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Abstract
This chapter describes a method of plant cytosolic ribosomes isolation typically used for further proteomic studies. Detailed description procedures including plant material disruption, various centrifugation steps, sucrose cushion centrifugation, and quality control of preparation are provided.
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Ji CY, Jin R, Xu Z, Kim HS, Lee CJ, Kang L, Kim SE, Lee HU, Lee JS, Kang CH, Chi YH, Lee SY, Xie Y, Li H, Ma D, Kwak SS. Overexpression of Arabidopsis P3B increases heat and low temperature stress tolerance in transgenic sweetpotato. BMC PLANT BIOLOGY 2017; 17:139. [PMID: 28806972 PMCID: PMC5557506 DOI: 10.1186/s12870-017-1087-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/31/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sweetpotato (Ipomoea batatas [L.] Lam) is suitable for growth on marginal lands due to its abiotic stress tolerance. However, severe environmental conditions including low temperature pose a serious threat to the productivity and expanded cultivation of this crop. In this study, we aimed to develop sweetpotato plants with enhanced tolerance to temperature stress. RESULTS P3 proteins are plant-specific ribosomal P-proteins that act as both protein and RNA chaperones to increase heat and cold stress tolerance in Arabidopsis. Here, we generated transgenic sweetpotato plants expressing the Arabidopsis ribosomal P3 (AtP3B) gene under the control of the CaMV 35S promoter (referred to as OP plants). Three OP lines (OP1, OP30, and OP32) were selected based on AtP3B transcript levels. The OP plants displayed greater heat tolerance and higher photosynthesis efficiency than wild type (WT) plants. The OP plants also exhibited enhanced low temperature tolerance, with higher photosynthesis efficiency and less membrane permeability than WT plants. In addition, OP plants had lower levels of hydrogen peroxide and higher activities of antioxidant enzymes such as peroxidase and catalase than WT plants under low temperature stress. The yields of tuberous roots and aerial parts of plants did not significantly differ between OP and WT plants under field cultivation. However, the tuberous roots of OP transgenic sweetpotato showed improved storage ability under low temperature conditions. CONCLUSIONS The OP plants developed in this study exhibited increased tolerance to temperature stress and enhanced storage ability under low temperature compared to WT plants, suggesting that they could be used to enhance sustainable agriculture on marginal lands.
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Affiliation(s)
- Chang Yoon Ji
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea
- Department of Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, South Korea
| | - Rong Jin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea
- Department of Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, South Korea
- Sweetpotato Research Center, Jiangsu Academy of Agricultural Science, Xuhuai Road, Xuzhou, Jiangsu, 221131, China
| | - Zhen Xu
- Sweetpotato Research Center, Jiangsu Academy of Agricultural Science, Xuhuai Road, Xuzhou, Jiangsu, 221131, China
| | - Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea
| | - Chan-Ju Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea
- Department of Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, South Korea
| | - Le Kang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea
- Department of Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, South Korea
| | - So-Eun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea
- Department of Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, South Korea
| | - Hyeong-Un Lee
- Bioenergy Crop Research Center, National Institute of Crop Science, Rural Development Administration, Muan, 58545, South Korea
| | - Joon Seol Lee
- Bioenergy Crop Research Center, National Institute of Crop Science, Rural Development Administration, Muan, 58545, South Korea
| | - Chang Ho Kang
- Division of Applied Life Science (BK21 Plus program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinjudae-ro, Jinju, 52828, South Korea
| | - Yong Hun Chi
- Division of Applied Life Science (BK21 Plus program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinjudae-ro, Jinju, 52828, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Plus program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinjudae-ro, Jinju, 52828, South Korea
| | - Yiping Xie
- Sweetpotato Research Center, Jiangsu Academy of Agricultural Science, Xuhuai Road, Xuzhou, Jiangsu, 221131, China
| | - Hongmin Li
- Sweetpotato Research Center, Jiangsu Academy of Agricultural Science, Xuhuai Road, Xuzhou, Jiangsu, 221131, China
| | - Daifu Ma
- Sweetpotato Research Center, Jiangsu Academy of Agricultural Science, Xuhuai Road, Xuzhou, Jiangsu, 221131, China
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, South Korea.
- Department of Environmental Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, South Korea.
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Ahsan N, Chen M, Salvato F, Wilson RS, Shyama Prasad Rao R, Thelen JJ. Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from Arabidopsis. J Proteomics 2017; 165:51-60. [DOI: 10.1016/j.jprot.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/26/2017] [Accepted: 06/05/2017] [Indexed: 01/21/2023]
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Merchante C, Stepanova AN, Alonso JM. Translation regulation in plants: an interesting past, an exciting present and a promising future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:628-653. [PMID: 28244193 DOI: 10.1111/tpj.13520] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 05/19/2023]
Abstract
Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever-changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high-throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein-RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well-established and uncharacterized translation-dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation.
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Affiliation(s)
- Catharina Merchante
- Departamento de Biologia Molecular y Bioquimica, Universidad de Malaga-Instituto de Hortofruticultura Subtropical y Mediterranea, IHSM-UMA-CSIC, Malaga, Andalucía, Spain
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
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AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in Arabidopsis by interacting with RNA binding proteins. J Biosci 2017; 42:57-68. [PMID: 28229965 DOI: 10.1007/s12038-016-9658-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
DNA methylation, mediated by double-stranded RNA, is a conserved epigenetic phenomenon that protects a genome from transposons, silences unwanted genes and has a paramount function in plant or animal development. Methyl CpG binding domain proteins are members of a class of proteins that bind to methylated DNA. The Arabidopsis thaliana genome encodes 13 methyl CpG binding domain (MBD) proteins, but the molecular/biological functions of most of these proteins are still not clear. In the present study, we identified four proteins that interact with AtMBD6. Interestingly, three of them contain RNA binding domains and are co-localized with AtMBD6 in the nucleus. The interacting partners includes AtRPS2C (a 40S ribosomal protein), AtNTF2 (nuclear transport factor 2) and AtAGO4 (Argonoute 4). The fourth protein that physically interacts with AtMBD6 is a histone-modifying enzyme, histone deacetylase 6 (AtHDA6), which is a known component of the RNA-mediated gene silencing system. Analysis of genomic DNA methylation in the atmbd6, atrps2c and atntf2 mutants, using methylation-sensitive PCR detected decreased DNA methylation at miRNA/siRNA producing loci, pseudogenes and other targets of RNA-directed DNA methylation. Our results indicate that AtMBD6 is involved in RNA-mediated gene silencing and it binds to RNA binding proteins like AtRPS2C, AtAGO4 and AtNTF2. AtMBD6 also interacts with histone deacetylase AtHDA6 that might have a role in chromatin condensation at the targets of RdDM.
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Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH. Resource: Mapping the Triticum aestivum proteome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:601-616. [PMID: 27775198 DOI: 10.1111/tpj.13402] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 05/22/2023]
Abstract
Yield and quality improvement of bread wheat (Triticum aestivum) is a focus in efforts to meet new demands from population growth and changing human diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome. We present a large scale, publicly accessible proteome mapping of wheat consisting of 24 organ and developmental samples. Tissue specific sub-proteomes and ubiquitously expressed markers of the wheat proteome are identified, alongside hierarchical assessment of protein functional classes, their presence in different tissues and correlations between the abundance of functional classes of proteins. Gene-specific identifications and protein family relationships are accounted for in the organisation of the data and 202 new protein-coding transcripts identified by proteogenomic mapping. The interactive database will serve as a vehicle to build, refine and deposit confirmed targeted proteomic assays for wheat proteins and protein families to assess function (www.wheatproteome.org).
