contribute a small fraction of the organelles’ proteome. Both mitochondrial and chloroplast DNA have originated endosymbiotically and most of their prokaryotic genes were either lost or transferred to the nuclear genome through endosymbiotic gene transfer during the course of evolution. Due to their immobile nature, plant nuclear and organellar genomes face continuous threat from diverse exogenous agents as well as some reactive by-products or intermediates released from various endogenous metabolic pathways. These factors eventually affect the overall plant growth and development and finally productivity. The detailed mechanism of DNA damage response and repair following accumulation of various forms of DNA lesions, including single and double-strand breaks (SSBs and DSBs) have been well documented for the nuclear genome and now it has been extended to the organelles also. Recently, it has been shown that both mitochondria and chloroplast possess a counterpart of most of the nuclear DNA damage repair pathways and share remarkable similarities with different damage repair proteins present in the nucleus. Among various repair pathways, homologous recombination (HR) is crucial for the repair as well as the evolution of organellar genomes. Along with the repair pathways, various other factors, such as the MSH1 and WHIRLY family proteins, WHY1, WHY2, and WHY3 are also known to be involved in maintaining low mutation rates and structural integrity of mitochondrial and chloroplast genome. SOG1, the central regulator in DNA damage response in plants, has also been found to mediate endoreduplication and cell-cycle progression through chloroplast to nucleus retrograde signaling in response to chloroplast genome instability. Various proteins associated with the maintenance of genome stability are targeted to both nuclear and organellar compartments, establishing communication between organelles as well as organelles and nucleus. Therefore, understanding the mechanism of DNA damage repair and inter compartmental crosstalk mechanism in various sub-cellular organelles following induction of DNA damage and identification of key components of such signaling cascades may eventually be translated into strategies for crop improvement under abiotic and genotoxic stress conditions. This review mainly highlights the current understanding as well as the importance of different aspects of organelle genome maintenance mechanisms in higher plants.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Samrat Banerjee
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Sayanti De
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Mehali Mitra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Pinaki Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
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11
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HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2021; 118:2021053118. [PMID: 33975946 PMCID: PMC8157925 DOI: 10.1073/pnas.2021053118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Compaction of bulky DNA is a universal issue for all DNA-based life forms. Chloroplast nucleoids (chloroplast DNA-protein complexes) are critical for chloroplast DNA maintenance and transcription, thereby supporting photosynthesis, but their detailed structure remains enigmatic. Our proteomic analysis of chloroplast nucleoids of the green alga Chlamydomonas reinhardtii identified a protein (HBD1) with a tandem repeat of two DNA-binding high mobility group box (HMG-box) domains, which is structurally similar to major mitochondrial nucleoid proteins transcription factor A, mitochondrial (TFAM), and ARS binding factor 2 protein (Abf2p). Disruption of the HBD1 gene by CRISPR-Cas9-mediated genome editing resulted in the scattering of chloroplast nucleoids. This phenotype was complemented when intact HBD1 was reintroduced, whereas a truncated HBD1 with a single HMG-box domain failed to complement the phenotype. Furthermore, ectopic expression of HBD1 in the mitochondria of yeast Δabf2 mutant successfully complemented the defects, suggesting functional similarity between HBD1 and Abf2p. Furthermore, in vitro assays of HBD1, including the electrophoretic mobility shift assay and DNA origami/atomic force microscopy, showed that HBD1 is capable of introducing U-turns and cross-strand bridges, indicating that proteins with two HMG-box domains would function as DNA clips to compact DNA in both chloroplast and mitochondrial nucleoids.
