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Ditz N, Braun HP, Eubel H. Protein assemblies in the Arabidopsis thaliana chloroplast compartment. FRONTIERS IN PLANT SCIENCE 2024; 15:1380969. [PMID: 39220006 PMCID: PMC11362043 DOI: 10.3389/fpls.2024.1380969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/30/2024] [Indexed: 09/04/2024]
Abstract
Introduction Equipped with a photosynthetic apparatus that uses the energy of solar radiation to fuel biosynthesis of organic compounds, chloroplasts are the metabolic factories of mature leaf cells. The first steps of energy conversion are catalyzed by a collection of protein complexes, which can dynamically interact with each other for optimizing metabolic efficiency under changing environmental conditions. Materials and methods For a deeper insight into the organization of protein assemblies and their roles in chloroplast adaption to changing environmental conditions, an improved complexome profiling protocol employing a MS-cleavable cross-linker is used to stabilize labile protein assemblies during the organelle isolation procedure. Results and discussion Changes in protein:protein interaction patterns of chloroplast proteins in response to four different light intensities are reported. High molecular mass assemblies of central chloroplast electron transfer chain components as well as the PSII repair machinery react to different light intensities. In addition, the chloroplast encoded RNA-polymerase complex was found to migrate at a molecular mass of ~8 MDa, well above its previously reported molecular mass. Complexome profiling data produced during the course of this study can be interrogated by interested readers via a web-based online resource (https://complexomemap.de/projectsinteraction-chloroplasts).
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Affiliation(s)
| | | | - Holger Eubel
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
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2
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Li J, Chen S, Zhang Y, Zhao W, Yang J, Fan Y. A novel PLS-DYW type PPR protein OsASL is essential for chloroplast development in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112134. [PMID: 38810885 DOI: 10.1016/j.plantsci.2024.112134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/30/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Oryza longistaminata (OL), an AA-genome African wild rice which can propagate clonally via rhizome, is an important germplasm for improvement of Asian cultivated rice, however recessive lethal alleles can hitchhike clonal propagation in heterozygous state. Selfing of OL is difficult due to its self-incompatibility, but simple selfing of hybrid progeny between OL and O. sativa is effective to disclose and eliminate recessive lethal alleles. Here, we identified an exhibited albino-lethal phenotype mutant, from an F2 population between OL and O. sativa, named it albino seedling-lethal (asl). The leaves of asl mutant showed abnormal chloroplast development. The albino characteristics of asl were determined to be governed by a set of recessive nuclear genes through genetic analysis. Map-based cloning experiments found that a single nucleotide variation (G to A) was detected in the exon of OsASL in OL, which causes a premature stop codon. OsASL encodes a PLS-type PPR protein with 12 pentratricopeptide repeat domains, and is translocalized to chloroplasts. Complementation and knockout transgenic experiments further confirmed that OsASL is responsible for the albino-lethal phenotype. Loss-of-function OsASL (i.e. osasl) resulted in devoid of intron splicing of chloroplast RNA atpF, ndhA, rpl2 and rps12, and also RNA editing of ndhB, but facilitates the RNA editing of rpl2 in the plastid. Transcriptome sequencing showed that OsASL was mainly involved in chlorophyll synthesis pathway. The expression of Chlorophyll-associated genes were significantly decreased in asl plants, especially PEP (plastid-encoded RNA polymerase)-mediated genes. Our results suggest that OsASL is crucial for RNA editing, RNA splicing of chloroplast RNA group II genes, and plays an essential role in chloroplast development during early leaf development in rice.
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Affiliation(s)
- Jie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Shufang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weidong Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiangyi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
| | - Yourong Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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3
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Zhu L, Li X, Yang Z, Hao C, Li H, Qin X. The yellow-cotyledon gene (ATYCO) is a crucial factor for thylakoid formation and photosynthesis regulation in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112208. [PMID: 39089330 DOI: 10.1016/j.plantsci.2024.112208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/12/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
Chloroplast development underpins plant growth, by facilitating not only photosynthesis but also other essential biochemical processes. Nonetheless, the regulatory mechanisms and functional components of chloroplast development remain largely uncharacterized due to their complexity. In our study, we identified a plastid-targeted gene, ATYCO/RP8/CDB1, as a critical factor in early chloroplast development in Arabidopsis thaliana. YCO knock-out mutant (yco) exhibited a seedling-lethal, albino phenotype, resulting from dysfunctional chloroplasts lacking thylakoid membranes. Conversely, YCO knock-down mutants produced a chlorophyll-deficient cotyledon and normal leaves when supplemented with sucrose. Transcription analysis also revealed that YCO deficiency could be partially compensated by sucrose supplementation, and that YCO played different roles in the cotyledons and the true leaves. In YCO knock-down mutants, the transcript levels of plastid-encoded RNA polymerase (PEP)-dependent genes and nuclear-encoded photosynthetic genes, as well as the accumulation of photosynthetic proteins, were significantly reduced in the cotyledons. Moreover, the chlorophyll-deficient phenotype in YCO knock-down line can be effectively suppressed by inhibition of PSI cyclic electron transport activity, implying an interaction between YCO and PSI cyclic electron transport. Taken together, our findings de underscore the vital role of YCO in early chloroplast development and photosynthesis.
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Affiliation(s)
- Lixia Zhu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xiuxiu Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Zonghui Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chenyang Hao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China.
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4
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Florez-Rueda AM, Miguel CM, Figueiredo DD. Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1134-1157. [PMID: 38709819 DOI: 10.1111/tpj.16786] [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: 10/13/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.
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Affiliation(s)
- Ana Marcela Florez-Rueda
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Karl-Liebknechts-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Célia M Miguel
- Faculty of Sciences, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Lisboa, Portugal
| | - Duarte D Figueiredo
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
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5
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Fujii S, Wada H, Kobayashi K. Orchestration of Photosynthesis-Associated Gene Expression and Galactolipid Biosynthesis during Chloroplast Differentiation in Plants. PLANT & CELL PHYSIOLOGY 2024; 65:1014-1028. [PMID: 38668647 PMCID: PMC11209550 DOI: 10.1093/pcp/pcae049] [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: 10/05/2023] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 06/28/2024]
Abstract
The chloroplast thylakoid membrane is composed of membrane lipids and photosynthetic protein complexes, and the orchestration of thylakoid lipid biosynthesis and photosynthesis-associated protein accumulation is considered important for thylakoid development. Galactolipids consist of ∼80% of the thylakoid lipids, and their biosynthesis is fundamental for chloroplast development. We previously reported that the suppression of galactolipid biosynthesis decreased the expression of photosynthesis-associated nuclear-encoded genes (PhAPGs) and photosynthesis-associated plastid-encoded genes (PhAPGs). However, the mechanism for coordinative regulation between galactolipid biosynthesis in plastids and the expression of PhANGs and PhAPGs remains largely unknown. To elucidate this mechanism, we investigated the gene expression patterns in galactolipid-deficient Arabidopsis seedlings during the de-etiolation process. We found that galactolipids are crucial for inducing both the transcript accumulation of PhANGs and PhAPGs and the accumulation of plastid-encoded photosynthesis-associated proteins in developing chloroplasts. Genetic analysis indicates the contribution of the GENOMES UNCOUPLED1 (GUN1)-mediated plastid-to-nucleus signaling pathway to PhANG regulation in response to galactolipid levels. Previous studies suggested that the accumulation of GUN1 reflects the state of protein homeostasis in plastids and alters the PhANG expression level. Thus, we propose a model that galactolipid biosynthesis determines the protein homeostasis in plastids in the initial phase of de-etiolation and optimizes GUN1-dependent signaling to regulate the PhANG expression. This mechanism might contribute to orchestrating the biosynthesis of lipids and proteins for the biogenesis of functional chloroplasts in plants.
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Affiliation(s)
- Sho Fujii
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561 Japan
| | - Hajime Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902 Japan
| | - Koichi Kobayashi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan
- Faculty of Liberal Arts, Science and Global Education, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan
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6
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Willige BC, Yoo CY, Saldierna Guzmán JP. What is going on inside of phytochrome B photobodies? THE PLANT CELL 2024; 36:2065-2085. [PMID: 38511271 PMCID: PMC11132900 DOI: 10.1093/plcell/koae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 03/22/2024]
Abstract
Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.
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Affiliation(s)
- Björn Christopher Willige
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Chan Yul Yoo
- School of Biological Sciences, University of Utah, UT 84112, USA
| | - Jessica Paola Saldierna Guzmán
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
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Nishimura Y. Plastid Nucleoids: Insights into Their Shape and Dynamics. PLANT & CELL PHYSIOLOGY 2024; 65:551-559. [PMID: 37542434 DOI: 10.1093/pcp/pcad090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/07/2023]
Abstract
Chloroplasts/plastids are unique organelles found in plant cells and some algae and are responsible for performing essential functions such as photosynthesis. The plastid genome, consisting of circular and linear DNA molecules, is packaged and organized into specialized structures called nucleoids. The composition and dynamics of these nucleoids have been the subject of intense research, as they are critical for proper plastid functions and development. In this mini-review, recent advances in understanding the organization and regulation of plastid nucleoids are overviewed, with a focus on the various proteins and factors that regulate the shape and dynamics of nucleoids, including DNA-binding proteins and membrane anchorage proteins. The dynamic nature of nucleoid organization, which is influenced by a variety of developmental cues and the cell cycle, is also examined.
