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Guo D, He B, Feng F, Lv D, Han T, Chen X. iTRAQ-based proteomic analysis reveals the effect of ribosomal proteins on essential-oil accumulation in Houttuynia cordata Thunb. PeerJ 2024; 12:e17519. [PMID: 38903882 PMCID: PMC11188929 DOI: 10.7717/peerj.17519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Houttuynia cordata Thunb., also known as Yuxingcao in Chinese, occupies a pivotal role in Asian traditional medicine and cuisine. The aerial parts and underground stems of H. cordata exhibit remarkable chemical diversity, particularly in essential oil. Nevertheless, the mechanisms regulating essential oil biosynthesis in H. cordata remain unclear. In this study, we present a quantitative overview of the proteomes across four tissues (flower, stem, leaf, and underground stem) of H. cordata, achieved through the application of the isobaric tag for relative and absolute quantitation (iTRAQ). Our research findings indicate that certain crucial ribosomal proteins and their interactions may significantly impact the production of essential oils in H. cordata. These results offer novel insights into the roles of ribosomal proteins and their associations in essential oil biosynthesis across various organisms of H. cordata.
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Affiliation(s)
- Dandan Guo
- School of Pharmacy, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Beixuan He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
| | - Fei Feng
- School of Pharmacy, Naval Medical University, Shanghai, China
| | - Diya Lv
- School of Pharmacy, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Ting Han
- School of Pharmacy, Naval Medical University, Shanghai, China
| | - Xiaofei Chen
- School of Pharmacy, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
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2
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Krämer C, Boehm CR, Liu J, Ting MKY, Hertle AP, Forner J, Ruf S, Schöttler MA, Zoschke R, Bock R. Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number. NATURE PLANTS 2024; 10:923-935. [PMID: 38802561 PMCID: PMC11208156 DOI: 10.1038/s41477-024-01709-9] [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: 11/22/2023] [Accepted: 04/24/2024] [Indexed: 05/29/2024]
Abstract
The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications.
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Affiliation(s)
- Carolin Krämer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Christian R Boehm
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Jinghan Liu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | | | - Alexander P Hertle
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Joachim Forner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Reimo Zoschke
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
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3
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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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4
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Shokri-Gharelo R, Derakhti-Dizaji M, Dadashi D, Chalekaei M, Rostami-Tobnag G. Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses. Biosystems 2024; 237:105165. [PMID: 38430956 DOI: 10.1016/j.biosystems.2024.105165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Abiotic stresses are predominant and main causes of the losses in the crop yield. A complexity of systems biology and involvement of numerous genes in the response to abiotic factors have challenged efforts to create tolerant cultivars with sustainable production. The root is the main organ of the plant and determines a plant tolerance under stressful conditions. In this study, we carried out a meta-analysis of expression datasets from wheat root to identify differentially expressed genes, followed by the weighted gene co-expression network analysis (WGCNA) to construct the weighted gene co-expression network. The aim was to identify consensus differentially expressed genes with regulatory functions, gene networks, and biological pathways involved in response of wheat root to a set of abiotic stresses. The meta-analysis using Fisher method (FDR<0.05) identified consensus 526 DEGs from 55,367 probe sets. Although the annotated expression data are limited for wheat, the functional analysis based on the data from model plants could identify the up-regulated seven regulatory genes involved in chromosome organization and response to oxygen-containing compounds. WGCNA identified four gene modules that were mostly associated with the ribosome biogenesis and polypeptide synthesis. This study's findings enhance our understanding of key players and gene networks related to wheat root response to multiple abiotic stresses.
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Affiliation(s)
- Reza Shokri-Gharelo
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran; Researcher of Sugar Beet Seed Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Morteza Derakhti-Dizaji
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran
| | - Davod Dadashi
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran
| | - Maryam Chalekaei
- Department of Agronomy and Plant Breeding, Agricultural College, University of Tehran, Iran
| | - Ghader Rostami-Tobnag
- Department of Horticulture, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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Dziubek D, Poeker L, Siemitkowska B, Graf A, Marino G, Alseekh S, Arrivault S, Fernie AR, Armbruster U, Geigenberger P. NTRC and thioredoxins m1/m2 underpin the light acclimation of plants on proteome and metabolome levels. PLANT PHYSIOLOGY 2024; 194:982-1005. [PMID: 37804523 PMCID: PMC10828201 DOI: 10.1093/plphys/kiad535] [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: 06/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023]
Abstract
During photosynthesis, plants must manage strong fluctuations in light availability on different time scales, leading to long-term acclimation and short-term responses. However, little is known about the regulation and coordination of these processes and the modulators involved. In this study, we used proteomics, metabolomics, and reverse genetics to investigate how different light environmental factors, such as intensity or variability, affect long-term and short-term acclimation responses of Arabidopsis (Arabidopsis thaliana) and the importance of the chloroplast redox network in their regulation. In the wild type, high light, but not fluctuating light, led to large quantitative changes in the proteome and metabolome, accompanied by increased photosynthetic dynamics and plant growth. This finding supports light intensity as a stronger driver for acclimation than variability. Deficiencies in NADPH-thioredoxin reductase C (NTRC) or thioredoxins m1/m2, but not thioredoxin f1, almost completely suppressed the re-engineering of the proteome and metabolome, with both the induction of proteins involved in stress and redox responses and the repression of those involved in cytosolic and plastid protein synthesis and translation being strongly attenuated. Moreover, the correlations of protein or metabolite levels with light intensity were severely disturbed, suggesting a general defect in the light-dependent acclimation response, resulting in impaired photosynthetic dynamics. These results indicate a previously unknown role of NTRC and thioredoxins m1/m2 in modulating light acclimation at proteome and metabolome levels to control dynamic light responses. NTRC, but not thioredoxins m1/m2 or f1, also improves short-term photosynthetic responses by balancing the Calvin-Benson cycle in fluctuating light.
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Affiliation(s)
- Dejan Dziubek
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Louis Poeker
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Beata Siemitkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Giada Marino
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Departments of Metabolomics and Crop Quantitative Genetics, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgari
| | - Stéphanie Arrivault
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Departments of Metabolomics and Crop Quantitative Genetics, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgari
| | - Ute Armbruster
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Institute of Molecular Photosynthesis, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS—Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Peter Geigenberger
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
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6
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Dou N, Li L, Fang Y, Fan S, Wu C. Comparative Physiological and Transcriptome Analyses of Tolerant and Susceptible Cultivars Reveal the Molecular Mechanism of Cold Tolerance in Anthurium andraeanum. Int J Mol Sci 2023; 25:250. [PMID: 38203421 PMCID: PMC10779044 DOI: 10.3390/ijms25010250] [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: 11/19/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Anthurium andraeanum is a tropical ornamental flower. The cost of Anthurium production is higher under low temperature (non-freezing) conditions; therefore, it is important to increase its cold tolerance. However, the molecular mechanisms underlying the response of Anthurium to cold stress remain elusive. In this study, comparative physiological and transcriptome sequencing analyses of two cultivars with contrasting cold tolerances were conducted to evaluate the cold stress response at the flowering stage. The activities of superoxide dismutase and peroxidase and the contents of proline, soluble sugar, and malondialdehyde increased under cold stress in the leaves of the cold tolerant cultivar Elegang (E) and cold susceptible cultivar Menghuang (MH), while the soluble protein content decreased in MH and increased in E. Using RNA sequencing, 24,695 differentially expressed genes (DEGs) were identified from comparisons between cultivars under the same conditions or between the treatment and control groups of a single cultivar, 9132 of which were common cold-responsive DEGs. Heat-shock proteins and pectinesterases were upregulated in E and downregulated in MH, indicating that these proteins are essential for Anthurium cold tolerance. Furthermore, four modules related to cold treatment were obtained by weighted gene co-expression network analysis. The expression of the top 20 hub genes in these modules was induced by cold stress in E or MH, suggesting they might be crucial contributors to cold tolerance. DEGs were significantly enriched in plant hormone signal transduction pathways, trehalose metabolism, and ribosomal proteins, suggesting these processes play important roles in Anthurium's cold stress response. This study provides a basis for elucidating the mechanism of cold tolerance in A. andraeanum and potential targets for molecular breeding.
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Affiliation(s)
- Na Dou
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan 250014, China (S.F.)
| | - Li Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan 250014, China (S.F.)
| | - Yifu Fang
- Institute of Ornamental Plants, Shandong Provincial Academy of Forestry, Wenhua East Road 42, Jinan 250010, China;
| | - Shoujin Fan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan 250014, China (S.F.)
| | - Chunxia Wu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Wenhua East Road 88, Jinan 250014, China (S.F.)
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7
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Gu X, Li L, Li S, Shi W, Zhong X, Su Y, Wang T. Adaptive evolution and co-evolution of chloroplast genomes in Pteridaceae species occupying different habitats: overlapping residues are always highly mutated. BMC PLANT BIOLOGY 2023; 23:511. [PMID: 37880608 PMCID: PMC10598918 DOI: 10.1186/s12870-023-04523-1] [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: 07/11/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND The evolution of protein residues depends on the mutation rates of their encoding nucleotides, but it may also be affected by co-evolution with other residues. Chloroplasts function as environmental sensors, transforming fluctuating environmental signals into different physiological responses. We reasoned that habitat diversity may affect their rate and mode of evolution, which might be evidenced in the chloroplast genome. The Pteridaceae family of ferns occupy an unusually broad range of ecological niches, which provides an ideal system for analysis. RESULTS We conducted adaptive evolution and intra-molecular co-evolution analyses of Pteridaceae chloroplast DNAs (cpDNAs). The results indicate that the residues undergoing adaptive evolution and co-evolution were mostly independent, with only a few residues being simultaneously involved in both processes, and these overlapping residues tend to exhibit high mutations. Additionally, our data showed that Pteridaceae chloroplast genes are under purifying selection. Regardless of whether we grouped species by lineage (which corresponded with ecological niches), we determined that positively selected residues mainly target photosynthetic genes. CONCLUSIONS Our work provides evidence for the adaptive evolution of Pteridaceae cpDNAs, especially photosynthetic genes, to different habitats and sheds light on the adaptive evolution and co-evolution of proteins.