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12
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Kuroiwa T, Yagisawa F, Fujiwara T, Misumi O, Nagata N, Imoto Y, Yoshida Y, Mogi Y, Miyagishima SY, Kuroiwa H. Smooth Loop-Like Mitochondrial Nucleus in the Primitive Red Alga <i>Cyanidioschyzon merolae</i> Revealed by Drying Treatment. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Fumi Yagisawa
- Center for Research Advancement and Collaboration, University of the Ryukyus
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics
| | - Osami Misumi
- Department of Biological Science and Chemistry, Faculty of Science, Yamaguchi University
| | - Noriko Nagata
- Department of Chemical and Biological Science, Japan Women’s University
| | - Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine
| | - Yamato Yoshida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Yuko Mogi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | | | - Haruko Kuroiwa
- Department of Chemical and Biological Science, Japan Women’s University
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13
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Yang Z, Li M, Sun Q. RHON1 Co-transcriptionally Resolves R-Loops for Arabidopsis Chloroplast Genome Maintenance. Cell Rep 2021; 30:243-256.e5. [PMID: 31914390 DOI: 10.1016/j.celrep.2019.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/24/2019] [Accepted: 12/02/2019] [Indexed: 01/10/2023] Open
Abstract
Preventing transcription-replication head-on conflict (HO-TRC)-triggered R-loop formation is essential for maintaining genome integrity in bacteria, plants, and mammals. The R-loop eraser RNase H can efficiently relax HO-TRCs. However, it is not clear how organisms resist HO-TRC-triggered R-loops when RNase H proteins are deficient. By screening factors that may relieve R-loop accumulation in the Arabidopsis atrnh1c mutant, we find that overexpression of the R-loop helicase RHON1 can rescue the defects of aberrantly accumulated HO-TRC-triggered R-loops co-transcriptionally. In addition, we find that RHON1 interacts with and orchestrates the transcriptional activity of plastid-encoded RNA polymerases to release the conflicts between transcription and replication. Our study illustrates that organisms employ multiple mechanisms to escape HO-TRC-triggered R-loop accumulation and thus maintain genome integrity.
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Affiliation(s)
- Zhuo Yang
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mengmeng Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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14
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Feng Y, Hashiya F, Hidaka K, Sugiyama H, Endo M. Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame. Chemistry 2020; 26:15282-15289. [PMID: 32830347 DOI: 10.1002/chem.202003071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/30/2020] [Indexed: 11/12/2022]
Abstract
The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high-speed atomic-force microscopy (HS-AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real-time movement of nucleosomes can be visualized. The arrangement and conformation of nucleosomes and the distance between two nucleosomes can be designed and controlled. In addition, four nucleosomes can be placed in a DNA frame. Multiple nucleosomes were well accessible in each conformation. Dynamic movement of the individual nucleosomes were precisely monitored in the DNA frame, and their assembly and interaction were directly observed. Neither mica surface modification nor chemical fixation of nucleosomes is used in this method, meaning that the DNA frame not only holds nucleosomes, but also retains their natural state. This method offers a promising platform for investigating nucleosome interactions and for studying chromatin structure.
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Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,present address: Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan
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15
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Zheng S, Poczai P, Hyvönen J, Tang J, Amiryousefi A. Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet 2020; 11:576124. [PMID: 33101394 PMCID: PMC7545089 DOI: 10.3389/fgene.2020.576124] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/28/2020] [Indexed: 11/13/2022] Open
Abstract
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
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Affiliation(s)
- Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Peter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland.,Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland.,Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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16
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Liang H, Zhang Y, Deng J, Gao G, Ding C, Zhang L, Yang R. The Complete Chloroplast Genome Sequences of 14 Curcuma Species: Insights Into Genome Evolution and Phylogenetic Relationships Within Zingiberales. Front Genet 2020; 11:802. [PMID: 32849804 PMCID: PMC7396571 DOI: 10.3389/fgene.2020.00802] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/06/2020] [Indexed: 11/13/2022] Open
Abstract
Zingiberaceae is taxonomically complex family where species are perennial herb. However, lack of chloroplast genomic information severely hinders our understanding of Zingiberaceae species in the research of evolution and phylogenetic relationships. In this study, the complete chloroplast (cp) genomes of fourteen Curcuma species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the 25 Zingiberaceae species. In each Zingiberaceae species, the 25 complete chloroplast genomes ranging from 155,890 bp (Zingiber spectabile) to 164,101 bp (Lanxangia tsaoko) contained 111 genes consisting of 77 protein coding genes, 4 ribosomal RNAs and 30 transfer RNAs. These chloroplast genomes are similar to most angiosperm that consisted of a four-part circular DNA molecules. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were found. Six divergent hotspots regions (matK-trnk, Rps16-trnQ, petN-psbM, rpl32, ndhA, and ycf1) were identified in the 25 Zingiberaceae chloroplast genomes, which could be potential molecular markers. In addition to Wurfbainia longiligularis, the ψycf1 was discovered among the 25 Zingiberaceae species. The shared protein coding genes from 52 Zingiberales plants and four other family species as out groups were used to construct phylogenetic trees distinguished by maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) and showed that Musaceae was the basal group in Zingiberales, and Curcuma had a close relationship with Stahlianthu. Besides this, Curcuma flaviflora was clustered together with Zingiber. Its distribution area (Southeast Asia) overlaps with the latter. Maybe hybridization occur in related groups within the same region. This may explain why Zingiberaceae species have a complex phylogeny, and more samples and genetic data were necessary to confirm their relationship. This study provide the reliable information and high-quality chloroplast genomes and genome resources for future Zingiberaceae research.