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Affiliation(s)
- Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - Josua Trösch
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
- School of Chemistry and Biochemistry, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
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Dinkins RD, Nagabhyru P, Graham MA, Boykin D, Schardl CL. Transcriptome response of Lolium arundinaceum to its fungal endophyte Epichloë coenophiala. THE NEW PHYTOLOGIST 2017; 213:324-337. [PMID: 27477008 DOI: 10.1111/nph.14103] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/10/2016] [Indexed: 05/21/2023]
Abstract
Tall fescue (Lolium arundinaceum) is one of the primary forage and turf grasses in temperate regions of the world. A number of favourable characteristics of tall fescue are enhanced by its seed-transmissible fungal symbiont (endophyte) Epichloë coenophiala. Our approach was to assemble the tall fescue transcriptome, then identify differentially expressed genes (DEGs) for endophyte-symbiotic (E+) vs endophyte-free (E-) clones in leaf blades, pseudostems, crowns and roots. RNA-seq reads were used to construct a tall fescue reference transcriptome and compare gene expression profiles. Over all tissues examined, 478 DEGs were identified between the E+ and E- clones for at least one tissue (more than two-fold; P < 0.0001, 238 E+ > E- and 240 E- > E+), although no genes were differentially expressed in all four tissues. Gene ontology (GO) terms, GO:0010200 (response to chitin), GO:0002679 (respiratory burst during defence response) and GO:0035556 (intracellular signal transduction) were significantly overrepresented among 25 E- > E+ DEGs in leaf blade, and a number of other DEGs were associated with defence and abiotic response. In particular, endophyte effects on various WRKY transcription factors may have implications for symbiotic stability, endophyte distribution in the plant, or defence against pathogens.
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Affiliation(s)
- Randy D Dinkins
- Forage-Animal Production Research Unit, USDA-ARS, Lexington, KY, 40546-0091, USA
| | - Padmaja Nagabhyru
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Michelle A Graham
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
| | - Deborah Boykin
- Jamie Whitten Delta States Research Center, USDA-ARS, Stoneville, MS, 38776, USA
| | - Christopher L Schardl
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546-0312, USA
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58
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Ribosomal protein L18aB is required for both male gametophyte function and embryo development in Arabidopsis. Sci Rep 2016; 6:31195. [PMID: 27502163 PMCID: PMC4977502 DOI: 10.1038/srep31195] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 01/01/2023] Open
Abstract
Ribosomal proteins are involved in numerous essential cell activities in plants. However, the regulatory role in specific plant developmental processes has not yet been fully elucidated. Here we identified the new ribosomal protein L18aB, which is specifically involved in sexual reproduction and plays a critical role in male gametophyte development and embryo pattern formation. In rpl18aB mutant plants, the mature pollen grains can germinate normally, but their competitiveness for growing in the style is significantly reduced. More interestingly, RPL18aB is required in early embryogenesis. rpl18aB embryos displayed irregular cell division orientations in the early pro-embryo and arrested at the globular stage with possible, secondary pattern formation defects. Further investigations revealed that the polar transportation of auxin is disturbed in the rpl18aB mutant embryos, which may explain the observed failure in embryo pattern formation. The cell type-specific complementation of RPL18aB in rpl18aB was not able to recover the phenotype, indicating that RPL18aB may play an essential role in early cell fate determination. This work unravels a novel role in embryo development for a ribosomal protein, and provides insight into regulatory mechanism of early embryogenesis.
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59
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The RNA-binding protein repertoire of Arabidopsis thaliana. Sci Rep 2016; 6:29766. [PMID: 27405932 PMCID: PMC4942612 DOI: 10.1038/srep29766] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/08/2016] [Indexed: 12/28/2022] Open
Abstract
RNA-binding proteins (RBPs) have essential roles in determining the fate of RNA from synthesis to decay and have been studied on a protein-by-protein basis, or computationally based on a number of well-characterised RNA-binding domains. Recently, high-throughput methods enabled the capture of mammalian RNA-binding proteomes. To gain insight into the role of Arabidopsis thaliana RBPs at the systems level, we have employed interactome capture techniques using cells from different ecotypes grown in cultures and leaves. In vivo UV-crosslinking of RNA to RBPs, oligo(dT) capture and mass spectrometry yielded 1,145 different proteins including 550 RBPs that either belong to the functional category 'RNA-binding', have known RNA-binding domains or have orthologs identified in mammals, C. elegans, or S. cerevisiae in addition to 595 novel candidate RBPs. We noted specific subsets of RBPs in cultured cells and leaves and a comparison of Arabidopsis, mammalian, C. elegans, and S. cerevisiae RBPs reveals a common set of proteins with a role in intermediate metabolism, as well as distinct differences suggesting that RBPs are also species and tissue specific. This study provides a foundation for studies that will advance our understanding of the biological significance of RBPs in plant developmental and stimulus specific responses.
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60
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Kang CH, Lee YM, Park JH, Nawkar GM, Oh HT, Kim MG, Lee SI, Kim WY, Yun DJ, Lee SY. Ribosomal P3 protein AtP3B of Arabidopsis acts as both protein and RNA chaperone to increase tolerance of heat and cold stresses. PLANT, CELL & ENVIRONMENT 2016; 39:1631-42. [PMID: 27004478 DOI: 10.1111/pce.12742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 05/16/2023]
Abstract
The P3 proteins are plant-specific ribosomal P-proteins; however, their molecular functions have not been characterized. In a screen for components of heat-stable high-molecular weight (HMW) complexes, we isolated the P3 protein AtP3B from heat-treated Arabidopsis suspension cultures. By size-exclusion chromatography (SEC), SDS-PAGE and native PAGE followed by immunoblotting with anti-AtP3B antibody, we showed that AtP3B was stably retained in HMW complexes following heat shock. The level of AtP3B mRNA increased in response to both high- and low-temperature stresses. Bacterially expressed recombinant AtP3B protein exhibited both protein and RNA chaperone activities. Knockdown of AtP3B by RNAi made plants sensitive to both high- and low-temperature stresses, whereas overexpression of AtP3B increased tolerance of both conditions. Together, our results suggest that AtP3B protects cells against both high- and low-temperature stresses. These findings provide novel insight into the molecular functions and in vivo roles of acidic ribosomal P-proteins, thereby expanding our knowledge of the protein production machinery.
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Affiliation(s)
- Chang Ho Kang
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Young Mee Lee
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
- Genetics and Breeding Research Center, NFRDI, Geoje, 656-842, Korea
| | - Joung Hun Park
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Ganesh M Nawkar
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Hun Taek Oh
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, 660-701, Korea
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), Jeonju, 560-500, Korea
| | - Woe Yeon Kim
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
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Katz MJ, Gándara L, De Lella Ezcurra AL, Wappner P. Hydroxylation and translational adaptation to stress: some answers lie beyond the STOP codon. Cell Mol Life Sci 2016; 73:1881-93. [PMID: 26874685 PMCID: PMC11108485 DOI: 10.1007/s00018-016-2160-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 01/08/2023]
Abstract
Regulation of protein synthesis contributes to maintenance of homeostasis and adaptation to environmental changes. mRNA translation is controlled at various levels including initiation, elongation and termination, through post-transcriptional/translational modifications of components of the protein synthesis machinery. Recently, protein and RNA hydroxylation have emerged as important enzymatic modifications of tRNAs, elongation and termination factors, as well as ribosomal proteins. These modifications enable a correct STOP codon recognition, ensuring translational fidelity. Recent studies are starting to show that STOP codon read-through is related to the ability of the cell to cope with different types of stress, such as oxidative and chemical insults, while correlations between defects in hydroxylation of protein synthesis components and STOP codon read-through are beginning to emerge. In this review we will discuss our current knowledge of protein synthesis regulation through hydroxylation of components of the translation machinery, with special focus on STOP codon recognition. We speculate on the possibility that programmed STOP codon read-through, modulated by hydroxylation of components of the protein synthesis machinery, is part of a concerted cellular response to stress.
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Affiliation(s)
- M J Katz
- Instituto Leloir, Buenos Aires, Argentina
| | - L Gándara
- Instituto Leloir, Buenos Aires, Argentina
| | | | - P Wappner
- Instituto Leloir, Buenos Aires, Argentina.
