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Qu G, Bao Y, Liao Y, Liu C, Zi H, Bai M, Liu Y, Tu D, Wang L, Chen S, Zhou G, Can M. Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes. Sci Rep 2022; 12:4970. [PMID: 35322069 PMCID: PMC8943043 DOI: 10.1038/s41598-022-08783-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/08/2022] [Indexed: 01/27/2023] Open
Abstract
Kobresia plants are important forage resources on the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants on the Qinghai-Tibetan Plateau. Previously, we have assembled the genome of Carex littledalei (Kobresia littledalei), which is a diploid with 29 chromosomes. In this study, we assembled genomes of Carex parvula (Kobresia pygmaea) and Carex kokanica (Kobresia royleana) via using Illumina and PacBio sequencing data, which were about 783.49 Mb and 673.40 Mb in size, respectively. And 45,002 or 36,709 protein-coding genes were further annotated in the genome of C. parvula or C. kokanica. Phylogenetic analysis indicated that Kobresia in Cyperaceae separated from Poaceae about 101.5 million years ago after separated from Ananas comosus in Bromeliaceae about 117.2 million years ago. C. littledalei and C. parvula separated about 5.0 million years ago, after separated from C. kokanica about 6.2 million years ago. In this study, transcriptome data of C. parvula at three different altitudes were also measured and analyzed. Kobresia plants genomes assembly and transcriptome analysis will assist research into mechanisms of plant adaptation to environments with high altitude and cold weather.
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Affiliation(s)
- Guangpeng Qu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China
| | - Yuhong Bao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China
| | - Yangci Liao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China
| | - Can Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, Beijing, China
| | - Magaweng Bai
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China
| | - Yunfei Liu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China
| | - Dengqunpei Tu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China
| | - Li Wang
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Shaofeng Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China
| | - Gang Zhou
- Novogene Bioinformatics Institute, Beijing, China.
| | - Muyou Can
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000, China.
- Institute of Grassland Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850000, China.
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Liang Y, Gong Z, Wang J, Zheng J, Ma Y, Min L, Chen Q, Li Z, Qu Y, Chen Q, Li X. Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.). PLANTS 2021; 10:plants10112517. [PMID: 34834881 PMCID: PMC8618236 DOI: 10.3390/plants10112517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022]
Abstract
Extreme high temperatures are threatening cotton production around the world due to the intensification of global warming. To cope with high-temperature stress, heat-tolerant cotton cultivars have been bred, but the heat-tolerant mechanism remains unclear. This study selected heat-tolerant (‘Xinluzao36′) and heat-sensitive (‘Che61-72′) cultivars of cotton treated with high-temperature stress as plant materials and performed comparative nanopore sequencing transcriptome analysis to reveal the potential heat-tolerant mechanism of cotton. Results showed that 120,605 nonredundant sequences were generated from the raw reads, and 78,601 genes were annotated. Differentially expressed gene (DEG) analysis showed that a total of 19,600 DEGs were screened; the DEGs involved in the ribosome, heat shock proteins, auxin and ethylene signaling transduction, and photosynthesis pathways may be attributed to the heat tolerance of the heat-tolerant cotton cultivar. This study also predicted a total of 5118 long non-coding RNAs (lncRNAs)and 24,462 corresponding target genes. Analysis of the target genes revealed that the expression of some ribosomal, heat shock, auxin and ethylene signaling transduction-related and photosynthetic proteins may be regulated by lncRNAs and further participate in the heat tolerance of cotton. This study deepens our understandings of the heat tolerance of cotton.
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Affiliation(s)
- Yajun Liang
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Zhaolong Gong
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Junduo Wang
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Juyun Zheng
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.M.); (L.M.)
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.M.); (L.M.)
| | - Qin Chen
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi 830022, China;
| | - Yanying Qu
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
| | - Quanjia Chen
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830001, China; (Y.L.); (Q.C.); (Y.Q.)
- Correspondence: (Q.C.); (X.L.)
| | - Xueyuan Li
- Xinjiang Academy of Agricultural Science, Urumqi 830001, China; (Z.G.); (J.W.); (J.Z.)
- Correspondence: (Q.C.); (X.L.)