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Affiliation(s)
- Heng Liang
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Yan Zhang
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Jiabin Deng
- School of Geography and Tourism, Guizhou Education University, Guiyang, China
| | - Gang Gao
- College of Life Sciences and Food Engineering, Yibin University, Yibin, China
| | - Chunbang Ding
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Yaan, China
| | - Ruiwu Yang
- College of Life Science, Sichuan Agricultural University, Yaan, China
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17
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Kuroiwa T, Ohnuma M, Imoto Y, Yagisawa F, Misumi O, Nagata N, Kuroiwa H. Evolutionary significance of the ring-like plastid nucleus in the primitive red alga Cyanidioschyzon merolae as revealed by drying. PROTOPLASMA 2020; 257:1069-1078. [PMID: 32185527 DOI: 10.1007/s00709-020-01496-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
Primary plastids originated from a free-living cyanobacterial ancestor and possess their own genomes-probably a few DNA copies. These genomes, which are organized in centrally located plastid nuclei (CN-type pt-nuclei), are produced from preexisting plastids by binary division. Ancestral algae with a CN-type pt-nucleus diverged and evolved into two basal eukaryotic lineages: red algae with circular (CL-type) pt-nuclei and green algae with scattered small (SN-type) pt-nuclei. Although the molecular dynamics of pt-nuclei in green algae and plants are now being analyzed, the process of the conversion of the original algae with a CN-type pt-nucleus to red algae with a CL-type one has not been studied. Here, we show that the CN-type pt-nucleus in the primitive red alga Cyanidioschyzon merolae can be changed to the CL-type by application of drying to produce slight cell swelling. This result implies that CN-type pt-nuclei are produced by compact packing of CL-type ones, which suggests that a C. merolae-like alga was the original progenitor of the red algal lineage. We also observed that the CL-type pt-nucleus has a chain-linked bead-like structure. Each bead is most likely a small unit of DNA, similar to CL-type pt-nuclei in brown algae. Our results thus suggest a C. merolae-like alga as the candidate for the secondary endosymbiont of brown algae.
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Affiliation(s)
- Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan.
| | - Mio Ohnuma
- Institute of Technology, Hiroshima College, 4272-1 Higashino, Osakikamijima-cho Toyota-gun, Hiroshima, 725-0231, Japan
| | - Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolf Street, Biophysics 100, Baltimore, MD, 21205, USA
| | - Fumi Yagisawa
- Center for Research Advancement and Collaboration, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Osami Misumi
- Department of Biological Science and Chemistry, Faculty of Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan
| | - Noriko Nagata
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Haruko Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
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18
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Yan J, Hong S, Guan Z, He W, Zhang D, Yin P. Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1. Nat Commun 2020; 11:1417. [PMID: 32184398 PMCID: PMC7078210 DOI: 10.1038/s41467-020-15242-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/17/2020] [Indexed: 11/24/2022] Open
Abstract
Holliday junctions (HJs) are key DNA intermediates in genetic recombination and are eliminated by nuclease, termed resolvase, to ensure genome stability. HJ resolvases have been identified across all kingdoms of life, members of which exhibit sequence-dependent HJ resolution. However, the molecular basis of sequence selectivity remains largely unknown. Here, we present the chloroplast resolvase MOC1, which cleaves HJ in a cytosine-dependent manner. We determine the crystal structure of MOC1 with and without HJs. MOC1 exhibits an RNase H fold, belonging to the retroviral integrase family. MOC1 functions as a dimer, and the HJ is embedded into the basic cleft of the dimeric enzyme. We characterize a base recognition loop (BR loop) that protrudes into and opens the junction. Residues from the BR loop intercalate into the bases, disrupt the C-G base pairing at the crossover and recognize the cytosine, providing the molecular basis for sequence-dependent HJ resolution by a resolvase.
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Affiliation(s)
- Junjie Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Sixing Hong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Wenjing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China.
