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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: 8] [Impact Index Per Article: 8.0] [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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Mahapatra K, Banerjee S, De S, Mitra M, Roy P, Roy S. An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update. Front Cell Dev Biol 2021; 9:671698. [PMID: 34447743 PMCID: PMC8383295 DOI: 10.3389/fcell.2021.671698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022] Open
Abstract
Besides the nuclear genome, plants possess two small extra chromosomal genomes in mitochondria and chloroplast, respectively, which contribute a small fraction of the organelles’ proteome. Both mitochondrial and chloroplast DNA have originated endosymbiotically and most of their prokaryotic genes were either lost or transferred to the nuclear genome through endosymbiotic gene transfer during the course of evolution. Due to their immobile nature, plant nuclear and organellar genomes face continuous threat from diverse exogenous agents as well as some reactive by-products or intermediates released from various endogenous metabolic pathways. These factors eventually affect the overall plant growth and development and finally productivity. The detailed mechanism of DNA damage response and repair following accumulation of various forms of DNA lesions, including single and double-strand breaks (SSBs and DSBs) have been well documented for the nuclear genome and now it has been extended to the organelles also. Recently, it has been shown that both mitochondria and chloroplast possess a counterpart of most of the nuclear DNA damage repair pathways and share remarkable similarities with different damage repair proteins present in the nucleus. Among various repair pathways, homologous recombination (HR) is crucial for the repair as well as the evolution of organellar genomes. Along with the repair pathways, various other factors, such as the MSH1 and WHIRLY family proteins, WHY1, WHY2, and WHY3 are also known to be involved in maintaining low mutation rates and structural integrity of mitochondrial and chloroplast genome. SOG1, the central regulator in DNA damage response in plants, has also been found to mediate endoreduplication and cell-cycle progression through chloroplast to nucleus retrograde signaling in response to chloroplast genome instability. Various proteins associated with the maintenance of genome stability are targeted to both nuclear and organellar compartments, establishing communication between organelles as well as organelles and nucleus. Therefore, understanding the mechanism of DNA damage repair and inter compartmental crosstalk mechanism in various sub-cellular organelles following induction of DNA damage and identification of key components of such signaling cascades may eventually be translated into strategies for crop improvement under abiotic and genotoxic stress conditions. This review mainly highlights the current understanding as well as the importance of different aspects of organelle genome maintenance mechanisms in higher plants.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Samrat Banerjee
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Sayanti De
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Mehali Mitra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Pinaki Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Burdwan, India
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Senthilkumar S, Ulaganathan K, Ghosh Dasgupta M. Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus. 3 Biotech 2021; 11:393. [PMID: 34458062 DOI: 10.1007/s13205-021-02943-0] [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] [Received: 04/13/2021] [Accepted: 07/25/2021] [Indexed: 12/25/2022] Open
Abstract
Chloroplast genome sequencing is an essential tool to understand genome evolution and phylogenetic relationship. The available methods for constructing chloroplast genome include chloroplast enrichment followed by long overlapping PCR or extraction and assembly of chloroplast-specific reads from whole-genome datasets. In the present study, we propose an alternate strategy of extraction and assembly of chloroplast-specific reads from leaf transcriptome data of Pterocarpus santalinus using bowtie2 aligner program. The assembled genome was compared with the published chloroplast genome of P. santalinus for genome size, number of predicted genes, microsatellite repeat motifs, and nucleotide repeats. A near-complete chloroplast genome was assembled from the transcriptome reads. The proposed method requires less computational time and know-how, limited virtual memory, and is cost-effective when compared to whole-genome sequencing. Assembly of Cp genome from transcriptome data will enhance the resolution of phylogenetic studies through comparative plastome analysis, facilitate accurate species/genotype discrimination and accelerate the development of transplastomic plants with enhanced biotic and abiotic tolerance. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02943-0.
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Affiliation(s)
- Shanmugavel Senthilkumar
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641002 Tamil Nadu India
| | - Kandasamy Ulaganathan
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007 Andhra Pradesh India
| | - Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641002 Tamil Nadu India
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Kössler S, Armarego-Marriott T, Tarkowská D, Turečková V, Agrawal S, Mi J, de Souza LP, Schöttler MA, Schadach A, Fröhlich A, Bock R, Al-Babili S, Ruf S, Sampathkumar A, Moreno JC. Lycopene β-cyclase expression influences plant physiology, development, and metabolism in tobacco plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2544-2569. [PMID: 33484250 PMCID: PMC8006556 DOI: 10.1093/jxb/erab029] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/19/2021] [Indexed: 05/12/2023]
Abstract
Carotenoids are important isoprenoids produced in the plastids of photosynthetic organisms that play key roles in photoprotection and antioxidative processes. β-Carotene is generated from lycopene by lycopene β-cyclase (LCYB). Previously, we demonstrated that the introduction of the Daucus carota (carrot) DcLCYB1 gene into tobacco (cv. Xanthi) resulted in increased levels of abscisic acid (ABA) and especially gibberellins (GAs), resulting in increased plant yield. In order to understand this phenomenon prior to exporting this genetic strategy to crops, we generated tobacco (Nicotiana tabacum cv. Petit Havana) mutants that exhibited a wide range of LCYB expression. Transplastomic plants expressing DcLCYB1 at high levels showed a wild-type-like growth, even though their pigment content was increased and their leaf GA1 content was reduced. RNA interference (RNAi) NtLCYB lines showed different reductions in NtLCYB transcript abundance, correlating with reduced pigment content and plant variegation. Photosynthesis (leaf absorptance, Fv/Fm, and light-saturated capacity of linear electron transport) and plant growth were impaired. Remarkably, drastic changes in phytohormone content also occurred in the RNAi lines. However, external application of phytohormones was not sufficient to rescue these phenotypes, suggesting that altered photosynthetic efficiency might be another important factor explaining their reduced biomass. These results show that LCYB expression influences plant biomass by different mechanisms and suggests thresholds for LCYB expression levels that might be beneficial or detrimental for plant growth.