- Departamento de Fisiología, Biología Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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62
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Palm D, Simm S, Darm K, Weis BL, Ruprecht M, Schleiff E, Scharf C. Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana. RNA Biol 2016; 13:441-54. [PMID: 26980300 DOI: 10.1080/15476286.2016.1154252] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), export of pre-ribosomal particles to the cytoplasm, and quality control mechanisms. Ribosome biogenesis is best established for Saccharomyces cerevisiae. Plant ortholog assignment to yeast RBFs revealed the absence of about 30% of the yeast RBFs in plants. In turn, few plant specific proteins have been identified by biochemical experiments to act in plant ribosome biogenesis. Nevertheless, a complete inventory of plant RBFs has not been established yet. We analyzed the proteome of the nucleus and nucleolus of Arabidopsis thaliana and the post-translational modifications of these proteins. We identified 1602 proteins in the nucleolar and 2544 proteins in the nuclear fraction with an overlap of 1429 proteins. For a randomly selected set of proteins identified by the proteomic approach we confirmed the localization inferred from the proteomics data by the localization of GFP fusion proteins. We assigned the identified proteins to various complexes and functions and found about 519 plant proteins that have a potential to act as a RBFs, but which have not been experimentally characterized yet. Last, we compared the distribution of RBFs and RPs in the various fractions with the distribution established for yeast.
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Affiliation(s)
| | - Stefan Simm
- a Institute for Molecular Biosciences.,b Cluster of Excellence Macromolecular Complexes
| | - Katrin Darm
- d Department of Otorhinolaryngology , Head and Neck Surgery
| | | | | | - Enrico Schleiff
- a Institute for Molecular Biosciences.,b Cluster of Excellence Macromolecular Complexes.,c Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt , Max von Laue Str. Nine, Frankfurt , Germany
| | - Christian Scharf
- d Department of Otorhinolaryngology , Head and Neck Surgery.,e Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Ferdinand-Sauerbruch-Straße DZ7 J.05.06, Greifswald , Germany
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de Michele R, McFarlane HE, Parsons HT, Meents MJ, Lao J, González Fernández-Niño SM, Petzold CJ, Frommer WB, Samuels AL, Heazlewood JL. Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings. J Proteome Res 2016; 15:900-13. [PMID: 26781341 DOI: 10.1021/acs.jproteome.5b00876] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The plant plasma membrane is the interface between the cell and its environment undertaking a range of important functions related to transport, signaling, cell wall biosynthesis, and secretion. Multiple proteomic studies have attempted to capture the diversity of proteins in the plasma membrane using biochemical fractionation techniques. In this study, two-phase partitioning was combined with free-flow electrophoresis to produce a population of highly purified plasma membrane vesicles that were subsequently characterized by tandem mass spectroscopy. This combined high-quality plasma membrane isolation technique produced a reproducible proteomic library of over 1000 proteins with an extended dynamic range including plasma membrane-associated proteins. The approach enabled the detection of a number of putative plasma membrane proteins not previously identified by other studies, including peripheral membrane proteins. Utilizing multiple data sources, we developed a PM-confidence score to provide a value indicating association to the plasma membrane. This study highlights over 700 proteins that, while seemingly abundant at the plasma membrane, are mostly unstudied. To validate this data set, we selected 14 candidates and transiently localized 13 to the plasma membrane using a fluorescent tag. Given the importance of the plasma membrane, this data set provides a valuable tool to further investigate important proteins. The mass spectrometry data are available via ProteomeXchange, identifier PXD001795.
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Affiliation(s)
- Roberto de Michele
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States.,Institute of Biosciences and Bioresources (CNR-IBBR), National Research Council of Italy , Palermo 90129, Italy
| | - Heather E McFarlane
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada.,Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany
| | - Harriet T Parsons
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Plant and Environmental Sciences, University of Copenhagen , Copenhagen C-1871, Denmark
| | - Miranda J Meents
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Susana M González Fernández-Niño
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States
| | - A Lacey Samuels
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne , Melbourne, Victoria 3010, Australia
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Dobrenel T, Mancera-Martínez E, Forzani C, Azzopardi M, Davanture M, Moreau M, Schepetilnikov M, Chicher J, Langella O, Zivy M, Robaglia C, Ryabova LA, Hanson J, Meyer C. The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6. FRONTIERS IN PLANT SCIENCE 2016; 7:1611. [PMID: 27877176 PMCID: PMC5100631 DOI: 10.3389/fpls.2016.01611] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/12/2016] [Indexed: 05/05/2023]
Abstract
Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.
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Affiliation(s)
- Thomas Dobrenel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- Université Paris-Sud–Université Paris-SaclayOrsay, France
- Umeå Plant Science Center, Department of Plant Physiology, Umeå UniversityUmeå, Sweden
| | - Eder Mancera-Martínez
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Céline Forzani
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
| | - Marianne Azzopardi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
| | | | - Manon Moreau
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix-Marseille Université, Faculté des Sciences de LuminyMarseille, France
| | - Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Johana Chicher
- Plateforme Protéomique Strasbourg-Esplanade, CNRS FRC1589, Institut de Biologie Moléculaire et CellulaireStrasbourg, France
| | | | - Michel Zivy
- Plateforme PAPPSO, UMR GQE-Le MoulonGif sur Yvette, France
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix-Marseille Université, Faculté des Sciences de LuminyMarseille, France
| | - Lyubov A. Ryabova
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, Université de StrasbourgStrasbourg, France
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå UniversityUmeå, Sweden
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-SaclayVersailles, France
- *Correspondence: Christian Meyer,
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Moin M, Bakshi A, Saha A, Dutta M, Madhav SM, Kirti PB. Rice Ribosomal Protein Large Subunit Genes and Their Spatio-temporal and Stress Regulation. FRONTIERS IN PLANT SCIENCE 2016; 7:1284. [PMID: 27605933 PMCID: PMC4995216 DOI: 10.3389/fpls.2016.01284] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/11/2016] [Indexed: 05/22/2023]
Abstract
Ribosomal proteins (RPs) are well-known for their role in mediating protein synthesis and maintaining the stability of the ribosomal complex, which includes small and large subunits. In the present investigation, in a genome-wide survey, we predicted that the large subunit of rice ribosomes is encoded by at least 123 genes including individual gene copies, distributed throughout the 12 chromosomes. We selected 34 candidate genes, each having 2-3 identical copies, for a detailed characterization of their gene structures, protein properties, cis-regulatory elements and comprehensive expression analysis. RPL proteins appear to be involved in interactions with other RP and non-RP proteins and their encoded RNAs have a higher content of alpha-helices in their predicted secondary structures. The majority of RPs have binding sites for metal and non-metal ligands. Native expression profiling of 34 ribosomal protein large (RPL) subunit genes in tissues covering the major stages of rice growth shows that they are predominantly expressed in vegetative tissues and seedlings followed by meiotically active tissues like flowers. The putative promoter regions of these genes also carry cis-elements that respond specifically to stress and signaling molecules. All the 34 genes responded differentially to the abiotic stress treatments. Phytohormone and cold treatments induced significant up-regulation of several RPL genes, while heat and H2O2 treatments down-regulated a majority of them. Furthermore, infection with a bacterial pathogen, Xanthomonas oryzae, which causes leaf blight also induced the expression of 80% of the RPL genes in leaves. Although the expression of RPL genes was detected in all the tissues studied, they are highly responsive to stress and signaling molecules indicating that their encoded proteins appear to have roles in stress amelioration besides house-keeping. This shows that the RPL gene family is a valuable resource for manipulation of stress tolerance in rice and other crops, which may be achieved by overexpressing and raising independent transgenic plants carrying the genes that became up-regulated significantly and instantaneously.