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19
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Factors Affecting Organelle Genome Stability in Physcomitrella patens. PLANTS 2020; 9:plants9020145. [PMID: 31979236 PMCID: PMC7076466 DOI: 10.3390/plants9020145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 01/25/2023]
Abstract
Organelle genomes are essential for plants; however, the mechanisms underlying the maintenance of organelle genomes are incompletely understood. Using the basal land plant Physcomitrella patens as a model, nuclear-encoded homologs of bacterial-type homologous recombination repair (HRR) factors have been shown to play an important role in the maintenance of organelle genome stability by suppressing recombination between short dispersed repeats. In this review, I summarize the factors and pathways involved in the maintenance of genome stability, as well as the repeats that cause genomic instability in organelles in P. patens, and compare them with findings in other plant species. I also discuss the relationship between HRR factors and organelle genome structure from the evolutionary standpoint.
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20
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Chevigny N, Schatz-Daas D, Lotfi F, Gualberto JM. DNA Repair and the Stability of the Plant Mitochondrial Genome. Int J Mol Sci 2020; 21:E328. [PMID: 31947741 PMCID: PMC6981420 DOI: 10.3390/ijms21010328] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.
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Affiliation(s)
| | | | | | - José Manuel Gualberto
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67081 Strasbourg, France; (N.C.); (D.S.-D.); (F.L.)
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21
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Zheng S, Poczai P, Hyvönen J, Tang J, Amiryousefi A. Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet 2020. [PMID: 33101394 DOI: 10.3389/fgene.576124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
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Affiliation(s)
- Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Peter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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22
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Structural basis of sequence-specific Holliday junction cleavage by MOC1. Nat Chem Biol 2019; 15:1241-1248. [PMID: 31611704 DOI: 10.1038/s41589-019-0377-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/02/2019] [Indexed: 02/04/2023]
Abstract
The Holliday junction (HJ) is a key intermediate during homologous recombination and DNA double-strand break repair. Timely HJ resolution by resolvases is critical for maintaining genome stability. The mechanisms underlying sequence-specific substrate recognition and cleavage by resolvases remain elusive. The monokaryotic chloroplast 1 protein (MOC1) specifically cleaves four-way DNA junctions in a sequence-specific manner. Here, we report the crystal structures of MOC1 from Zea mays, alone or bound to HJ DNA. MOC1 uses a unique β-hairpin to embrace the DNA junction. A base-recognition motif specifically interacts with the junction center, inducing base flipping and pseudobase-pair formation at the strand-exchanging points. Structures of MOC1 bound to HJ and different metal ions support a two-metal ion catalysis mechanism. Further molecular dynamics simulations and biochemical analyses reveal a communication between specific substrate recognition and metal ion-dependent catalysis. Our study thus provides a mechanism for how a resolvase turns substrate specificity into catalytic efficiency.
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23
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Plant Organelle Genome Replication. PLANTS 2019; 8:plants8100358. [PMID: 31546578 PMCID: PMC6843274 DOI: 10.3390/plants8100358] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/14/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022]
Abstract
Mitochondria and chloroplasts perform essential functions in respiration, ATP production, and photosynthesis, and both organelles contain genomes that encode only some of the proteins that are required for these functions. The proteins and mechanisms for organelle DNA replication are very similar to bacterial or phage systems. The minimal replisome may consist of DNA polymerase, a primase/helicase, and a single-stranded DNA binding protein (SSB), similar to that found in bacteriophage T7. In Arabidopsis, there are two genes for organellar DNA polymerases and multiple potential genes for SSB, but there is only one known primase/helicase protein to date. Genome copy number varies widely between type and age of plant tissues. Replication mechanisms are only poorly understood at present, and may involve multiple processes, including recombination-dependent replication (RDR) in plant mitochondria and perhaps also in chloroplasts. There are still important questions remaining as to how the genomes are maintained in new organelles, and how genome copy number is determined. This review summarizes our current understanding of these processes.