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Affiliation(s)
- Xiaolin Gu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lingling Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Sicong Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Wanxin Shi
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaona Zhong
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Testone G, Lamprillo M, Gonnella M, Arnesi G, Sobolev AP, Aiese Cigliano R, Giannino D. The Chloroplast Genome of Endive ( Cichorium endivia L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events. Genes (Basel) 2023; 14:1829. [PMID: 37761969 PMCID: PMC10531310 DOI: 10.3390/genes14091829] [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: 08/23/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (Cichorium endivia var. latifolium and var. crispum) are of nutritional and economic importance and are the target of ever-changing breeding programmes. A reference cp genome sequence was assembled and annotated (cultivar 'Confiance'), which was 152,809 base pairs long, organized into the angiosperm-typical quadripartite structure, harboring two inverted repeats separated by the large- and short- single copy regions. The annotation included 136 genes, 90 protein-coding genes, 38 transfer, and 8 ribosomal RNAs and the sequence generated a distinct phyletic group within Asteraceae with the well-separated C. endivia and intybus species. SSR variants within the reference genome were mostly of tri-nucleotide type, and the cytosine to uracil (C/U) RNA editing recurred. The cp genome was nearly fully transcribed, hence sequence polymorphism was investigated by RNA-Seq of seven cultivars, and the SNP number was higher in smooth- than curly-leafed ones. All cultivars maintained C/U changes in identical positions, suggesting that RNA editing patterns were conserved; most cultivars shared SNPs of moderate impact on protein changes in the ndhD, ndhA, and psbF genes, suggesting that their variability may have a potential role in adaptive response. The cp transcriptome expression was investigated in leaves of plants affected by pre-harvest rainfall and rainfall excess plus waterlogging events characterized by production loss, compared to those of a cycle not affected by extreme rainfall. Overall, the analyses evidenced stress- and cultivar-specific responses, and further revealed that genes of the Cytochrome b6/f, and PSI-PSII systems were commonly affected and likely to be among major targets of extreme rain-related stress.
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Affiliation(s)
- Giulio Testone
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
| | - Michele Lamprillo
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
| | - Maria Gonnella
- Institute of Sciences of Food Production, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy;
| | - Giuseppe Arnesi
- Enza Zaden Italia, Strada Statale Aurelia Km 96.400, Tarquinia, 01016 Viterbo, Italy;
| | - Anatoly Petrovich Sobolev
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
| | | | - Donato Giannino
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (G.T.); (M.L.); (A.P.S.)
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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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10
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Yang L, Deng S, Zhu Y, Da Q. Comparative chloroplast genomics of 34 species in subtribe Swertiinae (Gentianaceae) with implications for its phylogeny. BMC PLANT BIOLOGY 2023; 23:164. [PMID: 36977991 PMCID: PMC10044379 DOI: 10.1186/s12870-023-04183-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Subtribe Swertiinae, a medicinally significant and highly speciose Subtribe of family Gentianaceae. Despite previous extensive studies based on both morphology and molecular data, intergeneric and infrageneric relationships within subtribe Swertiinae remain controversial. METHODS Here, we employed four newly generated Swertia chloroplast genomes with thirty other published genomes to elucidate their genomic characteristics. RESULTS The 34 chloroplast genomes were small and ranged in size from 149,036 to 154,365 bp, each comprising two inverted repeat regions (size range 25,069-26,126 bp) that separated large single-copy (80,432-84,153 bp) and small single-copy (17,887-18,47 bp) regions, and all the chloroplast genomes showed similar gene orders, contents, and structures. These chloroplast genomes contained 129-134 genes each, including 84-89 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes of subtribe Swertiinae appeared to have lost some genes, such as rpl33, rpl2 and ycf15 genes. Comparative analyses revealed that two mutation hotspot regions (accD-psaI and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification in subtribe Swertiinae. Positive selection analyses showed that two genes (ccsA and psbB) had high Ka/Ks ratios, indicating that chloroplast genes may have undergone positive selection in their evolutionary history. Phylogenetic analysis showed that the 34 subtribe Swertiinae species formed a monophyletic clade, with Veratrilla, Gentianopsis and Pterygocalyx located at the base of the phylogenetic tree. Some genera of this subtribe, however, were not monophyletic, including Swertia, Gentianopsis, Lomatogonium, Halenia, Veratrilla and Gentianopsis. In addition, our molecular phylogeny was consistent with taxonomic classification of subtribe Swertiinae in the Roate group and Tubular group. The results of molecular dating showed that the divergence between subtrib Gentianinae and subtrib Swertiinae was estimated to occur in 33.68 Ma. Roate group and Tubular group in subtribe Swertiinae approximately diverged in 25.17 Ma. CONCLUSION Overall, our study highlighted the taxonomic utility of chloroplast genomes in subtribe Swertiinae, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of subtribe Swertiinae species.
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Affiliation(s)
- Lucun Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences, Xining, 81008, China.
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resource, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
| | - Shengxue Deng
- Qinghai Environmental Science Research and Design Institute Co. Ltd, Xining, 810007, China
| | - Yongqing Zhu
- Maqin County Forestry and Grassland Station, Maqin, 814000, China
| | - Qilin Da
- Bureau of Forestry in Hualong County, Hualong, 810900, China
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11
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Zhang H, Pei Y, He Q, Zhu W, Jahangir M, Haq SU, Khan A, Chen R. Salicylic acid-related ribosomal protein CaSLP improves drought and Pst.DC3000 tolerance in pepper. MOLECULAR HORTICULTURE 2023; 3:6. [PMID: 37789468 PMCID: PMC10514951 DOI: 10.1186/s43897-023-00054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/06/2023] [Indexed: 10/05/2023]
Abstract
The ribosomal protein contains complex structures that belong to polypeptide glycoprotein family, which are involved in plant growth and responses to various stresses. In this study, we found that capsicum annuum 40S ribosomal protein SA-like (CaSLP) was extensively accumulated in the cell nucleus and cell membrane, and the expression level of CaSLP was up-regulated by Salicylic acid (SA) and drought treatment. Significantly fewer peppers plants could withstand drought stress after CaSLP gene knockout. The transient expression of CaSLP leads to drought tolerance in pepper, and Arabidopsis's ability to withstand drought stress was greatly improved by overexpressing the CaSLP gene. Exogenous application of SA during spraying season enhanced drought tolerance. CaSLP-knockdown pepper plants demonstrated a decreased resistance of Pseudomonas syringae PV.tomato (Pst) DC3000 (Pst.DC3000), whereas ectopic expression of CaSLP increased the Pst.DC3000 stress resistance in Arabidopsis. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) results showed that CaNAC035 physically interacts with CaSLP in the cell nucleus. CaNAC035 was identified as an upstream partner of the CaPR1 promoter and activated transcription. Collectively the findings demonstrated that CaSLP plays an essential role in the regulation of drought and Pst.DC3000 stress resistance.
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Affiliation(s)
- Huafeng Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yingping Pei
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qiang He
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wang Zhu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Maira Jahangir
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Saeed Ul Haq
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Department of Horticulture, The University of Agriculture Peshawar, Peshawar, 25130, Pakistan
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Department of Horticulture, The University of Haripur, Haripur, 22620, Pakistan
| | - Rugang Chen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China.
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12
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Gao LL, Hong ZH, Wang Y, Wu GZ. Chloroplast proteostasis: A story of birth, life, and death. PLANT COMMUNICATIONS 2023; 4:100424. [PMID: 35964157 PMCID: PMC9860172 DOI: 10.1016/j.xplc.2022.100424] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 06/02/2023]
Abstract
Protein homeostasis (proteostasis) is a dynamic balance of protein synthesis and degradation. Because of the endosymbiotic origin of chloroplasts and the massive transfer of their genetic information to the nucleus of the host cell, many protein complexes in the chloroplasts are constituted from subunits encoded by both genomes. Hence, the proper function of chloroplasts relies on the coordinated expression of chloroplast- and nucleus-encoded genes. The biogenesis and maintenance of chloroplast proteostasis are dependent on synthesis of chloroplast-encoded proteins, import of nucleus-encoded chloroplast proteins from the cytosol, and clearance of damaged or otherwise undesired "old" proteins. This review focuses on the regulation of chloroplast proteostasis, its interaction with proteostasis of the cytosol, and its retrograde control over nuclear gene expression. We also discuss significant issues and perspectives for future studies and potential applications for improving the photosynthetic performance and stress tolerance of crops.
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Affiliation(s)
- Lin-Lin Gao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zheng-Hui Hong
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yinsong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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13
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Comparison of Boraginales Plastomes: Insights into Codon Usage Bias, Adaptive Evolution, and Phylogenetic Relationships. DIVERSITY 2022. [DOI: 10.3390/d14121104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Boraginales (Boraginaceae a.l.) comprise more than 2450 species worldwide. However, little knowledge exists of the characteristics of the complete plastid genome. In this study, three new sequences representing the first pt genome of Heliotropiaceae and Cordiaceae were assembled and compared with other Boraginales species. The pt genome sizes of Cordia dichotoma, Heliotropium arborescens, and Tournefortia montana were 151,990 bp, 156,243 bp, and 155,891 bp, respectively. Multiple optimal codons were identified, which may provide meaningful information for enhancing the gene expression of Boraginales species. Furthermore, codon usage bias analyses revealed that natural selection and other factors may dominate codon usage patterns in the Boraginales species. The boundaries of the IR/LSC and IR/SSC regions were significantly different, and we also found a signal of obvious IR region expansion in the pt genome of Nonea vesicaria and Arnebia euchroma. Genes with high nucleic acid diversity (pi) values were also calculated, which may be used as potential DNA barcodes to investigate the phylogenetic relationships in Boraginales. psaI, rpl33, rpl36, and rps19 were found to be under positive selection, and these genes play an important role in our understanding of the adaptive evolution of the Boraginales species. Phylogenetic analyses implied that Boraginales can be divided into two groups. The existence of two subfamilies (Lithospermeae and Boragineae) in Boraginaceae is also strongly supported. Our study provides valuable information on pt genome evolution and phylogenetic relationships in the Boraginales species.