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Essemine J, Qu M, Lyu MJA, Song Q, Khan N, Chen G, Wang P, Zhu XG. Photosynthetic and transcriptomic responses of two C 4 grass species with different NaCl tolerance. JOURNAL OF PLANT PHYSIOLOGY 2020; 253:153244. [PMID: 32818766 DOI: 10.1016/j.jplph.2020.153244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 05/15/2023]
Abstract
This report reveals the effects of salt on the photosynthetic electron transport and transcriptome of the glycophyte Setaria viridis (S. viridis) and its salt-tolerant close relative halophyte Spartina alterniflora (S. alterniflora). S. viridis was unable to survive exposed to sodium chloride (NaCl) levels higher than 100 mM, in contrast, S. alterniflora could tolerate NaCl up to 550 mM, with negligible effect on gas exchange related parameters and conductance of electrons transport chain (gETC). Under salt, the prompt fluorescence (OJIP-curves) exhibits an increase in the O- and J-steps in S. viridis and much less for S. alterniflora. Flowing NaCl stress, a dramatic decline in the photosystem II (PSII) primary photochemistry was observed for S. viridis, as reflected by the drastic drop in Fv/Fm, Fv/Fo and ΦPSII; however, no substantial change was recorded for these parameters in S. alterniflora. Interestingly, we found an increase in the primary PSII photochemistry (ΦPSII) for S. alterniflora with increasing either NaCl concentration or NaCl treatment duration. The NPQ magnitude was strongly enhanced for S. viridis even at a low NaCl (50 mM); however, it remains unchangeable or slightly increased for S. alterniflora at NaCl levels above 400 mM. After NaCl treatment, we found an increase in both the proportion of oxidized P700 and the amount of active P700 in S. viridis and almost no change for S. alterniflora. Under salt, the net photosynthetic rate (A) and stomatal conductance (gs) measurements demonstrate that A decreases earlier in S. viridis, even after one week exposure to only 50 mM NaCl; in contrast, in S. alterniflora, the effect of NaCl on A and gs was minor even after exposure for two weeks to high NaCl levels. For S. viridis exposed to 50 mM NaCl for 12 d, carbon dioxide (CO2) at a concentration of 2000 μL L-1 could not fully restore A to the control (Ctrl) level. Conversely, in S. alterniflora, high CO2 can fully restore A for all NaCl treatments except at 550 mM. RNA-seq data shows a major impact of NaCl on metabolic pathways in S. viridis and we found a number of transcription factors potentially related to NaCl responses. For S. alterniflora, no major changes in the transcriptomic levels were recorded under NaCl stress. To confirm our data analysis of RNA-seq, we performed quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis for randomly selected four genes for each species (8 genes in total) and we found that our results (up- and/or down-regulated genes) are fully consistent and match well our RNA-seq data. Overall, this study showed drastically different photosynthetic and transcriptomic responses of a salt-tolerant C4 grass species and one salt-sensitive C4 grass species to NaCl stress, which suggests that S. alterniflora could be used as a promising model species to study salt tolerance in C4 or monocot species.
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Affiliation(s)
- Jemaa Essemine
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Mingnan Qu
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Qingfeng Song
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Naveed Khan
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Peng Wang
- CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
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Essemine J, Lyu MJA, Qu M, Perveen S, Khan N, Song Q, Chen G, Zhu XG. Contrasting Responses of Plastid Terminal Oxidase Activity Under Salt Stress in Two C 4 Species With Different Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:1009. [PMID: 32733515 PMCID: PMC7359412 DOI: 10.3389/fpls.2020.01009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/19/2020] [Indexed: 05/07/2023]
Abstract
The present study reveals contrasting responses of photosynthesis to salt stress in two C4 species: a glycophyte Setaria viridis (SV) and a halophyte Spartina alterniflora (SA). Specifically, the effect of short-term salt stress treatment on the photosynthetic CO2 uptake and electron transport were investigated in SV and its salt-tolerant close relative SA. In this experiment, at the beginning, plants were grown in soil then were exposed to salt stress under hydroponic conditions for two weeks. SV demonstrated a much higher susceptibility to salt stress than SA; while, SV was incapable to survive subjected to about 100 mM, SA can tolerate salt concentrations up to 550 mM with slight effect on photosynthetic CO2 uptake rates and electrons transport chain conductance (gETC ). Regardless the oxygen concentration used, our results show an enhancement in the P700 oxidation with increasing O2 concentration for SV following NaCl treatment and almost no change for SA. We also observed an activation of the cyclic NDH-dependent pathway in SV by about 2.36 times upon exposure to 50 mM NaCl for 12 days (d); however, its activity in SA drops by about 25% compared to the control without salt treatment. Using PTOX inhibitor (n-PG) and that of the Qo-binding site of Cytb6/f (DBMIB), at two O2 levels (2 and 21%), to restrict electrons flow towards PSI, we successfully revealed the presence of a possible PTOX activity under salt stress for SA but not for SV. However, by q-PCR and western-blot analysis, we showed an increase in PTOX amount by about 3-4 times for SA under salt stress but not or very less for SV. Overall, this study provides strong proof for the existence of PTOX as an alternative electron pathway in C4 species (SA), which might play more than a photoprotective role under salt stress.
