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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] [MESH Headings] [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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2
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Hess WR, Wilde A, Mullineaux CW. Does mRNA targeting explain gene retention in chloroplasts? TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00267-X. [PMID: 39443276 DOI: 10.1016/j.tplants.2024.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/25/2024]
Abstract
During their evolution from cyanobacteria, plastids have relinquished most of their genes to the host cell nucleus, but have retained a core set of genes that are transcribed and translated within the organelle. Previous explanations have included incompatible codon or base composition, problems importing certain proteins across the double membrane, or the need for tight regulation in concert with the redox status of the electron transport chain. In this opinion article we propose the 'mRNA targeting hypothesis'. Studies in cyanobacteria suggest that mRNAs encoding core photosynthetic proteins have features that are crucial for membrane targeting and coordination of early steps in complex assembly. We propose that the requirement for intimate involvement of mRNA molecules at the thylakoid surface explains the retention of core photosynthetic genes in chloroplasts.
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Affiliation(s)
- Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Conrad W Mullineaux
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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3
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Kan S, Su X, Yang L, Zhou H, Qian M, Zhang W, Li C. From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation. BMC PLANT BIOLOGY 2024; 24:949. [PMID: 39394065 PMCID: PMC11468349 DOI: 10.1186/s12870-024-05669-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 10/07/2024] [Indexed: 10/13/2024]
Abstract
BACKGROUND Plastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy and carbon dioxide, converting them into chemical energy and oxygen, which are crucial for plant development and adaptation. However, little is known about the plastid genome to light adaptation. Petrocosmea, a member of the Gesneriaceae family, comprises approximately 70 species with diverse light environment, serve as an ideal subject for studying plastomes adapt to light. RESULTS In this study, we selected ten representative species of Petrocosmea from diverse light environments, assembled their plastid genomes, and conducted a comparative genomic analysis. We found that the plastid genome of Petrocosmea is highly conserved in both structure and gene content. The phylogenetic relationships reconstructed based on the plastid genes were divided into five clades, which is consistent with the results of previous studies. The vast majority of plastid protein-coding genes were under purifying selection, with only the rps8 and rps16 genes identified under positive selection in different light environments. Notably, significant differences of evolutionary rate were observed in NADH dehydrogenase, ATPase ribosome, and RNA polymerase between Clade A and the other clades. Additionally, we identified ycf1 and several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, and trnS-trnG) as candidate barcodes for this emerging ornamental horticulture. CONCLUSION We newly assembled ten plastid genomes of Petrocosmea and identified several hypervariable regions, providing genetic resources and candidate markers for this promising emerging ornamental horticulture. Furthermore, our study suggested that rps8 and rps16 were under positive selection and that the evolutionary patterns of NADH dehydrogenase, ATPase ribosome, and RNA polymerase were related to the diversity light environment in Petrocosmea. This revealed an evolutionary scenario for light adaptation of the plastid genome in plants.
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Affiliation(s)
- Shenglong Kan
- Marine College, Shandong University, Weihai, 264209, China
| | - Xiaoju Su
- Marine College, Shandong University, Weihai, 264209, China
| | - Liu Yang
- Marine College, Shandong University, Weihai, 264209, China
| | - Hongling Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, China
| | - Mu Qian
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, 250110, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, 264209, China.
| | - Chaoqun Li
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China.
- Shandong Engineering Research Center of Rose Breeding Technology and Germplasm Innovation, School of Life Sciences, Qilu Normal University, Jinan, 250200, China.
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4
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Rolo D, Schöttler MA, Sandoval-Ibáñez O, Bock R. Structure, function, and assembly of PSI in thylakoid membranes of vascular plants. THE PLANT CELL 2024; 36:4080-4108. [PMID: 38848316 PMCID: PMC11449065 DOI: 10.1093/plcell/koae169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
The photosynthetic apparatus is formed by thylakoid membrane-embedded multiprotein complexes that carry out linear electron transport in oxygenic photosynthesis. The machinery is largely conserved from cyanobacteria to land plants, and structure and function of the protein complexes involved are relatively well studied. By contrast, how the machinery is assembled in thylakoid membranes remains poorly understood. The complexes participating in photosynthetic electron transfer are composed of many proteins, pigments, and redox-active cofactors, whose temporally and spatially highly coordinated incorporation is essential to build functional mature complexes. Several proteins, jointly referred to as assembly factors, engage in the biogenesis of these complexes to bring the components together in a step-wise manner, in the right order and time. In this review, we focus on the biogenesis of the terminal protein supercomplex of the photosynthetic electron transport chain, PSI, in vascular plants. We summarize our current knowledge of the assembly process and the factors involved and describe the challenges associated with resolving the assembly pathway in molecular detail.
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Affiliation(s)
- David Rolo
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Omar Sandoval-Ibáñez
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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5
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Rojas M, Chotewutmontri P, Barkan A. Translational activation by a synthetic PPR protein elucidates control of psbA translation in Arabidopsis chloroplasts. THE PLANT CELL 2024; 36:4168-4178. [PMID: 38593198 PMCID: PMC11449048 DOI: 10.1093/plcell/koae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
Abstract
Translation initiation on chloroplast psbA mRNA in plants scales with light intensity, providing its gene product, D1, as needed to replace photodamaged D1 in Photosystem II. The psbA translational activator HIGH CHLOROPHYLL FLUORESCENCE 173 (HCF173) has been hypothesized to mediate this regulation. HCF173 belongs to the short-chain dehydrogenase/reductase superfamily, associates with the psbA 5'-untranslated region (5'-UTR), and has been hypothesized to enhance translation by binding an RNA segment that would otherwise pair with and mask the ribosome binding region. To test these hypotheses, we examined whether a synthetic pentatricopeptide repeat (sPPR) protein can substitute for HCF173 when bound to the HCF173 binding site. We show that an sPPR designed to bind HCF173's footprint in the psbA 5'-UTR bound the intended site in vivo and partially substituted for HCF173 to activate psbA translation. However, sPPR-activated translation did not respond to light. These results imply that HCF173 activates translation, at least in part, by sequestering the RNA it binds to maintain an accessible ribosome binding region, and that HCF173 is also required to regulate psbA translation in response to light. Translational activation can be added to the functions that can be programmed with sPPR proteins for synthetic biology applications in chloroplasts.
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Affiliation(s)
- Margarita Rojas
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97405, USA
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97405, USA
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6
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Rühle T, Leister D, Pasch V. Chloroplast ATP synthase: From structure to engineering. THE PLANT CELL 2024; 36:3974-3996. [PMID: 38484126 PMCID: PMC11449085 DOI: 10.1093/plcell/koae081] [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: 10/27/2023] [Accepted: 12/27/2023] [Indexed: 10/05/2024]
Abstract
F-type ATP synthases are extensively researched protein complexes because of their widespread and central role in energy metabolism. Progress in structural biology, proteomics, and molecular biology has also greatly advanced our understanding of the catalytic mechanism, post-translational modifications, and biogenesis of chloroplast ATP synthases. Given their critical role in light-driven ATP generation, tailoring the activity of chloroplast ATP synthases and modeling approaches can be applied to modulate photosynthesis. In the future, advances in genetic manipulation and protein design tools will significantly expand the scope for testing new strategies in engineering light-driven nanomotors.
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Affiliation(s)
- Thilo Rühle
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152 Planegg-Martinsried, Germany
| | - Viviana Pasch
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152 Planegg-Martinsried, Germany
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7
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Li Y, Liu Y, Ran G, Yu Y, Zhou Y, Zhu Y, Du Y, Pi L. The pentatricopeptide repeat protein DG1 promotes the transition to bilateral symmetry during Arabidopsis embryogenesis through GUN1-mediated plastid signals. THE NEW PHYTOLOGIST 2024; 244:542-557. [PMID: 39140987 DOI: 10.1111/nph.20056] [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: 05/31/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024]
Abstract
During Arabidopsis embryogenesis, the transition of the embryo's symmetry from radial to bilateral between the globular and heart stage is a crucial event, involving the formation of cotyledon primordia and concurrently the establishment of a shoot apical meristem (SAM). However, a coherent framework of how this transition is achieved remains to be elucidated. In this study, we investigated the function of DELAYED GREENING 1 (DG1) in Arabidopsis embryogenesis using a newly identified dg1-3 mutant. The absence of chloroplast-localized DG1 in the mutants led to embryos being arrested at the globular or heart stage, accompanied by an expansion of WUSCHEL (WUS) and SHOOT MERISTEMLESS (STM) expression. This finding pinpoints the essential role of DG1 in regulating the transition to bilateral symmetry. Furthermore, we showed that this regulation of DG1 may not depend on its role in plastid RNA editing. Nevertheless, we demonstrated that the DG1 function in establishing bilateral symmetry is genetically mediated by GENOMES UNCOUPLED 1 (GUN1), which represses the transition process in dg1-3 embryos. Collectively, our results reveal that DG1 functionally antagonizes GUN1 to promote the transition of the Arabidopsis embryo's symmetry from radial to bilateral and highlight the role of plastid signals in regulating pattern formation during plant embryogenesis.
