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Sloan DB, Broz AK, Kuster SA, Muthye V, Peñafiel-Ayala A, Marron JR, Lavrov DV, Brieba LG. Expansion of the MutS Gene Family in Plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603841. [PMID: 39071318 PMCID: PMC11275761 DOI: 10.1101/2024.07.17.603841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.
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Affiliation(s)
- Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Amanda K. Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Shady A. Kuster
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Viraj Muthye
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alejandro Peñafiel-Ayala
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
| | | | - Dennis V. Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Luis G. Brieba
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
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Islam MF, Yamatani H, Takami T, Kusaba M, Sakamoto W. Characterization of organelle DNA degradation mediated by DPD1 exonuclease in the rice genome-edited line. PLANT MOLECULAR BIOLOGY 2024; 114:71. [PMID: 38856917 PMCID: PMC11164812 DOI: 10.1007/s11103-024-01452-x] [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: 03/05/2024] [Accepted: 04/05/2024] [Indexed: 06/11/2024]
Abstract
Mitochondria and plastids, originated as ancestral endosymbiotic bacteria, contain their own DNA sequences. These organelle DNAs (orgDNAs) are, despite the limited genetic information they contain, an indispensable part of the genetic systems but exist as multiple copies, making up a substantial amount of total cellular DNA. Given this abundance, orgDNA is known to undergo tissue-specific degradation in plants. Previous studies have shown that the exonuclease DPD1, conserved among seed plants, degrades orgDNAs during pollen maturation and leaf senescence in Arabidopsis. However, tissue-specific orgDNA degradation was shown to differ among species. To extend our knowledge, we characterized DPD1 in rice in this study. We created a genome-edited (GE) mutant in which OsDPD1 and OsDPD1-like were inactivated. Characterization of this GE plant demonstrated that DPD1 was involved in pollen orgDNA degradation, whereas it had no significant effect on orgDNA degradation during leaf senescence. Comparison of transcriptomes from wild-type and GE plants with different phosphate supply levels indicated that orgDNA had little impact on the phosphate starvation response, but instead had a global impact in plant growth. In fact, the GE plant showed lower fitness with reduced grain filling rate and grain weight in natural light conditions. Taken together, the presented data reinforce the important physiological roles of orgDNA degradation mediated by DPD1.
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Affiliation(s)
- Md Faridul Islam
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Hiroshi Yamatani
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233, Watanuki, Takasaki, Gunma, 370-1292, Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Makoto Kusaba
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-3 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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Sakamoto W, Takami T. Plastid Inheritance Revisited: Emerging Role of Organelle DNA Degradation in Angiosperms. PLANT & CELL PHYSIOLOGY 2024; 65:484-492. [PMID: 37702423 DOI: 10.1093/pcp/pcad104] [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: 07/06/2023] [Revised: 08/15/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
Plastids are essential organelles in angiosperms and show non-Mendelian inheritance due to their evolution as endosymbionts. In approximately 80% of angiosperms, plastids are thought to be inherited from the maternal parent, whereas other species transmit plastids biparentally. Maternal inheritance can be generally explained by the stochastic segregation of maternal plastids after fertilization because the zygote is overwhelmed by the maternal cytoplasm. In contrast, biparental inheritance shows the transmission of organelles from both parents. In some species, maternal inheritance is not absolute and paternal leakage occurs at a very low frequency (∼10-5). A key process controlling the inheritance mode lies in the behavior of plastids during male gametophyte (pollen) development, with accumulating evidence indicating that the plastids themselves or their DNAs are eliminated during pollen maturation or at fertilization. Cytological observations in numerous angiosperm species have revealed several critical steps that mutually influence the degree of plastid transmission quantitatively among different species. This review revisits plastid inheritance from a mechanistic viewpoint. Particularly, we focus on a recent finding demonstrating that both low temperature and plastid DNA degradation mediated by the organelle exonuclease DEFECTIVE IN POLLEN ORGANELLE DNA DEGRADATION1 (DPD1) influence the degree of paternal leakage significantly in tobacco. Given these findings, we also highlight the emerging role of DPD1 in organelle DNA degradation.
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Affiliation(s)
- Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-2 Chuo, Kurashiki, Okayama, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-2 Chuo, Kurashiki, Okayama, 710-0046 Japan
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4
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He J, Huang Y, Li L, Lin S, Ma M, Wang Y, Lin S. Novel Plastid Genome Characteristics in Fugacium kawagutii and the Trend of Accelerated Evolution of Plastid Proteins in Dinoflagellates. Genome Biol Evol 2024; 16:evad237. [PMID: 38155596 PMCID: PMC10781511 DOI: 10.1093/gbe/evad237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023] Open
Abstract
Typical (peridinin-containing) dinoflagellates possess plastid genomes composed of small plasmids named "minicircles". Despite the ecological importance of dinoflagellate photosynthesis in corals and marine ecosystems, the structural characteristics, replication dynamics, and evolutionary forcing of dinoflagellate plastid genomes remain poorly understood. Here, we sequenced the plastid genome of the symbiodiniacean species Fugacium kawagutii and conducted comparative analyses. We identified psbT-coding minicircles, features previously not found in Symbiodiniaceae. The copy number of F. kawagutii minicircles showed a strong diel dynamics, changing between 3.89 and 34.3 copies/cell and peaking in mid-light period. We found that F. kawagutii minicircles are the shortest among all dinoflagellates examined to date. Besides, the core regions of the minicircles are highly conserved within genus in Symbiodiniaceae. Furthermore, the codon usage bias of the plastid genomes in Heterocapsaceae, Amphidiniaceae, and Prorocentraceae species are greatly influenced by selection pressure, and in Pyrocystaceae, Symbiodiniaceae, Peridiniaceae, and Ceratiaceae species are influenced by both natural selection pressure and mutation pressure, indicating a family-level distinction in codon usage evolution in dinoflagellates. Phylogenetic analysis using 12 plastid-encoded proteins and five nucleus-encoded plastid proteins revealed accelerated evolution trend of both plastid- and nucleus-encoded plastid proteins in peridinin- and fucoxanthin-dinoflagellate plastids compared to plastid proteins of nondinoflagellate algae. These findings shed new light on the structure and evolution of plastid genomes in dinoflagellates, which will facilitate further studies on the evolutionary forcing and function of the diverse dinoflagellate plastids. The accelerated evolution documented here suggests plastid-encoded sequences are potentially useful for resolving closely related dinoflagellates.
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Affiliation(s)
- Jiamin He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yulin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Sitong Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Minglei Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yujie Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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Jun SE, Shim JS, Park HJ. Beyond NPK: Mineral Nutrient-Mediated Modulation in Orchestrating Flowering Time. PLANTS (BASEL, SWITZERLAND) 2023; 12:3299. [PMID: 37765463 PMCID: PMC10535918 DOI: 10.3390/plants12183299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Flowering time in plants is a complex process regulated by environmental conditions such as photoperiod and temperature, as well as nutrient conditions. While the impact of major nutrients like nitrogen, phosphorus, and potassium on flowering time has been well recognized, the significance of micronutrient imbalances and their deficiencies should not be neglected because they affect the floral transition from the vegetative stage to the reproductive stage. The secondary major nutrients such as calcium, magnesium, and sulfur participate in various aspects of flowering. Micronutrients such as boron, zinc, iron, and copper play crucial roles in enzymatic reactions and hormone biosynthesis, affecting flower development and reproduction as well. The current review comprehensively explores the interplay between microelements and flowering time, and summarizes the underlying mechanism in plants. Consequently, a better understanding of the interplay between microelements and flowering time will provide clues to reveal the roles of microelements in regulating flowering time and to improve crop reproduction in plant industries.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea;
| | - Jae Sun Shim
- School of Biological Science and Technology, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hee Jin Park
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
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Sakamoto W, Takami T. Maternal plastid inheritance: two abating factors identified. Trends Genet 2023; 39:342-343. [PMID: 36935219 DOI: 10.1016/j.tig.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023]
Abstract
Organelle DNAs (orgDNAs) in mitochondria and plastids are generally inherited from the maternal parent; however, it is unclear how their inheritance mode is controlled, particularly in the plastids of seed plants. Chung et al. identify two factors that affect maternal inheritance in tobacco plastids: cold temperature and DNA amount in pollen.
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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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7
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Chilling stress and loss of an exonuclease lead to biparental inheritance of plastids. NATURE PLANTS 2023; 9:9-10. [PMID: 36650221 DOI: 10.1038/s41477-022-01330-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
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8
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Chung KP, Gonzalez-Duran E, Ruf S, Endries P, Bock R. Control of plastid inheritance by environmental and genetic factors. NATURE PLANTS 2023; 9:68-80. [PMID: 36646831 PMCID: PMC9873568 DOI: 10.1038/s41477-022-01323-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/26/2022] [Indexed: 06/01/2023]
Abstract
The genomes of cytoplasmic organelles (mitochondria and plastids) are maternally inherited in most eukaryotes, thus excluding organellar genomes from the benefits of sexual reproduction and recombination. The mechanisms underlying maternal inheritance are largely unknown. Here we demonstrate that two independently acting mechanisms ensure maternal inheritance of the plastid (chloroplast) genome. Conducting large-scale genetic screens for paternal plastid transmission, we discovered that mild chilling stress during male gametogenesis leads to increased entry of paternal plastids into sperm cells and strongly increased paternal plastid transmission. We further show that the inheritance of paternal plastid genomes is controlled by the activity of a genome-degrading exonuclease during pollen maturation. Our data reveal that (1) maternal inheritance breaks down under specific environmental conditions, (2) an organelle exclusion mechanism and a genome degradation mechanism act in concert to prevent paternal transmission of plastid genes and (3) plastid inheritance is determined by complex gene-environment interactions.