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Affiliation(s)
- Yoshiki Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kita-Shirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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Xu M, Zhang X, Cao J, Liu J, He Y, Guan Q, Tian X, Tang J, Li X, Ren D, Bu Q, Wang Z. OsPGL3A encodes a DYW-type pentatricopeptide repeat protein involved in chloroplast RNA processing and regulated chloroplast development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:29. [PMID: 38549701 PMCID: PMC10965880 DOI: 10.1007/s11032-024-01468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 04/24/2024]
Abstract
The chloroplast serves as the primary site of photosynthesis, and its development plays a crucial role in regulating plant growth and morphogenesis. The Pentatricopeptide Repeat Sequence (PPR) proteins constitute a vast protein family that function in the post-transcriptional modification of RNA within plant organelles. In this study, we characterized mutant of rice with pale green leaves (pgl3a). The chlorophyll content of pgl3a at the seedling stage was significantly reduced compared to the wild type (WT). Transmission electron microscopy (TEM) and quantitative PCR analysis revealed that pgl3a exhibited aberrant chloroplast development compared to the wild type (WT), accompanied by significant alterations in gene expression levels associated with chloroplast development and photosynthesis. The Mutmap analysis revealed that a single base deletionin the coding region of Os03g0136700 in pgl3a. By employing CRISPR/Cas9 mediated gene editing, two homozygous cr-pgl3a mutants were generated and exhibited a similar phenotype to pgl3a, thereby confirming that Os03g0136700 was responsible for pgl3a. Consequently, it was designated as OsPGL3A. OsPGL3A belongs to the DYW-type PPR protein family and is localized in chloroplasts. Furthermore, we demonstrated that the RNA editing efficiency of rps8-182 and rpoC2-4106, and the splicing efficiency of ycf3-1 were significantly decreased in pgl3a mutants compared to WT. Collectively, these results indicate that OsPGL3A plays a crucial role in chloroplast development by regulating the editing and splicing of chloroplast genes in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01468-7.
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Affiliation(s)
- Min Xu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xinying Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Jinzhe Cao
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Jiali Liu
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Yiyuan He
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qingjie Guan
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Jiaqi Tang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Xiufeng Li
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Zhenyu Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
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do Prado PFV, Ahrens FM, Liebers M, Ditz N, Braun HP, Pfannschmidt T, Hillen HS. Structure of the multi-subunit chloroplast RNA polymerase. Mol Cell 2024; 84:910-925.e5. [PMID: 38428434 DOI: 10.1016/j.molcel.2024.02.003] [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: 09/25/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.
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Affiliation(s)
- Paula F V do Prado
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Frederik M Ahrens
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Monique Liebers
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Noah Ditz
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Thomas Pfannschmidt
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Hauke S Hillen
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Research Group Structure and Function of Molecular Machines, University of Göttingen, 37077 Göttingen, Germany.
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10
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Vergara-Cruces Á, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW. Structure of the plant plastid-encoded RNA polymerase. Cell 2024; 187:1145-1159.e21. [PMID: 38428394 DOI: 10.1016/j.cell.2024.01.036] [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: 10/10/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 03/03/2024]
Abstract
Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation.
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Affiliation(s)
- Ángel Vergara-Cruces
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ishika Pramanick
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David Pearce
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Vinod K Vogirala
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Matthew J Byrne
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2050, Australia
| | - Michael W Webster
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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11
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Wu XX, Mu WH, Li F, Sun SY, Cui CJ, Kim C, Zhou F, Zhang Y. Cryo-EM structures of the plant plastid-encoded RNA polymerase. Cell 2024; 187:1127-1144.e21. [PMID: 38428393 DOI: 10.1016/j.cell.2024.01.026] [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: 10/10/2023] [Revised: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
Abstract
Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts.
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Affiliation(s)
- Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen-Hui Mu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Fan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shu-Yi Sun
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao-Jun Cui
- University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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12
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Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. Proc Natl Acad Sci U S A 2024; 121:e2311480121. [PMID: 38354263 PMCID: PMC10895346 DOI: 10.1073/pnas.2311480121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spanning approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP in the absence of iNTP bound at the active site and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG, or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms and organelle.
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Affiliation(s)
- M. Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
| | - Masahiko Imashimizu
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba305-8565, Japan
| | - Miron Leanca
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Rishi K. Vishwakarma
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
| | - Amber Riaz-Bradley
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Yulia Yuzenkova
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
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13
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Bychkov IA, Andreeva AA, Vankova R, Lacek J, Kudryakova NV, Kusnetsov VV. Modified Crosstalk between Phytohormones in Arabidopsis Mutants for PEP-Associated Proteins. Int J Mol Sci 2024; 25:1586. [PMID: 38338865 PMCID: PMC10855609 DOI: 10.3390/ijms25031586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Plastid-encoded RNA polymerase (PEP) forms a multisubunit complex in operating chloroplasts, where PEP subunits and a sigma factor are tightly associated with 12 additional nuclear-encoded proteins. Mutants with disrupted genes encoding PEP-associated proteins (PAPs) provide unique tools for deciphering mutual relationships among phytohormones. A block of chloroplast biogenesis in Arabidopsis pap mutants specifying highly altered metabolism in white tissues induced dramatic fluctuations in the content of major phytohormones and their metabolic genes, whereas hormone signaling circuits mostly remained functional. Reprogramming of the expression of biosynthetic and metabolic genes contributed to a greatly increased content of salicylic acid (SA) and a concomitant decrease in 1-aminocyclopropane-1-carboxylic acid (ACC) and oxophytodienoic acid (OPDA), precursors of ethylene and jasmonic acid, respectively, in parallel to reduced levels of abscisic acid (ABA). The lack of differences in the free levels of indole-3-acetic acid (IAA) between the pap mutants and wild-type plants was accompanied by fluctuations in the contents of IAA precursors and conjugated forms as well as multilayered changes in the expression of IAA metabolic genes. Along with cytokinin (CK) overproduction, all of these compensatory changes aim to balance plant growth and defense systems to ensure viability under highly modulated conditions.
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Affiliation(s)
- Ivan A. Bychkov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, Moscow 127276, Russia; (I.A.B.); (A.A.A.); (V.V.K.)
| | - Aleksandra A. Andreeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, Moscow 127276, Russia; (I.A.B.); (A.A.A.); (V.V.K.)
| | - Radomira Vankova
- Institute of Experimental Botany, Academy of Sciences CR, Rozvojova 263, 165 02 Prague, Czech Republic; (R.V.); (J.L.)
| | - Jozef Lacek
- Institute of Experimental Botany, Academy of Sciences CR, Rozvojova 263, 165 02 Prague, Czech Republic; (R.V.); (J.L.)
| | - Natalia V. Kudryakova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, Moscow 127276, Russia; (I.A.B.); (A.A.A.); (V.V.K.)
| | - Victor V. Kusnetsov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, Moscow 127276, Russia; (I.A.B.); (A.A.A.); (V.V.K.)
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14
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Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575193. [PMID: 38260627 PMCID: PMC10802570 DOI: 10.1101/2024.01.11.575193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spans approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding at the active site results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms.
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Affiliation(s)
- M. Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: Protein Technologies Center, Inspiration4 Advanced Research Center, Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Masahiko Imashimizu
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8565 Japan
| | - Miron Leanca
- The Centre for Bacterial Cell Biology, Newcastle University, UK
| | - Rishi K. Vishwakarma
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Yulia Yuzenkova
- The Centre for Bacterial Cell Biology, Newcastle University, UK
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
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15
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Tiwari LD, Bdolach E, Prusty MR, Bodenheimer S, Be'ery A, Faigenboim-Doron A, Yamamoto E, Panzarová K, Kashkush K, Shental N, Fridman E. Cytonuclear interactions modulate the plasticity of photosynthetic rhythmicity and growth in wild barley. PHYSIOLOGIA PLANTARUM 2024; 176:e14192. [PMID: 38351880 DOI: 10.1111/ppl.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
In plants, the contribution of the plasmotype (mitochondria and chloroplast) in controlling the circadian clock plasticity and possible consequences on cytonuclear genetic makeup have yet to be fully elucidated. A genome-wide association study in the wild barley (Hordeum vulgare ssp. spontaneum) B1K collection identified overlap with our previously mapped DRIVERS OF CLOCKS (DOCs) loci in wild-cultivated interspecific population. Moreover, we identified non-random segregation and epistatic interactions between nuclear DOCs loci and the chloroplastic RpoC1 gene, indicating an adaptive value for specific cytonuclear gene combinations. Furthermore, we show that DOC1.1, which harbours the candidate SIGMA FACTOR-B (SIG-B) gene, is linked with the differential expression of SIG-B and CCA1 genes and contributes to the circadian gating response to heat. High-resolution temporal growth and photosynthesis measurements of B1K also link the DOCs loci to differential growth, Chl content and quantum yield. To validate the involvement of the Plastid encoded polymerase (PEP) complex, we over-expressed the two barley chloroplastic RpoC1 alleles in Arabidopsis and identified significant differential plasticity under elevated temperatures. Finally, enhanced clock plasticity of de novo ENU (N-Ethyl-N-nitrosourea) -induced barley rpoB1 mutant further implicates the PEP complex as a key player in regulating the circadian clock output. Overall, this study highlights the contribution of specific cytonuclear interaction between rpoC1 (PEP gene) and SIG-B with distinct circadian timing regulation under heat, and their pleiotropic effects on growth implicate an adaptive value.