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Affiliation(s)
- Yajie Li
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Yiqiong Liu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Guiping Ran
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Yue Yu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Yifan Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxian Zhu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yujuan Du
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Limin Pi
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
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8
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Stolle DS, Osterhoff L, Treimer P, Lambertz J, Karstens M, Keller JM, Gerlach I, Bischoff A, Dünschede B, Rödiger A, Herrmann C, Baginsky S, Hofmann E, Zoschke R, Armbruster U, Nowaczyk MM, Schünemann D. STIC2 selectively binds ribosome-nascent chain complexes in the cotranslational sorting of Arabidopsis thylakoid proteins. EMBO J 2024; 43:4699-4719. [PMID: 39192033 PMCID: PMC11480477 DOI: 10.1038/s44318-024-00211-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
Chloroplast-encoded multi-span thylakoid membrane proteins are crucial for photosynthetic complexes, yet the coordination of their biogenesis remains poorly understood. To identify factors that specifically support the cotranslational biogenesis of the reaction center protein D1 of photosystem (PS) II, we generated and affinity-purified stalled ribosome-nascent chain complexes (RNCs) bearing D1 nascent chains. Stalled RNCs translating the soluble ribosomal subunit uS2c were used for comparison. Quantitative tandem-mass spectrometry of the purified RNCs identified around 140 proteins specifically associated with D1 RNCs, mainly involved in protein and cofactor biogenesis, including chlorophyll biosynthesis, and other metabolic pathways. Functional analysis of STIC2, a newly identified D1 RNC interactor, revealed its cooperation with chloroplast protein SRP54 in the de novo biogenesis and repair of D1, and potentially other cotranslationally-targeted reaction center subunits of PSII and PSI. The primary binding interface between STIC2 and the thylakoid insertase Alb3 and its homolog Alb4 was mapped to STIC2's β-sheet region, and the conserved Motif III in the C-terminal regions of Alb3/4.
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Affiliation(s)
- Dominique S Stolle
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Lena Osterhoff
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Paul Treimer
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Jan Lambertz
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Marie Karstens
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Ines Gerlach
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam, Germany
| | - Annika Bischoff
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Anja Rödiger
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christian Herrmann
- Physical Chemistry I, Faculty for Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Sacha Baginsky
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam, Germany
| | - Ute Armbruster
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Potsdam, Germany
- Molecular Photosynthesis, Faculty of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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9
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Abbasi-Vineh MA, Emadpour M. The First Introduction of an Exogenous 5' Untranslated Region for Control of Plastid Transgene Expression in Chlamydomonas reinhardtii. Mol Biotechnol 2024:10.1007/s12033-024-01279-3. [PMID: 39271617 DOI: 10.1007/s12033-024-01279-3] [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: 05/27/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024]
Abstract
The utilization of heterologous 5' untranslated regions (5'UTRs) for expressing foreign proteins in the chloroplast of Chlamydomonas reinhardtii (C. reinhardtii) has posed a persistent challenge over the years. This challenge stems from the lack of a defined and comprehensive set of translational cis-elements responsible for stability, ribosome binding, and translation initiation, which are mediated by trans-acting factors native to C. reinhardtii. In the current study, we aimed to address this bottleneck by employing the 5'UTR from gene 10 of the T7 bacteriophage (T7g10 5'UTR), fused to the promoter of C. reinhardtii small subunit ribosomal RNA (rrnS), to facilitate the translation of a reporter gene, YFP. Using a chimeric construct, the YFP mRNA was efficiently translated utilizing the heterologous T7g10 5'UTR. Furthermore, the accumulation of YFP protein under the control of the T7g10 5'UTR was approximately one third of that observed under the control of the endogenous psaA promoter/5'UTR in the C. reinhardtii chloroplast. The results of computational analyses demonstrated that the T7g10 5'UTR sequence shares common elements with the endogenous 5'UTRs of the chloroplast genes. Moreover, the findings of the current study highlighted the potential of employing bacteriophage 5'UTRs for the foreign protein accumulation from the chloroplast genome of C. reinhardtii.
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Affiliation(s)
- Mohammad Ali Abbasi-Vineh
- Department of Agricultural Biotechnology, Tarbiat Modares University (TMU), 1497713111, Tehran, Iran
| | - Masoumeh Emadpour
- Department of Agricultural Biotechnology, Tarbiat Modares University (TMU), 1497713111, Tehran, Iran.
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10
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Kwasniak-Owczarek M, Janska H. Experimental approaches to studying translation in plant semi-autonomous organelles. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5175-5187. [PMID: 38592734 PMCID: PMC11389837 DOI: 10.1093/jxb/erae151] [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: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Plant mitochondria and chloroplasts are semi-autonomous organelles originated from free-living bacteria that have retained reduced genomes during evolution. As a consequence, relatively few of the mitochondrial and chloroplast proteins are encoded in the organellar genomes and synthesized by the organellar ribosomes. Since both organellar genomes encode mainly components of the energy transduction systems, oxidative phosphorylation in mitochondria and photosynthetic apparatus in chloroplasts, understanding organellar translation is critical for a thorough comprehension of key aspects of mitochondrial and chloroplast activity affecting plant growth and development. Recent studies have clearly shown that translation is a key regulatory node in the expression of plant organellar genes, underscoring the need for an adequate methodology to study this unique stage of gene expression. The organellar translatome can be analysed by studying newly synthesized proteins or the mRNA pool recruited to the organellar ribosomes. In this review, we present experimental approaches used for studying translation in plant bioenergetic organelles. Their benefits and limitations, as well as the critical steps, are discussed. Additionally, we briefly mention several recently developed strategies to study organellar translation that have not yet been applied to plants.
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Affiliation(s)
- Malgorzata Kwasniak-Owczarek
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
| | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
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11
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Sun Y, Bakhtiari S, Valente-Paterno M, Wu Y, Nishimura Y, Shen W, Law C, Dhaliwal J, Dai D, Bui KH, Zerges W. Chloroplast biogenesis involves spatial coordination of nuclear and organellar gene expression in Chlamydomonas. PLANT PHYSIOLOGY 2024; 196:112-123. [PMID: 38709497 PMCID: PMC11376380 DOI: 10.1093/plphys/kiae256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/01/2024] [Accepted: 04/12/2024] [Indexed: 05/07/2024]
Abstract
The localization of translation can direct the polypeptide product to the proper intracellular compartment. Our results reveal translation by cytosolic ribosomes on a domain of the chloroplast envelope in the unicellular green alga Chlamydomonas (Chlamydomonas reinhardtii). We show that this envelope domain of isolated chloroplasts retains translationally active ribosomes and mRNAs encoding chloroplast proteins. This domain is aligned with localized translation by chloroplast ribosomes in the translation zone, a chloroplast compartment where photosystem subunits encoded by the plastid genome are synthesized and assembled. Roles of localized translation in directing newly synthesized subunits of photosynthesis complexes to discrete regions within the chloroplast for their assembly are suggested by differences in localization on the chloroplast of mRNAs encoding either subunit of the light-harvesting complex II or the small subunit of Rubisco. Transcription of the chloroplast genome is spatially coordinated with translation, as revealed by our demonstration of a subpopulation of transcriptionally active chloroplast nucleoids at the translation zone. We propose that the expression of chloroplast proteins by the nuclear-cytosolic and organellar genetic systems is organized in spatially aligned subcompartments of the cytoplasm and chloroplast to facilitate the biogenesis of the photosynthetic complexes.
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Affiliation(s)
- Yi Sun
- Department of Biology, Concordia University, Montreal, Quebec, Canada, H4B 1R6
| | - Shiva Bakhtiari
- Department of Biology, Concordia University, Montreal, Quebec, Canada, H4B 1R6
| | - Melissa Valente-Paterno
- Department of Biology, Concordia University, Montreal, Quebec, Canada, H4B 1R6
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada, H3A 0C7
| | - Yanxia Wu
- Department of Biology, Concordia University, Montreal, Quebec, Canada, H4B 1R6
| | - Yoshiki Nishimura
- Laboratory of Plant Molecular Genetics, Department of Botany, Graduate School of Sciences, Koyoto University, Oiwake-cho, Kita-Shirakawa, Kyoto-shi 606-8502, Japan
| | - Weike Shen
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Christopher Law
- Centre for Microscopy and Cell Imaging, Concordia University, Montreal, Quebec, Canada, H4B 1R6
| | - James Dhaliwal
- Department of Biology, Concordia University, Montreal, Quebec, Canada, H4B 1R6
| | - Daniel Dai
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada, H3A 0C7
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada, H3A 0C7
| | - William Zerges
- Department of Biology, Concordia University, Montreal, Quebec, Canada, H4B 1R6
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Böhm C, Inckemann R, Burgis M, Baumann J, Brinkmann CK, Lipinska KE, Gilles S, Freudigmann J, Seiler VN, Clark LG, Jewett MC, Voll LM, Niederholtmeyer H. Chloroplast Cell-Free Systems from Different Plant Species as a Rapid Prototyping Platform. ACS Synth Biol 2024; 13:2412-2424. [PMID: 39028299 PMCID: PMC11334176 DOI: 10.1021/acssynbio.4c00117] [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: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 07/20/2024]
Abstract
Climate change poses a significant threat to global agriculture, necessitating innovative solutions. Plant synthetic biology, particularly chloroplast engineering, holds promise as a viable approach to this challenge. Chloroplasts present a variety of advantageous traits for genetic engineering, but the development of genetic tools and genetic part characterization in these organelles is hindered by the lengthy time scales required to generate transplastomic organisms. To address these challenges, we have established a versatile protocol for generating highly active chloroplast-based cell-free gene expression (CFE) systems derived from a diverse range of plant species, including wheat (monocot), spinach, and poplar trees (dicots). We show that these systems work with conventionally used T7 RNA polymerase as well as the endogenous chloroplast polymerases, allowing for detailed characterization and prototyping of regulatory sequences at both transcription and translation levels. To demonstrate the platform for characterization of promoters and 5' and 3' untranslated regions (UTRs) in higher plant chloroplast gene expression, we analyze a collection of 23 5'UTRs, 10 3'UTRs, and 6 chloroplast promoters, assessed their expression in spinach and wheat extracts, and found consistency in expression patterns, suggesting cross-species compatibility. Looking forward, our chloroplast CFE systems open new avenues for plant synthetic biology, offering prototyping tools for both understanding gene expression and developing engineered plants, which could help meet the demands of a changing global climate.