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Affiliation(s)
- Kin Pan Chung
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | | | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Pierre Endries
- Universität Hamburg, Institut für Pflanzenwissenschaften und Mikrobiologie, Hamburg, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
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9
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Yoshitake Y, Shinozaki D, Yoshimoto K. Autophagy triggered by iron-mediated ER stress is an important stress response to the early phase of Pi starvation in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1370-1381. [PMID: 35306710 DOI: 10.1111/tpj.15743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Inorganic phosphate (Pi) is essential for plant growth. However, Pi is often limiting in soil. Hence, plants have established several mechanisms of response to Pi starvation. One of the important mechanisms is Pi recycling, which includes membrane lipid remodeling and plastid DNA degradation via catabolic enzymes. However, the involvement of other degradation systems in Pi recycling remains unclear. Autophagy, a system for degradation of intracellular components, contributes to recycling of some nutrients, such as nitrogen, carbon, and zinc, under starvation. In the present study, we found that autophagy-deficient mutants depleted Pi early and exhibited severe leaf growth defects under Pi starvation. The main cargo of autophagy induced by early Pi depleted conditions was the endoplasmic reticulum (ER), indicating that ER-phagy, a type of autophagy that selectively degrades the ER, is involved in the response to the early phase of Pi starvation for contribution to Pi recycling. This ER-phagy was suppressed in an INOSITOL-REQUIRING ENZYME 1 double mutant, ire1a ire1b, in which ER stress responses are defective, suggesting that the early Pi starvation induced ER-phagy is induced by ER stress. Furthermore, iron limitation and inhibition of lipid-reactive oxygen species accumulation suppressed the ER-phagy. Interestingly, membrane lipid remodeling, a response to late Pi starvation, was accelerated in the ire1a ire1b under early Pi-depleted conditions. Our findings reveal the existence of two different phases of responses to Pi starvation (i.e. early and late) and indicate that ER stress-mediated ER-phagy is involved in Pi recycling in the early phase to suppress acceleration of the late phase.
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Affiliation(s)
- Yushi Yoshitake
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
| | - Daiki Shinozaki
- Life Science Program, Graduate School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
| | - Kohki Yoshimoto
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
- Life Science Program, Graduate School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
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Nadeem M, Wu J, Ghaffari H, Kedir AJ, Saleem S, Mollier A, Singh J, Cheema M. Understanding the Adaptive Mechanisms of Plants to Enhance Phosphorus Use Efficiency on Podzolic Soils in Boreal Agroecosystems. FRONTIERS IN PLANT SCIENCE 2022; 13:804058. [PMID: 35371179 PMCID: PMC8965363 DOI: 10.3389/fpls.2022.804058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Being a macronutrient, phosphorus (P) is the backbone to complete the growth cycle of plants. However, because of low mobility and high fixation, P becomes the least available nutrient in podzolic soils; hence, enhancing phosphorus use efficiency (PUE) can play an important role in different cropping systems/crop production practices to meet ever-increasing demands in food, fiber, and fuel. Additionally, the rapidly decreasing mineral phosphate rocks/stocks forced to explore alternative resources and methods to enhance PUE either through improved seed P reserves and their remobilization, P acquisition efficiency (PAE), or plant's internal P utilization efficiency (IPUE) or both for sustainable P management strategies. The objective of this review article is to explore and document important domains to enhance PUE in crop plants grown on Podzol in a boreal agroecosystem. We have discussed P availabilities in podzolic soils, root architecture and morphology, root exudates, phosphate transporters and their role in P uptake, different contributors to enhance PAE and IPUE, and strategies to improve plant PUE in crops grown on podzolic soils deficient in P and acidic in nature.
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Affiliation(s)
- Muhammad Nadeem
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
| | - Jiaxu Wu
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
| | | | - Amana Jemal Kedir
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
- Environmental Science Program, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Shamila Saleem
- Department of Agriculture Extension, Government of Punjab, Khanewal, Pakistan
| | - Alain Mollier
- INRAE, UMR 1391 ISPA, Bordeaux Science Agro, Villenave d'Ornon, France
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Mumtaz Cheema
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, NL, Canada
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Kamireddy K, Sonbarse PP, Mishra SK, Agrawal L, Chauhan PS, Lata C, Parvatam G. Proteomic approach to identify the differentially abundant proteins during flavour development in tuberous roots of Decalepis hamiltonii Wight & Arn. 3 Biotech 2021; 11:173. [PMID: 33927964 DOI: 10.1007/s13205-021-02714-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/03/2021] [Indexed: 01/14/2023] Open
Abstract
2-Hydroxy-4-Methoxy Benzaldehyde (2H4MB) is a structural isomer of vanillin produced in the tuberous roots of D. hamiltonii. Both vanillin and 2H4MB share the common phenylpropanoid pathway for their synthesis. Unlike vanillin, in which the biosynthetic pathway was well elucidated in V. planifolia, the 2H4MB biosynthetic pathway is not known in any of its plant sources. To find the key enzymes/proteins that promote 2H4MB biosynthesis, a comparative proteomic approach was adapted. In this case, two developmental stages of tuberous roots of D. hamiltonii were selected, where the flavour content was highly variable. The flavour content in the two stages was estimated using quantitative HPLC. The flavour content in the first and second stages of tuber development was 160 and 510 µgg-1, respectively. Two-dimensional electrophoresis (2-DE) was performed for these two stages of tubers; this was followed by PDquest analysis. A total of 180 protein spots were differentially abundant of which 57 spots were selected and subjected to MALDI-TOF-TOF analysis. The largest percentage of identified proteins was involved in stress and defence (27.9%), followed by proteins related to bioenergy and metabolism (23.2%), Cellular homeostasis proteins (18.6%), signaling proteins (11.6%), Plant growth and development proteins (9.3%). Holistically, we found the upregulation of methyltransferase, cell division responsive proteins, plant growth and development proteins which directly relate to flavour development and maturation. Similarly, stress-responsive and signaling proteins, vacuole proteins and ATPases were down-regulated with an increase in flavour content. In this study, we could not identify the specific 2H4MB metabolic pathway proteins, however, we could be able to study the changes in physiological and primary metabolic proteins with 2H4MB accumulation. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02714-x.
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Affiliation(s)
- Kiran Kamireddy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh India
- Plant Cell Biotechnology Department, CSIR - Central Food Technological Research Institute, Mysore, Karnataka India
| | - Priyanka Purushottam Sonbarse
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh India
- Plant Cell Biotechnology Department, CSIR - Central Food Technological Research Institute, Mysore, Karnataka India
| | - Shashank K Mishra
- CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh India
| | - Lalit Agrawal
- CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh India
| | - Puneet S Chauhan
- CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh India
| | - Charu Lata
- CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh India
| | - Giridhar Parvatam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh India
- Plant Cell Biotechnology Department, CSIR - Central Food Technological Research Institute, Mysore, Karnataka India
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12
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Barthel D, Schuler H, Galli J, Borruso L, Geier J, Heer K, Burckhardt D, Janik K. Identification of Plant DNA in Adults of the Phytoplasma Vector Cacopsylla picta Helps Understanding Its Feeding Behavior. INSECTS 2020; 11:insects11120835. [PMID: 33255992 PMCID: PMC7761314 DOI: 10.3390/insects11120835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 01/04/2023]
Abstract
Simple Summary Cacopsylla picta is an insect vector of apple proliferation phytoplasma, the causative bacterial agent of apple proliferation disease. In this study, we provide an answer to the open question of whether adult Cacopsylla picta feed from other plants than their known host, the apple plant. We collected Cacopsylla picta specimens from apple trees and analyzed the composition of plant DNA ingested by these insects. By applying a state-of-the art sequencing approach, we show, for the first time, that Cacopsylla picta feeds from a wide range of woody and herbaceous plant species. Our results are important for a better understanding of the biology and feeding behavior of Cacopsylla picta. Since this insect is an efficient vector of apple proliferation phytoplasma, our results are also important to define potential reservoir plants that might be involved in the transmissive cycle of this pathogen. This study thus provides important data of practical relevance. Abstract Apple proliferation is an economically important disease and a threat for commercial apple cultivation. The causative pathogen, the bacterium ‘Candidatus Phytoplasma mali’, is mainly transmitted by Cacopsylla picta, a phloem-feeding insect that develops on the apple tree (Malus spp.). To investigate the feeding behavior of adults of the phytoplasma vector Cacopsylla picta in more detail, we used deep sequencing technology to identify plant-specific DNA ingested by the insect. Adult psyllids were collected in different apple orchards in the Trentino-South Tyrol region of northern Italy. DNA from the whole body of the insect was extracted and analyzed for the presence of plant DNA by performing PCR with two plant-specific primers that target the chloroplast regions trnH-psbA and rbcLa. DNA from 23 plant genera (trnH) and four plant families (rbcLa) of woody and herbaceous plant taxa was detected. Up to six and three plant genera and families, respectively, could be determined in single specimens. The results of this study contribute to a better understanding of the feeding behavior of adult Cacopsylla picta.