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Affiliation(s)
- Mazahar Moin
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Achala Bakshi
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Anusree Saha
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Mouboni Dutta
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Sheshu M. Madhav
- Department of Biotechnology, Indian Institute of Rice ResearchHyderabad, India
| | - P. B. Kirti
- Department of Plant Sciences, University of HyderabadHyderabad, India
- *Correspondence: P. B. Kirti,
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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: 128] [Impact Index Per Article: 14.2] [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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Breiman A, Fieulaine S, Meinnel T, Giglione C. The intriguing realm of protein biogenesis: Facing the green co-translational protein maturation networks. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:531-50. [PMID: 26555180 DOI: 10.1016/j.bbapap.2015.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/13/2023]
Abstract
The ribosome is the cell's protein-making factory, a huge protein-RNA complex, that is essential to life. Determining the high-resolution structures of the stable "core" of this factory was among the major breakthroughs of the past decades, and was awarded the Nobel Prize in 2009. Now that the mysteries of the ribosome appear to be more traceable, detailed understanding of the mechanisms that regulate protein synthesis includes not only the well-known steps of initiation, elongation, and termination but also the less comprehended features of the co-translational events associated with the maturation of the nascent chains. The ribosome is a platform for co-translational events affecting the nascent polypeptide, including protein modifications, folding, targeting to various cellular compartments for integration into membrane or translocation, and proteolysis. These events are orchestrated by ribosome-associated protein biogenesis factors (RPBs), a group of a dozen or more factors that act as the "welcoming committee" for the nascent chain as it emerges from the ribosome. In plants these factors have evolved to fit the specificity of different cellular compartments: cytoplasm, mitochondria and chloroplast. This review focuses on the current state of knowledge of these factors and their interaction around the exit tunnel of dedicated ribosomes. Particular attention has been accorded to the plant system, highlighting the similarities and differences with other organisms.
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Affiliation(s)
- Adina Breiman
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France; Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sonia Fieulaine
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France.
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Mazzoleni M, Figuet S, Martin-Laffon J, Mininno M, Gilgen A, Leroux M, Brugière S, Tardif M, Alban C, Ravanel S. Dual Targeting of the Protein Methyltransferase PrmA Contributes to Both Chloroplastic and Mitochondrial Ribosomal Protein L11 Methylation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:1697-710. [PMID: 26116422 DOI: 10.1093/pcp/pcv098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/22/2015] [Indexed: 05/09/2023]
Abstract
Methylation of ribosomal proteins has long been described in prokaryotes and eukaryotes, but our knowledge about the enzymes responsible for these modifications in plants is scarce. The bacterial protein methyltransferase PrmA catalyzes the trimethylation of ribosomal protein L11 (RPL11) at three distinct sites. The role of these modifications is still unknown. Here, we show that PrmA from Arabidopsis thaliana (AtPrmA) is dually targeted to chloroplasts and mitochondria. Mass spectrometry and enzymatic assays indicated that the enzyme methylates RPL11 in plasto- and mitoribosomes in vivo. We determined that the Arabidopsis and Escherichia coli PrmA enzymes share similar product specificity, making trimethylated residues, but, despite an evolutionary relationship, display a difference in substrate site specificity. In contrast to the bacterial enzyme that trimethylates the ε-amino group of two lysine residues and the N-terminal α-amino group, AtPrmA methylates only one lysine in the MAFCK(D/E)(F/Y)NA motif of plastidial and mitochondrial RPL11. The plant enzyme possibly methylates the N-terminus of plastidial RPL11, whereas mitochondrial RPL11 is N-α-acetylated by an unknown acetyltransferase. Lastly, we found that an Arabidopsis prma-null mutant is viable in standard environmental conditions and no molecular defect could be associated with a lack of RPL11 methylation in leaf chloroplasts or mitochondria. However, the conservation of PrmA during the evolution of photosynthetic eukaryotes together with the location of methylated residues at the binding site of translation factors to ribosomes suggests that RPL11 methylation in plant organelles could be involved, in combination with other post-translational modifications, in optimizing ribosome function.
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Affiliation(s)
- Meryl Mazzoleni
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sylvie Figuet
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Jacqueline Martin-Laffon
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Morgane Mininno
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Annabelle Gilgen
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Mélanie Leroux
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sabine Brugière
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Marianne Tardif
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Claude Alban
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Stéphane Ravanel
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
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Hummel M, Dobrenel T, Cordewener JJHG, Davanture M, Meyer C, Smeekens SJCM, Bailey-Serres J, America TAHP, Hanson J. Proteomic LC-MS analysis of Arabidopsis cytosolic ribosomes: Identification of ribosomal protein paralogs and re-annotation of the ribosomal protein genes. J Proteomics 2015; 128:436-49. [PMID: 26232565 DOI: 10.1016/j.jprot.2015.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/17/2015] [Accepted: 07/01/2015] [Indexed: 12/01/2022]
Abstract
UNLABELLED Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classic sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MS(E) with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68%) of the 242 cytosolic r-protein genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes. BIOLOGICAL SIGNIFICANCE Translation is one of the most energy demanding processes in a living cell and is therefore carefully regulated. Translational activity is tightly linked to growth control and growth regulating mechanism. Recently established translational profiling technologies, including the profiling of mRNAs associated with polysomes and the mapping of ribosome footprints on mRNAs, have revealed that the expression of gene expression is often fine-tuned by differential translation of gene transcripts. The eukaryotic ribosome, the hub of these important processes, consists of close to eighty different proteins (depending on species) and four large RNAs assembled into two highly conserved subunits. In plants and to lesser extent in yeast, the r-proteins are encoded by more than one actively transcribed gene. As r-protein gene paralogs frequently do not encode identical proteins and are regulated by growth conditions and development, in vivo ribosomes are heterogeneous in their protein content. The regulatory and physiological importance of this heterogeneity is unknown. Here, an improved annotation of the more than two hundred r-protein genes of Arabidopsis is presented that combines proteomic and advanced mRNA expression data. This proteomic investigation and re-annotation of Arabidopsis ribosomes establish a base for future investigations of translational control in plants.
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Affiliation(s)
- Maureen Hummel
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA
| | - Thomas Dobrenel
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden; Institut Jean-Pierre Bourgin, UMR 1318 INRA AgroParisTech, Saclay Plant Sciences, F-78026 Versailles, France
| | - Jan J H G Cordewener
- BU Bioscience, Plant Research International, P.O. Box 619, 6700 AP Wageningen, The Netherlands
| | - Marlène Davanture
- Plateforme PAPPSO, UMR de Génétique Végétale, Ferme du Moulon, Gif sur Yvette, France
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, UMR 1318 INRA AgroParisTech, Saclay Plant Sciences, F-78026 Versailles, France
| | - Sjef J C M Smeekens
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA
| | - Twan A H P America
- Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands; Netherlands Proteomics Centre, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.