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Affiliation(s)
- Clemens
V. Böhm
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - René Inckemann
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Michael Burgis
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Jessica Baumann
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | | | - Katarzyna E. Lipinska
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Sara Gilles
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Jonas Freudigmann
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | - Vinca N. Seiler
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | - Lauren G. Clark
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Lars M. Voll
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | - Henrike Niederholtmeyer
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
- Technical
University of Munich, Campus Straubing for Biotechnology and Sustainability, 94315 Straubing, Germany
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13
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Wang X, Ji D, Ma J, Chi W. Function of plastid translation in plant temperature acclimation: Retrograde signalling or extraribosomal 'moonlighting' functions? PLANT, CELL & ENVIRONMENT 2024. [PMID: 39101459 DOI: 10.1111/pce.15074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/06/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Summary StatementSpecific components of the plastid ribosome could act as pivotal limiting factors in plant temperature acclimation. We endeavour to elucidate the molecular nexus between plastid translation and temperature acclimation by incorporating the concept of extraribosomal ‘moonlighting’ functions of plastid ribosome proteins.
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Affiliation(s)
- Xiushun Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Daili Ji
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Ma
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Chi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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14
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Barboza Bispo R, Teixeira do Amaral A, Pinto VB, de Oliveira Santos T, Jário de Lima V, Rohem Simão B, Fischer A, Naldrett MJ, Alvarez S. Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn ( Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis. J Proteome Res 2024; 23:3108-3123. [PMID: 38648199 PMCID: PMC11302424 DOI: 10.1021/acs.jproteome.3c00772] [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: 11/14/2023] [Revised: 03/04/2024] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.
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Affiliation(s)
- Rosimeire Barboza Bispo
- Laboratório
de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro
de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos
dos Goytacazes, RJ, Brazil
| | - Antônio Teixeira do Amaral
- Laboratório
de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro
de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos
dos Goytacazes, RJ, Brazil
| | - Vitor Batista Pinto
- Laboratório
de Biologia Celular e Tecidual (LBCT), UENF,
Centro de Biociências e Biotecnologia (CBB), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Talles de Oliveira Santos
- Laboratório
de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro
de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos
dos Goytacazes, RJ, Brazil
| | - Valter Jário de Lima
- Laboratório
de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro
de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos
dos Goytacazes, RJ, Brazil
| | - Bruna Rohem Simão
- Laboratório
de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro
de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos
dos Goytacazes, RJ, Brazil
| | - Anne Fischer
- Proteomics
and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle
Center, 1901 Vine St, University of Nebraska−Lincoln
(UNL), Lincoln, Nebraska 68588, United States
| | - Michael J. Naldrett
- Proteomics
and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle
Center, 1901 Vine St, University of Nebraska−Lincoln
(UNL), Lincoln, Nebraska 68588, United States
| | - Sophie Alvarez
- Proteomics
and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle
Center, 1901 Vine St, University of Nebraska−Lincoln
(UNL), Lincoln, Nebraska 68588, United States
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15
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Legen J, Lenzen B, Kachariya N, Feltgen S, Gao Y, Mergenthal S, Weber W, Klotzsch E, Zoschke R, Sattler M, Schmitz-Linneweber C. A prion-like domain is required for phase separation and chloroplast RNA processing during cold acclimation in Arabidopsis. THE PLANT CELL 2024; 36:2851-2872. [PMID: 38723165 PMCID: PMC11289645 DOI: 10.1093/plcell/koae145] [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: 09/29/2023] [Accepted: 04/06/2024] [Indexed: 08/02/2024]
Abstract
Arabidopsis (Arabidopsis thaliana) plants can produce photosynthetic tissue with active chloroplasts at temperatures as low as 4°C, and this process depends on the presence of the nuclear-encoded, chloroplast-localized RNA-binding protein CP29A. In this study, we demonstrate that CP29A undergoes phase separation in vitro and in vivo in a temperature-dependent manner, which is mediated by a prion-like domain (PLD) located between the two RNA recognition motif domains of CP29A. The resulting droplets display liquid-like properties and are found near chloroplast nucleoids. The PLD is required to support chloroplast RNA splicing and translation in cold-treated tissue. Together, our findings suggest that plant chloroplast gene expression is compartmentalized by inducible condensation of CP29A at low temperatures, a mechanism that could play a crucial role in plant cold resistance.
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Affiliation(s)
- Julia Legen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Benjamin Lenzen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Nitin Kachariya
- Helmholtz Munich, Institute of Structural Biology, Ingolstädter Landstrasse 1, Munich 85764, Germany
- Department of Bioscience, Bavarian NMR Center, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Stephanie Feltgen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Simon Mergenthal
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Willi Weber
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Enrico Klotzsch
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Michael Sattler
- Helmholtz Munich, Institute of Structural Biology, Ingolstädter Landstrasse 1, Munich 85764, Germany
- Department of Bioscience, Bavarian NMR Center, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
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16
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Muino JM, Ruwe H, Qu Y, Maschmann S, Chen W, Zoschke R, Ohler U, Kaufmann K, Schmitz-Linneweber C. MatK impacts differential chloroplast translation by limiting spliced tRNA-K(UUU) abundance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39074058 DOI: 10.1111/tpj.16945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/31/2024]
Abstract
The protein levels of chloroplast photosynthetic genes and genes related to the chloroplast genetic apparatus vary to adapt to different conditions. However, the underlying mechanisms governing these variations remain unclear. The chloroplast intron Maturase K is encoded within the trnK intron and has been suggested to be required for splicing several group IIA introns, including the trnK intron. In this study, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) to identify MatK's preference for binding to group IIA intron domains I and VI within target transcripts. Importantly, these domains are crucial for splice site selection, and we discovered alternative 5'-splice sites in three MatK target introns. The resulting alternative trnK lariat structure showed increased accumulation during heat acclimation. The cognate codon of tRNA-K(UUU) is highly enriched in mRNAs encoding ribosomal proteins and a trnK-matK over-expressor exhibited elevated levels of the spliced tRNA-K(UUU). Ribosome profiling analysis of the overexpressor revealed a significant up-shift in the translation of ribosomal proteins compared to photosynthetic genes. Our findings suggest the existence of a novel regulatory mechanism linked to the abundance of tRNA-K(UUU), enabling the differential expression of functional chloroplast gene groups.
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Affiliation(s)
- Jose M Muino
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Hannes Ruwe
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Yujiao Qu
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Sascha Maschmann
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
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17
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Huo Y, Cheng M, Tang M, Zhang M, Yang X, Zheng Y, Zhao T, He P, Yu J. GhCTSF1, a short PPR protein with a conserved role in chloroplast development and photosynthesis, participates in intron splicing of rpoC1 and ycf3-2 transcripts in cotton. PLANT COMMUNICATIONS 2024; 5:100858. [PMID: 38444162 PMCID: PMC11211521 DOI: 10.1016/j.xplc.2024.100858] [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: 07/08/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Cotton is one of the most important textile fibers worldwide. As crucial agronomic traits, leaves play an essential role in the growth, disease resistance, fiber quality, and yield of cotton plants. Pentatricopeptide repeat (PPR) proteins are a large family of nuclear-encoded proteins involved in organellar or nuclear RNA metabolism. Using a virus-induced gene silencing assay, we found that cotton plants displayed variegated yellow leaf phenotypes with decreased chlorophyll content when expression of the PPR gene GhCTSF1 was silenced. GhCTSF1 encodes a chloroplast-localized protein that contains only two PPR motifs. Disruption of GhCTSF1 substantially reduces the splicing efficiency of rpoC1 intron 1 and ycf3 intron 2. Loss of function of the GhCTSF1 ortholog EMB1417 causes splicing defects in rpoC1 and ycf3-2, leading to impaired chloroplast structure and decreased photosynthetic rates in Arabidopsis. We also found that GhCTSF1 interacts with two splicing factors, GhCRS2 and GhWTF1. Defects in GhCRS2 and GhWTF1 severely affect intron splicing of rpoC1 and ycf3-2 in cotton, leading to defects in chloroplast development and a reduction in photosynthesis. Our results suggest that GhCTSF1 is specifically required for splicing rpoC1 and ycf3-2 in cooperation with GhCRS2 and GhWTF1.