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Affiliation(s)
- Dana Barthel
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), Italy
- Correspondence: (D.B.); (K.J.)
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, IT-39100 Bozen (Bolzano), Italy; (H.S.); (L.B.)
- Competence Centre Plant Health, Free University of Bozen-Bolzano, IT-39100 Bozen (Bolzano), Italy
| | - Jonas Galli
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria;
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen-Bolzano, IT-39100 Bozen (Bolzano), Italy; (H.S.); (L.B.)
| | - Jacob Geier
- Department of Botany, Leopold-Franzens-Universität Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria;
| | - Katrin Heer
- Faculty of Biology—Conservation Biology, Philipps Universität Marburg, Karl-von-Frisch-Straße 8, D-35043 Marburg, Germany;
| | - Daniel Burckhardt
- Naturhistorisches Museum, Augustinergasse 2, CH-4001 Basel, Switzerland;
| | - Katrin Janik
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), Italy
- Correspondence: (D.B.); (K.J.)
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13
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Phylogenetic Analysis and In Vitro Bifunctional Nuclease Assay of Arabidopsis BBD1 and BBD2. Molecules 2020; 25:molecules25092169. [PMID: 32384799 PMCID: PMC7249048 DOI: 10.3390/molecules25092169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 01/08/2023] Open
Abstract
Nucleases are a very diverse group of enzymes that play important roles in many crucial physiological processes in plants. We previously reported that the highly conserved region (HCR), domain of unknown function 151 (DUF151) and UV responsive (UVR) domain-containing OmBBD is a novel nuclease that does not share homology with other well-studied plant nucleases. Here, we report that DUF151 domain-containing proteins are present in bacteria, archaea and only Viridiplantae kingdom of eukarya, but not in any other eukaryotes. Two Arabidopsis homologs of OmBBD, AtBBD1 and AtBBD2, shared 43.69% and 44.38% sequence identity and contained all three distinct domains of OmBBD. We confirmed that the recombinant MBP-AtBBD1 and MBP-AtBBD2 exhibited non-substrate-specific DNase and RNase activity, like OmBBD. We also found that a metal cofactor is not necessarily required for DNase activity of AtBBD1 and AtBBD2, but their activities were much enhanced in the presence of Mg2+ or Mn2+. Using a yeast two-hybrid assay, we found that AtBBD1 and AtBBD2 each form a homodimer but not a heterodimer and that the HCR domain is possibly crucial for dimerization.
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14
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Marciniec R, Zięba E, Winiarczyk K. Distribution of plastids and mitochondria during male gametophyte formation in Tinantia erecta (Jacq.) Fenzl. PROTOPLASMA 2019; 256:1051-1063. [PMID: 30852672 PMCID: PMC6579867 DOI: 10.1007/s00709-019-01363-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/20/2019] [Indexed: 05/27/2023]
Abstract
During meiosis in microsporogenesis, autonomous cellular organelles, i.e., plastids and mitochondria, move and separate into daughter cells according to a specific pattern. This process called chondriokinesis is characteristic for a given plant species. The key criterion for classification of the chondriokinesis types was the arrangement of cell organelles during two meiosis phases: metaphase I and telophase I. The autonomous organelles participate in cytoplasmic inheritance; therefore, their precise distribution to daughter cells determines formation of identical viable microspores. In this study, the course of chondriokinesis during the development of the male gametophyte in Tinantia erecta was analyzed. The study was conducted using optical and transmission electron microscopes. During microsporogenesis in T. erecta, autonomous cell organelles moved in a manner defined as a neutral-equatorial type of chondriokinesis. Therefore, metaphase I plastids and mitochondria were evenly dispersed around the metaphase plate and formed an equatorial plate between the daughter nuclei in early telophase I. Changes in the ultrastructure of plastids and mitochondria during pollen microsporogenesis were also observed.
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Affiliation(s)
- Rafał Marciniec
- Department of Plant Anatomy and Cytology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Emil Zięba
- Confocal and Electron Microscopy Laboratory, Centre for Interdisciplinary Research, John Paul II Catholic University of Lublin, Al. Kraśnicka 102, 20-718, Lublin, Poland
| | - Krystyna Winiarczyk
- Department of Plant Anatomy and Cytology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
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15
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Sui W, Guo K, Li L, Liu S, Takano T, Zhang X. Arabidopsis Ca 2+-dependent nuclease AtCaN2 plays a negative role in plant responses to salt stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:213-222. [PMID: 30824054 DOI: 10.1016/j.plantsci.2018.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/16/2018] [Accepted: 12/08/2018] [Indexed: 06/09/2023]
Abstract
Eukaryotic nucleases are involved in processes such as DNA restriction digestion, repair, recombination, transposition, and programmed cell death (PCD). Studies on the role of nucleases have mostly focused on PCD during plant development, while the information on nucleases involved in responses to different abiotic stress conditions remains limited. Here, we identified a Ca2+-dependent nuclease, AtCaN2, in Arabidopsis thaliana and characterized its activity, expression patterns, and involvement in plant responses to salt stress. AtCaN2 showed a dual endonuclease and exonuclease activity, being able to degrade circular plasmids, RNA, single-stranded DNA, and double-stranded DNA. Expression analysis showed that AtCaN2 was strongly induced in senescent siliques and by salt stress. Overexpression of AtCaN2 decreased the plant tolerance to salt stress conditions, leading to an excessive H2O2 accumulation. However, an atcan2 mutant showed better tolerance to salt stress and a lower level of H2O2 accumulation. Moreover, the expression of several genes (AtAPX1, AtGPX8, and AtSOD1), encoding reactive oxygen species-scavenging enzymes (ascorbate peroxidase 1, glutathione peroxidase 8, and superoxide dismutase 1, respectively), was highly induced in the atcan2 mutant under salt stress conditions. In addition, salt-stress-induced cell death was increased in the AtCaN2-overexpressing transgenic plant but decreased in the atcan2 mutant. On the basis of these findings, we conclude that AtCaN2 plays a negative role in plant tolerance to salt stress. A AtCaN2 knock out could reduce ROS accumulation, decrease ROS-induced PCD, and improve overall plant tolerance.
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Affiliation(s)
- Wenting Sui
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China
| | - Kunyuan Guo
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China
| | - Li Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Tetsuo Takano
- Asian Natural Environment Science Center (ANESC), The University of Tokyo, 1-1-1 Midori Cho, Nishitokyo-shi, Tokyo 188-0002, Japan
| | - Xinxin Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China.
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16
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Shen J, Shou W, Zhang Y, Yuan G, Zhao Y, Chen J, Havey MJ. Rare maternal and biparental transmission of the cucumber mitochondrial DNA reveals sorting of polymorphisms among progenies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1223-1233. [PMID: 30758532 DOI: 10.1007/s00122-018-03274-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/22/2018] [Indexed: 05/28/2023]
Abstract
We used a mitochondrial (mt) mutant of cucumber to document rare maternal transmission of mt polymorphisms and demonstrate that polymorphisms can become more prevalent and sort to progenies to increase mt DNA diversity. The mitochondrial (mt) DNAs of most angiosperms show maternal inheritance, although relatively rare biparental or paternal transmission has been documented. The mt DNAs of plants in the genus Cucumis (family Cucurbitaceae) are paternally transmitted in intra- and interspecific crosses. MSC16 is an inbred line of cucumber (Cucumis sativus) with a mitochondrially associated mosaic (MSC) phenotype. MSC16 was crossed as the male parent to wild-type cultivar Calypso, and hybrid progenies were evaluated for the wild-type phenotype in order to screen for rare maternal or biparental transmission of the mt DNA. We then used standard and droplet digital (dd) PCR to study the transmission of polymorphic mt markers across three generations. We observed evidence for occasional maternal and biparental transmission of the mt DNA in cucumber. The transmission of specific regions of the maternal mt DNA could be as high as 17.8%, although the amounts of these maternal regions were often much lower relative to paternally transmitted regions. Different combinations of maternal and paternal mt polymorphisms were detected in progenies across generations, indicating that relatively rare maternal regions can be transmitted to progenies and become predominant to increase mt DNA diversity over generations.
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Affiliation(s)
- Jia Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weisong Shou
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yuejian Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Gaoya Yuan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinfeng Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Michael J Havey
- USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA.