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Mellor SB, Vinde MH, Nielsen AZ, Hanke GT, Abdiaziz K, Roessler MM, Burow M, Motawia MS, Møller BL, Jensen PE. Defining optimal electron transfer partners for light-driven cytochrome P450 reactions. Metab Eng 2019; 55:33-43. [PMID: 31091467 DOI: 10.1016/j.ymben.2019.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 12/16/2022]
Abstract
Plants and cyanobacteria are promising heterologous hosts for metabolic engineering, and particularly suited for expression of cytochrome P450 (P450s), enzymes that catalyse key steps in biosynthetic pathways leading to valuable natural products such as alkaloids, terpenoids and phenylpropanoids. P450s are often difficult to express and require a membrane-bound NADPH-dependent reductase, complicating their use in metabolic engineering and bio-production. We previously demonstrated targeting of heterologous P450s to thylakoid membranes both in N. benthamiana chloroplasts and cyanobacteria, and functional substitution of their native reductases with the photosynthetic apparatus via the endogenous soluble electron carrier ferredoxin. However, because ferredoxin acts as a sorting hub for photosynthetic reducing power, there is fierce competition for reducing equivalents, which limits photosynthesis-driven P450 output. This study compares the ability of four electron carriers to increase photosynthesis-driven P450 activity. These carriers, three plant ferredoxins and a flavodoxin-like engineered protein derived from cytochrome P450 reductase, show only modest differences in their electron transfer to our model P450, CYP79A1 in vitro. However, only the flavodoxin-like carrier supplies appreciable reducing power in the presence of competition for reduced ferredoxin, because it possesses a redox potential that renders delivery of reducing equivalents to endogenous processes inefficient. We further investigate the efficacy of these electron carrier proteins in vivo by expressing them transiently in N. benthamiana fused to CYP79A1. All but one of the fusion enzymes show improved sequestration of photosynthetic reducing power. Fusion with the flavodoxin-like carrier offers the greatest improvement in this comparison - nearly 25-fold on a per protein basis. Thus, this study demonstrates that synthetic electron transfer pathways with optimal redox potentials can alleviate the problem of endogenous competition for reduced ferredoxin and sets out a new metabolic engineering strategy useful for producing valuable natural products.
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Affiliation(s)
- Silas Busck Mellor
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Marcos Hamborg Vinde
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Agnieszka Zygadlo Nielsen
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Guy Thomas Hanke
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Kaltum Abdiaziz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Meike Burow
- DyNaMo Center of Excellence, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Villum Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Villum Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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Tamary E, Nevo R, Naveh L, Levin‐Zaidman S, Kiss V, Savidor A, Levin Y, Eyal Y, Reich Z, Adam Z. Chlorophyll catabolism precedes changes in chloroplast structure and proteome during leaf senescence. PLANT DIRECT 2019; 3:e00127. [PMID: 31245770 PMCID: PMC6508775 DOI: 10.1002/pld3.127] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 05/18/2023]
Abstract
The earliest visual changes of leaf senescence occur in the chloroplast as chlorophyll is degraded and photosynthesis declines. Yet, a comprehensive understanding of the sequence of catabolic events occurring in chloroplasts during natural leaf senescence is still missing. Here, we combined confocal and electron microscopy together with proteomics and biochemistry to follow structural and molecular changes during Arabidopsis leaf senescence. We observed that initiation of chlorophyll catabolism precedes other breakdown processes. Chloroplast size, stacking of thylakoids, and efficiency of PSII remain stable until late stages of senescence, whereas the number and size of plastoglobules increase. Unlike catabolic enzymes, whose level increase, the level of most proteins decreases during senescence, and chloroplast proteins are overrepresented among these. However, the rate of their disappearance is variable, mostly uncoordinated and independent of their inherent stability during earlier developmental stages. Unexpectedly, degradation of chlorophyll-binding proteins lags behind chlorophyll catabolism. Autophagy and vacuole proteins are retained at relatively high levels, highlighting the role of extra-plastidic degradation processes especially in late stages of senescence. The observation that chlorophyll catabolism precedes all other catabolic events may suggest that this process enables or signals further catabolic processes in chloroplasts.