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Affiliation(s)
- Yuzhu Huo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Mengxue Cheng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Meiju Tang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Meng Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaofan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yating Zheng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Tong Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Peng He
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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18
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Kim JE, Kim KM, Kim YS, Chung GY, Che SH, Na CS. Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation. Genes (Basel) 2024; 15:761. [PMID: 38927697 PMCID: PMC11203327 DOI: 10.3390/genes15060761] [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: 05/03/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.
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Affiliation(s)
- Ji Eun Kim
- Wild Plant Seed Office, Baekdudaegan National Arboretum, Bongwha 36209, Republic of Korea;
| | - Keyong Min Kim
- Arboretum Education Office, Baekdudaegan National Arboretum, Bongwha 36209, Republic of Korea
| | - Yang Su Kim
- Department of General Affairs, General Affairs Team, Gangeung-Wonju National University, Gangeung 25457, Republic of Korea
| | - Gyu Young Chung
- Department of Forest Science, Andong National University, Andong 36729, Republic of Korea
| | - Sang Hoon Che
- Forest Bioresources Department, Baekdudaegan National Arboretum, Bongwha 36209, Republic of Korea
| | - Chae Sun Na
- Wild Plant Seed Office, Baekdudaegan National Arboretum, Bongwha 36209, Republic of Korea;
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19
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Schmid LM, Manavski N, Chi W, Meurer J. Chloroplast Ribosome Biogenesis Factors. PLANT & CELL PHYSIOLOGY 2024; 65:516-536. [PMID: 37498958 DOI: 10.1093/pcp/pcad082] [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: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.
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Affiliation(s)
- Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
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20
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Liu XY, Jiang RC, Ma B, Wang Y, Yang YZ, Xu C, Sun F, Tan BC. Maize requires Embryo defective27 for embryogenesis and seedling development. PLANT PHYSIOLOGY 2024; 195:430-445. [PMID: 38198212 DOI: 10.1093/plphys/kiae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
The essential role of plastid translation in embryogenesis has been established in many plants, but a retrograde signal triggered by defective plastid translation machinery that may leads to embryogenesis arrest remains unknown. In this study, we characterized an embryo defective27 (emb27) mutant in maize (Zea mays), and cloning indicates that Emb27 encodes the plastid ribosomal protein S13. The null mutant emb27-1 conditions an emb phenotype with arrested embryogenesis; however, the leaky mutant emb27-2 exhibits normal embryogenesis but an albino seedling-lethal phenotype. The emb27-1/emb27-2 trans-heterozygotes display varying phenotypes from emb to normal seeds but albino seedlings. Analysis of the Emb27 transcription levels in these mutants revealed that the Emb27 expression level in the embryo corresponds with the phenotypic expression of the emb27 mutants. In the W22 genetic background, an Emb27 transcription level higher than 6% of the wild-type level renders normal embryogenesis, whereas lower than that arrests embryogenesis. Mutation of Emb27 reduces the level of plastid 16S rRNA and the accumulation of the plastid-encoded proteins. As a secondary effect, splicing of several plastid introns was impaired in emb27-1 and 2 other plastid translation-defective mutants, emb15 and emb16, suggesting that plastome-encoded factors are required for the splicing of these introns, such as Maturase K (MatK). Our results indicate that EMB27 is essential for plastid protein translation, embryogenesis, and seedling development in maize and reveal an expression threshold of Emb27 for maize embryogenesis.
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Affiliation(s)
- Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Rui-Cheng Jiang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bing Ma
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Chunhui Xu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Feng Sun
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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21
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Xu W, Li S, Bock R, Zhang J. A heat-inducible expression system for external control of gene expression in plastids. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:960-969. [PMID: 38059318 PMCID: PMC10955493 DOI: 10.1111/pbi.14238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/17/2023] [Accepted: 11/04/2023] [Indexed: 12/08/2023]
Abstract
Inducible expression systems can overcome the trade-off between high-level transgene expression and its pleiotropic effects on plant growth. In addition, they can facilitate the expression of biochemical pathways that produce toxic metabolites. Although a few inducible expression systems for the control of transgene expression in plastids have been developed, they all depend on chemical inducers and/or nuclear transgenes. Here we report a temperature-inducible expression system for plastids that is based on the bacteriophage λ leftward and rightward promoters (pL/pR) and the temperature-sensitive repressor cI857. We show that the expression of green fluorescent protein (GFP) in plastids can be efficiently repressed by cI857 under normal growth conditions, and becomes induced over time upon exposure to elevated temperatures in a light-dependent process. We further demonstrate that by introducing into plastids an expression system based on the bacteriophage T7 RNA polymerase, the temperature-dependent accumulation of GFP increased further and was ~24 times higher than expression driven by the pL/pR promoter alone, reaching ~0.48% of the total soluble protein. In conclusion, our heat-inducible expression system provides a new tool for the external control of plastid (trans) gene expression that is cost-effective and does not depend on chemical inducers.
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Affiliation(s)
- Wenbo Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Ralph Bock
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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22
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Mehra HS, Wang X, Russell BP, Kulkarni N, Ferrari N, Larson B, Vinyard DJ. Assembly and Repair of Photosystem II in Chlamydomonas reinhardtii. PLANTS (BASEL, SWITZERLAND) 2024; 13:811. [PMID: 38592843 PMCID: PMC10975043 DOI: 10.3390/plants13060811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Oxygenic photosynthetic organisms use Photosystem II (PSII) to oxidize water and reduce plastoquinone. Here, we review the mechanisms by which PSII is assembled and turned over in the model green alga Chlamydomonas reinhardtii. This species has been used to make key discoveries in PSII research due to its metabolic flexibility and amenability to genetic approaches. PSII subunits originate from both nuclear and chloroplastic gene products in Chlamydomonas. Nuclear-encoded PSII subunits are transported into the chloroplast and chloroplast-encoded PSII subunits are translated by a coordinated mechanism. Active PSII dimers are built from discrete reaction center complexes in a process facilitated by assembly factors. The phosphorylation of core subunits affects supercomplex formation and localization within the thylakoid network. Proteolysis primarily targets the D1 subunit, which when replaced, allows PSII to be reactivated and completes a repair cycle. While PSII has been extensively studied using Chlamydomonas as a model species, important questions remain about its assembly and repair which are presented here.
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Affiliation(s)
| | | | | | | | | | | | - David J. Vinyard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (H.S.M.); (X.W.); (B.P.R.); (N.K.); (N.F.); (B.L.)
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23
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Chai X, Wang X, Rong L, Luo M, Yuan L, Li Q, He B, Jiang J, Ji D, Ouyang M, Lu Q, Zhang L, Rochaix JD, Chi W. The translocon protein FtsHi1 is an ATP-dependent DNA/RNA helicase that prevents R-loop accumulation in chloroplasts. THE NEW PHYTOLOGIST 2024; 241:2209-2226. [PMID: 38084045 DOI: 10.1111/nph.19470] [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: 04/10/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
R-loops, three-stranded nucleic acid structures consisting of a DNA: RNA hybrid and displaced single-stranded DNA, play critical roles in gene expression and genome stability. How R-loop homeostasis is integrated into chloroplast gene expression remains largely unknown. We found an unexpected function of FtsHi1, an inner envelope membrane-bound AAA-ATPase in chloroplast R-loop homeostasis of Arabidopsis thaliana. Previously, this protein was shown to function as a component of the import motor complex for nuclear-encoded chloroplast proteins. However, this study provides evidence that FtsHi1 is an ATP-dependent helicase that efficiently unwinds both DNA-DNA and DNA-RNA duplexes, thereby preventing R-loop accumulation. Over-accumulation of R-loops could impair chloroplast transcription but not necessarily genome integrity. The dual function of FtsHi1 in both protein import and chloroplast gene expression may be important to coordinate the biogenesis of nuclear- and chloroplast-encoded subunits of multi-protein photosynthetic complexes. This study suggests a mechanical link between protein import and R-loop homeostasis in chloroplasts of higher plants.
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Affiliation(s)
- Xin Chai
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiushun Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manfei Luo
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Yuan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuxin Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jingjing Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Daili Ji
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qingtao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun St., Kaifeng, 475001, China
| | - Jean-David Rochaix
- Department of Molecular Biology, University of Geneva, 1211, Geneva, Switzerland
- Department of Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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24
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Gotsmann VL, Ting MKY, Haase N, Rudorf S, Zoschke R, Willmund F. Utilizing high-resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1614-1634. [PMID: 38047591 DOI: 10.1111/tpj.16577] [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: 06/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq yields genome-wide insight into translational dynamics and post-transcriptional control of gene expression. Here, we provide details on the Ribo-seq method and the subsequent analysis with the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas) for generating high-resolution data covering more than 10 000 different transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5' and 3' sections of transcripts and characteristics of eukaryotic translation termination, which are fundamentally distinct for chloroplast translation. In chloroplasts, a heterogeneous RPF size distribution along the coding sequence indicates specific regulatory phases during protein synthesis. For example, local accumulation of small RPFs correlates with local slowdown of psbA translation, possibly uncovering an uncharacterized regulatory step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light-harvesting complex proteins, LHCs. By providing high-quality datasets for all subcellular genomes and attaching our data to the Chlamydomonas reference genome, we aim to make ribosome profiles easily accessible for the broad research community. The data can be browsed without advanced bioinformatic background knowledge for translation output levels of specific genes and their splice variants and for monitoring genome annotation.