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17
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Shen J, Zhang Y, Havey MJ, Shou W. Copy numbers of mitochondrial genes change during melon leaf development and are lower than the numbers of mitochondria. HORTICULTURE RESEARCH 2019; 6:95. [PMID: 31645953 PMCID: PMC6804604 DOI: 10.1038/s41438-019-0177-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 06/04/2019] [Accepted: 06/24/2019] [Indexed: 05/17/2023]
Abstract
Melon is a useful plant species for studying mitochondrial genetics because it contains one of the largest and structurally diverse mitochondrial genomes among all plant species and undergoes paternal transmission of mitochondria. We used droplet digital (dd) PCR in combination with flow cytometric determination of nuclear DNA quantities to determine the absolute per-cell copy numbers of four mitochondrial genes (nad9, rps1, matR, and atp6) across four stages of melon leaf development. The copy numbers of these mitochondrial genes not only varied during leaf development but also differed among each other, and there was no correlation between the copy numbers of the mitochondrial genes and their transcript levels. The gene copy numbers varied from approximately 36.8 ± 4.5 (atp6 copies in the 15th leaf) to approximately 82.9 ± 5.7 (nad9 copies in the 9th leaf), while the mean number of mitochondria was approximately 416.6 ± 182.7 in the 15th leaf and 459.1 ± 228.2 in the 9th leaf. These observations indicate that the leaf cells of melon do not contain sufficient copies of mitochondrial genes to ensure that every mitochondrion possesses the entire mitochondrial genome. Given this cytological evidence, our results indicate that mtDNA in melon exists as a sub-genomic molecule rather than as a single-master circle and that the copy numbers of individual mitochondrial genes may vary greatly. An improved understanding of the molecular mechanism(s) controlling the relative prevalence and transmission of sub-genomic mtDNA molecules should provide insights into the continuity of the mitochondrial genome across generations.
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Affiliation(s)
- Jia Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 310021 Hangzhou, China
| | - Yuejian Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 310021 Hangzhou, China
| | - Michael J. Havey
- USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI 53706 USA
| | - Weisong Shou
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 310021 Hangzhou, China
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18
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Izumi M. Discovery of Mitochondrial Endonucleases. PLANT PHYSIOLOGY 2018; 178:1428-1429. [PMID: 30530758 PMCID: PMC6288738 DOI: 10.1104/pp.18.01197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Masanori Izumi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan
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19
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Takami T, Ohnishi N, Kurita Y, Iwamura S, Ohnishi M, Kusaba M, Mimura T, Sakamoto W. Organelle DNA degradation contributes to the efficient use of phosphate in seed plants. NATURE PLANTS 2018; 4:1044-1055. [PMID: 30420711 DOI: 10.1038/s41477-018-0291-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/27/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and chloroplasts (plastids) both harbour extranuclear DNA that originates from the ancestral endosymbiotic bacteria. These organelle DNAs (orgDNAs) encode limited genetic information but are highly abundant, with multiple copies in vegetative tissues, such as mature leaves. Abundant orgDNA constitutes a substantial pool of organic phosphate along with RNA in chloroplasts, which could potentially contribute to phosphate recycling when it is degraded and relocated. However, whether orgDNA is degraded nucleolytically in leaves remains unclear. In this study, we revealed the prevailing mechanism in which organelle exonuclease DPD1 degrades abundant orgDNA during leaf senescence. The DPD1 degradation system is conserved in seed plants and, more remarkably, we found that it was correlated with the efficient use of phosphate when plants were exposed to nutrient-deficient conditions. The loss of DPD1 compromised both the relocation of phosphorus to upper tissues and the response to phosphate starvation, resulting in reduced plant fitness. Our findings highlighted that DNA is also an internal phosphate-rich reservoir retained in organelles since their endosymbiotic origin.
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Affiliation(s)
- Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yuko Kurita
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Shoko Iwamura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Miwa Ohnishi
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
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20
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Ma F, Qi H, Hu YF, Jiang QR, Zhang LG, Xue P, Yang FQ, Wang R, Ju Y, Uchida H, Zhang Q. The Mitochondrial Endonuclease M20 Participates in the Down-Regulation of Mitochondrial DNA in Pollen Cells. PLANT PHYSIOLOGY 2018; 178:1537-1550. [PMID: 30301773 PMCID: PMC6288753 DOI: 10.1104/pp.18.00754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
Maintaining the appropriate number of mitochondrial DNA (mtDNA) molecules is crucial for supporting mitochondrial metabolism and function in both plant and animal cells. For example, a substantial decrease in mtDNA levels occurs as a key part of pollen development. The molecular mechanisms regulating mtDNA copy number are largely unclear, particularly with regard to those that reduce mtDNA levels. Here, we identified and purified a 20-kD endonuclease, M20, from maize (Zea mays) pollen mitochondria. We found M20 to be an His-Asn-His/Asn (H-N-H/N) nuclease that degrades linear and circular DNA in the presence of Mg2+ or Mn2+ Arabidopsis (Arabidopsis thaliana) AtM20, which shared high sequence similarity with maize M20, localized to the mitochondria, had a similar H-N-H/N structure, and degraded both linear and circular DNA. AtM20 transcript levels increased during pollen development, in parallel with a rapid reduction in mtDNA. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome-editing techniques were used to generate knockout lines of AtM20 (atm20), which exhibited a significant delay in the reduction in mtDNA levels in pollen vegetative cells but normal mtDNA levels in somatic cells. The delayed reduction in pollen mtDNA levels was rescued by the transgenic expression of AtM20 in atm20 plants. This study thus uncovers an endonucleolytic DNase in plant mitochondria and its crucial role in reducing mtDNA levels, pointing to the complex mechanism regulating mtDNA levels in plants.
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Affiliation(s)
- Fei Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Qi
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yu-Fei Hu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qian-Ru Jiang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Guang Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
| | - Peng Xue
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fu-Quan Yang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Wang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Ju
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
| | - Hidenobu Uchida
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
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21
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Biology in Bloom: A Primer on the Arabidopsis thaliana Model System. Genetics 2018; 208:1337-1349. [PMID: 29618591 DOI: 10.1534/genetics.118.300755] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
Arabidopsis thaliana could have easily escaped human scrutiny. Instead, Arabidopsis has become the most widely studied plant in modern biology despite its absence from the dinner table. Pairing diminutive stature and genome with prodigious resources and tools, Arabidopsis offers a window into the molecular, cellular, and developmental mechanisms underlying life as a multicellular photoautotroph. Many basic discoveries made using this plant have spawned new research areas, even beyond the verdant fields of plant biology. With a suite of resources and tools unmatched among plants and rivaling other model systems, Arabidopsis research continues to offer novel insights and deepen our understanding of fundamental biological processes.
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22
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Bell KL, Burgess KS, Botsch JC, Dobbs EK, Read TD, Brosi BJ. Quantitative and qualitative assessment of pollen
DNA
metabarcoding using constructed species mixtures. Mol Ecol 2018; 28:431-455. [DOI: 10.1111/mec.14840] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/20/2018] [Accepted: 07/28/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Karen L. Bell
- Department of Environmental Sciences Emory University Atlanta Georgia
| | - Kevin S. Burgess
- Columbus State University Department of Biology Columbus Georgia
| | | | - Emily K. Dobbs
- Department of Environmental Sciences Emory University Atlanta Georgia
| | - Timothy D. Read
- Division of Infectious Diseases Department of Human Genetics School of Medicine Emory University Atlanta Georgia
| | - Berry J. Brosi
- Department of Environmental Sciences Emory University Atlanta Georgia
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23
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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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24
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Ohnishi N, Zhang L, Sakamoto W. VIPP1 Involved in Chloroplast Membrane Integrity Has GTPase Activity in Vitro. PLANT PHYSIOLOGY 2018; 177:328-338. [PMID: 29622686 PMCID: PMC5933125 DOI: 10.1104/pp.18.00145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/29/2018] [Indexed: 05/04/2023]
Abstract
VESICLE-INDUCING PROTEIN IN PLASTID1 (VIPP1) is conserved among oxygenic photosynthetic organisms and appears to have diverged from the bacterial PspA protein. VIPP1 localizes to the chloroplast envelope and thylakoid membrane, where it forms homooligomers of high molecular mass. Although multiple roles of VIPP1 have been inferred, including thylakoid membrane formation, envelope maintenance, membrane fusion, and regulation of photosynthetic activity, its precise role in chloroplast membrane quality control remains unknown. VIPP1 forms an oligomer through its amino-terminal domain and triggers membrane fusion in an Mg2+-dependent manner. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) VIPP1 also exhibits dynamic complex disassembly in response to osmotic and heat stresses in vivo. These results suggest that VIPP1 mediates membrane fusion/remodeling in chloroplasts. Considering that protein machines that regulate intracellular membrane fusion/remodeling events often require a capacity for GTP binding and/or hydrolysis, we questioned whether VIPP1 has similar properties. We conducted an in vitro assay using a purified VIPP1-His fusion protein expressed in Escherichia coli cells. VIPP1-His showed GTP hydrolysis activity that was inhibited competitively by an unhydrolyzable GTP analog, GTPγS, and that depends on GTP binding. It is particularly interesting that the ancestral PspA from E. coli also possesses GTP hydrolysis activity. Although VIPP1 does not contain a canonical G domain, the amino-terminal α-helix was found to be important for both GTP binding and GTP hydrolysis as well as for oligomer formation. Collectively, our results reveal that the properties of VIPP1/PspA are similar to those of GTPases.