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Machida C, Nakagawa A, Kojima S, Takahashi H, Machida Y. The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:655-71. [PMID: 26108442 PMCID: PMC4744985 DOI: 10.1002/wdev.196] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/23/2015] [Accepted: 05/12/2015] [Indexed: 01/17/2023]
Abstract
Leaf primordia are born around meristem‐containing stem cells at shoot apices, grow along three axes (proximal–distal, adaxial–abaxial, medial–lateral), and develop into flat symmetric leaves with adaxial–abaxial polarity. Axis development and polarity specification of Arabidopsis leaves require a network of genes for transcription factor‐like proteins and small RNAs. Here, we summarize present understandings of adaxial‐specific genes, ASYMMETRIC LEAVES1 (AS1) and AS2. Their complex (AS1–AS2) functions in the regulation of the proximal–distal leaf length by directly repressing class 1 KNOX homeobox genes (BP, KNAT2) that are expressed in the meristem periphery below leaf primordia. Adaxial–abaxial polarity specification involves antagonistic interaction of adaxial and abaxial genes including AS1 and AS2 for the development of two respective domains. AS1–AS2 directly represses the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3) and indirectly represses ETT/ARF3 and ARF4 through tasiR‐ARF. Modifier mutations have been identified that abolish adaxialization and enhance the defect in the proximal–distal patterning in as1 and as2. AS1–AS2 and its modifiers synergistically repress both ARFs and class 1 KNOXs. Repression of ARFs is critical for establishing adaxial–abaxial polarity. On the other hand, abaxial factors KANADI1 (KAN1) and KAN2 directly repress AS2 expression. These data delineate a molecular framework for antagonistic gene interactions among adaxial factors, AS1, AS2, and their modifiers, and the abaxial factors ARFs as key regulators in the establishment of adaxial–abaxial polarity. Possible AS1–AS2 epigenetic repression and activities downstream of ARFs are discussed. WIREs Dev Biol 2015, 4:655–671. doi: 10.1002/wdev.196 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Chiba, Japan
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Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE. Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways. Mol Cell Proteomics 2015; 14:2243-60. [PMID: 26091701 DOI: 10.1074/mcp.m114.047183] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Indexed: 01/01/2023] Open
Abstract
The circadian clock provides adaptive advantages to an organism, resulting in increased fitness and survival. The phosphorylation events that regulate circadian-dependent signaling and the processes which post-translationally respond to clock-gated signals are largely unknown. To better elucidate post-translational events tied to the circadian system we carried out a survey of circadian-regulated protein phosphorylation events in Arabidopsis seedlings. A large-scale mass spectrometry-based quantitative phosphoproteomics approach employing TiO2-based phosphopeptide enrichment techniques identified and quantified 1586 phosphopeptides on 1080 protein groups. A total of 102 phosphopeptides displayed significant changes in abundance, enabling the identification of specific patterns of response to circadian rhythms. Our approach was sensitive enough to quantitate oscillations in the phosphorylation of low abundance clock proteins (early flowering4; ELF4 and pseudoresponse regulator3; PRR3) as well as other transcription factors and kinases. During constant light, extensive cyclic changes in phosphorylation status occurred in critical regulators, implicating direct or indirect regulation by the circadian system. These included proteins influencing transcriptional regulation, translation, metabolism, stress and phytohormones-mediated responses. We validated our analysis using the elf4-211 allele, in which an S45L transition removes the phosphorylation herein identified. We show that removal of this phosphorylatable site diminishes interaction with early flowering3 (ELF3), a key partner in a tripartite evening complex required for circadian cycling. elf4-211 lengthens period, which increases with increasing temperature, relative to the wild type, resulting in a more stable temperature compensation of circadian period over a wider temperature range.
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Affiliation(s)
- Mani Kant Choudhary
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea
| | - Yuko Nomura
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Lei Wang
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210; ‖Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hirofumi Nakagami
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - David E Somers
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
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72
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Egorova AM, Tarchevsky IA. Antipathogenic phenomenon of cycloheximide. DOKL BIOCHEM BIOPHYS 2015; 461:98-101. [PMID: 25937224 DOI: 10.1134/s160767291502009x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 11/23/2022]
Affiliation(s)
- A M Egorova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, ul. Lobachevskogo 2/31, Kazan, 420111, Tatarstan, Russia
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73
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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74
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Yan G, Yan X. Ribosomal proteomics: Strategies, approaches, and perspectives. Biochimie 2015; 113:69-77. [PMID: 25869001 DOI: 10.1016/j.biochi.2015.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
Abstract
Over the past few decades, proteomic research has seen unprecedented development due to technological advancement. However, whole-cell proteomics still has limitations with respect to sample complexity and the accuracy of determining protein locations. To deal with these limitations, several subcellular proteomic studies have been initiated. Nevertheless, compared to other subcellular proteomic fields, such as mitochondrial proteomics, ribosomal proteomics has lagged behind due to the long-held idea that the ribosome is just a translation machine. Recently, with the proposed ribosome filter hypothesis and subsequent studies of ribosome-specific regulatory capacity, ribosomal proteomics has become a promising chapter for both proteomic and ribosomal research. In this review, we discuss the current strategies and approaches in ribosomal proteomics and the efficacies as well as disadvantages of individual approaches for further improvement.
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Affiliation(s)
- Guokai Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Xianghua Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
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75
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Gunawardana Y, Fujiwara S, Takeda A, Woo J, Woelk C, Niranjan M. Outlier detection at the transcriptome-proteome interface. Bioinformatics 2015; 31:2530-6. [PMID: 25819671 DOI: 10.1093/bioinformatics/btv182] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/24/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In high-throughput experimental biology, it is widely acknowledged that while expression levels measured at the levels of transcriptome and the corresponding proteome do not, in general, correlate well, messenger RNA levels are used as convenient proxies for protein levels. Our interest is in developing data-driven computational models that can bridge the gap between these two levels of measurement at which different mechanisms of regulation may act on different molecular species causing any observed lack of correlations. To this end, we build data-driven predictors of protein levels using mRNA levels and known proxies of translation efficiencies as covariates. Previous work showed that in such a setting, outliers with respect to the model are reliable candidates for post-translational regulation. RESULTS Here, we present and compare two novel formulations of deriving a protein concentration predictor from which outliers may be extracted in a systematic manner. The first approach, outlier rejecting regression, allows explicit specification of a certain fraction of the data as outliers. In a regression setting, this is a non-convex optimization problem which we solve by deriving a difference of convex functions algorithm (DCA). With post-translationally regulated proteins, one expects their concentrations to be affected primarily by disruption of protein stability. Our second algorithm exploits this observation by minimizing an asymmetric loss using quantile regression and extracts outlier proteins whose measured concentrations are lower than what a genome-wide regression would predict. We validate the two approaches on a dataset of yeast transcriptome and proteome. Functional annotation check on detected outliers demonstrate that the methods are able to identify post-translationally regulated genes with high statistical confidence.
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Affiliation(s)
- Yawwani Gunawardana
- School of Electronics and Computer Science, University of Southampton, Southampton, UK
| | - Shuhei Fujiwara
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan and
| | - Akiko Takeda
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan and
| | - Jeongmin Woo
- Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
| | - Christopher Woelk
- Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
| | - Mahesan Niranjan
- School of Electronics and Computer Science, University of Southampton, Southampton, UK
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76
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Devis D, Firth SM, Liang Z, Byrne ME. Dosage Sensitivity of RPL9 and Concerted Evolution of Ribosomal Protein Genes in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1102. [PMID: 26734020 PMCID: PMC4679983 DOI: 10.3389/fpls.2015.01102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/22/2015] [Indexed: 05/19/2023]
Abstract
The ribosome in higher eukaryotes is a large macromolecular complex composed of four rRNAs and eighty different ribosomal proteins. In plants, each ribosomal protein is encoded by multiple genes. Duplicate genes within a family are often necessary to provide a threshold dose of a ribosomal protein but in some instances appear to have non-redundant functions. Here, we addressed whether divergent members of the RPL9 gene family are dosage sensitive or whether these genes have non-overlapping functions. The RPL9 family in Arabidopsis thaliana comprises two nearly identical members, RPL9B and RPL9C, and a more divergent member, RPL9D. Mutations in RPL9C and RPL9D genes lead to delayed growth early in development, and loss of both genes is embryo lethal, indicating that these are dosage-sensitive and redundant genes. Phylogenetic analysis of RPL9 as well as RPL4, RPL5, RPL27a, RPL36a, and RPS6 family genes in the Brassicaceae indicated that multicopy ribosomal protein genes have been largely retained following whole genome duplication. However, these gene families also show instances of tandem duplication, small scale deletion, and evidence of gene conversion. Furthermore, phylogenetic analysis of RPL9 genes in angiosperm species showed that genes within a species are more closely related to each other than to RPL9 genes in other species, suggesting ribosomal protein genes undergo convergent evolution. Our analysis indicates that ribosomal protein gene retention following whole genome duplication contributes to the number of genes in a family. However, small scale rearrangements influence copy number and likely drive concerted evolution of these dosage-sensitive genes.