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Affiliation(s)
- Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| | - Michael Kien Yin Ting
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nadin Haase
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
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25
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van Wijk KJ, Bentolila S, Leppert T, Sun Q, Sun Z, Mendoza L, Li M, Deutsch EW. Detection and editing of the updated Arabidopsis plastid- and mitochondrial-encoded proteomes through PeptideAtlas. PLANT PHYSIOLOGY 2024; 194:1411-1430. [PMID: 37879112 DOI: 10.1093/plphys/kiad572] [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: 07/10/2023] [Revised: 09/12/2023] [Accepted: 09/23/2023] [Indexed: 10/27/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) ecotype Col-0 has plastid and mitochondrial genomes encoding over 100 proteins. Public databases (e.g. Araport11) have redundancy and discrepancies in gene identifiers for these organelle-encoded proteins. RNA editing results in changes to specific amino acid residues or creation of start and stop codons for many of these proteins, but the impact of RNA editing at the protein level is largely unexplored due to the complexities of detection. Here, we assembled the nonredundant set of identifiers, their correct protein sequences, and 452 predicted nonsynonymous editing sites of which 56 are edited at lower frequency. We then determined accumulation of edited and/or unedited proteoforms by searching ∼259 million raw tandem MS spectra from ProteomeXchange, which is part of PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/). We identified all mitochondrial proteins and all except 3 plastid-encoded proteins (NdhG/Ndh6, PsbM, and Rps16), but no proteins predicted from the 4 ORFs were identified. We suggest that Rps16 and 3 of the ORFs are pseudogenes. Detection frequencies for each edit site and type of edit (e.g. S to L/F) were determined at the protein level, cross-referenced against the metadata (e.g. tissue), and evaluated for technical detection challenges. We detected 167 predicted edit sites at the proteome level. Minor frequency sites were edited at low frequency at the protein level except for cytochrome C biogenesis 382 at residue 124 (Ccb382-124). Major frequency sites (>50% editing of RNA) only accumulated in edited form (>98% to 100% edited) at the protein level, with the exception of Rpl5-22. We conclude that RNA editing for major editing sites is required for stable protein accumulation.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Stephane Bentolila
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, NY 14853, USA
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Margaret Li
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
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26
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Wu HYL, Ai Q, Teixeira RT, Nguyen PHT, Song G, Montes C, Elmore JM, Walley JW, Hsu PY. Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis. THE PLANT CELL 2024; 36:510-539. [PMID: 38000896 PMCID: PMC10896292 DOI: 10.1093/plcell/koad290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023]
Abstract
A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaoyun Ai
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rita Teresa Teixeira
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Phong H T Nguyen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - J Mitch Elmore
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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27
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Che R, Liu Y, Yan S, Yang C, Sun Y, Liu C, Ma F. Elongation factor MdEF-Tu coordinates with heat shock protein MdHsp70 to enhance apple thermotolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1250-1263. [PMID: 37991990 DOI: 10.1111/tpj.16561] [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: 05/13/2023] [Revised: 10/08/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
High-temperature stress results in protein misfolding/unfolding and subsequently promotes the accumulation of cytotoxic protein aggregates that can compromise cell survival. Heat shock proteins (HSPs) function as molecular chaperones that coordinate the refolding and degradation of aggregated proteins to mitigate the detrimental effects of high temperatures. However, the relationship between HSPs and protein aggregates in apples under high temperatures remains unclear. Here, we show that an apple (Malus domestica) chloroplast-localized, heat-sensitive elongation factor Tu (MdEF-Tu), positively regulates apple thermotolerance when it is overexpressed. Transgenic apple plants exhibited higher photosynthetic capacity and better integrity of chloroplasts during heat stress. Under high temperatures, MdEF-Tu formed insoluble aggregates accompanied by ubiquitination modifications. Furthermore, we identified a chaperone heat shock protein (MdHsp70), as an interacting protein of MdEF-Tu. Moreover, we observed obviously elevated MdHsp70 levels in 35S: MdEF-Tu apple plants that prevented the accumulation of ubiquitinated MdEF-Tu aggregates, which positively contributes to the thermotolerance of the transgenic plants. Overall, our results provide new insights into the molecular chaperone function of MdHsp70, which mediates the homeostasis of thermosensitive proteins under high temperatures.
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Affiliation(s)
- Runmin Che
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuerong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shengqi Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chao Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yubo Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Changhai Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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28
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Mehrez M, Lecampion C, Ke H, Gorsane F, Field B. Insights into the function of the chloroplastic ribosome-associated GTPase high frequency of lysogenization X in Arabidopsis thaliana. PLANT DIRECT 2024; 8:e559. [PMID: 38222931 PMCID: PMC10784650 DOI: 10.1002/pld3.559] [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: 03/03/2023] [Revised: 06/15/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Ribosome-associated GTPases are conserved enzymes that participate in ribosome biogenesis and ribosome function. In bacteria, recent studies have identified HflX as a ribosome-associated GTPase that is involved in both ribosome biogenesis and recycling under stress conditions. Plants possess a chloroplastic HflX homolog, but its function remains unknown. Here, we characterized the role of HflX in the plant Arabidopsis thaliana. Our findings show that HflX does not affect normal plant growth, nor does it play an essential role in acclimation to several different stresses, including heat, manganese, cold, and salt stress under the conditions tested. However, we found that HflX is required for plant resistance to chloroplast translational stress mediated by the antibiotic lincomycin. Our results suggest that HflX is a chloroplast ribosome-associated protein that may play a role in the surveillance of translation. These findings provide new insight into the function of HflX as a ribosome-associated GTPase in plants and highlight the importance of investigating conserved proteins in different organisms to gain a comprehensive understanding of their biological roles.
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Affiliation(s)
- Marwa Mehrez
- Aix‐Marseille Univ, CEA, CNRS, BIAM, UMR7265MarseilleFrance
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of TunisUniversity of Tunis El ManarTunisTunisia
| | | | - Hang Ke
- Aix‐Marseille Univ, CEA, CNRS, BIAM, UMR7265MarseilleFrance
| | - Faten Gorsane
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of TunisUniversity of Tunis El ManarTunisTunisia
- Faculty of Sciences of BizerteUniversity of CarthageZarzounaTunisia
| | - Ben Field
- Aix‐Marseille Univ, CEA, CNRS, BIAM, UMR7265MarseilleFrance
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29
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Chung KP, Loiacono FV, Neupert J, Wu M, Bock R. An RNA thermometer in the chloroplast genome of Chlamydomonas facilitates temperature-controlled gene expression. Nucleic Acids Res 2023; 51:11386-11400. [PMID: 37855670 PMCID: PMC10639063 DOI: 10.1093/nar/gkad816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
Riboregulators such as riboswitches and RNA thermometers provide simple, protein-independent tools to control gene expression at the post-transcriptional level. In bacteria, RNA thermometers regulate protein synthesis in response to temperature shifts. Thermometers outside of the bacterial world are rare, and in organellar genomes, no RNA thermometers have been identified to date. Here we report the discovery of an RNA thermometer in a chloroplast gene of the unicellular green alga Chlamydomonas reinhardtii. The thermometer, residing in the 5' untranslated region of the psaA messenger RNA forms a hairpin-type secondary structure that masks the Shine-Dalgarno sequence at 25°C. At 40°C, melting of the secondary structure increases accessibility of the Shine-Dalgarno sequence to initiating ribosomes, thus enhancing protein synthesis. By targeted nucleotide substitutions and transfer of the thermometer into Escherichia coli, we show that the secondary structure is necessary and sufficient to confer the thermometer properties. We also demonstrate that the thermometer provides a valuable tool for inducible transgene expression from the Chlamydomonas plastid genome, in that a simple temperature shift of the algal culture can greatly increase recombinant protein yields.
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Affiliation(s)
- Kin Pan Chung
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - F Vanessa Loiacono
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mengting Wu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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30
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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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31
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Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
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Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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32
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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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33
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Liu R, Wang L, Meng Y, Tian Y, Li F, Lu H. Theoretical and Experimental Studies on Plant Light-Dependent Protochlorophyllide Oxidoreductase as a Novel Target for Searching Potential Herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37467369 DOI: 10.1021/acs.jafc.3c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Herbicide resistance is a prevalent problem that has posed a foremost challenge to crop production worldwide. Light-dependent enzyme NADPH: protochlorophyllide oxidoreductase (LPOR) in plants is a metabolic target that could satisfy this unmet demand. Herein, for the first time, we embarked on proposing a new mode of action of herbicides by performing structure-based virtual screening targeting multiple LPOR binding sites, with the determination of further bioactivity on the lead series. The feasibility of exploiting high selectivity and safety herbicides targeting LPOR was discussed from the perspective of the origin and phylogeny. Besides, we revealed the structural rearrangement and the selection key for NADPH cofactor binding to LPOR. Based on these, multitarget virtual screening was performed and the result identified compounds 2 affording micromolar inhibition, in which the IC50 reached 4.74 μM. Transcriptome analysis revealed that compound 2 induced more genes related to chlorophyll synthesis in Arabidopsis thaliana, especially the LPOR genes. Additionally, we clarified that these compounds binding to the site enhanced the overall stability and local rigidity of the complex systems from molecular dynamics simulation. This study delivers a guideline on how to assess activity-determining features of inhibitors to LPOR and how to translate this knowledge into the design of novel and effective inhibitors against malignant weed that act by targeting LPOR.