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Affiliation(s)
- Eyal Tamary
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew UniversityRehovotIsrael
| | - Reinat Nevo
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Leah Naveh
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew UniversityRehovotIsrael
| | - Smadar Levin‐Zaidman
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Vladimir Kiss
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Alon Savidor
- de Botton Institute for Protein ProfilingThe Nancy and Stephen Grand Israel National Center for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Yishai Levin
- de Botton Institute for Protein ProfilingThe Nancy and Stephen Grand Israel National Center for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Yoram Eyal
- Institute of Plant SciencesThe Volcani Center ARORishon LeZionIsrael
| | - Ziv Reich
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Zach Adam
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew UniversityRehovotIsrael
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Scheiber IF, Pilátová J, Malych R, Kotabova E, Krijt M, Vyoral D, Mach J, Léger T, Camadro JM, Prášil O, Lesuisse E, Sutak R. Copper and iron metabolism in Ostreococcus tauri – the role of phytotransferrin, plastocyanin and a chloroplast copper-transporting ATPase. Metallomics 2019; 11:1657-1666. [DOI: 10.1039/c9mt00078j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have identified Ostreococcus tauri major iron uptake mediating protein, phytotransferrin (Ot-FEA1), whose expression and binding of iron is copper dependent.
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Kölsch A, Hejazi M, Stieger KR, Feifel SC, Kern JF, Müh F, Lisdat F, Lokstein H, Zouni A. Insights into the binding behavior of native and non-native cytochromes to photosystem I from Thermosynechococcus elongatus. J Biol Chem 2018; 293:9090-9100. [PMID: 29695502 DOI: 10.1074/jbc.ra117.000953] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/18/2018] [Indexed: 01/09/2023] Open
Abstract
The binding of photosystem I (PS I) from Thermosynechococcus elongatus to the native cytochrome (cyt) c6 and cyt c from horse heart (cyt cHH) was analyzed by oxygen consumption measurements, isothermal titration calorimetry (ITC), and rigid body docking combined with electrostatic computations of binding energies. Although PS I has a higher affinity for cyt cHH than for cyt c6, the influence of ionic strength and pH on binding is different in the two cases. ITC and theoretical computations revealed the existence of unspecific binding sites for cyt cHH besides one specific binding site close to P700 Binding to PS I was found to be the same for reduced and oxidized cyt cHH Based on this information, suitable conditions for cocrystallization of cyt cHH with PS I were found, resulting in crystals with a PS I:cyt cHH ratio of 1:1. A crystal structure at 3.4-Å resolution was obtained, but cyt cHH cannot be identified in the electron density map because of unspecific binding sites and/or high flexibility at the specific binding site. Modeling the binding of cyt c6 to PS I revealed a specific binding site where the distance and orientation of cyt c6 relative to P700 are comparable with cyt c2 from purple bacteria relative to P870 This work provides new insights into the binding modes of different cytochromes to PS I, thus facilitating steps toward solving the PS I-cyt c costructure and a more detailed understanding of natural electron transport processes.