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77
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Sauert M, Temmel H, Moll I. Heterogeneity of the translational machinery: Variations on a common theme. Biochimie 2014; 114:39-47. [PMID: 25542647 DOI: 10.1016/j.biochi.2014.12.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/16/2014] [Indexed: 12/22/2022]
Abstract
In all organisms the universal process of protein synthesis is performed by the ribosome, a complex multi-component assembly composed of RNA and protein elements. Although ribosome heterogeneity was observed already more than 40 years ago, the ribosome is still traditionally viewed as an unchangeable entity that has to be equipped with all ribosomal components and translation factors in order to precisely accomplish all steps in protein synthesis. In the recent years this concept was challenged by several studies highlighting a broad variation in the composition of the translational machinery in response to environmental signals, which leads to its adaptation and functional specialization. Here, we summarize recent reports on the variability of the protein synthesis apparatus in diverse organisms and discuss the multiple mechanisms and possibilities that can lead to functional ribosome heterogeneity. Collectively, these results indicate that all cells are equipped with a remarkable toolbox to fine tune gene expression at the level of translation and emphasize the physiological importance of ribosome heterogeneity for the immediate implementation of environmental information.
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Affiliation(s)
- Martina Sauert
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Centre for Molecular Biology, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Hannes Temmel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Centre for Molecular Biology, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Centre for Molecular Biology, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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78
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Wu L, Wang S, Wu J, Han Z, Wang R, Wu L, Zhang H, Chen Y, Hu X. Phosphoproteomic analysis of the resistant and susceptible genotypes of maize infected with sugarcane mosaic virus. Amino Acids 2014; 47:483-96. [PMID: 25488425 DOI: 10.1007/s00726-014-1880-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 11/18/2014] [Indexed: 10/24/2022]
Abstract
Protein phosphorylation plays a pivotal role in the regulation of many cellular events. No information is yet available, however, on protein phosphorylation in plants in response to virus infection. In this study, we characterized phosphoproteomes of resistant and susceptible genotypes of maize (Zea mays L.) in response to Sugarcane mosaic virus (SCMV) infection. Based on isotope tags for relative and absolute quantification technology, TiO2 enrichment method and LC-MS/MS analysis, we identified 65 and 59 phosphoproteins respectively, whose phosphorylation level regulated significantly in susceptible and resistant plants. Some identified phosphoproteins were shared by both genotypes, suggesting a partial overlapping of the responsive pathways to virus infection. While several phosphoproteins are well-known pathogen response phosphoproteins, virus infection differentially regulates most other phosphoproteins, which has not been reported in literature. Changes in protein phosphorylation status indicated that response to SCMV infection encompass a reformatting of major cellular processes. Our data provide new valuable insights into plant-virus interactions.
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Affiliation(s)
- Liuji Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
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79
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Gamm M, Peviani A, Honsel A, Snel B, Smeekens S, Hanson J. Increased sucrose levels mediate selective mRNA translation in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:306. [PMID: 25403240 PMCID: PMC4252027 DOI: 10.1186/s12870-014-0306-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/27/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Protein synthesis is a highly energy demanding process and is regulated according to cellular energy levels. Light and sugar availability affect mRNA translation in plant cells but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady-state mRNA and mRNA bound to translating ribosomes. RESULTS Steady-state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extent in both conditions. For a majority of the transcripts changes of the transcript levels were followed by changes in polysomal mRNA levels. However, for 243 mRNAs, a change in polysomal occupancy (defined as polysomal levels related to steady-state levels of the mRNA) was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased polysomal occupancy. CONCLUSIONS Our results suggest that sucrose regulate translation of these 243 mRNAs specifically in the light, through a novel regulatory mechanism. Our data shows that increased polysomal occupancy is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates.
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Affiliation(s)
- Magdalena Gamm
- />Molecular Plant Physiology, Institute of Environmental
Biology, Utrecht University, Utrecht, The Netherlands
| | - Alessia Peviani
- />Theoretical Biology and Bioinformatics, Department of Biology, Faculty
of Science, Utrecht University, Utrecht, The Netherlands
| | - Anne Honsel
- />Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden
| | - Berend Snel
- />Theoretical Biology and Bioinformatics, Department of Biology, Faculty
of Science, Utrecht University, Utrecht, The Netherlands
| | - Sjef Smeekens
- />Molecular Plant Physiology, Institute of Environmental
Biology, Utrecht University, Utrecht, The Netherlands
| | - Johannes Hanson
- />Molecular Plant Physiology, Institute of Environmental
Biology, Utrecht University, Utrecht, The Netherlands
- />Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden
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80
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Retzer K, Butt H, Korbei B, Luschnig C. The far side of auxin signaling: fundamental cellular activities and their contribution to a defined growth response in plants. PROTOPLASMA 2014; 251:731-46. [PMID: 24221297 PMCID: PMC4059964 DOI: 10.1007/s00709-013-0572-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/15/2013] [Indexed: 05/04/2023]
Abstract
Recent years have provided us with spectacular insights into the biology of the plant hormone auxin, leaving the impression of a highly versatile molecule involved in virtually every aspect of plant development. A combination of genetics, biochemistry, and cell biology has established auxin signaling pathways, leading to the identification of two distinct modes of auxin perception and downstream regulatory cascades. Major targets of these signaling modules are components of the polar auxin transport machinery, mediating directional distribution of the phytohormone throughout the plant body, and decisively affecting plant development. Alterations in auxin transport, metabolism, or signaling that occur as a result of intrinsic as well as environmental stimuli, control adjustments in morphogenetic programs, giving rise to defined growth responses attributed to the activity of the phytohormone. Some of the results obtained from the analysis of auxin, however, do not fit coherently into a picture of highly specific signaling events, but rather suggest mutual interactions between auxin and fundamental cellular pathways, like the control of intracellular protein sorting or translation. Crosstalk between auxin and these basic determinants of cellular activity and how they might shape auxin effects in the control of morphogenesis are the subject of this review.
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Affiliation(s)
- Katarzyna Retzer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Haroon Butt
- Department of Biological Sciences, Forman Christian College, Ferozepur Road, Lahore, 54600 Pakistan
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, BOKU, Wien Muthgasse 18, 1190 Wien, Austria
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81
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Zsögön A, Szakonyi D, Shi X, Byrne ME. Ribosomal Protein RPL27a Promotes Female Gametophyte Development in a Dose-Dependent Manner. PLANT PHYSIOLOGY 2014; 165:1133-1143. [PMID: 24872379 PMCID: PMC4081327 DOI: 10.1104/pp.114.241778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ribosomal protein mutations in Arabidopsis (Arabidopsis thaliana) result in a range of specific developmental phenotypes. Why ribosomal protein mutants have specific phenotypes is not fully known, but such defects potentially result from ribosome insufficiency, ribosome heterogeneity, or extraribosomal functions of ribosomal proteins. Here, we report that ovule development is sensitive to the level of Ribosomal Protein L27a (RPL27a) and is disrupted by mutations in the two paralogs RPL27aC and RPL27aB. Mutations in RPL27aC result in high levels of female sterility, whereas mutations in RPL27aB have a significant but lesser effect on fertility. Progressive reduction in RPL27a function results in increasing sterility, indicating a dose-dependent relationship between RPL27a and female fertility. RPL27a levels in both the sporophyte and gametophyte affect female gametogenesis, with different developmental outcomes determined by the dose of RPL27a. These results demonstrate that RPL27aC and RPL27aB act redundantly and reveal a function for RPL27a in coordinating complex interactions between sporophyte and gametophyte during ovule development.