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24
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Nilo-Poyanco R, Vizoso P, Sanhueza D, Balic I, Meneses C, Orellana A, Campos-Vargas R. A Prunus persica genome-wide RNA-seq approach uncovers major differences in the transcriptome among chilling injury sensitive and non-sensitive varieties. PHYSIOLOGIA PLANTARUM 2019; 166:772-793. [PMID: 30203620 DOI: 10.1111/ppl.12831] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/28/2018] [Accepted: 09/03/2018] [Indexed: 05/14/2023]
Abstract
Chilling injury represents a major constrain for crops productivity. Prunus persica, one of the most relevant rosacea crops, have early season varieties that are resistant to chilling injury, in contrast to late season varieties, which display chilling symptoms such as mealiness (dry, sandy fruit mesocarp) after prolonged storage at chilling temperatures. To uncover the molecular processes related to the ability of early varieties to withstand mealiness, postharvest and genome-wide RNA-seq assessments were performed in two early and two late varieties. Differences in juice content and ethylene biosynthesis were detected among early and late season fruits that became mealy after exposed to prolonged chilling. Principal component and data distribution analysis revealed that cold-stored late variety fruit displayed an exacerbated and unique transcriptome profile when compared to any other postharvest condition. A differential expression analysis performed using an empirical Bayes mixture modeling approach followed by co-expression and functional enrichment analysis uncover processes related to ethylene, lipids, cell wall, carotenoids and DNA metabolism, light response, and plastid homeostasis associated to the susceptibility or resistance of P. persica varieties to chilling stress. Several of the genes related to these processes are in quantitative trait loci (QTL) associated to mealiness in P. persica. Together, these analyses exemplify how P. persica can be used as a model for studying chilling stress in plants.
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Affiliation(s)
- Ricardo Nilo-Poyanco
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Paula Vizoso
- Centro de Propagación y Conservación Vegetal, Universidad Mayor, Santiago, Chile
| | - Dayan Sanhueza
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Iván Balic
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Departamento de Ciencias Biológicas, Universidad de Los Lagos, Osorno, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
| | - Reinaldo Campos-Vargas
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
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25
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Lee AJ, Wälti C. DNA nanostructures: A versatile lab-bench for interrogating biological reactions. Comput Struct Biotechnol J 2019; 17:832-842. [PMID: 31316727 PMCID: PMC6611922 DOI: 10.1016/j.csbj.2019.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/10/2023] Open
Abstract
At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.
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Affiliation(s)
- Andrew J. Lee
- Bioelectronics, The Pollard Institute, School of Electronic & Electrical Engineering, University of Leeds, LS2 9JT, United Kingdom
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26
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Gonçalves DJP, Simpson BB, Ortiz EM, Shimizu GH, Jansen RK. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Mol Phylogenet Evol 2019; 138:219-232. [PMID: 31146023 DOI: 10.1016/j.ympev.2019.05.022] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022]
Abstract
The current classification of angiosperms is based primarily on concatenated plastid markers and maximum likelihood (ML) inference. This approach has been justified by the assumption that plastid DNA (ptDNA) is inherited as a single locus and that its individual genes produce congruent trees. However, structural and functional characteristics of ptDNA suggest that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces. To examine this idea, we produced new complete plastid genome (plastome) sequences of 27 species and combined these data with publicly available sequences to produce a final dataset that includes 78 plastid genes for 89 species of rosids and five outgroups. We used four data matrices (i.e., gene, exon, codon-aligned, and amino acid) to infer species and gene trees using ML and multispecies coalescent (MSC) methods. Rosids include about one third of all angiosperms and their two major clades, fabids and malvids, were recovered in almost all analyses. However, we detected incongruence between species trees inferred with different matrices and methods and previously published plastid and nuclear phylogenies. We visualized and tested the significance of incongruence between gene trees and species trees. We then measured the distribution of phylogenetic signal across sites and genes supporting alternative placements of five controversial nodes at different taxonomic levels. Gene trees inferred with plastid data often disagree with species trees inferred using both ML (with unpartitioned or partitioned data) and MSC. Species trees inferred with both methods produced alternative topologies for a few taxa. Our results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus. Furthermore, concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees. We also show that phylogenies inferred with MSC are accurate. We therefore emphasize the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships. We also support the use of MSC with plastome matrices in future phylogenomic investigations.
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Affiliation(s)
- Deise J P Gonçalves
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA.