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14
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Wang Z, Sun J, Zu X, Gong J, Deng H, Hang R, Zhang X, Liu C, Deng X, Luo L, Wei X, Song X, Cao X. Pseudouridylation of chloroplast ribosomal RNA contributes to low temperature acclimation in rice. THE NEW PHYTOLOGIST 2022; 236:1708-1720. [PMID: 36093745 DOI: 10.1111/nph.18479] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Ribosomal RNAs (rRNAs) undergo many modifications during transcription and maturation; homeostasis of rRNA modifications is essential for chloroplast biogenesis in plants. The chloroplast acts as a hub to sense environmental signals, such as cold temperature. However, how RNA modifications contribute to low temperature responses remains unknown. Here we reveal that pseudouridine (Ψ) modification of rice chloroplast rRNAs mediated by the pseudouridine synthase (OsPUS1) contributes to cold tolerance at seedling stage. Loss-function of OsPUS1 leads to abnormal chloroplast development and albino seedling phenotype at low temperature. We find that OsPUS1 is accumulated upon cold and binds to chloroplast precursor rRNAs (pre-rRNAs) to catalyse the pseudouridylation on rRNA. These modifications on chloroplast rRNAs could be required for their processing, as the reduction of mature chloroplast rRNAs and accumulation of pre-rRNAs are observed in ospus1-1 at low temperature. Therefore, the ribosome activity and translation in chloroplasts is disturbed in ospus1-1. Furthermore, transcriptome and translatome analysis reveals that OsPUS1 balances growth and stress-responsive state, preventing excess reactive oxygen species accumulation. Taken together, our findings unveil a crucial function of Ψ in chloroplast ribosome biogenesis and cold tolerance in rice, with potential applications in crop improvement.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Zu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Gong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hongjing Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Runlai Hang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofan Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lilan Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
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15
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Rice TCD8 Encoding a Multi-Domain GTPase Is Crucial for Chloroplast Development of Early Leaf Stage at Low Temperatures. BIOLOGY 2022; 11:biology11121738. [PMID: 36552248 PMCID: PMC9774597 DOI: 10.3390/biology11121738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022]
Abstract
The multi-domain GTPase (MnmE) is conservative from bacteria to human and participates in tRNA modified synthesis. However, our understanding of how the MnmE is involved in plant chloroplast development is scarce, let alone in rice. A novel rice mutant, thermo-sensitive chlorophyll-deficient mutant 8 (tcd8) was identified in this study, which apparently presented an albino phenotype at 20 °C but a normal green over 24 °C, coincided with chloroplast development and chlorophyll content. Map-based cloning and complementary test revealed the TCD8 encoded a multi-domain GTPase localized in chloroplasts. In addition, the disturbance of TCD8 suppressed the transcripts of certain chloroplast-related genes at low temperature, although the genes were recoverable to nearly normal levels at high temperature (32 °C), indicating that TCD8 governs chloroplast development at low temperature. The multi-domain GTPase gene in rice is first reported in this study, which endorses the importance in exploring chloroplast development in rice.
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16
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Robles P, Quesada V. Unveiling the functions of plastid ribosomal proteins in plant development and abiotic stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 189:35-45. [PMID: 36041366 DOI: 10.1016/j.plaphy.2022.07.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Translation of mRNAs into proteins is a universal process and ribosomes are the molecular machinery that carries it out. In eukaryotic cells, ribosomes can be found in the cytoplasm, mitochondria, and also in the chloroplasts of photosynthetic organisms. A number of genetic studies have been performed to determine the function of plastid ribosomal proteins (PRPs). Tobacco has been frequently used as a system to study the ribosomal proteins encoded by the chloroplast genome. In contrast, Arabidopsis thaliana and rice are preferentially used models to study the function of nuclear-encoded PRPs by using direct or reverse genetics approaches. The results of these works have provided a relatively comprehensive catalogue of the roles of PRPs in different plant biology aspects, which highlight that some PRPs are essential, while others are not. The latter ones are involved in chloroplast biogenesis, lateral root formation, leaf morphogenesis, plant growth, photosynthesis or chlorophyll synthesis. Furthermore, small gene families encode some PRPs. In the last few years, an increasing number of findings have revealed a close association between PRPs and tolerance to adverse environmental conditions. Sometimes, the same PRP can be involved in both developmental processes and the response to abiotic stress. The aim of this review is to compile and update the findings hitherto published on the functional analysis of PRPs. The study of the phenotypic effects caused by the disruption of PRPs from different species reveals the involvement of PRPs in different biological processes and highlights the significant impact of plastid translation on plant biology.
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Affiliation(s)
- Pedro Robles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Víctor Quesada
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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17
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Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes. Int J Mol Sci 2022; 23:ijms231810611. [PMID: 36142529 PMCID: PMC9502317 DOI: 10.3390/ijms231810611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/23/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.
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18
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Du Q, Li J, Wang L, Chen H, Jiang M, Chen Z, Jiang C, Gao H, Wang B, Liu C. Complete chloroplast genomes of two medicinal Swertia species: the comparative evolutionary analysis of Swertia genus in the Gentianaceae family. PLANTA 2022; 256:73. [PMID: 36083348 DOI: 10.1007/s00425-022-03987-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The complete chloroplast genome of Swertia kouitchensis has been sequenced and assembled, compared with that of S. bimaculata to determine the evolutionary relationships among species of the Swertia in the Gentianaceae family. Swertia kouitchensis and S. bimaculata are from the Gentianaceae family. The complete chloroplast genome of S. kouitchensis was newly assembled, annotated, and analyzed by Illumina Hiseq 2500 platform. The chloroplast genomes of the two species encoded a total of 133, 134 genes, which included 88-89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA genes. One intron was contained in each of the eight protein-coding genes and eight tRNA-coding genes, whereas two introns were found in two genes (ycf3 and clpP). The most abundant codon of the two species was for isoleucine, and the least abundant codon was for cysteine. The number of microsatellite repeat sequences was twenty-eight and thirty-two identified in the chloroplast genomes of S. kouitchensis and S. bimaculata, respectively. A total of 1127 repeat sequences were identified in all the 23 Swertia chloroplast genomes, and they fell into four categories. Furthermore, five divergence hotspot regions can be applied to discriminate these 23 Swertia species through genomes comparison. One pair of genus-specific DNA barcodes primer has been accurately identified. Therefore, the diverse regions cloned by a specific primer may become an effective and powerful molecular marker for the identification of Swertia genus. Moreover, four genes (ccsA, ndhK, rpoC1, and rps12) were positive selective pressure. The phylogenetic tree showed that the 23 Swertia species were clustered into a large clade including four evident subbranches, whereas the two species of S. kouitchensis and S. bimaculata were separately clustered into the diverse but correlated species group.
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Affiliation(s)
- Qing Du
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China.
- College of Pharmacy, Key Laboratory of Medicinal Plant Resources of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Minzu University, No.3, Bayi Mid-road, Chengdong District, Xining City, Qinghai Province, 810007, People's Republic of China.
- Fresh Sky-Right (Beijing) International Science and Technology Co., Ltd, No.59, Banjing Road, Haidian District, Beijing, 100097, People's Republic of China.
| | - Jing Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
- Xiangnan University, No. 889, Chenzhou dadao, Chenzhou City, Hunan Province, 423000, People's Republic of China
| | - Liqiang Wang
- College of Pharmacy, Heze University, No.2269, University Road, Mudan District, Heze City, Shandong Province, 274015, People's Republic of China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), No. 3501, University Road, Changqing District, Jinan City, Shandong Province, 250399, People's Republic of China
| | - Zhuoer Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
- Xiangnan University, No. 889, Chenzhou dadao, Chenzhou City, Hunan Province, 423000, People's Republic of China
| | - Chuanbei Jiang
- Genepioneer Biotechnologies Inc, No. 9, Weidi Road, Qixia District, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Haidong Gao
- Genepioneer Biotechnologies Inc, No. 9, Weidi Road, Qixia District, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Bin Wang
- Xiangnan University, No. 889, Chenzhou dadao, Chenzhou City, Hunan Province, 423000, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China.
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19
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Dupouy G, McDermott E, Cashell R, Scian A, McHale M, Ryder P, de Groot J, Lucca N, Brychkova G, McKeown PC, Spillane C. Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana. PLANT REPRODUCTION 2022; 35:189-204. [PMID: 35247095 PMCID: PMC9352626 DOI: 10.1007/s00497-022-00440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Plastid ribosomal proteins (PRPs) can play essential roles in plastid ribosome functioning that affect plant function and development. However, the roles of many PRPs remain unknown, including elucidation of which PRPs are essential or display redundancy. Here, we report that the nuclear-encoded PLASTID RIBOSOMAL PROTEIN L5 (PRPL5) is essential for early embryo development in A. thaliana, as homozygous loss-of-function mutations in the PRPL5 gene impairs chloroplast development and leads to embryo failure to develop past the globular stage. We confirmed the prpl5 embryo-lethal phenotype by generating a mutant CRISPR/Cas9 line and by genetic complementation. As PRPL5 underwent transfer to the nuclear genome early in the evolution of Embryophyta, PRPL5 can be expected to have acquired a chloroplast transit peptide. We identify and validate the presence of an N-terminal chloroplast transit peptide, but unexpectedly also confirm the presence of a conserved and functional Nuclear Localization Signal on the protein C-terminal end. This study highlights the fundamental role of the plastid translation machinery during the early stages of embryo development in plants and raises the possibility of additional roles of plastid ribosomal proteins in the nucleus.