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Affiliation(s)
- Ruiyuan Liu
- College of Science, China Agricultural University, Beijing 100193, China
| | - Leng Wang
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yue Meng
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yiyi Tian
- College of Science, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Science, China Agricultural University, Beijing 100193, China
| | - Huizhe Lu
- College of Science, China Agricultural University, Beijing 100193, China
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34
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Tadini L, Jeran N, Domingo G, Zambelli F, Masiero S, Calabritto A, Costantini E, Forlani S, Marsoni M, Briani F, Vannini C, Pesaresi P. Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling. PLoS Genet 2023; 19:e1010344. [PMID: 37418499 PMCID: PMC10355426 DOI: 10.1371/journal.pgen.1010344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/09/2023] [Indexed: 07/09/2023] Open
Abstract
The chloroplast proteome is a dynamic mosaic of plastid- and nuclear-encoded proteins. Plastid protein homeostasis is maintained through the balance between de novo synthesis and proteolysis. Intracellular communication pathways, including the plastid-to-nucleus signalling and the protein homeostasis machinery, made of stromal chaperones and proteases, shape chloroplast proteome based on developmental and physiological needs. However, the maintenance of fully functional chloroplasts is costly and under specific stress conditions the degradation of damaged chloroplasts is essential to the maintenance of a healthy population of photosynthesising organelles while promoting nutrient redistribution to sink tissues. In this work, we have addressed this complex regulatory chloroplast-quality-control pathway by modulating the expression of two nuclear genes encoding plastid ribosomal proteins PRPS1 and PRPL4. By transcriptomics, proteomics and transmission electron microscopy analyses, we show that the increased expression of PRPS1 gene leads to chloroplast degradation and early flowering, as an escape strategy from stress. On the contrary, the overaccumulation of PRPL4 protein is kept under control by increasing the amount of plastid chaperones and components of the unfolded protein response (cpUPR) regulatory mechanism. This study advances our understanding of molecular mechanisms underlying chloroplast retrograde communication and provides new insight into cellular responses to impaired plastid protein homeostasis.
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Affiliation(s)
- Luca Tadini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Nicolaj Jeran
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Federico Zambelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Simona Masiero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Anna Calabritto
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Elena Costantini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Sara Forlani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Milena Marsoni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Candida Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
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35
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Pang Y, Liao Q, Peng H, Qian C, Wang F. CO 2 mesophyll conductance regulated by light: a review. PLANTA 2023; 258:11. [PMID: 37289402 DOI: 10.1007/s00425-023-04157-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/17/2023] [Indexed: 06/09/2023]
Abstract
MAIN CONCLUSION Light quality and intensity regulate plant mesophyll conductance, which has played an essential role in photosynthesis by controlling leaf structural and biochemical properties. Mesophyll conductance (gm), a crucial physiological factor influencing the photosynthetic rate of leaves, is used to describe the resistance of CO2 from the sub-stomatal cavity into the chloroplast up to the carboxylation site. Leaf structural and biochemical components, as well as external environmental factors such as light, temperature, and water, all impact gm. As an essential factor of plant photosynthesis, light affects plant growth and development and plays a vital role in regulating gm as well as determining photosynthesis and yield. This review aimed to summarize the mechanisms of gm response to light. Both structural and biochemical perspectives were combined to reveal the effects of light quality and intensity on the gm, providing a guide for selecting the optimal conditions for intensifying photosynthesis in plants.
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Affiliation(s)
- Yadan Pang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400712, China
| | - Qiuhong Liao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213, China
| | - Honggui Peng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400712, China
| | - Chun Qian
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400712, China
| | - Fang Wang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213, China.
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36
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Smirnova J, Loerke J, Kleinau G, Schmidt A, Bürger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R. Structure of the actively translating plant 80S ribosome at 2.2 Å resolution. NATURE PLANTS 2023; 9:987-1000. [PMID: 37156858 PMCID: PMC10281867 DOI: 10.1038/s41477-023-01407-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/29/2023] [Indexed: 05/10/2023]
Abstract
In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.
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Affiliation(s)
- Julia Smirnova
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Justus Loerke
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andrea Schmidt
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jörg Bürger
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Etienne H Meyer
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Institut für Pflanzenphysiologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Patrick Scheerer
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ralph Bock
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Reimo Zoschke
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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37
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Small I, Melonek J, Bohne AV, Nickelsen J, Schmitz-Linneweber C. Plant organellar RNA maturation. THE PLANT CELL 2023; 35:1727-1751. [PMID: 36807982 PMCID: PMC10226603 DOI: 10.1093/plcell/koad049] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 05/30/2023]
Abstract
Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery-and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to individual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.
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Affiliation(s)
- Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Joanna Melonek
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | | | - Jörg Nickelsen
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
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38
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Postel Z, Mauri T, Lensink MF, Touzet P. What is the potential impact of genetic divergence of plastid ribosomal genes between Silene nutans lineages in hybrids? An in silico approach using the 3D structure of the plastid ribosome. FRONTIERS IN PLANT SCIENCE 2023; 14:1167478. [PMID: 37223795 PMCID: PMC10201985 DOI: 10.3389/fpls.2023.1167478] [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: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/25/2023]
Abstract
Introduction Following the integration of cyanobacteria into the eukaryotic cells, many genes were transferred from the plastid to the nucleus. As a result, plastid complexes are encoded both by plastid and nuclear genes. Tight co-adaptation is required between these genes as plastid and nuclear genomes differ in several characteristics, such as mutation rate and inheritance patterns. Among these are complexes from the plastid ribosome, composed of two main subunits: a large and a small one, both composed of nuclear and plastid gene products. This complex has been identified as a potential candidate for sheltering plastid-nuclear incompatibilities in a Caryophyllaceae species, Silene nutans. This species is composed of four genetically differentiated lineages, which exhibit hybrid breakdown when interlineage crosses are conducted. As this complex is composed of numerous interacting plastid-nuclear gene pairs, in the present study, the goal was to reduce the number of gene pairs that could induce such incompatibilities. Method We used the previously published 3D structure of the spinach ribosome to further elucidate which of the potential gene pairs might disrupt plastid-nuclear interactions within this complex. After modeling the impact of the identified mutations on the 3D structure, we further focused on one strongly mutated plastid-nuclear gene pair: rps11-rps21. We used the centrality measure of the mutated residues to further understand if the modified interactions and associated modified centralities might be correlated with hybrid breakdown. Results and discussion This study highlights that lineage-specific mutations in essential plastid and nuclear genes might disrupt plastid-nuclear protein interactions of the plastid ribosome and that reproductive isolation correlates with changes in residue centrality values. Because of this, the plastid ribosome might be involved in hybrid breakdown in this system.
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Affiliation(s)
- Zoé Postel
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Théo Mauri
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marc F. Lensink
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
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Sierra J, Escobar-Tovar L, Leon P. Plastids: diving into their diversity, their functions, and their role in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2508-2526. [PMID: 36738278 DOI: 10.1093/jxb/erad044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/31/2023] [Indexed: 06/06/2023]
Abstract
Plastids are a group of essential, heterogenous semi-autonomous organelles characteristic of plants that perform photosynthesis and a diversity of metabolic pathways that impact growth and development. Plastids are remarkably dynamic and can interconvert in response to specific developmental and environmental cues, functioning as a central metabolic hub in plant cells. By far the best studied plastid is the chloroplast, but in recent years the combination of modern techniques and genetic analyses has expanded our current understanding of plastid morphological and functional diversity in both model and non-model plants. These studies have provided evidence of an unexpected diversity of plastid subtypes with specific characteristics. In this review, we describe recent findings that provide insights into the characteristics of these specialized plastids and their functions. We concentrate on the emerging evidence that supports the model that signals derived from particular plastid types play pivotal roles in plant development, environmental, and defense responses. Furthermore, we provide examples of how new technologies are illuminating the functions of these specialized plastids and the overall complexity of their differentiation processes. Finally, we discuss future research directions such as the use of ectopic plastid differentiation as a valuable tool to characterize factors involved in plastid differentiation. Collectively, we highlight important advances in the field that can also impact future agricultural and biotechnological improvement in plants.
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Affiliation(s)
- Julio Sierra
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, México
| | - Lina Escobar-Tovar
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, México
| | - Patricia Leon
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, México
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40
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Zhang Y, Ananyev G, Matsuoka A, Dismukes GC, Maliga P. Cyanobacterial photosystem II reaction center design in tobacco chloroplasts increases biomass in low light. PLANT PHYSIOLOGY 2023; 191:2229-2244. [PMID: 36510848 PMCID: PMC10069877 DOI: 10.1093/plphys/kiac578] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/29/2022] [Indexed: 06/17/2023]
Abstract
The D1 polypeptide of the photosystem II (PSII) reaction center complex contains domains that regulate primary photochemical yield and charge recombination rate. Many prokaryotic oxygenic phototrophs express two or more D1 isoforms differentially in response to environmental light needs, a capability absent in flowering plants and algae. We report that tobacco (Nicotiana tabacum) plants carrying the Synechococcus (Synechococcus elongatus PCC 7942) low-light mutation (LL-E130Q) in the D1 polypeptide (NtLL) acquire the cyanobacterial photochemical phenotype: faster photodamage in high light and significantly more charge separations in productive linear electron flow in low light. This flux increase produces 16.5% more (dry) biomass under continuous low-light illumination (100 μE m-2 s-1, 24 h). This gain is offset by the predicted lower photoprotection at high light. By contrast, the introduction of the Synechococcus high-light mutation (HL-A152S) into tobacco D1 (NtHL) has slightly increased photoprotection, achieved by photochemical quenching, but no apparent impact on biomass yield compared to wild type under the tested conditions. The universal design principle of all PSII reaction centers trades off energy conversion for photoprotection in different proportions across all phototrophs and provides a useful guidance for testing in crop plants. The observed biomass advantage under continuous low light can be transferred between evolutionarily isolated lineages to benefit growth under artificial lighting conditions. However, removal of the selective marker gene was essential to observe the growth phenotype, indicating growth penalty imposed by use of the particular spectinomycin-resistance gene.