| | - Beryl B Simpson
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA
| | - Edgardo M Ortiz
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Department of Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Emil-Ramann Strasse 2, Freising D-85354, Germany
| | - Gustavo H Shimizu
- Department of Plant Biology, University of Campinas, 13083-970 Campinas, SP, Brazil
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Genomics and Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Sakamoto W, Takami T. Chloroplast DNA Dynamics: Copy Number, Quality Control and Degradation. PLANT & CELL PHYSIOLOGY 2018; 59:1120-1127. [PMID: 29860378 DOI: 10.1093/pcp/pcy084] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/01/2018] [Indexed: 05/16/2023]
Abstract
Endosymbiotically originated chloroplast DNA (cpDNA) encodes part of the genetic information needed to fulfill chloroplast function, including fundamental processes such as photosynthesis. In the last two decades, advances in genome analysis led to the identification of a considerable number of cpDNA sequences from various species. While these data provided the consensus features of cpDNA organization and chloroplast evolution in plants, how cpDNA is maintained through development and is inherited remains to be fully understood. In particular, the fact that cpDNA exists as multiple copies despite its limited genetic capacity raises the important question of how copy number is maintained or whether cpDNA is subjected to quantitative fluctuation or even developmental degradation. For example, cpDNA is abundant in leaves, where it forms punctate structures called nucleoids, which seemingly alter their morphologies and numbers depending on the developmental status of the chloroplast. In this review, we summarize our current understanding of 'cpDNA dynamics', focusing on the changes in DNA abundance. A special focus is given to the cpDNA degradation mechanism, which appears to be mediated by Defective in Pollen organelle DNA degradation 1 (DPD1), a recently discovered organelle exonuclease. The physiological significance of cpDNA degradation in flowering plants is also discussed.
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Affiliation(s)
- Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
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Kamimura Y, Tanaka H, Kobayashi Y, Shikanai T, Nishimura Y. Chloroplast nucleoids as a transformable network revealed by live imaging with a microfluidic device. Commun Biol 2018; 1:47. [PMID: 30271930 PMCID: PMC6123815 DOI: 10.1038/s42003-018-0055-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/17/2018] [Indexed: 12/14/2022] Open
Abstract
Chloroplast DNA is organized into DNA–protein conglomerates called chloroplast nucleoids, which are replicated, transcribed, and inherited. We applied live-imaging technology with a microfluidic device to examine the nature of chloroplast nucleoids in Chlamydomonas reinhardtii. We observed the dynamic and reversible dispersion of globular chloroplast nucleoids into a network structure in dividing chloroplasts. In the monokaryotic chloroplast (moc) mutant, in which chloroplast nucleoids are unequally distributed following chloroplast division due to a defect in MOC1, the early stages of chloroplast nucleoid formation occurred mainly in the proximal area. This suggests the chloroplast nucleoid transformable network consists of a highly compact core with proximal areas associated with cpDNA replication and nucleoid formation. Yoshitaka Kamimura and colleagues combine live-imaging technology with microfluidics to examine chloroplast DNA organization in nucleoids. They find that these structures form a network structure in dividing chloroplasts, and propose a mechanism for their inheritance in organelle replication.
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Affiliation(s)
- Yoshitaka Kamimura
- Department of Botany, Laboratory of Plant Molecular Genetics, Kyoto University, Oiwake-cho, Kita-shirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hitomi Tanaka
- Department of Botany, Laboratory of Plant Molecular Genetics, Kyoto University, Oiwake-cho, Kita-shirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yusuke Kobayashi
- Department of Cell Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Toshiharu Shikanai
- Department of Botany, Laboratory of Plant Molecular Genetics, Kyoto University, Oiwake-cho, Kita-shirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshiki Nishimura
- Department of Botany, Laboratory of Plant Molecular Genetics, Kyoto University, Oiwake-cho, Kita-shirakawa, Sakyo-ku, Kyoto, 606-8502, Japan.
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Abstract
Successful chromosome segregation depends on the timely removal of DNA recombination and replication intermediates that interlink sister chromatids. These intermediates are acted upon by structure-selective endonucleases that promote incisions close to the junction point. GEN1, a member of the Rad2/XPG endonuclease family, was identified on the basis of its ability to cleave Holliday junction recombination intermediates. Resolution occurs by a nick and counter-nick mechanism in strands that are symmetrically related across the junction point, leading to the formation of ligatable nicked duplex products. The actions of GEN1 are, however, not restricted to HJs, as 5'-flaps and replication fork structures also serve as excellent in vitro substrates for the nuclease. In the cellular context, GEN1 activity is observed late in the cell cycle, as most of the protein is excluded from the nucleus, such that it gains access to DNA intermediates after the breakdown of nuclear envelope. Nuclear exclusion ensures the protection of replication forks and other DNA secondary structures important for normal metabolic processes. In this chapter, we describe the purification of recombinant GEN1 and detail biochemical assays involving the use of synthetic DNA substrates and cruciform-containing plasmids.
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Kobayashi Y, Misumi O, Nishimura Y. Finding Holliday Junction Resolvases: A Crucial Factor for Chloroplast Nucleoid Segregation. CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yusuke Kobayashi
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University
| | - Osami Misumi
- Department of Biological Science and Chemistry, Faculty of Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Yoshiki Nishimura
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University
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