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Affiliation(s)
- Gilles Dupouy
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Emma McDermott
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Ronan Cashell
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Anna Scian
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Marcus McHale
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Joelle de Groot
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Noel Lucca
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland.
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20
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A De Novo Transcriptome Analysis Identifies Cold-Responsive Genes in the Seeds of Taxillus chinensis (DC.) Danser. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9247169. [PMID: 35845948 PMCID: PMC9279050 DOI: 10.1155/2022/9247169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/30/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022]
Abstract
Taxillus chinensis (DC.) Danser, a parasitic plant of the Loranthaceae family, grows by attacking other plants. It has a long history of being used in Chinese medicine to treat multiple chronic diseases. We previously observed that T. chinensis seeds are sensitive to cold. In this study, we performed transcriptome sequencing for T. chinensis seeds treated by cold (0°C) for 0 h, 12 h, 24 h, and 36 h. TRINITY assembled 257,870 transcripts from 223,512 genes. The GC content and N50 were calculated as 42.29% and 1,368, respectively. Then, we identified 42,183 CDSs and 35,268 likely proteins in the assembled transcriptome, which contained 1,622 signal peptides and 6,795 transmembrane domains. Next, we identified 17,217 genes (FPKM > 5) and 2,333 differentially expressed genes (DEGs) in T. chinensis seeds under cold stress. The MAPK pathway, as an early cold response, was significantly enriched by the DEGs in the T. chinensis seeds after 24 h of cold treatment. Known cold-responsive genes encoding abscisic acid-associated, aquaporin, C-repeat binding factor (CBF), cold-regulated protein, heat shock protein, protein kinase, ribosomal protein, transcription factor (TF), zinc finger protein, and ubiquitin were deregulated in the T. chinensis seeds under cold stress. Notably, the upregulation of CBF gene might be the consequences of the downregulation of MYB and GATA TFs. Additionally, we identified that genes encoding CDC20, YLS9, EXORDIUM, and AUX1 and wound-responsive family protein might be related to novel mechanisms of T. chinensis seeds exposed to cold. This study is first to report the differential transcriptional induction in T. chinensis seeds under cold stress. It will improve our understanding of parasitic plants in response to cold and provide a valuable resource for future studies.
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21
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Xiong HB, Pan HM, Long QY, Wang ZY, Qu WT, Mei T, Zhang N, Xu XF, Yang ZN, Yu QB. AtNusG, a chloroplast nucleoid protein of bacterial origin linking chloroplast transcriptional and translational machineries, is required for proper chloroplast gene expression in Arabidopsis thaliana. Nucleic Acids Res 2022; 50:6715-6734. [PMID: 35736138 PMCID: PMC9262611 DOI: 10.1093/nar/gkac501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 05/25/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022] Open
Abstract
In Escherichia coli, transcription-translation coupling is mediated by NusG. Although chloroplasts are descendants of endosymbiotic prokaryotes, the mechanism underlying this coupling in chloroplasts remains unclear. Here, we report transcription-translation coupling through AtNusG in chloroplasts. AtNusG is localized in chloroplast nucleoids and is closely associated with the chloroplast PEP complex by interacting with its essential component PAP9. It also comigrates with chloroplast ribosomes and interacts with their two components PRPS5 (uS5c) and PRPS10 (uS10c). These data suggest that the transcription and translation machineries are coupled in chloroplasts. In the atnusg mutant, the accumulation of chloroplast-encoded photosynthetic gene transcripts, such as psbA, psbB, psbC and psbD, was not obviously changed, but that of their proteins was clearly decreased. Chloroplast polysomic analysis indicated that the decrease in these proteins was due to the reduced efficiency of their translation in this mutant, leading to reduced photosynthetic efficiency and enhanced sensitivity to cold stress. These data indicate that AtNusG-mediated coupling between transcription and translation in chloroplasts ensures the rapid establishment of photosynthetic capacity for plant growth and the response to environmental changes. Therefore, our study reveals a conserved mechanism of transcription-translation coupling between chloroplasts and E. coli, which perhaps represents a regulatory mechanism of chloroplast gene expression. This study provides insights into the underlying mechanisms of chloroplast gene expression in higher plants.
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Affiliation(s)
| | | | | | - Zi-Yuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wan-Tong Qu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Tong Mei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Nan Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Feng Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhong-Nan Yang
- Correspondence may also be addressed to Zhong-Nan Yang. Tel: +86 21 64324650;
| | - Qing-Bo Yu
- To whom correspondence should be addressed. Tel: +86 21 64324812;
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22
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Long J, Xing W, Wang Y, Wu Z, Li W, Zou Y, Sun J, Zhang F, Pi Z. Comparative proteomic analysis on chloroplast proteins provides new insights into the effects of low temperature in sugar beet. BOTANICAL STUDIES 2022; 63:18. [PMID: 35670889 PMCID: PMC9174413 DOI: 10.1186/s40529-022-00349-6] [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: 10/11/2021] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Low temperature, which is one of the main environmental factors that limits geographical distribution and sucrose yield, is a common abiotic stress during the growth and development of sugar beet. As a regulatory hub of plant response to abiotic stress, activity in the chloroplasts is related to many molecular and physiological processes, particularly in response to low temperature stress. RESULTS The contents of chlorophyll (Chl) and malondialdehyde (MDA), relative electrical conductivity (REL), and superoxide dismutase (SOD) activity were measured. The results showed that sugar beet could manage low temperature stress by regulating the levels of Chl, REL and MDA, and the activity of SOD. The physiological responses indicated that sugar beets respond positively to low temperature treatments and are not significantly damaged. Moreover, to determine the precise time to response low temperature in sugar beet, well-known abiotic stresses-responsive transcript factor family, namely DEHYDRATION RESPONSIVE ELEMENT BINDING PROTEIN (DREB), was selected as the marker gene. The results of phylogenetic analyses showed that BvDREBA1 and BvDREBA4 were in the same branch as the cold- and drought-responsive AtDREB gene. In addition, the expression of BvDREBs reached its maximum level at 24 h after low temperature by RNA-Seq and qRT-PCR analysis. Furthermore, the changes in chloroplast proteome after low temperature at 24 h were detected using a label-free technique. A total of 416 differentially expressed proteins were identified. GO enrichment analysis showed that 16 GO terms were significantly enriched, particularly chloroplast stroma, chloroplast envelope, and chloroplast thylakoid membrane. It is notable that the transport of photosynthetic proteins (BvLTD and BvTOC100), the formation of starch granules (BvPU1, BvISA3, and BvGWD3) and the scavenging of reactive oxygen species (BvCu/Zn-SOD, BvCAT, BvPrx, and BvTrx) were the pathways used by sugar beets to respond to low temperatures at an early stage. CONCLUSIONS These results provide a preliminarily analysis of how chloroplasts of sugar beet respond to low temperature stress at the translational level and provide a theoretical basis for breeding low temperature resistant varieties of sugar beet.
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Affiliation(s)
- Jiali Long
- School of Life Sciences, Heilongjiang University, Harbin, 150080, Heilongjiang, China
| | - Wang Xing
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, Heilongjiang, China
| | - Yuguang Wang
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, Heilongjiang, China
| | - Zedong Wu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, Heilongjiang, China
| | - Wenjing Li
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, Heilongjiang, China
| | - Yi Zou
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, Heilongjiang, China
| | - Jiaping Sun
- School of Life Sciences, Heilongjiang University, Harbin, 150080, Heilongjiang, China
| | - Fushun Zhang
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, Heilongjiang, China.
| | - Zhi Pi
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, Heilongjiang, China.
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23
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 PMCID: PMC9048916 DOI: 10.1093/plcell/koac056] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/04/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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24
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 DOI: 10.1093/plcell/koac056%jtheplantcell] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/28/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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25
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Wang ZY, Qu WT, Mei T, Zhang N, Yang NY, Xu XF, Xiong HB, Yang ZN, Yu QB. AtRsmD Is Required for Chloroplast Development and Chloroplast Function in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:860945. [PMID: 35548310 PMCID: PMC9083416 DOI: 10.3389/fpls.2022.860945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 05/25/2023]
Abstract
AtRsmD was recently demonstrated to be a chloroplast 16S rRNA methyltransferase (MTase) for the m2G915 modification in Arabidopsis. Here, its function of AtRsmD for chloroplast development and photosynthesis was further analyzed. The AtRsmD gene is highly expressed in green photosynthetic tissues. AtRsmD is associated with the thylakoid in chloroplasts. The atrsmd-2 mutant exhibited impaired photosynthetic efficiency in emerging leaves under normal growth conditions. A few thylakoid lamellas could be observed in the chloroplast from the atrsmd-2 mutant, and these thylakoids were loosely organized. Knockout of the AtRsmD gene had minor effects on chloroplast ribosome biogenesis and RNA loading on chloroplast ribosomes, but it reduced the amounts of chloroplast-encoded photosynthesis-related proteins in the emerging leaves, for example, D1, D2, CP43, and CP47, which reduced the accumulation of the photosynthetic complex. Nevertheless, knockout of the AtRsmD gene did not cause a general reduction in chloroplast-encoded proteins in Arabidopsis grown under normal growth conditions. Additionally, the atrsmd-2 mutant exhibited more sensitivity to lincomycin, which specifically inhibits the elongation of nascent polypeptide chains. Cold stress exacerbated the effect on chloroplast ribosome biogenesis in the atrsmd-2 mutant. All these data suggest that the AtRsmD protein plays distinct regulatory roles in chloroplast translation, which is required for chloroplast development and chloroplast function.