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Affiliation(s)
- Lalit Dev Tiwari
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Eyal Bdolach
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Manas Ranjan Prusty
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Schewach Bodenheimer
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avital Be'ery
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Adi Faigenboim-Doron
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Eyal Fridman
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
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16
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Wang X, Qi Y, Liu N, Zhang Q, Xie S, Lei Y, Li B, Shao J, Yu F, Liu X. Interaction of PALE CRESS with PAP2/pTAC2 and PAP3/pTAC10 affects the accumulation of plastid-encoded RNA polymerase complexes in Arabidopsis. THE NEW PHYTOLOGIST 2023; 240:1433-1448. [PMID: 37668229 DOI: 10.1111/nph.19243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023]
Abstract
The transcription of photosynthesis genes in chloroplasts is largely mediated by the plastid-encoded RNA polymerase (PEP), which resembles prokaryotic-type RNA polymerases, but with plant-specific accessory subunits known as plastid transcriptionally active chromosome proteins (pTACs) or PEP-associated proteins (PAPs). However, whether additional factors are involved in the biogenesis of PEP complexes remains unknown. Here, we investigated the function of an essential gene, PALE CRESS (PAC), in the accumulation of PEP complexes in chloroplasts. We established that an Arabidopsis leaf variegation mutant, variegated 6-1 (var6-1), is a hypomorphic allele of PAC. Unexpectedly, we revealed that a fraction of VAR6/PAC is associated with thylakoid membranes, where it interacts with PEP complexes. The accumulation of PEP complexes is defective in both var6-1 and the null allele var6-2. Further protein interaction assays confirmed that VAR6/PAC interacts directly with the PAP2/pTAC2 and PAP3/pTAC10 subunits of PEP complexes. Moreover, we generated viable hypomorphic alleles of the essential gene PAP2/pTAC2, and revealed a genetic interaction between PAC and PAP2/pTAC2 in photosynthesis gene expression and PEP complex accumulation. Our findings establish that VAR6/PAC affects PEP complex accumulation through interactions with PAP2/pTAC2 and PAP3/pTAC10, and provide new insights into the accumulation of PEP and chloroplast development.
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Affiliation(s)
- Xiaomin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yafei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Na Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qiaoxin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Sha Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yang Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bilang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jingxia Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
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17
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Sajib SA, Kandel M, Prity SA, Oukacine C, Gakière B, Merendino L. Role of plastids and mitochondria in the early development of seedlings in dark growth conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1272822. [PMID: 37841629 PMCID: PMC10570830 DOI: 10.3389/fpls.2023.1272822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Establishment of the seedlings is a crucial stage of the plant life cycle. The success of this process is essential for the growth of the mature plant. In Nature, when seeds germinate under the soil, seedlings follow a dark-specific program called skotomorphogenesis, which is characterized by small, non-green cotyledons, long hypocotyl, and an apical hook-protecting meristematic cells. These developmental structures are required for the seedlings to emerge quickly and safely through the soil and gain autotrophy before the complete depletion of seed resources. Due to the lack of photosynthesis during this period, the seed nutrient stocks are the primary energy source for seedling development. The energy is provided by the bioenergetic organelles, mitochondria, and etioplast (plastid in the dark), to the cell in the form of ATP through mitochondrial respiration and etio-respiration processes, respectively. Recent studies suggest that the limitation of the plastidial or mitochondrial gene expression induces a drastic reprogramming of the seedling morphology in the dark. Here, we discuss the dark signaling mechanisms involved during a regular skotomorphogenesis and how the dysfunction of the bioenergetic organelles is perceived by the nucleus leading to developmental changes. We also describe the probable involvement of several plastid retrograde pathways and the interconnection between plastid and mitochondria during seedling development. Understanding the integration mechanisms of organellar signals in the developmental program of seedlings can be utilized in the future for better emergence of crops through the soil.
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Affiliation(s)
- Salek Ahmed Sajib
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Margot Kandel
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Sadia Akter Prity
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Cylia Oukacine
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Bertrand Gakière
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Livia Merendino
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
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18
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Zhang Y, Tian L, Lu C. Chloroplast gene expression: Recent advances and perspectives. PLANT COMMUNICATIONS 2023; 4:100611. [PMID: 37147800 PMCID: PMC10504595 DOI: 10.1016/j.xplc.2023.100611] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/07/2023]
Abstract
Chloroplasts evolved from an ancient cyanobacterial endosymbiont more than 1.5 billion years ago. During subsequent coevolution with the nuclear genome, the chloroplast genome has remained independent, albeit strongly reduced, with its own transcriptional machinery and distinct features, such as chloroplast-specific innovations in gene expression and complicated post-transcriptional processing. Light activates the expression of chloroplast genes via mechanisms that optimize photosynthesis, minimize photodamage, and prioritize energy investments. Over the past few years, studies have moved from describing phases of chloroplast gene expression to exploring the underlying mechanisms. In this review, we focus on recent advances and emerging principles that govern chloroplast gene expression in land plants. We discuss engineering of pentatricopeptide repeat proteins and its biotechnological effects on chloroplast RNA research; new techniques for characterizing the molecular mechanisms of chloroplast gene expression; and important aspects of chloroplast gene expression for improving crop yield and stress tolerance. We also discuss biological and mechanistic questions that remain to be answered in the future.
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Affiliation(s)
- Yi Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lin Tian
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Congming Lu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
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19
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Heß D, Holzhausen A, Hess WR. Insight into the nodal cells transcriptome of the streptophyte green alga Chara braunii S276. PHYSIOLOGIA PLANTARUM 2023; 175:e14025. [PMID: 37882314 DOI: 10.1111/ppl.14025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 10/27/2023]
Abstract
Charophyceae are the most complex streptophyte algae, possessing tissue-like structures, rhizoids and a cellulose-pectin-based cell wall akin to embryophytes. Together with the Zygnematophyceae and the Coleochaetophycae, the Charophyceae form a grade in which the Zygnematophyceae share a last common ancestor with land plants. The availability of genomic data, its short life cycle, and the ease of non-sterile cultivation in the laboratory have made the species Chara braunii an emerging model system for streptophyte terrestrialization and early land plant evolution. In this study, tissue containing nodal cells was prepared under the stereomicroscope, and an RNA-seq dataset was generated and compared to transcriptome data from whole plantlets. In both samples, transcript coverage was high for genes encoding ribosomal proteins and a homolog of the putative PAX3- and PAX7-binding protein 1. Gene ontology was used to classify the putative functions of the differently expressed genes. In the nodal cell sample, main upregulated molecular functions were related to protein, nucleic acid, ATP- and DNA binding. Looking at specific genes, several signaling-related genes and genes encoding sugar-metabolizing enzymes were found to be expressed at a higher level in the nodal cell sample, while photosynthesis-and chloroplast-related genes were expressed at a comparatively lower level. We detected the transcription of 21 different genes encoding DUF4360-containing cysteine-rich proteins. The data contribute to the growing understanding of Charophyceae developmental biology by providing a first insight into the transcriptome composition of Chara nodal cells.
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Affiliation(s)
- Daniel Heß
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Anja Holzhausen
- Plant Cell Biology, Department of Biology, Philipps University Marburg, Marburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
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20
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Pan H, Zagorchev L, Chen L, Tao Y, Cai C, Jiang M, Sun Z, Li J. Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus. BMC Genomics 2023; 24:310. [PMID: 37291497 DOI: 10.1186/s12864-023-09427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Cuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species. RESULTS In the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize. CONCLUSION Our results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.
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Affiliation(s)
- Hangkai Pan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lyuben Zagorchev
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov Blvd., Sofia, 1164, Bulgaria
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Yutian Tao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Electronics and Information Engineering, Taizhou University, Taizhou, 318000, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China.
- School of Advanced Study, Taizhou University, Taizhou, 318000, China.
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Sajib SA, Grübler B, Oukacine C, Delannoy E, Courtois F, Mauve C, Lurin C, Gakière B, Pfannschmidt T, Merendino L. Limiting etioplast gene expression induces apical hook twisting during skotomorphogenesis of Arabidopsis seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:293-309. [PMID: 36748183 DOI: 10.1111/tpj.16134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 05/10/2023]
Abstract
When covered by a layer of soil, seedling development follows a dark-specific program (skotomorphogenesis). In the dark, seedlings consist of small, non-green cotyledons, a long hypocotyl, and an apical hook to protect meristematic cells. We recently highlighted the role played by mitochondria in the high energy-consuming reprogramming of Arabidopsis skotomorphogenesis. Here, the role played by plastids, another energy-supplying organelle, in skotomorphogenesis is investigated. This study was conducted in dark conditions to exclude light signals so as to better focus on those produced by plastids. It was found that limitation of plastid gene expression (PGE) induced an exaggerated apical hook bending. Inhibition of PGE was obtained at the levels of transcription and translation using the antibiotics rifampicin (RIF) and spectinomycin, respectively, as well as plastid RPOTp RNA polymerase mutants. RIF-treated seedlings also showed expression induction of marker nuclear genes for mitochondrial stress, perturbation of mitochondrial metabolism, increased ROS levels, and an augmented capacity of oxygen consumption by mitochondrial alternative oxidases (AOXs). AOXs act to prevent overreduction of the mitochondrial electron transport chain. Previously, we reported that AOX1A, the main AOX isoform, is a key component in the developmental response to mitochondrial respiration deficiency. In this work, we suggest the involvement of AOX1A in the response to PGE dysfunction and propose the importance of signaling between plastids and mitochondria. Finally, it was found that seedling architecture reprogramming in response to RIF was independent of canonical organelle retrograde pathways and the ethylene signaling pathway.