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Affiliation(s)
- Adrian Kölsch
- From the Biophysics of Photosynthesis, Institute for Biology, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115 Berlin, Germany,
| | - Mahdi Hejazi
- From the Biophysics of Photosynthesis, Institute for Biology, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115 Berlin, Germany
| | - Kai R Stieger
- Biosystems Technology, Institute for Applied Life Sciences, University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Sven C Feifel
- Biosystems Technology, Institute for Applied Life Sciences, University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Jan F Kern
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Frank Müh
- Department of Theoretical Biophysics, Institute for Theoretical Physics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria, and
| | - Fred Lisdat
- Biosystems Technology, Institute for Applied Life Sciences, University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, CZ-121 16 Praha 2, Czech Republic
| | - Athina Zouni
- From the Biophysics of Photosynthesis, Institute for Biology, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115 Berlin, Germany,
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9
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Wan Y, Tang K, Zhang D, Xie S, Zhu X, Wang Z, Lang Z. Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana. Genome Biol 2015; 16:272. [PMID: 26667818 PMCID: PMC4714525 DOI: 10.1186/s13059-015-0839-2] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 11/18/2015] [Indexed: 12/25/2022] Open
Abstract
Background m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, differential m6A patterns between organs have not been well characterized. Results Over two-third of the transcripts in Arabidopsis are modified by m6A. In contrast to a recent observation of m6A enrichment in 5′ mRNA, we find that m6A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m6A methylation extent compared to their transcript level. The 290 highly methylated transcripts are mainly associated with transporters, stress responses, redox, regulation factors, and some non-coding RNAs. On average, the proportion of transcripts showing differential methylation between two plant organs is higher than that showing differential transcript levels. The transcripts with extensively higher m6A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m6A may be another important contributor to organ differentiation in Arabidopsis. Highly expressed genes are relatively less methylated and vice versa, and different RNAs have distinct m6A patterns, which hint at mRNA fate. Intriguingly, most of the transposable element transcripts maintained a fragmented form with a relatively low transcript level and high m6A methylation in the cells. Conclusions This is the first study to comprehensively analyze m6A patterns in a variety of RNAs, the relationship between transcript level and m6A methylation extent, and differential m6A patterns across organs in Arabidopsis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0839-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yizhen Wan
- State Key Lab Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. .,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Dayong Zhang
- Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shaojun Xie
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaohong Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zegang Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Zhaobo Lang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA. .,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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Fristedt R, Williams-Carrier R, Merchant SS, Barkan A. A thylakoid membrane protein harboring a DnaJ-type zinc finger domain is required for photosystem I accumulation in plants. J Biol Chem 2014; 289:30657-30667. [PMID: 25228689 DOI: 10.1074/jbc.m114.587758] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Photosystem I (PSI) is a large pigment-protein complex and one of the two photosystems that drive electron transfer in oxygenic photosynthesis. We identified a nuclear gene required specifically for the accumulation of PSI in a forward genetic analysis of chloroplast biogenesis in maize. This gene, designated psa2, belongs to the "GreenCut" gene set, a group of genes found in green algae and plants but not in non-photosynthetic organisms. Disruption of the psa2 ortholog in Arabidopsis likewise resulted in the specific loss of PSI proteins. PSA2 harbors a conserved domain found in DnaJ chaperones where it has been shown to form a zinc finger and to have protein-disulfide isomerase activity. Accordingly, PSA2 exhibited protein-disulfide reductase activity in vitro. PSA2 localized to the thylakoid lumen and was found in a ∼250-kDa complex harboring the peripheral PSI protein PsaG but lacking several core PSI subunits. PSA2 mRNA is coexpressed with mRNAs encoding various proteins involved in the biogenesis of the photosynthetic apparatus with peak expression preceding that of genes encoding structural components. PSA2 protein abundance was not decreased in the absence of PSI but was reduced in the absence of the PSI assembly factor Ycf3. These findings suggest that a complex harboring PSA2 and PsaG mediates thiol transactions in the thylakoid lumen that are important for the assembly of PSI.
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Affiliation(s)
- Rikard Fristedt
- Department of Chemistry and Biochemistry and UCLA, Los Angeles, California 90095; Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | | | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and UCLA, Los Angeles, California 90095; Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403.
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Jensen PE, Bassi R, Boekema EJ, Dekker JP, Jansson S, Leister D, Robinson C, Scheller HV. Structure, function and regulation of plant photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:335-52. [PMID: 17442259 DOI: 10.1016/j.bbabio.2007.03.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 03/03/2007] [Accepted: 03/06/2007] [Indexed: 12/20/2022]
Abstract
Photosystem I (PSI) is a multisubunit protein complex located in the thylakoid membranes of green plants and algae, where it initiates one of the first steps of solar energy conversion by light-driven electron transport. In this review, we discuss recent progress on several topics related to the functioning of the PSI complex, like the protein composition of the complex in the plant Arabidopsis thaliana, the function of these subunits and the mechanism by which nuclear-encoded subunits can be inserted into or transported through the thylakoid membrane. Furthermore, the structure of the native PSI complex in several oxygenic photosynthetic organisms and the role of the chlorophylls and carotenoids in the antenna complexes in light harvesting and photoprotection are reviewed. The special role of the 'red' chlorophylls (chlorophyll molecules that absorb at longer wavelength than the primary electron donor P700) is assessed. The physiology and mechanism of the association of the major light-harvesting complex of photosystem II (LHCII) with PSI during short term adaptation to changes in light quality and quantity is discussed in functional and structural terms. The mechanism of excitation energy transfer between the chlorophylls and the mechanism of primary charge separation is outlined and discussed. Finally, a number of regulatory processes like acclimatory responses and retrograde signalling is reviewed with respect to function of the thylakoid membrane. We finish this review by shortly discussing the perspectives for future research on PSI.