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Affiliation(s)
- Agustin Zsögön
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Dóra Szakonyi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Xiuling Shi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary E Byrne
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
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82
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Cai Q, Fu L, Wang Z, Gan N, Dai X, Wang Y. α-N-methylation of damaged DNA-binding protein 2 (DDB2) and its function in nucleotide excision repair. J Biol Chem 2014; 289:16046-56. [PMID: 24753253 DOI: 10.1074/jbc.m114.558510] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DDB2 exhibits a high affinity toward UV-damaged DNA, and it is involved in the initial steps of global genome nucleotide excision repair. Mutations in the DDB2 gene cause the genetic complementation group E of xeroderma pigmentosum, an autosomal recessive disease manifested clinically by hypersensitivity to sunlight exposure and an increased predisposition to skin cancer. Here we found that, in human cells, the initiating methionine residue in DDB2 was removed and that the N-terminal alanine could be methylated on its α-amino group in human cells, with trimethylation being the major form. We also demonstrated that the α-N-methylation of DDB2 is catalyzed by the N-terminal RCC1 methyltransferase. In addition, a methylation-defective mutant of DDB2 displayed diminished nuclear localization and was recruited at a reduced efficiency to UV-induced cyclobutane pyrimidine dimer foci. Moreover, loss of this methylation conferred compromised ATM (ataxia telangiectasia mutated) activation, decreased efficiency in cyclobutane pyrimidine dimer repair, and elevated sensitivity of cells toward UV light exposure. Our study provides new knowledge about the posttranslational regulation of DDB2 and expands the biological functions of protein α-N-methylation to DNA repair.
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Affiliation(s)
- Qian Cai
- From the Environmental Toxicology Graduate Program and
| | - Lijuan Fu
- From the Environmental Toxicology Graduate Program and
| | - Zi Wang
- From the Environmental Toxicology Graduate Program and
| | - Nanqin Gan
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Yinsheng Wang
- From the Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521-0403
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83
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Casanova-Sáez R, Candela H, Micol JL. Combined haploinsufficiency and purifying selection drive retention of RPL36a paralogs in Arabidopsis. Sci Rep 2014; 4:4122. [PMID: 24535089 PMCID: PMC3927210 DOI: 10.1038/srep04122] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 01/31/2014] [Indexed: 12/19/2022] Open
Abstract
Whole-genome duplication events have driven to a large degree the evolution of angiosperm genomes. Although the majority of redundant gene copies after a genome duplication are lost, subfunctionalization or gene balance account for the retention of gene copies. The Arabidopsis 80S ribosome represents an excellent model to test the gene balance hypothesis as it consists of 80 ribosomal proteins, all of them encoded by genes belonging to small gene families. Here, we present the isolation of mutant alleles of the APICULATA2 (API2) and RPL36aA paralogous genes, which encode identical ribosomal proteins but share a similarity of 89% in their coding sequences. RPL36aA was found expressed at a higher level than API2 in the wild type. The loss-of-function api2 and rpl36aa mutations are recessive and affect leaf development in a similar way. Their double mutant combinations with asymmetric leaves2-1 (as2-1) caused leaf polarity defects that were stronger in rpl36aa as2-1 than in api2 as2-1. Our results highlight the role of combined haploinsufficiency and purifying selection in the retention of these paralogous genes in the Arabidopsis genome.
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Affiliation(s)
- Rubén Casanova-Sáez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
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84
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Nelson CJ, Li L, Millar AH. Quantitative analysis of protein turnover in plants. Proteomics 2014; 14:579-92. [DOI: 10.1002/pmic.201300240] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/02/2013] [Accepted: 10/14/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Clark J. Nelson
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
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85
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Ito J, Parsons HT, Heazlewood JL. The Arabidopsis cytosolic proteome: the metabolic heart of the cell. FRONTIERS IN PLANT SCIENCE 2014; 5:21. [PMID: 24550929 PMCID: PMC3914213 DOI: 10.3389/fpls.2014.00021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/19/2014] [Indexed: 05/09/2023]
Abstract
The plant cytosol is the major intracellular fluid that acts as the medium for inter-organellar crosstalk and where a plethora of important biological reactions take place. These include its involvement in protein synthesis and degradation, stress response signaling, carbon metabolism, biosynthesis of secondary metabolites, and accumulation of enzymes for defense and detoxification. This central role is highlighted by estimates indicating that the majority of eukaryotic proteins are cytosolic. Arabidopsis thaliana has been the subject of numerous proteomic studies on its different subcellular compartments. However, a detailed study of enriched cytosolic fractions from Arabidopsis cell culture has been performed only recently, with over 1,000 proteins reproducibly identified by mass spectrometry. The number of proteins allocated to the cytosol nearly doubles to 1,802 if a series of targeted proteomic characterizations of complexes is included. Despite this, few groups are currently applying advanced proteomic approaches to this important metabolic space. This review will highlight the current state of the Arabidopsis cytosolic proteome since its initial characterization a few years ago.
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Affiliation(s)
- Jun Ito
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
| | - Harriet T. Parsons
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
- Department of Plant and Environmental Sciences, University of Copenhagen, CopenhagenDenmark
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
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86
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Pitkänen L, Tuomainen P, Eskelin K. Analysis of plant ribosomes with asymmetric flow field-flow fractionation. Anal Bioanal Chem 2014; 406:1629-37. [PMID: 24281322 DOI: 10.1007/s00216-013-7454-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/17/2013] [Accepted: 10/18/2013] [Indexed: 11/30/2022]
Abstract
Ribosome profiling is a technique used to separate ribosomal subunits, 80S ribosomes (monosomes), and polyribosomes (polysomes) from other RNA-protein complexes. It is traditionally performed in sucrose gradients. In this study, we used asymmetric flow field-flow fractionation (AsFlFFF) to characterize ribosome profiles of Nicotiana benthamiana plants. With the optimized running conditions, we were able to separate free molecules from ribosomal subunits and intact ribosomes. We used various chemical and enzymatic treatments to validate the positions of subunits, monosomes, and polysomes in the AsFlFFF fractograms. We also characterized the protein and RNA content of AsFlFFF fractions by gel electrophoresis and western blotting. The reverse transcription polymerase chain reaction (RT-PCR) analysis showed that ribosomes remained bound to messenger RNAs (mRNAs) during the analysis. Therefore, we conclude that AsFlFFF can be used for ribosome profiling to study the mRNAs that are being translated. It can also be used to study the protein composition of ribosomes that are active in translation at that particular moment.
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Affiliation(s)
- Leena Pitkänen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
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87
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Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochem Biophys Res Commun 2014; 445:535-41. [PMID: 24486316 DOI: 10.1016/j.bbrc.2014.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 01/14/2014] [Indexed: 01/12/2023]
Abstract
Ribosomes, as the center of protein translation in the cell, require careful regulation via multiple pathways. While regulation of ribosomal synthesis and function has been widely studied on the transcriptional and translational "levels," the biological roles of ribosomal post-translational modifications (PTMs) are largely not understood. Here, we explore this matter by using quantitative mass spectrometry to compare the prevalence of ribosomal methylation and acetylation for yeast in the log phase and the stationary phase of growth. We find that of the 27 modified peptides identified, two peptides experience statistically significant changes in abundance: a 1.9-fold decrease in methylation for k(Me)VSGFKDEVLETV of ribosomal protein S1B (RPS1B), and a 10-fold increase in dimethylation for r(DiMe)GGFGGR of ribosomal protein S2 (RPS2). While the biological role of RPS1B methylation has largely been unexplored, RPS2 methylation is a modification known to have a role in processing and export of ribosomal RNA. This suggests that yeast in the stationary phase increase methylation of RPS2 in order to regulate ribosomal synthesis. These results demonstrate the utility of mass spectrometry for quantifying dynamic changes in ribosomal PTMs.
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Affiliation(s)
- Daniel T Ladror
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Brian L Frey
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark E Levenstein
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Jacklyn M Artymiuk
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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88
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Matthes A, Köhl K, Schulze WX. SILAC and alternatives in studying cellular proteomes of plants. Methods Mol Biol 2014; 1188:65-83. [PMID: 25059605 DOI: 10.1007/978-1-4939-1142-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Quantitative proteomics by metabolic labeling has a high impact on the growing field of plant systems biology. SILAC has been pioneered and optimized for plant cell culture systems allowing for SILAC-based quantitative experiments in specialized experimental setups. In comparison to other model organisms, the application of SILAC to whole plants is challenging. As autotrophic organisms, plants under their natural growth conditions can hardly be fully labeled with stable isotope-coded amino acids. The metabolic labeling with inorganic nitrogen is therefore the method of choice for most whole-plant physiological questions. Plants can easily metabolize different inorganic nitrogen isotopes. The incorporation of the labeled inorganic nitrogen then results in proteins and metabolites with distinct molecular mass, which can be detected on a mass spectrometer. In comparative quantitative experiments, similarly as in SILAC experiments, treated and untreated samples are differentially labeled by nitrogen isotopes and jointly processed, thereby minimizing sample-to-sample variation. In recent years, heavy nitrogen labeling has become a widely used strategy in quantitative proteomics and novel approaches were developed for metabolite identification. Here we present a typical hydroponics setup, the workflow for processing of samples, mass spectrometry and data analysis for large-scale metabolic labeling experiments of whole plants.