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Affiliation(s)
- Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Lingang Zhang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
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25
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Arimura SI. Fission and Fusion of Plant Mitochondria, and Genome Maintenance. PLANT PHYSIOLOGY 2018; 176:152-161. [PMID: 29138352 PMCID: PMC5761811 DOI: 10.1104/pp.17.01025] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/07/2017] [Indexed: 05/18/2023]
Abstract
Dynamic changes maintain a multipartite mitochondrial genome meets the changing needs of plant cells.
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Affiliation(s)
- Shin-Ichi Arimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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26
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Kurusu T, Kuchitsu K. Autophagy, programmed cell death and reactive oxygen species in sexual reproduction in plants. JOURNAL OF PLANT RESEARCH 2017; 130:491-499. [PMID: 28364377 DOI: 10.1007/s10265-017-0934-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/14/2017] [Indexed: 05/18/2023]
Abstract
Autophagy is one of the major cellular processes of recycling of proteins, metabolites and intracellular organelles, and plays crucial roles in the regulation of innate immunity, stress responses and programmed cell death (PCD) in many eukaryotes. It is also essential in development and sexual reproduction in many animals. In plants, although autophagy-deficient mutants of Arabidopsis thaliana show phenotypes in abiotic and biotic stress responses, their life cycle seems normal and thus little had been known until recently about the roles of autophagy in development and reproduction. Rice mutants defective in autophagy show sporophytic male sterility and immature pollens, indicating crucial roles of autophagy during pollen maturation. Enzymatic production of reactive oxygen species (ROS) by respiratory burst oxidase homologues (Rbohs) play multiple roles in regulating anther development, pollen tube elongation and fertilization. Significance of autophagy and ROS in the regulation of PCD of transient cells during plant sexual reproduction is discussed in comparison with animals.
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Affiliation(s)
- Takamitsu Kurusu
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
- Imaging Frontier Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kazuyuki Kuchitsu
- Imaging Frontier Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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27
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Yu Z, O'Farrell PH, Yakubovich N, DeLuca SZ. The Mitochondrial DNA Polymerase Promotes Elimination of Paternal Mitochondrial Genomes. Curr Biol 2017; 27:1033-1039. [PMID: 28318978 DOI: 10.1016/j.cub.2017.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/22/2017] [Accepted: 02/07/2017] [Indexed: 01/09/2023]
Abstract
Mitochondrial DNA (mtDNA) is typically inherited from only one parent [1-3]. In animals, this is usually the mother. Maternal inheritance is often presented as the passive outcome of the difference in cytoplasmic content of egg and sperm; however, active programs enforce uniparental inheritance at two levels, eliminating paternal mitochondrial genomes or destroying mitochondria delivered to the zygote by the sperm [4-13]. Both levels operate in Drosophila [8, 12, 13]. As sperm formation begins, hundreds of doomed mitochondrial genomes are visualized within the two huge mitochondria of each spermatid. These genomes abruptly disappear during spermatogenesis. Genome elimination, which is not in the interests of the restricted genomes, is directed by nuclear genes. Mutation of EndoG, which encodes a mitochondria-targeted endonuclease, retarded elimination [8]. Here, we show that knockdown of the nuclear-encoded mtDNA polymerase (Pol γ-α), Tamas, produces a more complete block of mtDNA elimination. Tamas is found in large particles that localize to mtDNA during genome elimination. We discount a simple possible mechanism by showing that the 3'-exonuclease function of the polymerase is not needed. While DNA elimination is a surprising function for DNA polymerase, it could provide a robust nexus for nuclear control of mitochondrial genome copy number, since use of common interactions for elimination and replication might limit options for the mitochondrial genome to escape restriction. We suggest that the DNA polymerase may play this role more widely and that inappropriate activation of its elimination ability might underlie association of DNA loss syndromes with mutations of the human mtDNA polymerase [14-16].
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Affiliation(s)
- Zhongsheng Yu
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94107, USA
| | - Patrick H O'Farrell
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94107, USA.
| | - Nikita Yakubovich
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94107, USA
| | - Steven Z DeLuca
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94107, USA.
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Primavesi LF, Wu H, Mudd EA, Day A, Jones HD. Visualisation of plastid degradation in sperm cells of wheat pollen. PROTOPLASMA 2017; 254:229-237. [PMID: 26795342 DOI: 10.1007/s00709-015-0935-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
Like most angiosperms, wheat (Triticum aestivum) shows maternal inheritance of plastids. It is thought that this takes place by cytoplasmic stripping at fertilisation rather than the absence of plastids in sperm cells. To determine the fate of plastids during sperm cell development, plastid-targeted green fluorescent protein was used to visualise these organelles in nuclear transgenic wheat lines. Fewer than thirty small 1-2-μm plastids were visible in early uninucleate pollen cells. These dramatically increased to several hundred larger (4 μm) plastids during pollen maturation and went through distinct morphological changes. Only small plastids were visible in generative cells (n = 25) and young sperm cells (n = 9). In mature sperm cells, these green fluorescent protein (GFP)-tagged plastids were absent. This is consistent with maternal inheritance of plastids resulting from their degradation in mature sperm cells in wheat.
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Affiliation(s)
| | - Huixia Wu
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Elisabeth A Mudd
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Anil Day
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Huw D Jones
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
- IBERS, University of Aberystwyth, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK.
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Bell KL, de Vere N, Keller A, Richardson RT, Gous A, Burgess KS, Brosi BJ. Pollen DNA barcoding: current applications and future prospects. Genome 2016; 59:629-40. [DOI: 10.1139/gen-2015-0200] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.
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Affiliation(s)
- Karen L. Bell
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
| | | | - Annemarie Gous
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Berry J. Brosi
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
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Paul P, Röth S, Schleiff E. Importance of organellar proteins, protein translocation and vesicle transport routes for pollen development and function. PLANT REPRODUCTION 2016; 29:53-65. [PMID: 26874709 DOI: 10.1007/s00497-016-0274-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/18/2016] [Indexed: 05/27/2023]
Abstract
Protein translocation. Cellular homeostasis strongly depends on proper distribution of proteins within cells and insertion of membrane proteins into the destined membranes. The latter is mediated by organellar protein translocation and the complex vesicle transport system. Considering the importance of protein transport machineries in general it is foreseen that these processes are essential for pollen function and development. However, the information available in this context is very scarce because of the current focus on deciphering the fundamental principles of protein transport at the molecular level. Here we review the significance of protein transport machineries for pollen development on the basis of pollen-specific organellar proteins as well as of genetic studies utilizing mutants of known organellar proteins. In many cases these mutants exhibit morphological alterations highlighting the requirement of efficient protein transport and translocation in pollen. Furthermore, expression patterns of genes coding for translocon subunits and vesicle transport factors in Arabidopsis thaliana are summarized. We conclude that with the exception of the translocation systems in plastids-the composition and significance of the individual transport systems are equally important in pollen as in other cell types. Apparently for plastids only a minimal translocon, composed of only few subunits, exists in the envelope membranes during maturation of pollen. However, only one of the various transport systems known from thylakoids seems to be required for the function of the "simple thylakoid system" existing in pollen plastids. In turn, the vesicle transport system is as complex as seen for other cell types as it is essential, e.g., for pollen tube formation.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany
| | - Sascha Röth
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany.
- Cluster of Excellence Frankfurt, Goethe University, 60438, Frankfurt Am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, 60438, Frankfurt Am Main, Germany.
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31
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Review and future prospects for DNA barcoding methods in forensic palynology. Forensic Sci Int Genet 2016; 21:110-6. [DOI: 10.1016/j.fsigen.2015.12.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/19/2015] [Accepted: 12/15/2015] [Indexed: 11/18/2022]
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Shen J, Zhao J, Bartoszewski G, Malepszy S, Havey M, Chen J. Persistence and Protection of Mitochondrial DNA in the Generative Cell of Cucumber is Consistent with its Paternal Transmission. PLANT & CELL PHYSIOLOGY 2015; 56:2271-82. [PMID: 26412781 DOI: 10.1093/pcp/pcv140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/18/2015] [Indexed: 05/25/2023]
Abstract
Plants predominantly show maternal transmission of mitochondrial DNA (mtDNA). One known exception is cucumber, in which the mtDNA is paternally inherited. However, the mechanisms regulating this unique mode of transmission are unclear. Here we monitored the amounts of mtDNA throughout the development of cucumber microspores into pollen and observed that mtDNA decreases in the vegetative cell, but persists in the generative cell that ultimately produces the sperm cells. We characterized the cucumber homolog (CsDPD1) of the Arabidopsis gene defective in pollen organelle DNA degradation 1 (AtDPD1), which plays a direct role in mtDNA degradation. CsDPD1 rescued an Arabidopsis AtDPD1 mutant, indicating the same function in both plants. Expression of CsDPD1 coincided with the decrease of mtDNA in pollen, except in the generative cell where both the expression of CsDPD1 and mtDNA levels remained high. Our cytological results confirmed that the persistence of mtDNA in the cucumber generative cell is consistent with its paternal transmission. Our molecular analyses suggest that protection of mtDNA in the generative cell may be the critical factor for paternal mtDNA transmission, rather than mtDNA degradation mediated by CsDPD1. Taken together, these findings indicate that a mechanism may protect paternal mtDNA from degradation and is likely to be the genetic basis of paternal mtDNA transmission.