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Affiliation(s)
- Salek Ahmed Sajib
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif sur Yvette, France
| | - Björn Grübler
- University of Grenoble Alpes, CNRS, INRAE, CEA, IRIG-LPCV, 38000, Grenoble, France
| | - Cylia Oukacine
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif sur Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif sur Yvette, France
| | - Florence Courtois
- University of Grenoble Alpes, CNRS, INRAE, CEA, IRIG-LPCV, 38000, Grenoble, France
| | - Caroline Mauve
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif sur Yvette, France
| | - Claire Lurin
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif sur Yvette, France
| | - Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif sur Yvette, France
| | - Thomas Pfannschmidt
- Institut for Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Livia Merendino
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif sur Yvette, France
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22
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Melicher P, Dvořák P, Šamaj J, Takáč T. Protein-protein interactions in plant antioxidant defense. FRONTIERS IN PLANT SCIENCE 2022; 13:1035573. [PMID: 36589041 PMCID: PMC9795235 DOI: 10.3389/fpls.2022.1035573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The regulation of reactive oxygen species (ROS) levels in plants is ensured by mechanisms preventing their over accumulation, and by diverse antioxidants, including enzymes and nonenzymatic compounds. These are affected by redox conditions, posttranslational modifications, transcriptional and posttranscriptional modifications, Ca2+, nitric oxide (NO) and mitogen-activated protein kinase signaling pathways. Recent knowledge about protein-protein interactions (PPIs) of antioxidant enzymes advanced during last decade. The best-known examples are interactions mediated by redox buffering proteins such as thioredoxins and glutaredoxins. This review summarizes interactions of major antioxidant enzymes with regulatory and signaling proteins and their diverse functions. Such interactions are important for stability, degradation and activation of interacting partners. Moreover, PPIs of antioxidant enzymes may connect diverse metabolic processes with ROS scavenging. Proteins like receptor for activated C kinase 1 may ensure coordination of antioxidant enzymes to ensure efficient ROS regulation. Nevertheless, PPIs in antioxidant defense are understudied, and intensive research is required to define their role in complex regulation of ROS scavenging.
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23
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Liebers M, Cozzi C, Uecker F, Chambon L, Blanvillain R, Pfannschmidt T. Biogenic signals from plastids and their role in chloroplast development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7105-7125. [PMID: 36002302 DOI: 10.1093/jxb/erac344] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Plant seeds do not contain differentiated chloroplasts. Upon germination, the seedlings thus need to gain photoautotrophy before storage energies are depleted. This requires the coordinated expression of photosynthesis genes encoded in nuclear and plastid genomes. Chloroplast biogenesis needs to be additionally coordinated with the light regulation network that controls seedling development. This coordination is achieved by nucleus to plastid signals called anterograde and plastid to nucleus signals termed retrograde. Retrograde signals sent from plastids during initial chloroplast biogenesis are also called biogenic signals. They have been recognized as highly important for proper chloroplast biogenesis and for seedling development. The molecular nature, transport, targets, and signalling function of biogenic signals are, however, under debate. Several studies disproved the involvement of a number of key components that were at the base of initial models of retrograde signalling. New models now propose major roles for a functional feedback between plastid and cytosolic protein homeostasis in signalling plastid dysfunction as well as the action of dually localized nucleo-plastidic proteins that coordinate chloroplast biogenesis with light-dependent control of seedling development. This review provides a survey of the developments in this research field, summarizes the unsolved questions, highlights several recent advances, and discusses potential new working modes.
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Affiliation(s)
- Monique Liebers
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Carolina Cozzi
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Finia Uecker
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Louise Chambon
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, F-38000 Grenoble, France
| | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, F-38000 Grenoble, France
| | - Thomas Pfannschmidt
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
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24
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Li Y, Jian Y, Mao Y, Meng F, Shao Z, Wang T, Zheng J, Wang Q, Liu L. "Omics" insights into plastid behavior toward improved carotenoid accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:1001756. [PMID: 36275568 PMCID: PMC9583013 DOI: 10.3389/fpls.2022.1001756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yue Jian
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yuanyu Mao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Fanliang Meng
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhiyong Shao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Tonglin Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jirong Zheng
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Lihong Liu
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
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25
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Bychkov IA, Andreeva AA, Kudryakova NV, Pojidaeva ES, Kusnetsov VV. The role of PAP4/FSD3 and PAP9/FSD2 in heat stress responses of chloroplast genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 322:111359. [PMID: 35738478 DOI: 10.1016/j.plantsci.2022.111359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/01/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Chloroplasts' mechanisms of adaptation to elevated temperatures are largely determined by the gene expression of the plastid transcription apparatus. Gene disruption of iron-containing superoxide dismutase PAP4/FSD3 and PAP9/FSD2, which are parts of the DNA-RNA polymerase complex of plastids, contributed to a decrease in resistance to oxidative stress caused by the prolonged action of elevated temperatures (5 days, 30 °C). Under heat stress conditions, pap4/fsd3 and pap9/fsd2 mutants showed a decline in chlorophyll content and photosynthesis level, as measured by photosynthetic parameters, and a different amplitude of HSP gene response to heat stress. The expression of nuclear- and plastid-encoded photosynthesis genes and corresponding proteins was strongly inhibited in the mutants as compared with wild-type plants and was further suppressed or displayed no additional changes at 30 °C. NEP-dependent plastid genes, as well as NEP genes RPOTp and RPOTmp, were also downregulated in the mutants by high temperature or remained stable, unlike in wild-type seedlings where these genes were strongly upregulated. The results obtained correspond to the concept of the complex effect of various forms of reactive oxygen species under all types of stresses, including heat stress, and confirm the hypothesis of a new regulatory function in plastid transcription acquired by enzymatic proteins during evolution.
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Affiliation(s)
- Ivan A Bychkov
- К.А. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow 127276, Russia
| | - Aleksandra A Andreeva
- К.А. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow 127276, Russia
| | - Natalia V Kudryakova
- К.А. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow 127276, Russia.
| | - Elena S Pojidaeva
- К.А. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow 127276, Russia
| | - Victor V Kusnetsov
- К.А. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow 127276, Russia
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26
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Barrero-Gil J, Bouza-Morcillo L, Espinosa-Cores L, Piñeiro M, Jarillo JA. H4 acetylation by the NuA4 complex is required for plastid transcription and chloroplast biogenesis. NATURE PLANTS 2022; 8:1052-1063. [PMID: 36038656 DOI: 10.1038/s41477-022-01229-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Chloroplast biogenesis is crucial in plant development, as it is essential for the transition to autotrophic growth. This process is light-induced and relies on the orchestrated transcription of nuclear and plastid genes, enabling the effective assembly and regulation of the photosynthetic machinery. Here we reveal a new regulation level for this process by showing the involvement of chromatin remodelling in the nuclear control of plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologues of yeast EPL1 protein, components of the NuA4 histone acetyltransferase complex, are essential for plastid transcription and correct chloroplast development and performance. We show that EPL1 proteins are light-regulated and necessary for concerted expression of nuclear genes encoding most components of chloroplast transcriptional machinery, directly mediating H4K5ac deposition at these loci and promoting the expression of plastid genes required for chloroplast biogenesis. These data unveil a NuA4-mediated mechanism regulating chloroplast biogenesis that links the transcription of nuclear and plastid genomes during chloroplast development.
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Affiliation(s)
- Javier Barrero-Gil
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain
| | - Laura Bouza-Morcillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain
| | - Loreto Espinosa-Cores
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain.
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Madrid, Spain.
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27
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Three-Dimensional Envelope and Subunit Interactions of the Plastid-Encoded RNA Polymerase from Sinapis alba. Int J Mol Sci 2022; 23:ijms23179922. [PMID: 36077319 PMCID: PMC9456514 DOI: 10.3390/ijms23179922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
RNA polymerases (RNAPs) are found in all living organisms. In the chloroplasts, the plastid-encoded RNA polymerase (PEP) is a prokaryotic-type multimeric RNAP involved in the selective transcription of the plastid genome. One of its active states requires the assembly of nuclear-encoded PEP-Associated Proteins (PAPs) on the catalytic core, producing a complex of more than 900 kDa, regarded as essential for chloroplast biogenesis. In this study, sequence alignments of the catalytic core subunits across various chloroplasts of the green lineage and prokaryotes combined with structural data show that variations are observed at the surface of the core, whereas internal amino acids associated with the catalytic activity are conserved. A purification procedure compatible with a structural analysis was used to enrich the native PEP from Sinapis alba chloroplasts. A mass spectrometry (MS)-based proteomic analysis revealed the core components, the PAPs and additional proteins, such as FLN2 and pTAC18. MS coupled with crosslinking (XL-MS) provided the initial structural information in the form of protein clusters, highlighting the relative position of some subunits with the surfaces of their interactions. Using negative stain electron microscopy, the PEP three-dimensional envelope was calculated. Particles classification shows that the protrusions are very well-conserved, offering a framework for the future positioning of all the PAPs. Overall, the results show that PEP-associated proteins are firmly and specifically associated with the catalytic core, giving to the plastid transcriptional complex a singular structure compared to other RNAPs.
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28
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Foyer CH, Hanke G. ROS production and signalling in chloroplasts: cornerstones and evolving concepts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:642-661. [PMID: 35665548 PMCID: PMC9545066 DOI: 10.1111/tpj.15856] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 05/05/2023]
Abstract
Reactive oxygen species (ROS) such as singlet oxygen, superoxide (O2●- ) and hydrogen peroxide (H2 O2 ) are the markers of living cells. Oxygenic photosynthesis produces ROS in abundance, which act as a readout of a functional electron transport system and metabolism. The concept that photosynthetic ROS production is a major driving force in chloroplast to nucleus retrograde signalling is embedded in the literature, as is the role of chloroplasts as environmental sensors. The different complexes and components of the photosynthetic electron transport chain (PETC) regulate O2●- production in relation to light energy availability and the redox state of the stromal Cys-based redox systems. All of the ROS generated in chloroplasts have the potential to act as signals and there are many sulphhydryl-containing proteins and peptides in chloroplasts that have the potential to act as H2 O2 sensors and function in signal transduction. While ROS may directly move out of the chloroplasts to other cellular compartments, ROS signalling pathways can only be triggered if appropriate ROS-sensing proteins are present at or near the site of ROS production. Chloroplast antioxidant systems serve either to propagate these signals or to remove excess ROS that cannot effectively be harnessed in signalling. The key challenge is to understand how regulated ROS delivery from the PETC to the Cys-based redox machinery is organised to transmit redox signals from the environment to the nucleus. Redox changes associated with stromal carbohydrate metabolism also play a key role in chloroplast signalling pathways.