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Affiliation(s)
- Stella Kössler
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Tegan Armarego-Marriott
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Palacký University, Šlechtitelů, Olomouc, Czech Republic
| | - Veronika Turečková
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Palacký University, Šlechtitelů, Olomouc, Czech Republic
| | - Shreya Agrawal
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Jianing Mi
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Leonardo Perez de Souza
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Anne Schadach
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Anja Fröhlich
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Salim Al-Babili
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stephanie Ruf
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
| | - Juan C Moreno
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg1 D-14476, Potsdam-Golm, Germany
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Li S, Chang L, Zhang J. Advancing organelle genome transformation and editing for crop improvement. PLANT COMMUNICATIONS 2021; 2:100141. [PMID: 33898977 PMCID: PMC8060728 DOI: 10.1016/j.xplc.2021.100141] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/15/2020] [Accepted: 01/01/2021] [Indexed: 05/05/2023]
Abstract
Plant cells contain three organelles that harbor DNA: the nucleus, plastids, and mitochondria. Plastid transformation has emerged as an attractive platform for the generation of transgenic plants, also referred to as transplastomic plants. Plastid genomes have been genetically engineered to improve crop yield, nutritional quality, and resistance to abiotic and biotic stresses, as well as for recombinant protein production. Despite many promising proof-of-concept applications, transplastomic plants have not been commercialized to date. Sequence-specific nuclease technologies are widely used to precisely modify nuclear genomes, but these tools have not been applied to edit organelle genomes because the efficient homologous recombination system in plastids facilitates plastid genome editing. Unlike plastid transformation, successful genetic transformation of higher plant mitochondrial genome transformation was tested in several research group, but not successful to date. However, stepwise progress has been made in modifying mitochondrial genes and their transcripts, thus enabling the study of their functions. Here, we provide an overview of advances in organelle transformation and genome editing for crop improvement, and we discuss the bottlenecks and future development of these technologies.
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Affiliation(s)
- Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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Tabatabaei I, Dal Bosco C, Bednarska M, Ruf S, Meurer J, Bock R. A highly efficient sulfadiazine selection system for the generation of transgenic plants and algae. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:638-649. [PMID: 30144344 PMCID: PMC6381783 DOI: 10.1111/pbi.13004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/17/2018] [Indexed: 05/02/2023]
Abstract
The genetic transformation of plant cells is critically dependent on the availability of efficient selectable marker gene. Sulfonamides are herbicides that, by inhibiting the folic acid biosynthetic pathway, suppress the growth of untransformed cells. Sulfonamide resistance genes that were previously developed as selectable markers for plant transformation were based on the assumption that, in plants, the folic acid biosynthetic pathway resides in the chloroplast compartment. Consequently, the Sul resistance protein, a herbicide-insensitive dihydropteroate synthase, was targeted to the chloroplast. Although these vectors produce transgenic plants, the transformation efficiencies are low compared to other markers. Here, we show that this inefficiency is due to the erroneous assumption that the folic acid pathway is located in chloroplasts. When the RbcS transit peptide was replaced by a transit peptide for protein import into mitochondria, the compartment where folic acid biosynthesis takes place in yeast, much higher resistance to sulfonamide and much higher transformation efficiencies are obtained, suggesting that current sul vectors are likely to function due to low-level mistargeting of the resistance protein to mitochondria. We constructed a series of optimized transformation vectors and demonstrate that they produce transgenic events at very high frequency in both the seed plant tobacco and the green alga Chlamydomonas reinhardtii. Co-transformation experiments in tobacco revealed that sul is even superior to nptII, the currently most efficient selectable marker gene, and thus provides an attractive marker for the high-throughput genetic transformation of plants and algae.
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Affiliation(s)
- Iman Tabatabaei
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Cristina Dal Bosco
- Department für Biologie ILudwig‐Maximilians‐Universität MünchenMünchenGermany
- Present address:
Pioneer Hi‐Bred Northern Europe Service Division GmbHEschbachGermany
| | - Marta Bednarska
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Stephanie Ruf
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jörg Meurer
- Department für Biologie ILudwig‐Maximilians‐Universität MünchenMünchenGermany
| | - Ralph Bock
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
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