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Affiliation(s)
- Jia Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Juan Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Lands-ape Architecture, Warsaw University of Life Sciences, ul. Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Lands-ape Architecture, Warsaw University of Life Sciences, ul. Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Michael Havey
- USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China
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Cai Q, Guo L, Shen ZR, Wang DY, Zhang Q. Elevation of Pollen Mitochondrial DNA Copy Number by WHIRLY2: Altered Respiration and Pollen Tube Growth in Arabidopsis. PLANT PHYSIOLOGY 2015; 169. [PMID: 26195569 PMCID: PMC4577393 DOI: 10.1104/pp.15.00437] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In plants, the copy number of the mitochondrial DNA (mtDNA) can be much lower than the number of mitochondria. The biological significance and regulatory mechanisms of this phenomenon remain poorly understood. Here, using the pollen vegetative cell, we examined the role of the Arabidopsis (Arabidopsis thaliana) mtDNA-binding protein WHIRLY2 (AtWHY2). AtWHY2 decreases during pollen development, in parallel with the rapid degradation of mtDNA; to examine the importance of this decrease, we used the pollen vegetative cell-specific promoter Lat52 to express AtWHY2. The transgenic plants (LWHY2) had very high mtDNA levels in pollen, more than 10 times more than in the wild type (ecotype Columbia-0). LWHY2 plants were fertile, morphologically normal, and set seeds; however, reciprocal crosses with heterozygous plants showed reduced transmission of LWHY2-1 through the male and slower growth of LWHY2-1 pollen tubes. We found that LWHY2-1 pollen had significantly more reactive oxygen species and less ATP compared with the wild type, indicating an effect on mitochondrial respiration. These findings reveal that AtWHY2 affects mtDNA copy number in pollen and suggest that low mtDNA copy numbers might be the normal means by which plant cells maintain mitochondrial genetic information.
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Affiliation(s)
- Qiang Cai
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China (Q.C., L.G., Z.-R.S., Q.Z., S.); andKey Laboratory of Ministry of Education for Resource Biology and Biotechnology in Western China, School of Life Science, Northwest University, Xi'an 710069, China (D.-Y.W.)
| | - Liang Guo
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China (Q.C., L.G., Z.-R.S., Q.Z., S.); andKey Laboratory of Ministry of Education for Resource Biology and Biotechnology in Western China, School of Life Science, Northwest University, Xi'an 710069, China (D.-Y.W.)
| | - Zhao-Rui Shen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China (Q.C., L.G., Z.-R.S., Q.Z., S.); andKey Laboratory of Ministry of Education for Resource Biology and Biotechnology in Western China, School of Life Science, Northwest University, Xi'an 710069, China (D.-Y.W.)
| | - Dan-Yang Wang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China (Q.C., L.G., Z.-R.S., Q.Z., S.); andKey Laboratory of Ministry of Education for Resource Biology and Biotechnology in Western China, School of Life Science, Northwest University, Xi'an 710069, China (D.-Y.W.)
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China (Q.C., L.G., Z.-R.S., Q.Z., S.); andKey Laboratory of Ministry of Education for Resource Biology and Biotechnology in Western China, School of Life Science, Northwest University, Xi'an 710069, China (D.-Y.W.)
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López-Fernández MP, Burrieza HP, Rizzo AJ, Martínez-Tosar LJ, Maldonado S. Cellular and molecular aspects of quinoa leaf senescence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:178-187. [PMID: 26259186 DOI: 10.1016/j.plantsci.2015.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 06/04/2023]
Abstract
During leaf senescence, degradation of chloroplasts precede to changes in nuclei and other cytoplasmic organelles, RuBisCO stability is progressively lost, grana lose their structure, plastidial DNA becomes distorted and degraded, the number of plastoglobuli increases and abundant senescence-associated vesicles containing electronically dense particles emerge from chloroplasts pouring their content into the central vacuole. This study examines quinoa leaf tissues during development and senescence using a range of well-established markers of programmed cell death (PCD), including: morphological changes in nuclei and chloroplasts, degradation of RuBisCO, changes in chlorophyll content, DNA degradation, variations in ploidy levels, and changes in nuclease profiles. TUNEL reaction and DNA electrophoresis demonstrated that DNA fragmentation in nuclei occurs at early senescence, which correlates with induction of specific nucleases. During senescence, metabolic activity is high and nuclei endoreduplicate, peaking at 4C. At this time, TEM images showed some healthy nuclei with condensed chromatin and nucleoli. We have found that DNA fragmentation, induction of senescence-associated nucleases and endoreduplication take place during leaf senescence. This provides a starting point for further research aiming to identify key genes involved in the senescence of quinoa leaves.
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Affiliation(s)
- María Paula López-Fernández
- IBBEA (Instituto de Biodiversidad y Biología Experimental y Aplicada), CONICET (Consejo Nacional de Investigaciones Científicas Técnicas). Argentina; DBBE (Departamento de Biodiversidad y Biología Experimental), FCEN (Facultad de Ciencias Exactas y Naturales), UBA (Universidad de Buenos Aires), Int. Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina
| | - Hernán Pablo Burrieza
- IBBEA (Instituto de Biodiversidad y Biología Experimental y Aplicada), CONICET (Consejo Nacional de Investigaciones Científicas Técnicas). Argentina; DBBE (Departamento de Biodiversidad y Biología Experimental), FCEN (Facultad de Ciencias Exactas y Naturales), UBA (Universidad de Buenos Aires), Int. Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina
| | - Axel Joel Rizzo
- DBBE (Departamento de Biodiversidad y Biología Experimental), FCEN (Facultad de Ciencias Exactas y Naturales), UBA (Universidad de Buenos Aires), Int. Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina
| | - Leandro Julián Martínez-Tosar
- IBBEA (Instituto de Biodiversidad y Biología Experimental y Aplicada), CONICET (Consejo Nacional de Investigaciones Científicas Técnicas). Argentina
| | - Sara Maldonado
- IBBEA (Instituto de Biodiversidad y Biología Experimental y Aplicada), CONICET (Consejo Nacional de Investigaciones Científicas Técnicas). Argentina; DBBE (Departamento de Biodiversidad y Biología Experimental), FCEN (Facultad de Ciencias Exactas y Naturales), UBA (Universidad de Buenos Aires), Int. Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina.
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35
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Martín M, Noarbe DM, Serrot PH, Sabater B. The rise of the photosynthetic rate when light intensity increases is delayed in ndh gene-defective tobacco at high but not at low CO2 concentrations. FRONTIERS IN PLANT SCIENCE 2015; 6:34. [PMID: 25709611 PMCID: PMC4321573 DOI: 10.3389/fpls.2015.00034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 01/13/2015] [Indexed: 05/02/2023]
Abstract
The 11 plastid ndh genes have hovered frequently on the edge of dispensability, being absent in the plastid DNA of many algae and certain higher plants. We have compared the photosynthetic activity of tobacco (Nicotiana tabacum, cv. Petit Havana) with five transgenic lines (ΔndhF, pr-ΔndhF, T181D, T181A, and ndhF FC) and found that photosynthetic performance is impaired in transgenic ndhF-defective tobacco plants at rapidly fluctuating light intensities and higher than ambient CO2 concentrations. In contrast to wild type and ndhF FC, which reach the maximum photosynthetic rate in less than 1 min when light intensity suddenly increases, ndh defective plants (ΔndhF and T181A) show up to a 5 min delay in reaching the maximum photosynthetic rate at CO2 concentrations higher than the ambient 360 ppm. Net photosynthesis was determined at different CO2 concentrations when sequences of 130, 870, 61, 870, and 130 μmol m(-2) s(-1) PAR sudden light changes were applied to leaves and photosynthetic efficiency and entropy production (Sg) were determined as indicators of photosynthesis performance. The two ndh-defective plants, ΔndhF and T181A, had lower photosynthetic efficiency and higher Sg than wt, ndhF FC and T181D tobacco plants, containing full functional ndh genes, at CO2 concentrations above 400 ppm. We propose that the Ndh complex improves cyclic electron transport by adjusting the redox level of transporters during the low light intensity stage. In ndhF-defective strains, the supply of electrons through the Ndh complex fails, transporters remain over-oxidized (specially at high CO2 concentrations) and the rate of cyclic electron transport is low, impairing the ATP level required to rapidly reach high CO2 fixation rates in the following high light phase. Hence, ndh genes could be dispensable at low but not at high atmospheric concentrations of CO2.