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Affiliation(s)
- Yuan Zhang
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Gennady Ananyev
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Aki Matsuoka
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | - Pal Maliga
- Author for correspondence: (P.M.); (G.C.D.)
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Ghandour R, Gao Y, Laskowski J, Barahimipour R, Ruf S, Bock R, Zoschke R. Transgene insertion into the plastid genome alters expression of adjacent native chloroplast genes at the transcriptional and translational levels. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:711-725. [PMID: 36529916 PMCID: PMC10037153 DOI: 10.1111/pbi.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 11/14/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
In plant biotechnology and basic research, chloroplasts have been used as chassis for the expression of various transgenes. However, potential unintended side effects of transgene insertion and high-level transgene expression on the expression of native chloroplast genes are often ignored and have not been studied comprehensively. Here, we examined expression of the chloroplast genome at both the transcriptional and translational levels in five transplastomic tobacco (Nicotiana tabacum) lines carrying the identical aadA resistance marker cassette in diverse genomic positions. Although none of the lines exhibits a pronounced visible phenotype, the analysis of three lines that contain the aadA insertion in different locations within the petL-petG-psaJ-rpl33-rps18 transcription unit demonstrates that transcriptional read-through from the aadA resistance marker is unavoidable, and regularly causes overexpression of downstream sense-oriented chloroplast genes at the transcriptional and translational levels. Investigation of additional lines that harbour the aadA intergenically and outside of chloroplast transcription units revealed that expression of the resistance marker can also cause antisense effects by interference with transcription/transcript accumulation and/or translation of downstream antisense-oriented genes. In addition, we provide evidence for a previously suggested role of genomically encoded tRNAs in chloroplast transcription termination and/or transcript processing. Together, our data uncover principles of neighbouring effects of chloroplast transgenes and suggest general strategies for the choice of transgene insertion sites and expression elements to minimize unintended consequences of transgene expression on the transcription and translation of native chloroplast genes.
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Affiliation(s)
- Rabea Ghandour
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Yang Gao
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | | | | | - Stephanie Ruf
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
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Liu K, Lee KP, Duan J, Kim EY, Singh RM, Di M, Meng Z, Kim C. Cooperative role of AtRsmD and AtRimM proteins in modification and maturation of 16S rRNA in plastids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:310-324. [PMID: 36752655 DOI: 10.1111/tpj.16135] [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: 08/12/2022] [Accepted: 02/01/2023] [Indexed: 05/10/2023]
Abstract
Chloroplast pre-ribosomal RNA (rRNA) undergoes maturation, which is critical for ribosome assembly. While the central and auxiliary factors in rRNA maturation have been elucidated in bacteria, their mode of action remains largely unexplored in chloroplasts. We now reveal chloroplast-specific factors involved in 16S rRNA maturation, Arabidopsis thaliana orthologs of bacterial RsmD methyltransferase (AtRsmD) and ribosome maturation factor RimM (AtRimM). A forward genetic screen aimed to find suppressors of the Arabidopsis yellow variegated 2 (var2) mutant defective in photosystem II quality control found a causal nonsense mutation in AtRsmD. The substantially impaired 16S rRNA maturation and translation due to the mutation rescued the leaf variegation phenotype by lowering the levels of chloroplast-encoded proteins, including photosystem II core proteins, in var2. The subsequent co-immunoprecipitation coupled with mass spectrometry analyses and bimolecular fluorescence complementation assay found that AtRsmD interacts with AtRimM. Consistent with their interaction, loss of AtRimM also considerably impairs 16S rRNA maturation with decelerated m2 G915 modification in 16S rRNA catalyzed by AtRsmD. The atrimM mutation also rescued var2 mutant phenotypes, corroborating the functional interplay between AtRsmD and AtRimM towards modification and maturation of 16S rRNA and chloroplast proteostasis. The maturation and post-transcriptional modifications of rRNA are critical to assembling ribosomes responsible for protein translation. Here, we revealed that the cooperative regulation of 16S rRNA m2 G915 modifications by AtRsmD methyltransferase and ribosome assembly factor AtRimM contributes to 16S rRNA maturation, ribosome assembly, and proteostasis in chloroplasts.
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Affiliation(s)
- Kaiwei Liu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Keun Pyo Lee
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianli Duan
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Rahul Mohan Singh
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Minghui Di
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuoling Meng
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Zhang X, Han Y, Han X, Zhang S, Xiong L, Chen T. Peptide chain release factor DIG8 regulates plant growth by affecting ROS-mediated sugar transportation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1172275. [PMID: 37063204 PMCID: PMC10102589 DOI: 10.3389/fpls.2023.1172275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts have important roles in photosynthesis, stress sensing and retrograde signaling. However, the relationship between chloroplast peptide chain release factor and ROS-mediated plant growth is still unclear. In the present study, we obtained a loss-of-function mutant dig8 by EMS mutation. The dig8 mutant has few lateral roots and a pale green leaf phenotype. By map-based cloning, the DIG8 gene was located on AT3G62910, with a point mutation leading to amino acid substitution in functional release factor domain. Using yeast-two-hybrid and BiFC, we confirmed DIG8 protein was characterized locating in chloroplast by co-localization with plastid marker and interacting with ribosome-related proteins. Through observing by transmission electron microscopy, quantifying ROS content and measuring the transport efficiency of plasmodesmata in dig8 mutant, we found that abnormal thylakoid stack formation and chloroplast dysfunction in the dig8 mutant caused increased ROS activity leading to callose deposition and lower PD permeability. A local sugar supplement partially alleviated the growth retardation phenotype of the mutant. These findings shed light on chloroplast peptide chain release factor-affected plant growth by ROS stress.
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Affiliation(s)
- Xiangxiang Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Yuliang Han
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Xiao Han
- College of Life Sciences, Fuzhou University, Fuzhou, China
| | - Siqi Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Liming Xiong
- Department of Biology, Hong Kong Baptist University, Kowloon Tang, Hong Kong, Hong Kong SAR, China
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
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Chen H, Wang Q, Fan M, Zhang X, Feng P, Zhu L, Wu J, Cheng X, Wang J. A Single Nucleotide Variation of CRS2 Affected the Establishment of Photosynthetic System in Rice. Int J Mol Sci 2023; 24:ijms24065796. [PMID: 36982870 PMCID: PMC10054620 DOI: 10.3390/ijms24065796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Chloroplasts are essential sites for plant photosynthesis, and the biogenesis of the photosynthetic complexes involves the interaction of nuclear genes and chloroplast genes. In this study, we identified a rice pale green leaf mutant, crs2. The crs2 mutant showed different degrees of low chlorophyll phenotypes at different growth stages, especially at the seedling stage. Fine mapping and DNA sequencing of crs2 revealed a single nucleotide substitution (G4120A) in the eighth exons of CRS2, causing a G-to-R mutation of the 229th amino acid of CRS2 (G229R). The results of complementation experiments confirmed that this single-base mutation in crs2 is responsible for the phenotype of the crs2 mutant. CRS2 encodes a chloroplast RNA splicing 2 protein localized in the chloroplast. Western blot results revealed an abnormality in the abundance of the photosynthesis-related protein in crs2. However, the mutation of CRS2 leads to the enhancement of antioxidant enzyme activity, which could reduce ROS levels. Meanwhile, with the release of Rubisco activity, the photosynthetic performance of crs2 was improved. In summary, the G229R mutation in CRS2 causes chloroplast protein abnormalities and affects photosystem performance in rice; the above findings facilitate the elucidation of the physiological mechanism of chloroplast proteins affecting photosynthesis.
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Affiliation(s)
- Hongwei Chen
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Qi Wang
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingqian Fan
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Xijuan Zhang
- Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Pulin Feng
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Lin Zhu
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Jiayi Wu
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyi Cheng
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (X.C.); or (J.W.)
| | - Jiayu Wang
- Key Laboratory of Rice Biology & Genetic Breeding in Northeast China, Ministry of Agriculture and Rural Areas, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (X.C.); or (J.W.)