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Affiliation(s)
- Poul Erik Jensen
- Plant Biochemistry Laboratory, Department of Plant Biology, Faculty of Life Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.
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Hansson A, Amann K, Zygadlo A, Meurer J, Scheller HV, Jensen PE. Knock-out of the chloroplast-encoded PSI-J subunit of photosystem I in Nicotiana tabacum. FEBS J 2007; 274:1734-46. [PMID: 17331187 DOI: 10.1111/j.1742-4658.2007.05722.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The plastid-encoded psaJ gene encodes a hydrophobic low-molecular-mass subunit of photosystem I (PSI) containing one transmembrane helix. Homoplastomic transformants with an inactivated psaJ gene were devoid of PSI-J protein. The mutant plants were slightly smaller and paler than wild-type because of a 13% reduction in chlorophyll content per leaf area caused by an approximately 20% reduction in PSI. The amount of the peripheral antenna proteins, Lhca2 and Lhca3, was decreased to the same level as the core subunits, but Lhca1 and Lhca4 were present in relative excess. The functional size of the PSI antenna was not affected, suggesting that PSI-J is not involved in binding of light-harvesting complex I. The specific PSI activity, measured as NADP(+) photoreduction in vitro, revealed a 55% reduction in electron transport through PSI in the mutant. No significant difference in the second-order rate constant for electron transfer from reduced plastocyanin to oxidized P700 was observed in the absence of PSI-J. Instead, a large fraction of PSI was found to be inactive. Immunoblotting analysis revealed a secondary loss of the luminal PSI-N subunit in PSI particles devoid of PSI-J. Presumably PSI-J affects the conformation of PSI-F, which in turn affects the binding of PSI-N. This together renders a fraction of the PSI particles inactive. Thus, PSI-J is an important subunit that, together with PSI-F and PSI-N, is required for formation of the plastocyanin-binding domain of PSI. PSI-J is furthermore important for stability or assembly of the PSI complex.
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Affiliation(s)
- Andreas Hansson
- Plant Biochemistry Laboratory, Department of Plant Biology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg, Denmark
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Dühring U, Ossenbühl F, Wilde A. Late assembly steps and dynamics of the cyanobacterial photosystem I. J Biol Chem 2007; 282:10915-21. [PMID: 17303568 DOI: 10.1074/jbc.m609206200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The dynamics of photosystem I assembly in cyanobacteria have been addressed using in vivo pulse-chase labeling of Synechocystis sp. PCC 6803 proteins in combination with blue native polyacrylamide gel electrophoresis. The analyses indicate the existence of three different monomeric photosystem I complexes and also the high stability of photosystem I trimers. We show that in addition to a complete photosystem I monomer, containing all 11 subunits, we detected a PsaK-less monomer and a short-lived PsaL/PsaK-less complex. The latter two monomers were missing in the ycf37 mutant of Synechocystis sp. PCC 6803 that accumulates also less trimers. Pulse-chase experiments suggest that the three monomeric complexes have different functions in the biogenesis of the trimer. Based on these findings we propose a model where PsaK is incorporated in the latest step of photosystem I assembly. The PsaK-less photosystem I monomer may represent an intermediate complex that is important for the exchange of the two PsaK variants during high light acclimation. Implications of the presented data with respect to Ycf37 function are discussed.