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Affiliation(s)
- Mercedes Martín
- Department of Life Sciences, University of Alcalá, Alcalá de HenaresSpain
| | - Dolores M. Noarbe
- Department of Physical Chemistry, University of Alcalá, Alcalá de HenaresSpain
| | - Patricia H. Serrot
- Department of Life Sciences, University of Alcalá, Alcalá de HenaresSpain
| | - Bartolomé Sabater
- Department of Life Sciences, University of Alcalá, Alcalá de HenaresSpain
- *Correspondence: Bartolomé Sabater, Department of Life Sciences, University of Alcalá, Alcalá de Henares, 28805 Madrid, Spain e-mail:
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Furuta KM, Yadav SR, Lehesranta S, Belevich I, Miyashima S, Heo JO, Vatén A, Lindgren O, De Rybel B, Van Isterdael G, Somervuo P, Lichtenberger R, Rocha R, Thitamadee S, Tähtiharju S, Auvinen P, Beeckman T, Jokitalo E, Helariutta Y. Plant development. Arabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation. Science 2014; 345:933-7. [PMID: 25081480 DOI: 10.1126/science.1253736] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Photoassimilates such as sugars are transported through phloem sieve element cells in plants. Adapted for effective transport, sieve elements develop as enucleated living cells. We used electron microscope imaging and three-dimensional reconstruction to follow sieve element morphogenesis in Arabidopsis. We show that sieve element differentiation involves enucleation, in which the nuclear contents are released and degraded in the cytoplasm at the same time as other organelles are rearranged and the cytosol is degraded. These cellular reorganizations are orchestrated by the genetically redundant NAC domain-containing transcription factors, NAC45 and NAC86 (NAC45/86). Among the NAC45/86 targets, we identified a family of genes required for enucleation that encode proteins with nuclease domains. Thus, sieve elements differentiate through a specialized autolysis mechanism.
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Affiliation(s)
- Kaori Miyashima Furuta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Shri Ram Yadav
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Satu Lehesranta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Ilya Belevich
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Shunsuke Miyashima
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Jung-ok Heo
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Anne Vatén
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Ove Lindgren
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium. Department of Plant System Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
| | - Gert Van Isterdael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium. Department of Plant System Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
| | - Panu Somervuo
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Raffael Lichtenberger
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Raquel Rocha
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Siripong Thitamadee
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Sari Tähtiharju
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Petri Auvinen
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium. Department of Plant System Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
| | - Eija Jokitalo
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland.
| | - Ykä Helariutta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland. Cardiff University Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK. The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.
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Sakamoto W, Takami T. Nucleases in higher plants and their possible involvement in DNA degradation during leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3835-43. [PMID: 24634485 DOI: 10.1093/jxb/eru091] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
During leaf senescence, macromolecules such as proteins and lipids are known to be degraded for redistribution into upper tissues. Similarly, nucleic acids appear to undergo fragmentation or degradation during senescence, but the physiological role of nucleic acid degradation, particularly of genomic DNA degradation, remains unclear. To date, more than a dozen of plant deoxyribonucleases have been reported, whereas it remains to be verified whether any of them degrade DNA during leaf senescence. This review summarizes current knowledge related to the plant nucleases that are induced developmentally or in a tissue-specific manner and are known to degrade DNA biochemically. Of these, several endonucleases (BFN1, CAN1, and CAN2) and an exonuclease (DPD1) in Arabidopsis seem to act in leaf senescence because they were shown to be inducible at the transcript level. This review specifically examines DPD1, which is dual-targeted to chloroplasts and mitochondria. Results show that, among the exonuclease family to which DPD1 belongs, DPD1 expression is extraordinary when estimated using a microarray database. DPD1 is the only example among the nucleases in which DNA degradation has been confirmed in vivo in pollen by mutant analysis. These data imply a significant role of organelle DNA degradation during leaf senescence and implicate DPD1 as a potential target for deciphering nucleotide salvage in plants.
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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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38
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Hu J, Huang W, Huang Q, Qin X, Yu C, Wang L, Li S, Zhu R, Zhu Y. Mitochondria and cytoplasmic male sterility in plants. Mitochondrion 2014; 19 Pt B:282-8. [PMID: 24566371 DOI: 10.1016/j.mito.2014.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
Abstract
Mitochondria are essential organelles in cells not only because they supply over 90% of the cell's energy but also because their dysfunction is associated with disease. Owing to the importance of mitochondria, there are many questions about mitochondria that must be answered. Cytoplasmic male sterility (CMS) is a mysterious natural phenomenon, and the mechanism of the origin of CMS is unknown. Despite successful utilization of CMS and restoration of fertility (Rf) in practice, the underlying mechanisms of these processes remain elusive. This review summarizes the genes involved in CMS and Rf, with a special focus on recent studies reporting the mechanisms of the CMS and Rf pathways, and concludes with potential working models.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Qi Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Xiaojian Qin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Changchun Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Lili Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Hubei 430072, China.
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39
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McCauley DE. Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes. THE NEW PHYTOLOGIST 2013; 200:966-77. [PMID: 23952142 DOI: 10.1111/nph.12431] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/25/2013] [Indexed: 05/25/2023]
Abstract
Plant mitochondrial genomes are usually transmitted to the progeny from the maternal parent. However, cases of paternal transmission are known and are perhaps more common than once thought. This review will consider recent evidence, both direct and indirect, of paternal transmission (leakage) of the mitochondrial genome of seed plants, especially in natural populations, and how this can result in offspring that carry a mixture of maternally and paternally derived copies of the genome; a type of heteroplasmy. It will further consider how this heteroplasmy facilitates recombination between genetically distinct partners; a process that can enhance mitochondrial genotypic diversity. This will then form the basis for a discussion of five evolutionary questions that arise from these observations. Questions include how plant mitochondrial genome evolution can be placed on a sexual to asexual continuum, whether cytoplasmic male sterility (CMS) facilitates the evolution of paternal leakage, whether paternal leakage is more likely in populations undergoing admixture, how leakage influences patterns of gene flow, and whether heteroplasmy occurs in natural populations at a frequency greater than predicted by crossing experiments. It is proposed that each of these questions offers fertile ground for future research on a diversity of plant species.
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Affiliation(s)
- David E McCauley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
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Kabeya Y, Miyagishima SY. Chloroplast DNA replication is regulated by the redox state independently of chloroplast division in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2013; 161:2102-12. [PMID: 23447524 PMCID: PMC3613479 DOI: 10.1104/pp.113.216291] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chloroplasts arose from a cyanobacterial endosymbiont and multiply by division. In algal cells, chloroplast division is regulated by the cell cycle so as to occur only once, in the S phase. Chloroplasts possess multiple copies of their own genome that must be replicated during chloroplast proliferation. In order to examine how chloroplast DNA replication is regulated in the green alga Chlamydomonas reinhardtii, we first asked whether it is regulated by the cell cycle, as is the case for chloroplast division. Chloroplast DNA is replicated in the light and not the dark phase, independent of the cell cycle or the timing of chloroplast division in photoautotrophic culture. Inhibition of photosynthetic electron transfer blocked chloroplast DNA replication. However, chloroplast DNA was replicated when the cells were grown heterotrophically in the dark, raising the possibility that chloroplast DNA replication is coupled with the reducing power supplied by photosynthesis or the uptake of acetate. When dimethylthiourea, a reactive oxygen species scavenger, was added to the photoautotrophic culture, chloroplast DNA was replicated even in the dark. In contrast, when methylviologen, a reactive oxygen species inducer, was added, chloroplast DNA was not replicated in the light. Moreover, the chloroplast DNA replication activity in both the isolated chloroplasts and nucleoids was increased by dithiothreitol, while it was repressed by diamide, a specific thiol-oxidizing reagent. These results suggest that chloroplast DNA replication is regulated by the redox state that is sensed by the nucleoids and that the disulfide bonds in nucleoid-associated proteins are involved in this regulatory activity.
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41
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Sato M, Sato K. Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1979-84. [PMID: 23524114 DOI: 10.1016/j.bbamcr.2013.03.010] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/06/2013] [Accepted: 03/10/2013] [Indexed: 10/27/2022]
Abstract
The mitochondrion is an organelle that has its own DNA (mtDNA). Mitochondria play essential roles in energy production and in various cellular processes such as metabolism and signal transduction. In most animals, including humans, although the sperm-derived paternal mitochondria enter the oocyte cytoplasm after fertilization, their mtDNA is never transmitted to the offspring. This pattern of mtDNA inheritance is well known as "maternal inheritance." However, how the paternal mitochondria and mtDNA are eliminated from the cytoplasm of gametes or zygotes remains an enigma. Recently, a variety of mechanisms, including specific nuclease-dependent systems, ubiquitin-proteasome system, and autophagy have been shown to degrade the paternal mtDNA or the paternal mitochondria themselves in order to prevent paternal mtDNA transmission. In this review, we will address the current state of knowledge of the molecular mechanisms underlying the elimination of paternal mtDNA or mitochondrial structures for ensuring the maternal transmission of mtDNA.