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Affiliation(s)
- Christine H. Foyer
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | - Guy Hanke
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
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29
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Palomar VM, Jaksich S, Fujii S, Kuciński J, Wierzbicki AT. High-resolution map of plastid-encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1139-1151. [PMID: 35765883 PMCID: PMC9540123 DOI: 10.1111/tpj.15882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 05/16/2023]
Abstract
Plastids contain their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplast DNA using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq). We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with levels of RNA accumulation, which demonstrates the impact of PEP on chloroplast gene expression. Presented data are available through a publicly available Plastid Genome Visualization Tool (Plavisto) at https://plavisto.mcdb.lsa.umich.edu/.
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Affiliation(s)
- V. Miguel Palomar
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
| | - Sarah Jaksich
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
| | - Sho Fujii
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
- Department of Botany, Graduate School of ScienceKyoto UniversityKyoto606‐8502Japan
- Department of Biology, Faculty of Agriculture and Life ScienceHirosaki UniversityHirosaki036‐8561Japan
| | - Jan Kuciński
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
| | - Andrzej T. Wierzbicki
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
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30
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Fujii S, Kobayashi K, Lin YC, Liu YC, Nakamura Y, Wada H. Impacts of phosphatidylglycerol on plastid gene expression and light induction of nuclear photosynthetic genes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2952-2970. [PMID: 35560187 DOI: 10.1093/jxb/erac034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/31/2022] [Indexed: 06/15/2023]
Abstract
Phosphatidylglycerol (PG) is the only major phospholipid in the thylakoid membrane of chloroplasts. PG is essential for photosynthesis, and loss of PG in Arabidopsis thaliana results in severe defects of growth and chloroplast development, with decreased chlorophyll accumulation, impaired thylakoid formation, and down-regulation of photosynthesis-associated genes encoded in nuclear and plastid genomes. However, how the absence of PG affects gene expression and plant growth remains unclear. To elucidate this mechanism, we investigated transcriptional profiles of a PG-deficient Arabidopsis mutant pgp1-2 under various light conditions. Microarray analysis demonstrated that reactive oxygen species (ROS)-responsive genes were up-regulated in pgp1-2. However, ROS production was not enhanced in the mutant even under strong light, indicating limited impacts of photooxidative stress on the defects of pgp1-2. Illumination to dark-adapted pgp1-2 triggered down-regulation of photosynthesis-associated nuclear-encoded genes (PhANGs), while plastid-encoded genes were constantly suppressed. Overexpression of GOLDEN2-LIKE1 (GLK1), a transcription factor gene regulating chloroplast development, in pgp1-2 up-regulated PhANGs but not plastid-encoded genes along with chlorophyll accumulation. Our data suggest a broad impact of PG biosynthesis on nuclear-encoded genes partially via GLK1 and a specific involvement of this lipid in plastid gene expression and plant development.
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Affiliation(s)
- Sho Fujii
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
- Department of Botany, Graduate School of Science, Kyoto University, Kita-Shirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Koichi Kobayashi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho, Naka-ku, Sakai, Osaka, Japan
- Faculty of Liberal Arts and Sciences, Osaka Prefecture University, 1-1 Gakuencho, Naka-ku, Sakai, Osaka, Japan
| | - Ying-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chi Liu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yuki Nakamura
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Japan
| | - Hajime Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
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31
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PAP8/pTAC6 Is Part of a Nuclear Protein Complex and Displays RNA Recognition Motifs of Viral Origin. Int J Mol Sci 2022; 23:ijms23063059. [PMID: 35328480 PMCID: PMC8954402 DOI: 10.3390/ijms23063059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Chloroplast biogenesis depends on a complex transcriptional program involving coordinated expression of plastid and nuclear genes. In particular, photosynthesis-associated plastid genes are expressed by the plastid-encoded polymerase (PEP) that undergoes a structural rearrangement during chloroplast formation. The prokaryotic-type core enzyme is rebuilt into a larger complex by the addition of nuclear-encoded PEP-associated proteins (PAP1 to PAP12). Among the PAPs, some have been detected in the nucleus (PAP5 and PAP8), where they could serve a nuclear function required for efficient chloroplast biogenesis. Here, we detected PAP8 in a large nuclear subcomplex that may include other subunits of the plastid-encoded RNA polymerase. We have made use of PAP8 recombinant proteins in Arabidopsis thaliana to decouple its nucleus- and chloroplast-associated functions and found hypomorphic mutants pointing at essential amino acids. While the origin of the PAP8 gene remained elusive, we have found in its sequence a micro-homologous domain located within a large structural homology with a rhinoviral RNA-dependent RNA polymerase, highlighting potential RNA recognition motifs in PAP8. PAP8 in vitro RNA binding activity suggests that this domain is functional. Hence, we propose that the acquisition of PAPs may have occurred during evolution by different routes, including lateral gene transfer.
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Yang Z, Liu M, Ding S, Zhang Y, Yang H, Wen X, Chi W, Lu C, Lu Q. Plastid Deficient 1 Is Essential for the Accumulation of Plastid-Encoded RNA Polymerase Core Subunit β and Chloroplast Development in Arabidopsis. Int J Mol Sci 2021; 22:ijms222413648. [PMID: 34948448 PMCID: PMC8705867 DOI: 10.3390/ijms222413648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/05/2022] Open
Abstract
Plastid-encoded RNA polymerase (PEP)-dependent transcription is an essential process for chloroplast development and plant growth. It is a complex event that is regulated by numerous nuclear-encoded proteins. In order to elucidate the complex regulation mechanism of PEP activity, identification and characterization of PEP activity regulation factors are needed. Here, we characterize Plastid Deficient 1 (PD1) as a novel regulator for PEP-dependent gene expression and chloroplast development in Arabidopsis. The PD1 gene encodes a protein that is conserved in photoautotrophic organisms. The Arabidopsis pd1 mutant showed albino and seedling-lethal phenotypes. The plastid development in the pd1 mutant was arrested. The PD1 protein localized in the chloroplasts, and it colocalized with nucleoid protein TRXz. RT-quantitative real-time PCR, northern blot, and run-on analyses indicated that the PEP-dependent transcription in the pd1 mutant was dramatically impaired, whereas the nuclear-encoded RNA polymerase-dependent transcription was up-regulated. The yeast two-hybrid assays and coimmunoprecipitation experiments showed that the PD1 protein interacts with PEP core subunit β (PEP-β), which has been verified to be essential for chloroplast development. The immunoblot analysis indicated that the accumulation of PEP-β was barely detected in the pd1 mutant, whereas the accumulation of the other essential components of the PEP complex, such as core subunits α and β′, were not affected in the pd1 mutant. These observations suggested that the PD1 protein is essential for the accumulation of PEP-β and chloroplast development in Arabidopsis, potentially by direct interaction with PEP-β.
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Affiliation(s)
- Zhipan Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Y.); (M.L.); (S.D.); (H.Y.); (X.W.); (W.C.)
| | - Mingxin Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Y.); (M.L.); (S.D.); (H.Y.); (X.W.); (W.C.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunhua Ding
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Y.); (M.L.); (S.D.); (H.Y.); (X.W.); (W.C.)
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China;
| | - Huixia Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Y.); (M.L.); (S.D.); (H.Y.); (X.W.); (W.C.)
| | - Xiaogang Wen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Y.); (M.L.); (S.D.); (H.Y.); (X.W.); (W.C.)
| | - Wei Chi
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Y.); (M.L.); (S.D.); (H.Y.); (X.W.); (W.C.)
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China;
- Correspondence: (C.L.); (Q.L.)
| | - Qingtao Lu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Y.); (M.L.); (S.D.); (H.Y.); (X.W.); (W.C.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (C.L.); (Q.L.)
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Kong M, Wu Y, Wang Z, Qu W, Lan Y, Chen X, Liu Y, Shahnaz P, Yang Z, Yu Q, Mi H. A Novel Chloroplast Protein RNA Processing 8 Is Required for the Expression of Chloroplast Genes and Chloroplast Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:700975. [PMID: 34956248 PMCID: PMC8695849 DOI: 10.3389/fpls.2021.700975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
Chloroplast development involves the coordinated expression of both plastids- and nuclear-encoded genes in higher plants. However, the underlying mechanism still remains largely unknown. In this study, we isolated and characterized an Arabidopsis mutant with an albino lethality phenotype named RNA processing 8 (rp8). Genetic complementation analysis demonstrated that the gene AT4G37920 (RP8) was responsible for the mutated phenotype. The RP8 gene was strongly expressed in photosynthetic tissues at both transcription and translation protein levels. The RP8 protein is localized in the chloroplast and associated with the thylakoid. Disruption of the RP8 gene led to a defect in the accumulation of the rpoA mature transcript, which reduced the level of the RpoA protein, and affected the transcription of PEP-dependent genes. The abundance of the chloroplast rRNA, including 23S, 16S, 4.5S, and 5S rRNA, were reduced in the rp8 mutant, respectively, and the amounts of chloroplast ribosome proteins, such as, PRPS1(uS1c), PRPS5(uS5c), PRPL2 (uL2c), and PRPL4 (uL4c), were substantially decreased in the rp8 mutant, which indicated that knockout of RP8 seriously affected chloroplast translational machinery. Accordingly, the accumulation of photosynthetic proteins was seriously reduced. Taken together, these results indicate that the RP8 protein plays an important regulatory role in the rpoA transcript processing, which is required for the expression of chloroplast genes and chloroplast development in Arabidopsis.