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Affiliation(s)
- Ulf Dühring
- Institute of Biology, Humboldt University Berlin, 10115 Berlin, Germany
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Zygadlo A, Robinson C, Scheller HV, Mant A, Jensen PE. The properties of the positively charged loop region in PSI-G are essential for its "spontaneous" insertion into thylakoids and rapid assembly into the photosystem I complex. J Biol Chem 2006; 281:10548-54. [PMID: 16478728 DOI: 10.1074/jbc.m512687200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PSI-G subunit of photosystem I (PSI) is an 11-kDa membrane protein that plays an important role in electron transport between plastocyanin and PSI and is involved in the stability of the PSI complex. Within the complex, the PSI-G subunit is bound to PSI-B and is in contact with Lhca1. PSI-G has two transmembrane spans connected by a positively charged stromal loop. The loop is inaccessible to proteases, indicating a tightly bound location within the PSI complex. Here, we have studied the insertion mechanism and assembly of PSI-G. We show that the protein inserts into thylakoids by a direct or "spontaneous" pathway that does not involve the activities of any known chloroplast protein-targeting machinery. Surprisingly, the positively charged stromal loop region plays a major role in this process. Mutagenesis or deletions within this region almost invariably lead to a marked lowering of insertion efficiency, strongly indicating a critical role for the loop in the organization of the transmembrane regions prior to or during membrane insertion. Finally, we have examined the assembly of newly inserted PSI-G into the PSI complex, since very little is known of the assembly pathway for this large multimeric complex. Interestingly, we find that inserted PSI-G can be found within the full PSI complex within the import assay time frame after insertion into thylakoids, strongly suggesting that PSI-G normally associates at the end of the assembly process. This is consistent with its location on the periphery of the complex.
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Affiliation(s)
- Agnieszka Zygadlo
- Plant Biochemistry Laboratory, Department of Plant Biology, The Royal Veterinary and Agricultural University, 1870 Frederiksberg, Denmark
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Khrouchtchova A, Hansson M, Paakkarinen V, Vainonen JP, Zhang S, Jensen PE, Scheller HV, Vener AV, Aro EM, Haldrup A. A previously found thylakoid membrane protein of 14 kDa (TMP14) is a novel subunit of plant photosystem I and is designated PSI-P. FEBS Lett 2005; 579:4808-12. [PMID: 16109415 DOI: 10.1016/j.febslet.2005.07.061] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 07/22/2005] [Accepted: 07/25/2005] [Indexed: 11/17/2022]
Abstract
We show that the thylakoid membrane phosphoprotein TMP14 is a novel subunit of plant photosystem I (PSI). Blue native/SDS-PAGE and sucrose gradient fractionation demonstrated the association of the protein exclusively with PSI. We designate the protein PSI-P. The presence of PSI-P subunit in Arabidopsis mutants lacking other PSI subunits was analyzed and suggested a location in the proximity of PSI-L, -H and -O subunits. The PSI-P protein was not differentially phosphorylated in state 1 and state 2.
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Affiliation(s)
- Anastassia Khrouchtchova
- Plant Biochemistry Laboratory, Department of Plant Biology, The Royal Veterinary and Agricultural University, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
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Rosgaard L, Zygadlo A, Scheller HV, Mant A, Jensen PE. Insertion of the plant photosystem I subunit G into the thylakoid membrane. FEBS J 2005; 272:4002-10. [PMID: 16045770 DOI: 10.1111/j.1742-4658.2005.04824.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Subunit G of photosystem I is a nuclear-encoded protein, predicted to form two transmembrane alpha-helices separated by a loop region. We use in vitro import assays to show that the positively charged loop domain faces the stroma, whilst the N- and C-termini most likely face the lumen. PSI-G constructs in which a His- or Strep-tag is placed at the C-terminus or in the loop region insert with the same topology as wild-type photosystem I subunit G (PSI-G). However, the presence of the tags in the loop make the membrane-inserted protein significantly more sensitive to trypsin, apparently by disrupting the interaction between the loop and the PSI core. Knock-out plants lacking PSI-G were transformed with constructs encoding the C-terminal and loop-tagged PSI-G proteins. Experiments on thylakoids from the transgenic lines show that the C-terminally tagged versions of PSI-G adopt the same topology as wild-type PSI-G, whereas the loop-tagged versions affect the sensitivity of the loop region to trypsin, thus confirming the in vitro observations. Furthermore, purification of PSI complexes from transgenic plants revealed that all the tagged versions of PSI-G are incorporated and retained in the PSI complex, although the C-terminally tagged variants of PSI-G were preferentially retained. This suggests that the loop region of PSI-G is important for proper integration into the PSI core. Our experiments demonstrate that it is possible to produce His- and Strep-tagged PSI in plants, and provide further evidence that the topology of membrane proteins is dictated by the distribution of positive charges, which resist translocation across membranes.
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Affiliation(s)
- Lisa Rosgaard
- Plant Biochemistry Laboratory, Department of Plant Biology, The Royal Veterinary & Agricultural University, Frederiksberg, Denmark
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