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26
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Liu J, Lindstrom AJ, Gong X. Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis. BMC PLANT BIOLOGY 2022; 22:116. [PMID: 35291941 PMCID: PMC8922756 DOI: 10.1186/s12870-022-03491-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic discordance, in resolving the phylogeny within a lineage. Here we examine plastome characteristics of Cycas L., the most diverse genus among extant cycads, and investigate the deep phylogenetic relationships within Cycas by sampling 47 plastomes representing all major clades from six sections. RESULTS All Cycas plastomes shared consistent gene content and structure with only one gene loss detected in Philippine species C. wadei. Three novel plastome regions (psbA-matK, trnN-ndhF, chlL-trnN) were identified as containing the highest nucleotide variability. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection except ndhB. Phylogenomic analyses that alternatively included concatenated and coalescent methods, both identified four clades but with conflicting topologies at shallow nodes. Specifically, we found three species-rich Cycas sections, namely Stangerioides, Indosinenses and Cycas, were not or only weakly supported as monophyly based on plastomic phylogeny. Tree space analyses based on different tree-inference methods both revealed three gene clusters, of which the cluster with moderate genetic properties showed the best congruence with the favored phylogeny. CONCLUSIONS Our exploration in plastomic data for Cycas supports the idea that plastid protein-coding genes may exhibit discordance in phylogenetic signals. The incongruence between molecular phylogeny and morphological classification reported here may largely be attributed to the uniparental attribute of plastid, which cannot offer sufficient information to resolve the phylogeny. Contrasting to a previous consensus that genes with longer sequences and a higher proportion of variances are superior for phylogeny reconstruction, our result implies that the most effective phylogenetic signals could come from loci that own moderate variation, GC content, sequence length, and underwent modest selection.
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Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, 20250, Bangsalae, Sattahip, Chonburi, Thailand.
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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27
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Dalla Costa TP, Silva MC, de Santana Lopes A, Gomes Pacheco T, de Oliveira JD, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes. PLANTA 2022; 255:57. [PMID: 35113261 DOI: 10.1007/s00425-022-03841-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.
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Affiliation(s)
- Tanara P Dalla Costa
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Maria C Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José D de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Valter A de Baura
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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28
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Li X, Li D, Ma S, Yang Y. Integration of transcriptomic and proteomic analyses of cold shock response in Kosmotoga olearia, a typical thermophile with an incredible minimum growth temperature at 20 °C. Braz J Microbiol 2022; 53:71-88. [PMID: 34997565 PMCID: PMC8882551 DOI: 10.1007/s42770-021-00662-5] [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: 04/06/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023] Open
Abstract
Kosmotoga olearia TBF 19.5.1 is a typical thermophile with optimal growth at 65 °C and also exhibits visible growth at an incredible minimum temperature (20 °C). It is considered an ideal model for investigating the evolutionary transition from thermophiles to mesophiles within Thermotogae. However, knowledge relevant to molecular mechanisms of K. olearia responding to cold shock is still limited. In this study, transcriptomics and proteomics were integrated to investigate the global variations at the transcript and protein level during cold shock in K. olearia. As a result, total 734 differentially expressed genes and 262 differentially expressed proteins were identified. The cold-responsive genes and proteins were associated with signaling transduction, transcription, translation and repair, cell wall/membrane reconstruction, amino acid biosynthesis, and stress response. However, most genes and proteins, involved in carbon metabolism, fatty acid biosynthesis, and energy production, were repressed. This work provides the first integrative transcriptomics and proteomics analyses of the cold shock response in K. olearia, and it offered new insights into the mechanisms of cold adaptation and post-transcriptional regulation of the distinctive thermophile within Thermotogae.
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Affiliation(s)
- Xia Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China ,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041 China
| | - Dan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China ,School of Liquor-Making Engineering, Sichuan University Jinjiang College, Meishan, 620680 China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041 China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
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29
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Tang X, Shi F, Wang Y, Huang S, Zhao Y, Feng H. Proteomic analysis of a plastid gene encoding RPS4 mutant in Chinese cabbage (Brassica campestris L. ssp. pekinensis). Funct Integr Genomics 2021; 22:113-130. [PMID: 34881421 DOI: 10.1007/s10142-021-00808-6] [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: 12/04/2020] [Revised: 02/20/2021] [Accepted: 09/18/2021] [Indexed: 10/19/2022]
Abstract
Plastids are important plant cell organelles containing a genome and bacterial-type 70S ribosomes-primarily composed of plastid ribosomal proteins and ribosomal RNAs. In this study, a chlorophyll-deficient mutant (cdm) obtained from double-haploid Chinese cabbage 'FT' was identified as a plastome mutant with an A-to-C base substitution in the plastid gene encoding the ribosomal protein RPS4. To further elucidate the function and regulatory mechanisms of RPS4, a comparative proteomic analysis was conducted between cdm and its wild-type 'FT' plants by isobaric tags and a relative and absolute quantitation (iTRAQ)-based strategy. A total of 6,245 proteins were identified, 540 of which were differentially abundant proteins (DAPs) in the leaves of cdm as compared to those of 'FT'-including 233 upregulated and 307 downregulated proteins. Upregulated DAPs were mainly involved in translation, organonitrogen compound biosynthetic process, ribosomes, and spliceosomes. Meanwhile, downregulated DAPs were mainly involved in photosynthesis, photosynthetic reaction centres, photosynthetic light harvesting, carbon fixation, and chlorophyll binding. These results indicated an important role of RPS4 in the regulation of growth and development of Chinese cabbage, possibly by regulating plastid translation activity by affecting the expression of specific photosynthesis- and cold stress-related proteins. Moreover, a multiple reaction monitoring (MRM) test and quantitative real-time polymerase chain reaction analysis confirmed our iTRAQ results. Quantitative proteomic analysis allowed us to confirm diverse changes in the metabolic pathways between cdm and 'FT' plants. This work provides new insights into the regulation of chlorophyll biosynthesis and photosynthesis in Chinese cabbage.
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Affiliation(s)
- Xiaoyan Tang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding College of Horticulture, Anhui Agricultural University, 130 Changjiang West Road, Shushan District, Hefei, China
| | - Fengyan Shi
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yiheng Wang
- Biotechnology Research Institute, Xiqing District, Tianjin Academy of Agricultural Sciences, Jinjing Road 17 km, Tianjin, 300384, China
| | - Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Ying Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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30
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Zhang Y, Yu J, Xia M, Chi X, Khan G, Chen S, Zhang F. Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau. Ecol Evol 2021; 11:16034-16046. [PMID: 34824809 PMCID: PMC8601884 DOI: 10.1002/ece3.8274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/07/2022] Open
Abstract
Genus Comastoma (subt. Swertiinae, Gentianaceae) contains species, such as "Zangyinchen," that are important herbs in Tibetan medicine. The phylogenetic relationship of this within Gentianaceae and the circumscriptions of its species have long been controversial with conflicting morphological and molecular data reported. Here, we used whole chloroplast genome sequences for Comastoma species and related taxa to reconstruct their phylogeny and clarify their taxonomic relationships. The results revealed that the length of all plastome sequenced varied from 149 to 151 kb and have high similarity in structure and gene content. Phylogenomic analysis showed that Comastoma is a monophyletic group, closely related to the genus Lomatogonium. The divergence time estimation showed that Gentianaceae diverged at about 21.81 Ma, while the split of Comastoma occurred at 7.70 Ma. However, the results suggested the crown age of species formation in this genus is after 4.19 Ma. Our results suggest that QTP uplift, the alternation of Quaternary glaciation and interglaciation, and monsoon changes might have acted as drivers of speciation in Comastoma.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mingze Xia
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Gulzar Khan
- Institute for Biology and Environmental SciencesCarl von Ossietzky‐University OldenburgOldenburgGermany
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
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Shariatipour N, Heidari B, Tahmasebi A, Richards C. Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:709817. [PMID: 34712248 PMCID: PMC8546302 DOI: 10.3389/fpls.2021.709817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/06/2021] [Indexed: 05/02/2023]
Abstract
Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.
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Affiliation(s)
- Nikwan Shariatipour
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ahmad Tahmasebi
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- USDA ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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Cauz-Santos LA, da Costa ZP, Callot C, Cauet S, Zucchi MI, Bergès H, van den Berg C, Vieira MLC. A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes. Genome Biol Evol 2021; 12:1841-1857. [PMID: 32722748 PMCID: PMC7586853 DOI: 10.1093/gbe/evaa155] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with ∼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in Passiflora capsularis and Passiflora costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.
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Affiliation(s)
- Luiz Augusto Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Maria Imaculada Zucchi
- Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, SP, Brazil
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Cássio van den Berg
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, BA, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
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Plastid Transformation in Tomato: A Vegetable Crop and Model Species. Methods Mol Biol 2021; 2317:217-228. [PMID: 34028771 DOI: 10.1007/978-1-0716-1472-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Tomato (Solanum lycopersicum L.), a member of the nightshade family (Solanaceae), is one of the most important vegetable crops and has long been an important model species in plant biology. Plastid biology in tomato is especially interesting due to the chloroplast-to-chromoplast conversion occurring during fruit ripening. Moreover, as tomato represents a major food crop with a fleshy fruit that can be eaten raw, the development of a plastid transformation protocol for tomato was of particular interest to plant biotechnologists. Recent methodological improvements have made tomato plastid transformation more efficient, and facilitated applications in metabolic engineering and molecular farming. This chapter describes the basic methods involved in the generation and analysis of tomato plants with transgenic chloroplast genomes and summarizes recent applications of tomato plastid transformation in plant biotechnology.