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Affiliation(s)
- Mengmeng Kong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yaozong Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ziyuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wantong Qu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yixin Lan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yanyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Perveen Shahnaz
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zhongnan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qingbo Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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Canonge J, Roby C, Hamon C, Potin P, Pfannschmidt T, Philippot M. Occurrence of albinism during wheat androgenesis is correlated with repression of the key genes required for proper chloroplast biogenesis. PLANTA 2021; 254:123. [PMID: 34786602 DOI: 10.1007/s00425-021-03773-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The phenomenon of albinism in wheat androgenesis is linked to the transcriptional repression of specific genes involved in chloroplast biogenesis during the first weeks of in vitro culture. Isolated microspore culture is widely used to accelerate breeding programs and produce new cultivars. However, in cereals and particularly in wheat, the use of this technique is limited due to the high proportion of regenerated albino plantlets. The causes and mechanisms leading to the formation of albino plantlets in wheat remain largely unknown and, to date, no concrete solution has been found to make it possible to overcome this barrier. We performed a molecular study of proplastid-to-chloroplast differentiation within wheat microspore cultures by analyzing the expression of 20 genes specifically involved in chloroplast biogenesis. Their expression levels were compared between two wheat genotypes that exhibit differential capacities to regenerate green plantlets, i.e., Pavon and Paledor, which produce high and low rates of green plants, respectively. We observed that chloroplast biogenesis within wheat microspores was affected as of the very early stages of the androgenesis process. A successful transition from a NEP- to a PEP-dependent transcription during early plastid development was found to be strongly correlated with the formation of green plantlets, while failure of this transition was strongly correlated with the regeneration of albino plantlets. The very low expression of plastid-encoded 16S and 23S rRNAs within plastids of the recalcitrant genotype Paledor suggests a low translation activity in albino plastids. Furthermore, a delay in the activation of the transcription of nuclear encoded key genes like GLK1 related to chloroplast biogenesis was observed in multicellular structures and pro-embryos of the genotype Paledor. These data help to understand the phenomenon of albinism in wheat androgenesis, which appears to be linked to the transcriptional activation of specific genes involved in the initial steps of chloroplast biogenesis that occurs between days 7 and 21 of in vitro culture.
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Affiliation(s)
- Julie Canonge
- Vegenov, Pen ar Prat, 29250, Saint-Pol-de-Léon, France
- CNRS, Sorbonne Université Sciences, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | | | - Céline Hamon
- Vegenov, Pen ar Prat, 29250, Saint-Pol-de-Léon, France
| | - Philippe Potin
- CNRS, Sorbonne Université Sciences, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Thomas Pfannschmidt
- Institut für Botanik, Pflanzenphysiologie, Leibniz-Universität Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
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Liu X, Zhang X, Cao R, Jiao G, Hu S, Shao G, Sheng Z, Xie L, Tang S, Wei X, Hu P. CDE4 encodes a pentatricopeptide repeat protein involved in chloroplast RNA splicing and affects chloroplast development under low-temperature conditions in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1724-1739. [PMID: 34219386 DOI: 10.1111/jipb.13147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/30/2021] [Indexed: 05/24/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins play important roles in the post-transcriptional modification of organellar RNAs in plants. However, the function of most PPR proteins remains unknown. Here, we characterized the rice (Oryza sativa L.) chlorophyll deficient 4 (cde4) mutant which exhibits an albino phenotype during early leaf development, with decreased chlorophyll contents and abnormal chloroplasts at low-temperature (20°C). Positional cloning revealed that CDE4 encodes a P-type PPR protein localized in chloroplasts. In the cde4 mutant, plastid-encoded polymerase (PEP)-dependent transcript levels were significantly reduced, but transcript levels of nuclear-encoded genes were increased compared to wild-type plants at 20°C. CDE4 directly binds to the transcripts of the chloroplast genes rpl2, ndhA, and ndhB. Intron splicing of these transcripts was defective in the cde4 mutant at 20°C, but was normal at 32°C. Moreover, CDE4 interacts with the guanylate kinase VIRESCENT 2 (V2); overexpression of V2 enhanced CDE4 protein stability, thereby rescuing the cde4 phenotype at 20°C. Our results suggest that CDE4 participates in plastid RNA splicing and plays an important role in rice chloroplast development under low-temperature conditions.
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Affiliation(s)
- Xinyong Liu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xichun Zhang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- Guizhou Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ruijie Cao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
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Andreeva AA, Kudryakova NV, Kuznetsov VV, Kusnetsov VV. Ontogenetic, Light, and Circadian Regulation of PAP Protein Genes during Seed Germination of Arabidopsis thaliana. DOKL BIOCHEM BIOPHYS 2021; 500:312-316. [PMID: 34697734 DOI: 10.1134/s1607672921050021] [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: 04/23/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/23/2022]
Abstract
The expression profiles of the PAP genes, encoding proteins associated with plastid multisubunit RNA polymerase, were studied in dry seeds, during germination, and at the early stages of Arabidopsis thaliana seedling formation. A detailed analysis of the PAP transcript levels by RT-PCR showed that the transition of seeds from dormancy to active growth is accompanied by a drastic increase in the transcript accumulation of all studied genes on the first day of germination, both in the light and in the dark. Further changes in transcript levels differed among PAP genes and were apparently determined by their functional specificity. It was established for the first time that the expression of individual PAP genes is regulated by circadian rhythms, in addition to factors of ontogenetic and light nature.
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Affiliation(s)
- A A Andreeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - N V Kudryakova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia.
| | - Vl V Kuznetsov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - V V Kusnetsov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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A Transcription Factor Regulates Gene Expression in Chloroplasts. Int J Mol Sci 2021; 22:ijms22136769. [PMID: 34202438 PMCID: PMC8268430 DOI: 10.3390/ijms22136769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/21/2023] Open
Abstract
The chloroplast is a semi-autonomous organelle with its own genome. The expression of chloroplast genes depends on both chloroplasts and the nucleus. Although many nucleus-encoded proteins have been shown to localize in chloroplasts and are essential for chloroplast gene expression, it is not clear whether transcription factors can regulate gene expression in chloroplasts. Here we report that the transcription factor NAC102 localizes in both chloroplasts and nucleus in Arabidopsis. Specifically, NAC102 localizes in chloroplast nucleoids. Yeast two-hybrid assay and co-immunoprecipitation assay suggested that NAC102 interacts with chloroplast RNA polymerases. Furthermore, overexpression of NAC102 in chloroplasts leads to reduced chloroplast gene expression and chlorophyll content, indicating that NAC102 functions as a repressor in chloroplasts. Our study not only revealed that transcription factors are new regulators of chloroplast gene expression, but also discovered that transcription factors can function in chloroplasts in addition to the canonical organelle nucleus.
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Cejudo FJ, González MC, Pérez-Ruiz JM. Redox regulation of chloroplast metabolism. PLANT PHYSIOLOGY 2021; 186:9-21. [PMID: 33793865 PMCID: PMC8154093 DOI: 10.1093/plphys/kiaa062] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/16/2020] [Indexed: 05/08/2023]
Abstract
Regulation of enzyme activity based on thiol-disulfide exchange is a regulatory mechanism in which the protein disulfide reductase activity of thioredoxins (TRXs) plays a central role. Plant chloroplasts are equipped with a complex set of up to 20 TRXs and TRX-like proteins, the activity of which is supported by reducing power provided by photosynthetically reduced ferredoxin (FDX) with the participation of a FDX-dependent TRX reductase (FTR). Therefore, the FDX-FTR-TRXs pathway allows the regulation of redox-sensitive chloroplast enzymes in response to light. In addition, chloroplasts contain an NADPH-dependent redox system, termed NTRC, which allows the use of NADPH in the redox network of these organelles. Genetic approaches using mutants of Arabidopsis (Arabidopsis thaliana) in combination with biochemical and physiological studies have shown that both redox systems, NTRC and FDX-FTR-TRXs, participate in fine-tuning chloroplast performance in response to changes in light intensity. Moreover, these studies revealed the participation of 2-Cys peroxiredoxin (2-Cys PRX), a thiol-dependent peroxidase, in the control of the reducing activity of chloroplast TRXs as well as in the rapid oxidation of stromal enzymes upon darkness. In this review, we provide an update on recent findings regarding the redox regulatory network of plant chloroplasts, focusing on the functional relationship of 2-Cys PRXs with NTRC and the FDX-FTR-TRXs redox systems for fine-tuning chloroplast performance in response to changes in light intensity and darkness. Finally, we consider redox regulation as an additional layer of control of the signaling function of the chloroplast.