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Legen J, Dühnen S, Gauert A, Götz M, Schmitz-Linneweber C. A CRR2-Dependent sRNA Sequence Supports Papillomavirus Vaccine Expression in Tobacco Chloroplasts. Metabolites 2023; 13:metabo13030315. [PMID: 36984756 PMCID: PMC10054877 DOI: 10.3390/metabo13030315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction: Human papillomavirus (HPV) infection is the leading cause of cervical cancer, and vaccination with HPV L1 capsid proteins has been successful in controlling it. However, vaccination coverage is not universal, particularly in developing countries, where 80% of all cervical cancer cases occur. Cost-effective vaccination could be achieved by expressing the L1 protein in plants. Various efforts have been made to produce the L1 protein in plants, including attempts to express it in chloroplasts for high-yield performance. However, manipulating chloroplast gene expression requires complex and difficult-to-control expression elements. In recent years, a family of nuclear-encoded, chloroplast-targeted RNA-binding proteins, the pentatricopeptide repeat (PPR) proteins, were described as key regulators of chloroplast gene expression. For example, PPR proteins are used by plants to stabilize and translate chloroplast mRNAs. Objectives: To demonstrate that a PPR target site can be used to drive HPV L1 expression in chloroplasts. Methods: To test our hypothesis, we used biolistic chloroplast transformation to establish tobacco lines that express two variants of the HPV L1 protein under the control of the target site of the PPR protein CHLORORESPIRATORY REDUCTION2 (CRR2). The transgenes were inserted into a dicistronic operon driven by the plastid rRNA promoter. To determine the effectiveness of the PPR target site for the expression of the HPV L1 protein in the chloroplasts, we analyzed the accumulation of the transgenic mRNA and its processing, as well as the accumulation of the L1 protein in the transgenic lines. Results: We established homoplastomic lines carrying either the HPV18 L1 protein or an HPV16B Enterotoxin::L1 fusion protein. The latter line showed severe growth retardation and pigment loss, suggesting that the fusion protein is toxic to the chloroplasts. Despite the presence of dicistronic mRNAs, we observed very little accumulation of monocistronic transgenic mRNA and no significant increase in CRR2-associated small RNAs. Although both lines expressed the L1 protein, quantification using an external standard suggested that the amounts were low. Conclusions: Our results suggest that PPR binding sites can be used to drive vaccine expression in plant chloroplasts; however, the factors that modulate the effectiveness of target gene expression remain unclear. The identification of dozens of PPR binding sites through small RNA sequencing expands the set of expression elements available for high-value protein production in chloroplasts.
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Affiliation(s)
- Julia Legen
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Sara Dühnen
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Anton Gauert
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Michael Götz
- BioEnergy GmbH, Dietersberg 1, 92334 Berching, Germany
| | - Christian Schmitz-Linneweber
- Molecular Genetics, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany
- Correspondence: ; Tel.: +49-20-2093-49700
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Hu Y, Sun Y, Zhu QH, Fan L, Li J. Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years. Curr Genomics 2023; 23:369-384. [PMID: 37920556 PMCID: PMC10173419 DOI: 10.2174/1389202924666221201140603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 12/11/2022] Open
Abstract
The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.
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Affiliation(s)
- Yiyu Hu
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yanqing Sun
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jianhua Li
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Mehrez M, Romand S, Field B. New perspectives on the molecular mechanisms of stress signalling by the nucleotide guanosine tetraphosphate (ppGpp), an emerging regulator of photosynthesis in plants and algae. THE NEW PHYTOLOGIST 2023; 237:1086-1099. [PMID: 36349398 PMCID: PMC10107265 DOI: 10.1111/nph.18604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The nucleotides guanosine tetraphosphate and guanosine pentaphosphate (together (p)ppGpp) are found in a wide range of prokaryotic and eukaryotic organisms where they are associated with stress signalling. In this review, we will discuss recent research highlighting the role of (p)ppGpp signalling as a conserved regulator of photosynthetic activity in the chloroplasts of plants and algae, and the latest discoveries that open up new perspectives on the emerging roles of (p)ppGpp in acclimation to environmental stress. We explore how rapid advances in the study of (p)ppGpp signalling in prokaryotes are now revealing large gaps in our understanding of the molecular mechanisms of signalling by (p)ppGpp and related nucleotides in plants and algae. Filling in these gaps is likely to lead to the discovery of conserved as well as new plant- and algal-specific (p)ppGpp signalling mechanisms that will offer new insights into the taming of the chloroplast and the regulation of stress tolerance.
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Affiliation(s)
- Marwa Mehrez
- Aix‐Marseille University, CEA, CNRS, BIAM, UMR726513009MarseilleFrance
- Faculty of Sciences of Tunis, Laboratory of Molecular Genetics, Immunology and BiotechnologyUniversity of Tunis El Manar2092TunisTunisia
| | - Shanna Romand
- Aix‐Marseille University, CEA, CNRS, BIAM, UMR726513009MarseilleFrance
| | - Ben Field
- Aix‐Marseille University, CEA, CNRS, BIAM, UMR726513009MarseilleFrance
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Chloroplasts evolved an additional layer of translational regulation based on non-AUG start codons for proteins with different turnover rates. Sci Rep 2023; 13:896. [PMID: 36650197 PMCID: PMC9845219 DOI: 10.1038/s41598-022-27347-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Chloroplasts have evolved from photosynthetic cyanobacteria-like progenitors through endosymbiosis. The chloroplasts of present-day land plants have their own transcription and translation systems that show several similarities with prokaryotic organisms. A remarkable feature of the chloroplast translation system is the use of non-AUG start codons in the protein synthesis of certain genes that are evolutionarily conserved from Algae to angiosperms. However, the biological significance of such use of non-AUG codons is not fully understood. The present study was undertaken to unravel the significance of non-AUG start codons in vivo using the chloroplast genetic engineering approach. For this purpose, stable transplastomic tobacco plants expressing a reporter gene i.e. uidA (GUS) under four different start codons (AUG/UUG/GUG/CUG) were generated and β-glucuronidase (GUS) expression was compared. To investigate further the role of promoter sequences proximal to the start codon, uidA was expressed under two different chloroplast gene promoters psbA and psbC that use AUG and a non-AUG (GUG) start codons, respectively, and also showed significant differences in the DNA sequence surrounding the start codon. Further, to delineate the role of RNA editing that creates AUG start codon by editing non-AUG codons, if any, which is another important feature of the chloroplast transcription and translation system, transcripts were sequenced. In addition, a proteomic approach was used to identify the translation initiation site(s) of GUS and the N-terminal amino acid encoded when expressed under different non-AUG start codons. The results showed that chloroplasts use non-AUG start codons in combination with the translation initiation site as an additional layer of gene regulation to over-express proteins that are required at high levels due to their high rates of turnover.
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Rozov SM, Zagorskaya AA, Konstantinov YM, Deineko EV. Three Parts of the Plant Genome: On the Way to Success in the Production of Recombinant Proteins. PLANTS (BASEL, SWITZERLAND) 2022; 12:38. [PMID: 36616166 PMCID: PMC9824153 DOI: 10.3390/plants12010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are the most important product of current industrial biotechnology. They are indispensable in medicine (for diagnostics and treatment), food and chemical industries, and research. Plant cells combine advantages of the eukaryotic protein production system with simplicity and efficacy of the bacterial one. The use of plants for the production of recombinant proteins is an economically important and promising area that has emerged as an alternative to traditional approaches. This review discusses advantages of plant systems for the expression of recombinant proteins using nuclear, plastid, and mitochondrial genomes. Possibilities, problems, and prospects of modifications of the three parts of the genome in light of obtaining producer plants are examined. Examples of successful use of the nuclear expression platform for production of various biopharmaceuticals, veterinary drugs, and technologically important proteins are described, as are examples of a high yield of recombinant proteins upon modification of the chloroplast genome. Potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated. Although these opportunities have not yet been exploited, potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated.
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Affiliation(s)
- Sergey M. Rozov
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Alla A. Zagorskaya
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Yuri M. Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, Lermontova Str. 132, Irkutsk 664033, Russia
| | - Elena V. Deineko
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
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Assembly and Annotation of Red Spruce ( Picea rubens) Chloroplast Genome, Identification of Simple Sequence Repeats, and Phylogenetic Analysis in Picea. Int J Mol Sci 2022; 23:ijms232315243. [PMID: 36499570 PMCID: PMC9739956 DOI: 10.3390/ijms232315243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/11/2022] Open
Abstract
We have sequenced the chloroplast genome of red spruce (Picea rubens) for the first time using the single-end, short-reads (44 bp) Illumina sequences, assembled and functionally annotated it, and identified simple sequence repeats (SSRs). The contigs were assembled using SOAPdenovo2 following the retrieval of chloroplast genome sequences using the black spruce (Picea mariana) chloroplast genome as the reference. The assembled genome length was 122,115 bp (gaps included). Comparatively, the P. rubens chloroplast genome reported here may be considered a near-complete draft. Global genome alignment and phylogenetic analysis based on the whole chloroplast genome sequences of Picea rubens and 10 other Picea species revealed high sequence synteny and conservation among 11 Picea species and phylogenetic relationships consistent with their known classical interrelationships and published molecular phylogeny. The P. rubens chloroplast genome sequence showed the highest similarity with that of P. mariana and the lowest with that of P. sitchensis. We have annotated 107 genes including 69 protein-coding genes, 28 tRNAs, 4 rRNAs, few pseudogenes, identified 42 SSRs, and successfully designed primers for 26 SSRs. Mononucleotide A/T repeats were the most common followed by dinucleotide AT repeats. A similar pattern of microsatellite repeats occurrence was found in the chloroplast genomes of 11 Picea species.
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