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Liu H, Zhang Y, Lu S, Chen H, Wu J, Zhu X, Zou B, Hua J. HsfA1d promotes hypocotyl elongation under chilling via enhancing expression of ribosomal protein genes in Arabidopsis. THE NEW PHYTOLOGIST 2021; 231:646-660. [PMID: 33893646 DOI: 10.1111/nph.17413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
How plants maintain growth under nonfreezing low temperatures (chilling) is not well understood. Here we use hypocotyl elongation under dark to investigate the molecular mechanisms for chilling growth in Arabidopsis thaliana. The function of HsfA1d (Heat shock transcription factor A1d) in chilling growth is investigated by physiological and molecular characterization of its mutants. Subcellular localization of HsfA1d under chilling is analyzed. Potential target genes of HsfA1d were identified by transcriptome analysis, chromatin immunoprecipitation, transcriptional activation assay and mutant characterization. HsfA1d is a positive regulator of hypocotyl elongation under chilling. It promotes expression of a large number of ribosome biogenesis genes to a moderate but significant extent under chilling. HsfA1d could bind to the promoter regions of two ribosome protein genes tested and promote their expression. The loss-of-function of one ribosome gene also reduced hypocotyl elongation under chilling. In addition, HsfA1d did not have increased nuclear accumulation under chilling and its basal nuclear accumulation is promoted by a salicylic acid receptor under chilling. This study thus unveils a new HsfA1d-mediated pathway that promotes the expression of cytosolic and plastid cytosolic and plastid ribosomal protein genes which may maintain overall protein translation for plant growth in chilling.
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Affiliation(s)
- Huimin Liu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan Lu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Chen
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiawen Wu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiang Zhu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baohong Zou
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Hua
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY, 14853, USA
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Zhou K, Zhang C, Xia J, Yun P, Wang Y, Ma T, Li Z. Albino seedling lethality 4; Chloroplast 30S Ribosomal Protein S1 is Required for Chloroplast Ribosome Biogenesis and Early Chloroplast Development in Rice. RICE (NEW YORK, N.Y.) 2021; 14:47. [PMID: 34046768 PMCID: PMC8160077 DOI: 10.1186/s12284-021-00491-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Ribosomes responsible for transcription and translation of plastid-encoded proteins in chloroplasts are essential for chloroplast development and plant growth. Although most ribosomal proteins in plastids have been identified, the molecular mechanisms regulating chloroplast biogenesis remain to be investigated. RESULTS Here, we identified albinic seedling mutant albino seedling lethality 4 (asl4) caused by disruption of 30S ribosomal protein S1 that is targeted to the chloroplast. The mutant was defective in early chloroplast development and chlorophyll (Chl) biosynthesis. A 2855-bp deletion in the ASL4 allele was verified as responsible for the mutant phenotype by complementation tests. Expression analysis revealed that the ASL4 allele was highly expressed in leaf 4 sections and newly expanded leaves during early leaf development. Expression levels were increased by exposure to light following darkness. Some genes involved in chloroplast biogenesis were up-regulated and others down-regulated in asl4 mutant tissues compared to wild type. Plastid-encoded plastid RNA polymerase (PEP)-dependent photosynthesis genes and nuclear-encoded phage-type RNA polymerase (NEP)-dependent housekeeping genes were separately down-regulated and up-regulated, suggesting that plastid transcription was impaired in the mutant. Transcriptome and western blot analyses showed that levels of most plastid-encoded genes and proteins were reduced in the mutant. The decreased contents of chloroplast rRNAs and ribosomal proteins indicated that chloroplast ribosome biogenesis was impaired in the asl4 mutant. CONCLUSIONS Rice ASL4 encodes 30S ribosomal protein S1, which is targeted to the chloroplast. ASL4 is essential for chloroplast ribosome biogenesis and early chloroplast development. These data will facilitate efforts to further elucidate the molecular mechanism of chloroplast biogenesis.
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Affiliation(s)
- Kunneng Zhou
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Caijuan Zhang
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Jiafa Xia
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Peng Yun
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Yuanlei Wang
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Tingchen Ma
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China
| | - Zefu Li
- Anhui Province Key Laboratory of Rice Genetics and Breeding, (Rice Research Institute Anhui Academy of Agricultural Sciences), Hefei, 230031, China.
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Caroca R, Howell KA, Malinova I, Burgos A, Tiller N, Pellizzer T, Annunziata MG, Hasse C, Ruf S, Karcher D, Bock R. Knockdown of the plastid-encoded acetyl-CoA carboxylase gene uncovers functions in metabolism and development. PLANT PHYSIOLOGY 2021; 185:1091-1110. [PMID: 33793919 PMCID: PMC8133629 DOI: 10.1093/plphys/kiaa106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
De novo fatty acid biosynthesis in plants relies on a prokaryotic-type acetyl-CoA carboxylase (ACCase) that resides in the plastid compartment. The enzyme is composed of four subunits, one of which is encoded in the plastid genome, whereas the other three subunits are encoded by nuclear genes. The plastid gene (accD) encodes the β-carboxyltransferase subunit of ACCase and is essential for cell viability. To facilitate the functional analysis of accD, we pursued a transplastomic knockdown strategy in tobacco (Nicotiana tabacum). By introducing point mutations into the translational start codon of accD, we obtained stable transplastomic lines with altered ACCase activity. Replacement of the standard initiator codon AUG with UUG strongly reduced AccD expression, whereas replacement with GUG had no detectable effects. AccD knockdown mutants displayed reduced ACCase activity, which resulted in changes in the levels of many but not all species of cellular lipids. Limiting fatty acid availability caused a wide range of macroscopic, microscopic, and biochemical phenotypes, including impaired chloroplast division, reduced seed set, and altered storage metabolism. Finally, while the mutants displayed reduced growth under photoautotrophic conditions, they showed exaggerated growth under heterotrophic conditions, thus uncovering an unexpected antagonistic role of AccD activity in autotrophic and heterotrophic growth.
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Affiliation(s)
- Rodrigo Caroca
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Katharine A Howell
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Irina Malinova
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Asdrúbal Burgos
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Nadine Tiller
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Tommaso Pellizzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | | | - Claudia Hasse
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
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Xu Y, Li Y, Wang Q, Zheng C, Zhao D, Shi F, Liu X, Tao J, Zong S. Identification of key genes associated with overwintering in Anoplophora glabripennis larva using gene co-expression network analysis. PEST MANAGEMENT SCIENCE 2021; 77:805-816. [PMID: 32909651 DOI: 10.1002/ps.6082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/06/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Anoplophora glabripennis (Coleoptera: Cerambycidae) is a major quarantine pest in forestry. It is widely distributed throughout many regions such as Asia, Europe, and North America, and has enormous destructive potential for forests. The larvae of A. glabripennis overwinter in a dormant state with strong cold tolerance, and whether the larvae survive winter determines the population density in the following year. However, the molecular mechanisms of this process are not clear. RESULTS RNA sequencing (RNA-Seq) analysis of A. glabripennis larvae at five overwintering stages identified 6876 differentially expressed genes (DEGs). Among these, 46 functional genes that might respond to low temperature were identified. Weighted gene co-expression network analysis revealed that the MEturquoise module was correlated with the overwintering process. The STPK, PP2A, DGAT, and HSF genes were identified as hub genes using visualization of gene network. In addition, four genes related to sugar transport, gluconeogenesis and glycosylation were screened, which may be involved in the metabolic regulation of overwintering larvae. The protein-protein interaction network indicated that ribosomal protein and ATP synthase may play an important role in connecting with other proteins. The expression levels of fifteen hub genes were further validated by quantitative RT-PCR, and the results were consistent with RNA-Seq. CONCLUSION This study demonstrates key genes that may reveal the molecular mechanism of overwintering in A. glabripennis larvae. The genes may be the potential targets to prevent larvae from surviving the cold winter by developing new biological agents using genetic engineering.
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Affiliation(s)
- Yabei Xu
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Yurong Li
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Qianqian Wang
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Chunchun Zheng
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Dongfang Zhao
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Fengming Shi
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Xinhai Liu
- Ulanqab Municipal Bureau of Parks, Ulanqab, China
| | - Jing Tao
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Shixiang Zong
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
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Lin P, Bai HR, He L, Huang QX, Zeng QH, Pan YZ, Jiang BB, Zhang F, Zhang L, Liu QL. Proteome-wide and lysine crotonylation profiling reveals the importance of crotonylation in chrysanthemum (Dendranthema grandiforum) under low-temperature. BMC Genomics 2021; 22:51. [PMID: 33446097 PMCID: PMC7809856 DOI: 10.1186/s12864-020-07365-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/30/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Low-temperature severely affects the growth and development of chrysanthemum which is one kind of ornamental plant well-known and widely used in the world. Lysine crotonylation is a recently identified post-translational modification (PTM) with multiple cellular functions. However, lysine crotonylation under low-temperature stress has not been studied. RESULTS Proteome-wide and lysine crotonylation of chrysanthemum at low-temperature was analyzed using TMT (Tandem Mass Tag) labeling, sensitive immuno-precipitation, and high-resolution LC-MS/MS. The results showed that 2017 crotonylation sites were identified in 1199 proteins. Treatment at 4 °C for 24 h and - 4 °C for 4 h resulted in 393 upregulated proteins and 500 downregulated proteins (1.2-fold threshold and P < 0.05). Analysis of biological information showed that lysine crotonylation was involved in photosynthesis, ribosomes, and antioxidant systems. The crotonylated proteins and motifs in chrysanthemum were compared with other plants to obtain orthologous proteins and conserved motifs. To further understand how lysine crotonylation at K136 affected APX (ascorbate peroxidase), we performed a site-directed mutation at K136 in APX. Site-directed crotonylation showed that lysine decrotonylation at K136 reduced APX activity, and lysine complete crotonylation at K136 increased APX activity. CONCLUSION In summary, our study comparatively analyzed proteome-wide and crotonylation in chrysanthemum under low-temperature stress and provided insights into the mechanisms of crotonylation in positively regulated APX activity to reduce the oxidative damage caused by low-temperature stress. These data provided an important basis for studying crotonylation to regulate antioxidant enzyme activity in response to low-temperature stress and a new research ideas for chilling-tolerance and freezing-tolerance chrysanthemum molecular breeding.