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Affiliation(s)
- Francisco Javier Cejudo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla—Consejo Superior de Investigaciones Científicas, Avda. Américo Vespucio 49, 41092 Sevilla, Spain
- Author for communication:
| | - María-Cruz González
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla—Consejo Superior de Investigaciones Científicas, Avda. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Juan Manuel Pérez-Ruiz
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla—Consejo Superior de Investigaciones Científicas, Avda. Américo Vespucio 49, 41092 Sevilla, Spain
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Xu C, Shen Y, Li C, Lu F, Zhang MD, Meeley RB, McCarty DR, Tan BC. Emb15 encodes a plastid ribosomal assembly factor essential for embryogenesis in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:214-227. [PMID: 33450100 DOI: 10.1111/tpj.15160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Ribosome assembly factors guide the complex process by which ribosomal proteins and the ribosomal RNAs form a functional ribosome. However, the assembly of plant plastid ribosomes is poorly understood. In the present study, we discovered a maize (Zea mays) plastid ribosome assembly factor based on our characterization of the embryo defective 15 (emb15) mutant. Loss of function of Emb15 retards embryo development at an early stage, but does not substantially affect the endosperm, and causes an albino phenotype in other genetic backgrounds. EMB15 localizes to plastids and possesses a ribosome maturation factor M (RimM) domain in the N-terminus and a predicted UDP-GlcNAc pyrophosphorylase domain in the C-terminus. The EMB15 RimM domain originated in bacteria and the UDP-GlcNAc pyrophosphorylase domain originated in fungi; these two domains came together in the ancestor of land plants during evolution. The N-terminus of EMB15 complemented the growth defect of an Escherichia coli strain with a RimM deletion and rescued the albino phenotype of emb15 homozygous mutants. The RimM domain mediates the interaction between EMB15 and the plastid ribosomal protein PRPS19. Plastid 16S rRNA maturation is also significantly impaired in emb15. These observations suggest that EMB15 functions in maize seed development as a plastid ribosome assembly factor, and the C-terminal domain is not important under normal conditions.
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Affiliation(s)
- Chunhui Xu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Yun Shen
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Cuiling Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Fan Lu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Meng-Di Zhang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Robert B Meeley
- DuPont Pioneer AgBiotech Research, Johnston, Iowa, 50131-1004, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
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Ji Y, Lehotai N, Zan Y, Dubreuil C, Díaz MG, Strand Å. A fully assembled plastid-encoded RNA polymerase complex detected in etioplasts and proplastids in Arabidopsis. PHYSIOLOGIA PLANTARUM 2021; 171:435-446. [PMID: 33155308 DOI: 10.1111/ppl.13256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
The plastid-encoded genes of higher plants are transcribed by at least two types of RNA polymerases, the nuclear-encoded RNA polymerase (NEP) and the plastid-encoded RNA polymerase (PEP). In mature photosynthesizing leaves, the vast majority of the genes are transcribed by PEP. However, the regulatory mechanisms controlling plastid transcription during early light response is unclear. Chloroplast development is suggested to be associated with a shift in the usage of the primary RNA polymerase from NEP to PEP as the expression of the plastid-encoded photosynthesis genes is induced upon light exposure. Assembly of the PEP complex has been suggested as a rate-limiting step for full activation of plastid-encoded photosynthesis gene expression. However, two sigma factor mutants, sig2 and sig6, with reduced PEP activity, showed significantly lower expression of the plastid-encoded photosynthesis genes already in the dark and during the first hours of light exposure indicating that PEP activity is required for basal expression of plastid-encoded photosynthesis genes in the dark and during early light response. Furthermore, in etioplasts and proplastids a fully assembled PEP complex was revealed on Blue Native PAGE. Our results indicate that a full assembly of the PEP complex is possible in the dark and that PEP drives basal transcriptional activity of plastid-encoded photosynthesis genes in the dark. Assembly of the complex is most likely not a rate-limiting step for full activation of plastid-encoded photosynthesis gene expression which is rather achieved either by the abundance of the PEP complex or by some posttranslational regulation of the individual PEP components.
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Affiliation(s)
- Yan Ji
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nóra Lehotai
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Yanjun Zan
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Carole Dubreuil
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- CEA-Commissariat à l'Energie Atomique et aux Énergies Alternatives, CEA Tech, Centre Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Manuel Guinea Díaz
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Åsa Strand
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
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Shimizu T, Masuda T. The Role of Tetrapyrrole- and GUN1-Dependent Signaling on Chloroplast Biogenesis. PLANTS 2021; 10:plants10020196. [PMID: 33494334 PMCID: PMC7911674 DOI: 10.3390/plants10020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Abstract
Chloroplast biogenesis requires the coordinated expression of the chloroplast and nuclear genomes, which is achieved by communication between the developing chloroplasts and the nucleus. Signals emitted from the plastids, so-called retrograde signals, control nuclear gene expression depending on plastid development and functionality. Genetic analysis of this pathway identified a set of mutants defective in retrograde signaling and designated genomes uncoupled (gun) mutants. Subsequent research has pointed to a significant role of tetrapyrrole biosynthesis in retrograde signaling. Meanwhile, the molecular functions of GUN1, the proposed integrator of multiple retrograde signals, have not been identified yet. However, based on the interactions of GUN1, some working hypotheses have been proposed. Interestingly, GUN1 contributes to important biological processes, including plastid protein homeostasis, through transcription, translation, and protein import. Furthermore, the interactions of GUN1 with tetrapyrroles and their biosynthetic enzymes have been revealed. This review focuses on our current understanding of the function of tetrapyrrole retrograde signaling on chloroplast biogenesis.
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Wu CS, Sudianto E, Chaw SM. Tight association of genome rearrangements with gene expression in conifer plastomes. BMC PLANT BIOLOGY 2021; 21:33. [PMID: 33419387 PMCID: PMC7796615 DOI: 10.1186/s12870-020-02809-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/20/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. RESULTS We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. CONCLUSIONS Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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Gajecka M, Marzec M, Chmielewska B, Jelonek J, Zbieszczyk J, Szarejko I. Changes in plastid biogenesis leading to the formation of albino regenerants in barley microspore culture. BMC PLANT BIOLOGY 2021; 21:22. [PMID: 33413097 PMCID: PMC7792217 DOI: 10.1186/s12870-020-02755-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/24/2020] [Indexed: 06/06/2023]
Abstract
BACKGROUND Microspore embryogenesis is potentially the most effective method of obtaining doubled haploids (DH) which are utilized in breeding programs to accelerate production of new cultivars. However, the regeneration of albino plants significantly limits the exploitation of androgenesis for DH production in cereals. Despite many efforts, the precise mechanisms leading to development of albino regenerants have not yet been elucidated. The objective of this study was to reveal the genotype-dependent molecular differences in chloroplast differentiation that lead to the formation of green and albino regenerants in microspore culture of barley. RESULTS We performed a detailed analysis of plastid differentiation at successive stages of androgenesis in two barley cultivars, 'Jersey' and 'Mercada' that differed in their ability to produce green regenerants. We demonstrated the lack of transition from the NEP-dependent to PEP-dependent transcription in plastids of cv. 'Mercada' that produced mostly albino regenerants in microspore culture. The failed NEP-to-PEP transition was associated with the lack of activity of Sig2 gene encoding a sigma factor necessary for transcription of plastid rRNA genes. A very low level of 16S and 23S rRNA transcripts and impaired plastid translation machinery resulted in the inhibition of photomorphogenesis in regenerating embryos and albino regenerants. Furthermore, the plastids present in differentiating 'Mercada' embryos contained a low number of plastome copies whose replication was not always completed. Contrary to 'Mercada', cv. 'Jersey' that produced 90% green regenerants, showed the high activity of PEP polymerase, the highly increased expression of Sig2, plastid rRNAs and tRNAGlu, which indicated the NEP inhibition. The increased expression of GLKs genes encoding transcription factors required for induction of photomorphogenesis was also observed in 'Jersey' regenerants. CONCLUSIONS Proplastids present in microspore-derived embryos of albino-producing genotypes did not pass the early checkpoints of their development that are required for induction of further light-dependent differentiation of chloroplasts. The failed activation of plastid-encoded RNA polymerase during differentiation of embryos was associated with the genotype-dependent inability to regenerate green plants in barley microspore culture. The better understanding of molecular mechanisms underlying formation of albino regenerants may be helpful in overcoming the problem of albinism in cereal androgenesis.
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Affiliation(s)
- Monika Gajecka
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Jagiellonska 28, Katowice, 40-032, Poland
| | - Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Jagiellonska 28, Katowice, 40-032, Poland
| | - Beata Chmielewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Jagiellonska 28, Katowice, 40-032, Poland
| | - Janusz Jelonek
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Jagiellonska 28, Katowice, 40-032, Poland
| | - Justyna Zbieszczyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Jagiellonska 28, Katowice, 40-032, Poland
| | - Iwona Szarejko
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Jagiellonska 28, Katowice, 40-032, Poland.
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Favier A, Gans P, Boeri Erba E, Signor L, Muthukumar SS, Pfannschmidt T, Blanvillain R, Cobessi D. The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features. FRONTIERS IN PLANT SCIENCE 2021; 12:668897. [PMID: 34276730 PMCID: PMC8278866 DOI: 10.3389/fpls.2021.668897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/28/2021] [Indexed: 05/09/2023]
Abstract
In Angiosperms, the plastid-encoded RNA polymerase (PEP) is a multimeric enzyme, essential for the proper expression of the plastid genome during chloroplast biogenesis. It is especially required for the light initiated expression of photosynthesis genes and the subsequent build-up of the photosynthetic apparatus. The PEP complex is composed of a prokaryotic-type core of four plastid-encoded subunits and 12 nuclear-encoded PEP-associated proteins (PAPs). Among them, there are two iron superoxide dismutases, FSD2/PAP9 and FSD3/PAP4. Superoxide dismutases usually are soluble enzymes not bound into larger protein complexes. To investigate this unusual feature, we characterized PAP9 using molecular genetics, fluorescence microscopy, mass spectrometry, X-ray diffraction, and solution-state NMR. Despite the presence of a predicted nuclear localization signal within the sequence of the predicted chloroplast transit peptide, PAP9 was mainly observed within plastids. Mass spectrometry experiments with the recombinant Arabidopsis PAP9 suggested that monomers and dimers of PAP9 could be associated to the PEP complex. In crystals, PAP9 occurred as a dimeric enzyme that displayed a similar fold to that of the FeSODs or manganese SOD (MnSODs). A zinc ion, instead of the expected iron, was found to be penta-coordinated with a trigonal-bipyramidal geometry in the catalytic center of the recombinant protein. The metal coordination involves a water molecule and highly conserved residues in FeSODs. Solution-state NMR and DOSY experiments revealed an unfolded C-terminal 34 amino-acid stretch in the stand-alone protein and few internal residues interacting with the rest of the protein. We hypothesize that this C-terminal extension had appeared during evolution as a distinct feature of the FSD2/PAP9 targeting it to the PEP complex. Close vicinity to the transcriptional apparatus may allow for the protection against the strongly oxidizing aerial environment during plant conquering of terrestrial habitats.
