1
|
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.
Collapse
Affiliation(s)
- Yoshiki Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kita-Shirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| |
Collapse
|
2
|
Kobayashi Y, Odahara M, Sekine Y, Hamaji T, Fujiwara S, Nishimura Y, Miyagishima SY. Holliday Junction Resolvase MOC1 Maintains Plastid and Mitochondrial Genome Integrity in Algae and Bryophytes. PLANT PHYSIOLOGY 2020; 184:1870-1883. [PMID: 32978278 PMCID: PMC7723093 DOI: 10.1104/pp.20.00763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
When DNA double-strand breaks occur, four-stranded DNA structures called Holliday junctions (HJs) form during homologous recombination. Because HJs connect homologous DNA by a covalent link, resolution of HJ is crucial to terminate homologous recombination and segregate the pair of DNA molecules faithfully. We recently identified Monokaryotic Chloroplast1 (MOC1) as a plastid DNA HJ resolvase in algae and plants. Although Cruciform cutting endonuclease1 (CCE1) was identified as a mitochondrial DNA HJ resolvase in yeasts, homologs or other mitochondrial HJ resolvases have not been identified in other eukaryotes. Here, we demonstrate that MOC1 depletion in the green alga Chlamydomonas reinhardtii and the moss Physcomitrella patens induced ectopic recombination between short dispersed repeats in ptDNA. In addition, MOC1 depletion disorganized thylakoid membranes in plastids. In some land plant lineages, such as the moss P. patens, a liverwort and a fern, MOC1 dually targeted to plastids and mitochondria. Moreover, mitochondrial targeting of MOC1 was also predicted in charophyte algae and some land plant species. Besides causing instability of plastid DNA, MOC1 depletion in P. patens induced short dispersed repeat-mediated ectopic recombination in mitochondrial DNA and disorganized cristae in mitochondria. Similar phenotypes in plastids and mitochondria were previously observed in mutants of plastid-targeted (RECA2) and mitochondrion-targeted (RECA1) recombinases, respectively. These results suggest that MOC1 functions in the double-strand break repair in which a recombinase generates HJs and MOC1 resolves HJs in mitochondria of some lineages of algae and plants as well as in plastids in algae and plants.
Collapse
Affiliation(s)
- Yusuke Kobayashi
- College of Science, Graduate School of Science and Engineering, Ibaraki University, Bunkyo, Mito, Ibaraki 310-8512, Japan
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masaki Odahara
- Department of Life Science, College of Science, Rikkyo (St. Paul's) University, Toshima-ku, Tokyo 171-8501, Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo (St. Paul's) University, Toshima-ku, Tokyo 171-8501, Japan
| | - Takashi Hamaji
- Department of Botany, Laboratory of Plant Molecular Genetics, Kyoto University, Oiwake-cho, Kita-shirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sumire Fujiwara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshiki Nishimura
- Department of Botany, Laboratory of Plant Molecular Genetics, Kyoto University, Oiwake-cho, Kita-shirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Johnston IG. Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells. MOLECULAR PLANT 2019; 12:764-783. [PMID: 30445187 DOI: 10.1016/j.molp.2018.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.
Collapse
Affiliation(s)
- Iain G Johnston
- School of Biosciences, University of Birmingham, Birmingham, UK; Birmingham Institute for Forest Research, University of Birmingham, Birmingham, UK.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|