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Affiliation(s)
- Ping Lin
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Hui-Ru Bai
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Ling He
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qiu-Xiang Huang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qin-Han Zeng
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuan-Zhi Pan
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Bei-Bei Jiang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qing-Lin Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China.
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Li M, Hensel G, Melzer M, Junker A, Tschiersch H, Ruwe H, Arend D, Kumlehn J, Börner T, Stein N. Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley. FRONTIERS IN PLANT SCIENCE 2021; 12:732608. [PMID: 34659298 PMCID: PMC8517540 DOI: 10.3389/fpls.2021.732608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/10/2021] [Indexed: 05/12/2023]
Abstract
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained if at least one member of the pair undergoes neo- or sub-functionalization. Phylogenetic analyses of the ohnologous genes ALBOSTRIANS (HvAST/HvCMF7) and ALBOSTRIANS-LIKE (HvASL/HvCMF3) of barley (Hordeum vulgare) revealed them as members of a subfamily of genes coding for CCT motif (CONSTANS, CONSTANS-LIKE and TIMING OF CAB1) proteins characterized by a single CCT domain and a putative N-terminal chloroplast transit peptide. Recently, we showed that HvCMF7 is needed for chloroplast ribosome biogenesis. Here we demonstrate that mutations in HvCMF3 lead to seedlings delayed in development. They exhibit a yellowish/light green - xantha - phenotype and successively develop pale green leaves. Compared to wild type, plastids of mutant seedlings show a decreased PSII efficiency, impaired processing and reduced amounts of ribosomal RNAs; they contain less thylakoids and grana with a higher number of more loosely stacked thylakoid membranes. Site-directed mutagenesis of HvCMF3 identified a previously unknown functional domain, which is highly conserved within this subfamily of CCT domain containing proteins. HvCMF3:GFP fusion constructs were localized to plastids and nucleus. Hvcmf3Hvcmf7 double mutants exhibited a xantha-albino or albino phenotype depending on the strength of molecular lesion of the HvCMF7 allele. The chloroplast ribosome deficiency is discussed as the primary observed defect of the Hvcmf3 mutants. Based on our observations, the genes HvCMF3 and HvCMF7 have similar but not identical functions in chloroplast development of barley supporting our hypothesis of neo-/sub-functionalization between both ohnologous genes.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Henning Tschiersch
- Heterosis Research Group, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Daniel Arend
- Research Group Bioinformatics and Information Technology, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
- *Correspondence: Thomas Börner,
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
- Nils Stein,
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Abstract
Expression of transgenes from the plastid genome offers a number of attractions to biotechnologists, with the potential to attain very high protein accumulation levels arguably being the most attractive one. High-level transgene expression is of particular importance in resistance engineering (e.g., for expression of insecticidal proteins) and molecular farming (e.g., for expression of pharmaceutical proteins and industrial enzymes). Over the past decades, the production of many commercially valuable proteins in chloroplast-transgenic (transplastomic) plants has been attempted, including pharmaceutical proteins (e.g., subunit vaccines and protein antibiotics) and industrial enzymes. Although in some cases, spectacularly high foreign protein accumulation levels have been obtained, expression levels were disappointingly poor in other cases. In this review, I summarize our current knowledge about the factors influencing the efficiency of plastid transgene expression, and highlight possible optimization strategies to alleviate problems with poor expression levels. I also discuss available techniques for inducible expression of chloroplast transgenes.
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Sun T. Expanded Function of the P-Type Pentatricopeptide Repeat Protein ATP4 in RNA Editing. PLANT PHYSIOLOGY 2020; 184:1625-1626. [PMID: 33277330 PMCID: PMC7723080 DOI: 10.1104/pp.20.01406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Tianhu Sun
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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Zhang J, Guo Y, Fang Q, Zhu Y, Zhang Y, Liu X, Lin Y, Barkan A, Zhou F. The PPR-SMR Protein ATP4 Is Required for Editing the Chloroplast rps8 mRNA in Rice and Maize. PLANT PHYSIOLOGY 2020; 184:2011-2021. [PMID: 32928899 PMCID: PMC7723101 DOI: 10.1104/pp.20.00849] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/01/2020] [Indexed: 05/20/2023]
Abstract
Chloroplast gene expression involves the participation of hundreds of pentatricopeptide repeat (PPR) RNA binding proteins, and proteins in the PLS subfamily typically specify sites of RNA editing, whereas those in the P-subfamily typically stabilize RNA, activate translation, or promote intron splicing. Several P-type PPR proteins include a small MutS-related (SMR) domain, but the biochemical contribution of the SMR domain remains enigmatic. Here, we describe a rice (Oryza sativa) mutant, osatp4, lacking the ortholog of ATP4, a PPR-SMR protein in maize (Zea mays). osatp4 mutants were chlorotic and had a plastid-ribosome deficiency when grown in the cold. Like maize ATP4, OsATP4 was required for the accumulation of dicistronic rpl16-rpl14 transcripts. Surprisingly, OsATP4 was also required for the editing of a specific nucleotide in the ribosomal protein S8 transcripts, rps8, and this function was conserved in maize. By contrast, rps8 RNA was edited normally in the maize PROTON gradient regulation3 mutant, pgr3, which also lacks rpl16-rpl14 transcripts, indicating that the editing defect in atp4 mutants is not a secondary effect of altered rpl16-rpl14 RNA metabolism. Expression of the edited rps8 isoform in transgenic osatp4 mutants complemented the cold-sensitive phenotype, indicating that a rps8 expression defect accounts for the cold-sensitivity. We suggest that ATP4 stimulates rps8 editing by facilitating access of a previously characterized PLS-type RNA editing factor to its cognate cis-element upstream of the edited nucleotide.
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Affiliation(s)
- Jinghong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yipo Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongli Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuejiao Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Zhu Y, Wu W, Shao W, Chen J, Shi X, Ma X, Xu YZ, Huang W, Huang J. SPLICING FACTOR1 Is Important in Chloroplast Development under Cold Stress. PLANT PHYSIOLOGY 2020; 184:973-987. [PMID: 32732348 PMCID: PMC7536683 DOI: 10.1104/pp.20.00706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/20/2020] [Indexed: 05/20/2023]
Abstract
RNA SPLICING FACTOR1 (SF1) is responsible for recognizing the branch point site (BPS) sequence in introns and is critical for pre-mRNA splicing. In Arabidopsis (Arabidopsis thaliana), splicing factor1 (AtSF1) has been shown to retain the conserved function, but it is unexpected that null atsf1 mutants are viable. Here, we identified an allele of atsf1, named suppressor of thf1-4 (sot4), from suppressor screening for leaf variegation of thylakoid formation1 The sot4 mutant resulting from the G-to-R mutation at the highly conserved 198th amino acid residue within the functionally unknown domain exhibits leaf virescence associated with less accumulation of mature plastid ribosomal RNA, particularly under cold stress. Interestingly, the same point mutation in yeast Saccharomyces cerevisiae MUD synthetic-lethal 5p (SF1/Msl5p) also causes hypersensitivity to coldness and a low splicing activity for the introns with suboptimal BPS sequences. Transcriptomic profiling and reverse-transcription quantitative PCR analyses showed that expression of many genes were up- or downregulated in atsf1 via insufficient intron splicing. Our search for a BPS consensus from the retained introns in atsf1 transcriptomes, combined with RNA electrophoresis mobility shift assays, revealed that AtSF1 directly binds to the BPS consensus containing 5'-CU(U/A)AU-3'. Taken together, our data provide insight into a role for AtSF1 in regulating intron splicing efficiency, which helps plants acclimate to coldness.
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Affiliation(s)
- Yajuan Zhu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjuan Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Jingli Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoning Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoyu Ma
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yong-Zhen Xu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weihua Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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Pacheco TG, Lopes ADS, Welter JF, Yotoko KSC, Otoni WC, Vieira LDN, Guerra MP, Nodari RO, Balsanelli E, Pedrosa FDO, de Souza EM, Rogalski M. Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features. PLANT MOLECULAR BIOLOGY 2020; 104:21-37. [PMID: 32533420 DOI: 10.1007/s11103-020-01020-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Fátima Welter
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Karla Suemy Clemente Yotoko
- Laboratório de Bioinformática e Evolução, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais, Departamento de Biologia Vegetal, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Dong X, Duan S, Wang H, Jin H. Plastid ribosomal protein LPE2 is involved in photosynthesis and the response to C/N balance in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1418-1432. [PMID: 31944575 PMCID: PMC7540278 DOI: 10.1111/jipb.12907] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 01/09/2020] [Indexed: 05/31/2023]
Abstract
The balance between cellular carbon (C) and nitrogen (N) must be tightly coordinated to sustain optimal growth and development in plants. In chloroplasts, photosynthesis converts inorganic C to organic C, which is important for maintenance of C content in plant cells. However, little is known about the role of chloroplasts in C/N balance. Here, we identified a nuclear-encoded protein LOW PHOTOSYNTHETIC EFFICIENCY2 (LPE2) that it is required for photosynthesis and C/N balance in Arabidopsis. LPE2 is specifically localized in the chloroplast. Both loss-of-function mutants, lpe2-1 and lpe2-2, showed lower photosynthetic activity, characterized by slower electron transport and lower PSII quantum yield than the wild type. Notably, LPE2 is predicted to encode the plastid ribosomal protein S21 (RPS21). Deficiency of LPE2 significantly perturbed the thylakoid membrane composition and plastid protein accumulation, although the transcription of plastid genes is not affected obviously. More interestingly, transcriptome analysis indicated that the loss of LPE2 altered the expression of C and N response related genes in nucleus, which is confirmed by quantitative real-time-polymerase chain reaction. Moreover, deficiency of LPE2 suppressed the response of C/N balance in physiological level. Taken together, our findings suggest that LPE2 plays dual roles in photosynthesis and the response to C/N balance.