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Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pierre Gans
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | - Luca Signor
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, Grenoble, France
- *Correspondence: Robert Blanvillain,
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- David Cobessi,
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Kurkela J, Fredman J, Salminen TA, Tyystjärvi T. Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase. Mol Microbiol 2021; 115:1-11. [PMID: 32920946 DOI: 10.1111/mmi.14603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
The conserved omega (ω) subunit of RNA polymerase (RNAP) is the only nonessential subunit of bacterial RNAP core. The small ω subunit (7 kDa-11.5 kDa) contains three conserved α helices, and helices α2 and α3 contain five fully conserved amino acids of ω. Four conserved amino acids stabilize the correct folding of the ω subunit and one is located in the vicinity of the β' subunit of RNAP. Otherwise ω shows high variation between bacterial taxa, and although the main interaction partner of ω is always β', many interactions are taxon-specific. ω-less strains show pleiotropic phenotypes, and based on in vivo and in vitro results, a few roles for the ω subunits have been described. Interactions of the ω subunit with the β' subunit are important for the RNAP core assembly and integrity. In addition, the ω subunit plays a role in promoter selection, as ω-less RNAP cores recruit fewer primary σ factors and more alternative σ factors than intact RNAP cores in many species. Furthermore, the promoter selection of an ω-less RNAP holoenzyme bearing the primary σ factor seems to differ from that of an intact RNAP holoenzyme.
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Affiliation(s)
- Juha Kurkela
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Fredman
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Tiina A Salminen
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
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Li T, Pan W, Yuan Y, Liu Y, Li Y, Wu X, Wang F, Cui L. Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:684619. [PMID: 34335653 PMCID: PMC8319850 DOI: 10.3389/fpls.2021.684619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/23/2021] [Indexed: 05/17/2023]
Abstract
Plant mitochondrial transcription termination factor (mTERF) family regulates organellar gene expression (OGE) and is functionally characterized in diverse species. However, limited data are available about its functions in the agriculturally important cereal barley (Hordeum vulgare L.). In this study, we identified 60 mTERFs in the barley genome (HvmTERFs) through a comprehensive search against the most updated barley reference genome, Morex V2. Then, phylogenetic analysis categorized these genes into nine subfamilies, with approximately half of the HvmTERFs belonging to subfamily IX. Members within the same subfamily generally possessed conserved motif composition and exon-intron structure. Both segmental and tandem duplication contributed to the expansion of HvmTERFs, and the duplicated gene pairs were subjected to strong purifying selection. Expression analysis suggested that many HvmTERFs may play important roles in barley development (e.g., seedlings, leaves, and developing inflorescences) and abiotic stresses (e.g., cold, salt, and metal ion), and HvmTERF21 and HvmTERF23 were significant induced by various abiotic stresses and/or phytohormone treatment. Finally, the nucleotide diversity was decreased by only 4.5% for HvmTERFs during the process of barley domestication. Collectively, this is the first report to characterize HvmTERFs, which will not only provide important insights into further evolutionary studies but also contribute to a better understanding of the potential functions of HvmTERFs and ultimately will be useful in future gene functional studies.
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Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Yiyuan Yuan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Ying Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaoyu Wu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Fei Wang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Licao Cui
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Żur I, Gajecka M, Dubas E, Krzewska M, Szarejko I. Albino Plant Formation in Androgenic Cultures: An Old Problem and New Facts. Methods Mol Biol 2021; 2288:3-23. [PMID: 34270002 DOI: 10.1007/978-1-0716-1335-1_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High frequency of albino plant formation in isolated microspore or anther cultures is a great problem limiting the possibility of their exploitation on a wider scale. It is highly inconvenient as androgenesis-based doubled haploid (DH) technology provides the simplest and shortest way to total homozygosity, highly valued by plant geneticists, biotechnologists and especially, plant breeders, and this phenomenon constitutes a serious limitation of these otherwise powerful tools. The genotype-dependent tendency toward albino plant formation is typical for many monocotyledonous plants, including cereals like wheat, barley, rice, triticale, oat and rye - the most important from the economical point of view. Despite many efforts, the precise mechanism underlying chlorophyll deficiency has not yet been elucidated. In this chapter, we review the data concerning molecular and physiological control over proper/disturbed chloroplast biogenesis, old hypotheses explaining the mechanism of chlorophyll deficiency, and recent studies which shed new light on this phenomenon.
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Affiliation(s)
- Iwona Żur
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland.
| | - Monika Gajecka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Ewa Dubas
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - Monika Krzewska
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
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Cytokinin-Regulated Expression of Arabidopsis thaliana PAP Genes and Its Implication for the Expression of Chloroplast-Encoded Genes. Biomolecules 2020; 10:biom10121658. [PMID: 33322466 PMCID: PMC7764210 DOI: 10.3390/biom10121658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
Cytokinins (CKs) are known to regulate the biogenesis of chloroplasts under changing environmental conditions and at different stages of plant ontogenesis. However, the underlying mechanisms are still poorly understood. Apparently, the mechanisms can be duplicated in several ways, including the influence of nuclear genes that determine the expression of plastome through the two-component CK regulatory circuit. In this study, we evaluated the role of cytokinins and CK signaling pathway on the expression of nuclear genes for plastid RNA polymerase-associated proteins (PAPs). Cytokinin induced the expression of all twelve Arabidopsis thalianaPAP genes irrespective of their functions via canonical CK signaling pathway but this regulation might be indirect taking into consideration their different functions and versatile structure of promoter regions. The disruption of PAP genes contributed to the abolishment of positive CK effect on the accumulation of the chloroplast gene transcripts and transcripts of the nuclear genes for plastid transcription machinery as can be judged from the analysis of pap1 and pap6 mutants. However, the CK regulatory circuit in the mutants remained practically unperturbed. Knock-out of PAP genes resulted in cytokinin overproduction as a consequence of the strong up-regulation of the genes for CK synthesis.
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Exploring the Functional Relationship between y-Type Thioredoxins and 2-Cys Peroxiredoxins in Arabidopsis Chloroplasts. Antioxidants (Basel) 2020; 9:antiox9111072. [PMID: 33142810 PMCID: PMC7694023 DOI: 10.3390/antiox9111072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 11/17/2022] Open
Abstract
Thioredoxins (Trxs) are small, ubiquitous enzymes that catalyze disulphide–dithiol interchange in target enzymes. The large set of chloroplast Trxs, including f, m, x and y subtypes, use reducing equivalents fueled by photoreduced ferredoxin (Fdx) for fine-tuning photosynthetic performance and metabolism through the control of the activity of redox-sensitive proteins. Although biochemical analyses suggested functional diversity of chloroplast Trxs, genetic studies have established that deficiency in a particular Trx subtype has subtle phenotypic effects, leading to the proposal that the Trx isoforms are functionally redundant. In addition, chloroplasts contain an NADPH-dependent Trx reductase with a joint Trx domain, termed NTRC. Interestingly, Arabidopsis mutants combining the deficiencies of x- or f-type Trxs and NTRC display very severe growth inhibition phenotypes, which are partially rescued by decreased levels of 2-Cys peroxiredoxins (Prxs). These findings indicate that the reducing capacity of Trxs f and x is modulated by the redox balance of 2-Cys Prxs, which is controlled by NTRC. In this study, we explored whether NTRC acts as a master regulator of the pool of chloroplast Trxs by analyzing its functional relationship with Trxs y. While Trx y interacts with 2-Cys Prxs in vitro and in planta, the analysis of Arabidopsis mutants devoid of NTRC and Trxs y suggests that Trxs y have only a minor effect, if any, on the redox state of 2-Cys Prxs.
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50
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Bychkov IA, Kudryakova NV, Kuznetsov VV, Kusnetsov VV. Cold Stress Activates the Expression of Genes of the Chloroplast Transcription Apparatus in Arabidopsis thaliana Plants. DOKL BIOCHEM BIOPHYS 2020; 494:235-239. [PMID: 33119824 DOI: 10.1134/s160767292005004x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 05/30/2020] [Accepted: 05/30/2020] [Indexed: 11/23/2022]
Abstract
The physiological and molecular responses of Arabidopsis thaliana plants to cold stress were studied. Exposure to a low non-freezing temperature (4°C, 5 days) caused a decrease in the physiological functions and activity of a number of photosynthetic genes and elevation in expression of the cold stress gene COR15a, the product of which protects chloroplasts. It was shown for the first time that in parallel to a general inhibition of physiological functions under hypothermia, an increase in the expression of most genes for the chloroplast transcription apparatus was observed. This is obviously one of the compensatory mechanisms of adaptation aimed to maintain cellular homeostasis and physiological functions under hypothermia.
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Affiliation(s)
- I A Bychkov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia.
| | - N V Kudryakova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Vl V Kuznetsov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - V V Kusnetsov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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