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Affiliation(s)
- Miyuki Sato
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
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42
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Zhang B, Carrie C, Ivanova A, Narsai R, Murcha MW, Duncan O, Wang Y, Law SR, Albrecht V, Pogson B, Giraud E, Van Aken O, Whelan J. LETM proteins play a role in the accumulation of mitochondrially encoded proteins in Arabidopsis thaliana and AtLETM2 displays parent of origin effects. J Biol Chem 2012; 287:41757-73. [PMID: 23043101 PMCID: PMC3516725 DOI: 10.1074/jbc.m112.383836] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 10/01/2012] [Indexed: 11/06/2022] Open
Abstract
The Arabidopsis thaliana genome contains two genes with homology to the mitochondrial protein LETM1 (leucine zipper-EF-hand-containing transmembrane protein). Inactivation of both genes, Atletm1 and Atletm2, together is lethal. Plants that are hemizygous for AtLETM2 and homozygous for Atletm1 (letm1(-/-) LETM2(+/-)) displayed a mild retarded growth phenotype during early seedling growth. It was shown that accumulation of mitochondrial proteins was reduced in hemizygous (letm1(-/-) LETM2(+/-)) plants. Examination of respiratory chain proteins by Western blotting, blue native PAGE, and enzymatic activity assays revealed that the steady state level of ATP synthase was reduced in abundance, whereas the steady state levels of other respiratory chain proteins remained unchanged. The absence of a functional maternal AtLETM2 allele in an Atletm1 mutant background resulted in early seed abortion. Reciprocal crosses revealed that maternally, but not paternally, derived AtLETM2 was absolutely required for seed development. This requirement for a functional maternal allele of AtLETM2 was confirmed using direct sequencing of reciprocal crosses of Col-0 and Ler accessions. Furthermore, AtLETM2 promoter β-glucuronidase constructs displayed exclusive maternal expression patterns.
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Affiliation(s)
- Botao Zhang
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Chris Carrie
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Aneta Ivanova
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Reena Narsai
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
- Centre for Computational Systems Biology, Bayliss Building M316 University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia and
| | - Monika W. Murcha
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Owen Duncan
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Yan Wang
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Simon R. Law
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Verónica Albrecht
- the Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton 2601, Australian Capital Territory, Australia
| | - Barry Pogson
- the Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton 2601, Australian Capital Territory, Australia
| | - Estelle Giraud
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - Olivier Van Aken
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
| | - James Whelan
- From the Australian Research Council Centre of Excellence in Plant Energy Biology and
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43
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A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:253-9. [PMID: 22683762 DOI: 10.1016/j.bbamcr.2012.05.029] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/26/2012] [Accepted: 05/28/2012] [Indexed: 01/08/2023]
Abstract
Over 100 proteins are found in both mitochondria and chloroplasts, via a variety of processes known generally as 'dual-targeting'. Dual-targeting has attracted interest from many different research groups because of its profound implications concerning the mechanisms of protein import into these organelles and the evolution of both the protein import machinery and the targeting sequences within the imported proteins. Beyond these aspects, dual-targeting is also interesting for its implications concerning shared functions between mitochondria and chloroplasts, and especially the control of the activities of these two very different energy organelles. We discuss each of these points in the light of the latest relevant research findings and make some suggestions for where research might be most illuminating in the near future. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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DeLuca SZ, O'Farrell PH. Barriers to male transmission of mitochondrial DNA in sperm development. Dev Cell 2012; 22:660-8. [PMID: 22421049 DOI: 10.1016/j.devcel.2011.12.021] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/09/2011] [Accepted: 12/25/2011] [Indexed: 11/19/2022]
Abstract
Across the eukaryotic phylogeny, offspring usually inherit their mitochondrial genome from only one of two parents: in animals, the female. Although mechanisms that eliminate paternally derived mitochondria from the zygote have been sought, the developmental stage at which paternal transmission of mitochondrial DNA is restricted is unknown in most animals. Here, we show that the mitochondria of mature Drosophila sperm lack DNA, and we uncover two processes that eliminate mitochondrial DNA during spermatogenesis. Visualization of mitochondrial DNA nucleoids revealed their abrupt disappearance from developing spermatids in a process requiring the mitochondrial nuclease, Endonuclease G. In Endonuclease G mutants, persisting nucleoids are swept out of spermatids by a cellular remodeling process that trims and shapes spermatid tails. Our results show that mitochondrial DNA is eliminated during spermatogenesis, thereby removing the capacity of sperm to transmit the mitochondrial genome to the next generation.
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Affiliation(s)
- Steven Z DeLuca
- Department of Biochemistry, UCSF, San Francisco, CA 94110, USA
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45
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Su X, Zhu X, Zhang C, Xiao X, Zhao M. In situ, real-time monitoring of the 3' to 5' exonucleases secreted by living cells. Anal Chem 2012; 84:5059-65. [PMID: 22559334 DOI: 10.1021/ac300745f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes containing 3'-5' exonuclease activities play vital roles in maintaining genome stability. Though a wide variety of methods have been developed for detection of these enzymes, few of them can be directly applied for in situ and real-time monitoring of the secretion of these active substances by living cells. Taking advantages of the free 3'-end of stacked guanine-quenched photoinduced electron transfer fluorescent probes, here we demonstrate a novel assay capable of in situ and real-time monitoring of the 3'-5' exonucleases secreted by living cells. The detection limit of the new method achieved as low as 0.04 U/mL, allowing direct monitoring of the target enzymes in an extracellular environment without preconcentration steps. False positive signals caused by other nonspecific enzymes were easily ruled out by the use of a control probe with the 3'-end modified with exonuclease-resistant phosphorothioate guanines. Using Alexa Fluor 488 as the fluorophore, the probe is adaptable to a wide range of pH conditions. The approach was successfully applied for in situ, real-time monitoring of the 3'-5' exonucleases secreted by suspension cells of Arabidopsis thaliana. It also holds great potential for in situ and real-time detection of many other DNA end-processing enzymes produced by other types of cells.
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Affiliation(s)
- Xin Su
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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46
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Tang LY, Matsushima R, Sakamoto W. Mutations defective in ribonucleotide reductase activity interfere with pollen plastid DNA degradation mediated by DPD1 exonuclease. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:637-49. [PMID: 22239102 DOI: 10.1111/j.1365-313x.2012.04904.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Organellar DNAs in mitochondria and plastids are present in multiple copies and make up a substantial proportion of total cellular DNA despite their limited genetic capacity. We recently demonstrated that organellar DNA degradation occurs during pollen maturation, mediated by the Mg(2+) -dependent organelle exonuclease DPD1. To further understand organellar DNA degradation, we characterized a distinct mutant (dpd2). In contrast to the dpd1 mutant, which retains both plastid and mitochondrial DNAs, dpd2 showed specific accumulation of plastid DNAs. Multiple abnormalities in vegetative and reproductive tissues of dpd2 were also detected. DPD2 encodes the large subunit of ribonucleotide reductase, an enzyme that functions at the rate-limiting step of de novo nucleotide biosynthesis. We demonstrated that the defects in ribonucleotide reductase indirectly compromise the activity of DPD1 nuclease in plastids, thus supporting a different regulation of organellar DNA degradation in pollen. Several lines of evidence provided here reinforce our previous conclusion that the DPD1 exonuclease plays a central role in organellar DNA degradation, functioning in DNA salvage rather than maternal inheritance during pollen development.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Exoribonucleases/genetics
- Exoribonucleases/metabolism
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genetic Complementation Test
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Microscopy, Electron, Scanning
- Microscopy, Fluorescence
- Mutation
- Phenotype
- Plants, Genetically Modified
- Plastids/genetics
- Pollen/genetics
- Pollen/ultrastructure
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleotide Reductases/genetics
- Ribonucleotide Reductases/metabolism
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Affiliation(s)
- Lay Yin Tang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
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47
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Liu L. Ultrastructural study on dynamics of plastids and mitochondria during microgametogenesis in watermelon. Micron 2012; 43:412-7. [DOI: 10.1016/j.micron.2011.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Revised: 10/06/2011] [Accepted: 10/14/2011] [Indexed: 11/16/2022]
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48
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Oshima M, Handa H. The identification of quantitative trait loci that control the paternal inheritance of a mitochondrial plasmid in rapeseed ( Brassica napus L.). Genes Genet Syst 2012; 87:19-27. [DOI: 10.1266/ggs.87.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Masao Oshima
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Hirokazu Handa
- Graduate School of Life and Environmental Sciences, University of Tsukuba
- Plant Genome Research Unit, National Institute of Agrobiological Sciences
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49
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Tang LY, Sakamoto W. Tissue-specific organelle DNA degradation mediated by DPD1 exonuclease. PLANT SIGNALING & BEHAVIOR 2011; 6:1391-3. [PMID: 21852754 PMCID: PMC3258073 DOI: 10.4161/psb.6.9.16595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 05/21/2023]
Abstract
Organelle DNA in plastids and mitochondria is present in multiple copies and undergoes degradation developmentally. For example, organelle DNA that is detectable cytologically using DNA-fluorescent dye disappears during pollen development. Nevertheless, nucleases involved in this degradation process remain unknown. Our recent study identified the organelle nuclease, DPD1, which has Mg2+ -dependent exonuclease activity in vitro. The discovery of DPD1 emerged from Arabidopsis mutant screening and concomitant isolation of dpd1 mutants that retain organelle DNA in mature pollen. DPD1 is conserved only in angiosperms: not in other photosynthetic organisms. Despite these findings, the physiological significance of organelle DNA degradation during pollen development remains unclear because dpd1 exhibits no apparent defects in pollen viability or in the maternal inheritance of organelle DNA. We discuss a possible role of organelle DNA degradation mediated by DPD1, based on a DPD1 expression profile studied using in silico analyses.
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Affiliation(s)
- Lay Yin Tang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
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