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Affiliation(s)
- Xiaoxiao Dong
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
| | - Sujuan Duan
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
- School of Pharmaceutical SciencesGuangzhou University of Chinese MedicineGuangzhou510006China
| | - Hong‐Bin Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
| | - Hong‐Lei Jin
- School of Pharmaceutical SciencesGuangzhou University of Chinese MedicineGuangzhou510006China
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The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress. Int J Mol Sci 2020; 21:ijms21176082. [PMID: 32846932 PMCID: PMC7503970 DOI: 10.3390/ijms21176082] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes and gene-expression machinery. Most genes from the prokaryotic ancestors of chloroplasts were transferred into the nucleus over the course of evolution. However, the importance of chloroplast gene expression in environmental stress responses have recently become more apparent. Here, we discuss the emerging roles of the distinct chloroplast gene expression processes in plant responses to environmental stresses. For example, the transcription and translation of psbA play an important role in high-light stress responses. A better understanding of the connection between chloroplast gene expression and environmental stress responses is crucial for breeding stress-tolerant crops better able to cope with the rapidly changing environment.
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Prakash C, Pandey M, Talwar S, Singh Y, Kanojiya S, Pandey AK, Kumar N. Extra-ribosomal functions of Mtb RpsB in imparting stress resilience and drug tolerance to mycobacteria. Biochimie 2020; 177:87-97. [PMID: 32828823 DOI: 10.1016/j.biochi.2020.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/31/2020] [Accepted: 08/09/2020] [Indexed: 01/21/2023]
Abstract
Emerging observations suggest that ribosomal proteins (RPs) play important extra-ribosomal roles in maintenance of cellular homeostasis. However, the mechanistic insights into these processes have not been extensively explored, especially in pathogenic bacteria. Here, we present our findings on potential extra-ribosomal functions of Mycobacterium tuberculosis (Mtb) RPs. We observed that Mtb RpsB and RpsQ are differentially localized to cell wall fraction in M. tuberculosis (H37Rv), while their M. smegmatis (Msm) homologs are primarily cytosolic. Cellular fractionation of ectopically expressed Mtb RPs in surrogate host (M. smegmatis) also shows their association with cell membrane/cell wall without any gross changes in cell morphology. M. smegmatis expressing Mtb RpsB exhibited altered redox homeostasis, decreased drug-induced ROS, reduced cell wall permeability and increased tolerance to various proteotoxic stress (oxidative stress, SDS and starvation). Mtb RpsB expression was also associated with increased resistance specifically towards Isoniazid, Ethionamide and Streptomycin. The enhanced drug tolerance was specific to Mtb RpsB and not observed upon ectopic expression of M. smegmatis homolog (Msm RpsB). Interestingly, C-terminus deletion in Mtb RpsB affected its localization and reversed the stress-resilient phenotypes. We also observed that M. tuberculosis (H37Rv) with upregulated RpsB levels had higher intracellular survival in macrophage. All these observations hint towards existence of moonlighting roles of Mtb RpsB in imparting stress resilience to mycobacteria. This work open avenues for further exploration of alternative pathways associated with fitness and drug tolerance in mycobacteria.
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Affiliation(s)
- Chetan Prakash
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Manitosh Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India; Department of Life Sciences, ITM University, Gwalior 475001, Madhya Pradesh, India
| | - Sakshi Talwar
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Yatendra Singh
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Sanjeev Kanojiya
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Amit Kumar Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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Zhang X, Sun Y, Landis JB, Lv Z, Shen J, Zhang H, Lin N, Li L, Sun J, Deng T, Sun H, Wang H. Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes. BMC PLANT BIOLOGY 2020; 20:340. [PMID: 32680458 PMCID: PMC7368685 DOI: 10.1186/s12870-020-02518-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied. RESULTS We sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one (atpB) of the three widely used plastid markers (rbcL, atpB and matK) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal protein (RPL and RPS) genes and the RNA polymerase (RPO) genes have higher substitution rates and genetic variations among plastid genes in Gentianeae. Our study revealed that just one (matK) of the three (matK, ndhB and rbcL) widely used markers show high phylogenetic informativeness (PI) value. Due to the high PI and lowest gene-tree discordance, rpoC2 is advocated as a promising plastid DNA barcode for taxonomic studies of Gentianeae. Furthermore, our analyses revealed a positive correlation of evolutionary rates with genetic variation of plastid genes, but a negative correlation with gene-tree discordance under purifying selection. CONCLUSIONS Overall, our results demonstrate the heterogeneity of nucleotide substitution rates and genetic characteristics among plastid genes providing new insights into plastome evolution, while highlighting the necessity of considering gene-tree discordance into phylogenomic studies based on plastome-scale data.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92507, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
| | - Zhenyu Lv
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jun Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiao Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Mattila H, Mishra KB, Kuusisto I, Mishra A, Novotná K, Šebela D, Tyystjärvi E. Effects of low temperature on photoinhibition and singlet oxygen production in four natural accessions of Arabidopsis. PLANTA 2020; 252:19. [PMID: 32671474 PMCID: PMC7363673 DOI: 10.1007/s00425-020-03423-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/08/2020] [Indexed: 05/27/2023]
Abstract
Low temperature decreases PSII damage in vivo, confirming earlier in vitro results. Susceptibility to photoinhibition differs among Arabidopsis accessions and moderately decreases after 2-week cold-treatment. Flavonols may alleviate photoinhibition. The rate of light-induced inactivation of photosystem II (PSII) at 22 and 4 °C was measured from natural accessions of Arabidopsis thaliana (Rschew, Tenela, Columbia-0, Coimbra) grown under optimal conditions (21 °C), and at 4 °C from plants shifted to 4 °C for 2 weeks. Measurements were done in the absence and presence of lincomycin (to block repair). PSII activity was assayed with the chlorophyll a fluorescence parameter Fv/Fm and with light-saturated rate of oxygen evolution using a quinone acceptor. When grown at 21 °C, Rschew was the most tolerant to photoinhibition and Coimbra the least. Damage to PSII, judged from fitting the decrease in oxygen evolution or Fv/Fm to a first-order equation, proceeded more slowly or equally at 4 than at 22 °C. The 2-week cold-treatment decreased photoinhibition at 4 °C consistently in Columbia-0 and Coimbra, whereas in Rschew and Tenela the results depended on the method used to assay photoinhibition. The rate of singlet oxygen production by isolated thylakoid membranes, measured with histidine, stayed the same or slightly decreased with decreasing temperature. On the other hand, measurements of singlet oxygen from leaves with Singlet Oxygen Sensor Green suggest that in vivo more singlet oxygen is produced at 4 °C. Under high light, the PSII electron acceptor QA was more reduced at 4 than at 22 °C. Singlet oxygen production, in vitro or in vivo, did not decrease due to the cold-treatment. Epidermal flavonols increased during the cold-treatment and, in Columbia-0 and Coimbra, the amount correlated with photoinhibition tolerance.
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Affiliation(s)
- Heta Mattila
- Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014, Turku, Finland
| | - Kumud B Mishra
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986, 4a, Brno, 603 00, Czech Republic
| | - Iiris Kuusisto
- Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014, Turku, Finland
| | - Anamika Mishra
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986, 4a, Brno, 603 00, Czech Republic
| | - Kateřina Novotná
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986, 4a, Brno, 603 00, Czech Republic
| | - David Šebela
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986, 4a, Brno, 603 00, Czech Republic
| | - Esa Tyystjärvi
- Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014, Turku, Finland.
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Gomes Pacheco T, Morais da Silva G, de Santana Lopes A, de Oliveira JD, Rogalski JM, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae). PLANTA 2020; 252:17. [PMID: 32666132 DOI: 10.1007/s00425-020-03427-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Complete plastome sequence of Tropaeolum pentaphyllum revealed molecular markers, hotspots of nucleotide polymorphism, RNA editing sites and phylogenetic aspects Tropaeolaceae Juss. ex DC. comprises approximately 95 species across North and South Americas. Tropaeolum pentaphyllum Lam. is an unconventional and endangered species with occurrence in some countries of South America. Although this species presents nutritional, medicinal and ornamental uses, genetic studies involving natural populations or promising genotypes are practically non-existent. Here, we report the nucleotide sequence of T. pentaphyllum plastome. It represents the first complete plastome sequence of the family Tropaeolaceae to be fully sequenced and analyzed in detail. The sequencing data revealed that the T. pentaphyllum plastome is highly similar to the plastomes of other Brassicales. Notwithstanding, our analyses detected some specific features concerning events of IR expansion and structural changes in some genes such as matK, rpoA, and rpoC2. We also detected 251 SSR loci, nine hotspots of nucleotide polymorphism, and two specific RNA editing sites in the plastome of T. pentaphyllum. Moreover, plastid phylogenomic inference indicated a closed relationship between the families Tropaeolaceae and Akaniaceae, which formed a sister group to Moringaceae-Caricaceae. Finally, our data bring new molecular markers and evolutionary features to be applied in the natural population, germplasm collection, and genotype selection aiming conservation, genetic diversity evaluation, and exploitation of this endangered species.
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Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José Daniel de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Marcia Rogalski
- Núcleo de Ciências Biológicas e Ambientais, Instituto Federal do Rio Grande do Sul, Distrito Engenheiro Luiz Englert, Sertão, RS, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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