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Affiliation(s)
- Annemarie Matthes
- Max Planck Institut für molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Golm, Germany
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89
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Estavillo GM, Verhertbruggen Y, Scheller HV, Pogson BJ, Heazlewood JL, Ito J. Isolation of the plant cytosolic fraction for proteomic analysis. Methods Mol Biol 2014; 1072:453-67. [PMID: 24136540 DOI: 10.1007/978-1-62703-631-3_31] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The cytosol is the fluid portion of the cell that is not partitioned by membranes. It contains a highly diverse collection of substances and is central to many essential cellular processes ranging from signal transduction, metabolite production and transport, protein biosynthesis and degradation to stress response and defense. Despite its importance, only a few proteomic studies have been performed on the plant cytosol. This is largely due to difficulties in isolating relatively pure samples from plant material free of disrupted organelle material. In this chapter we outline methods for isolating the cytosolic fraction from Arabidopsis cell cultures and seedlings and provide guidance on assessing purity for analysis by mass spectrometry.
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Affiliation(s)
- Gonzalo M Estavillo
- ARC Centre of Excellence in Plant Energy Biology and Research School of Biology, The Australian National University, Canberra, Australia
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90
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Wang J, Lan P, Gao H, Zheng L, Li W, Schmidt W. Expression changes of ribosomal proteins in phosphate- and iron-deficient Arabidopsis roots predict stress-specific alterations in ribosome composition. BMC Genomics 2013; 14:783. [PMID: 24225185 PMCID: PMC3830539 DOI: 10.1186/1471-2164-14-783] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/11/2013] [Indexed: 12/22/2022] Open
Abstract
Background Ribosomes are essential ribonucleoprotein complexes that are engaged in translation and thus indispensable for growth. Arabidopsis thaliana ribosomes are composed of 80 distinct ribosomal proteins (RPs), each of which is encoded by two to seven highly similar paralogous genes. Little information is available on how RP genes respond to a shortage of essential mineral nutrients such as phosphate (Pi) or iron (Fe). In the present study, the expression of RP genes and the differential accumulation of RPs upon Pi or Fe deficiency in Arabidopsis roots were comprehensively analyzed. Results Comparison of 3,106 Pi-responsive genes with 3,296 Fe-responsive genes revealed an overlap of 579 genes that were differentially expressed under both conditions in Arabidopsis roots. Gene ontology (GO) analysis revealed that these 579 genes were mainly associated with abiotic stress responses. Among the 247 RP genes retrieved from the TAIR10 release of the Arabidopsis genome (98 small subunit RP genes, 143 large subunit RP genes and six ribosome-related genes), seven RP genes were not detected in Arabidopsis roots by RNA sequencing under control conditions. Transcripts from 20 and 100 RP genes showed low and medium abundance, respectively; 120 RP genes were highly expressed in Arabidopsis roots. As anticipated, gene ontology (GO) analysis indicated that most RP genes were related to translation and ribosome assembly, but some of the highly expressed RP genes were also involved in the responses to cold, UV-B, and salt stress. Only three RP genes derived from three ‘sets’ of paralogous genes were differentially expressed between Pi-sufficient and Pi-deficient roots, all of which were induced by Pi starvation. In Fe-deficient plants, 81 RP genes from 51 ’sets’ of paralagous RP genes were significantly down-regulated in response to Fe deficiency. The biological processes ’translation’ (GO: 0006412), ’ribosome biogenesis (GO: 0042254), and ’response to salt (GO: 0009651), cold (GO: 0009409), and UV-B stresses (GO: 0071493)’ were enriched in this subset of RP genes. At the protein level, 21 and two RPs accumulated differentially under Pi- and Fe-deficient conditions, respectively. Neither the differentially expressed RP genes nor the differentially expressed RPs showed any overlap between the two growth types. Conclusions In the present study three and 81 differentially expressed RP genes were identified under Pi and Fe deficiency, respectively. At protein level, 21 and two RP proteins were differentially accumulated under Pi- and Fe-deficient conditions. Our study shows that the expression of paralogous genes encoding RPs was regulated in a stress-specific manner in Arabidopsis roots, presumably resulting in an altered composition of ribosomes and biased translation. These findings may aid in uncovering an unexplored mechanism by which plants adapt to changing environmental conditions.
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Affiliation(s)
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy Sciences, Nanjing 210008, China.
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91
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Ge XH, Ding L, Li ZY. Nucleolar dominance and different genome behaviors in hybrids and allopolyploids. PLANT CELL REPORTS 2013; 32:1661-73. [PMID: 23864197 DOI: 10.1007/s00299-013-1475-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/01/2013] [Indexed: 05/05/2023]
Abstract
Many plants are allopolyploids with different nuclear genomes from two or more progenitors, but cytoplasmic genomes typically inherited from the female parent. The importance of this speciation mechanism has stimulated the extensive investigations of genetic consequences of genome mergers in several experimental systems during last 20 years. The dynamic nature of polyploid genomes is recognized, and widespread changes to gene expression are revealed by transcriptomic analysis. These progresses show different stabilities of parental genomes and their unequal contributions to the transcriptome, proteome, and phenotype. We review the results in systems where extensive genetic analyses have been conducted and propose possible mechanisms for biased behavior of parental genomes in allopolyploids, including the role of nucleolar dominance. It is hypothesized that the novel ribosomes with rRNAs from uniparental genome and the ribosomal proteins of biparental origins have some impacts on the biased cellular and genetic behaviors of parental genomes in hybrids and allopolyploids.
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Affiliation(s)
- Xian-Hong Ge
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Crop Molecular Breeding, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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92
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Gunawardana Y, Niranjan M. Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes. Bioinformatics 2013; 29:3060-6. [PMID: 24045772 DOI: 10.1093/bioinformatics/btt537] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Despite much dynamical cellular behaviour being achieved by accurate regulation of protein concentrations, messenger RNA abundances, measured by microarray technology, and more recently by deep sequencing techniques, are widely used as proxies for protein measurements. Although for some species and under some conditions, there is good correlation between transcriptome and proteome level measurements, such correlation is by no means universal due to post-transcriptional and post-translational regulation, both of which are highly prevalent in cells. Here, we seek to develop a data-driven machine learning approach to bridging the gap between these two levels of high-throughput omic measurements on Saccharomyces cerevisiae and deploy the model in a novel way to uncover mRNA-protein pairs that are candidates for post-translational regulation. RESULTS The application of feature selection by sparsity inducing regression (l₁ norm regularization) leads to a stable set of features: i.e. mRNA, ribosomal occupancy, ribosome density, tRNA adaptation index and codon bias while achieving a feature reduction from 37 to 5. A linear predictor used with these features is capable of predicting protein concentrations fairly accurately (R² = 0.86). Proteins whose concentration cannot be predicted accurately, taken as outliers with respect to the predictor, are shown to have annotation evidence of post-translational modification, significantly more than random subsets of similar size P < 0.02. In a data mining sense, this work also shows a wider point that outliers with respect to a learning method can carry meaningful information about a problem domain.
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Affiliation(s)
- Yawwani Gunawardana
- School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
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93
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Dai X, Otake K, You C, Cai Q, Wang Z, Masumoto H, Wang Y. Identification of novel α-n-methylation of CENP-B that regulates its binding to the centromeric DNA. J Proteome Res 2013; 12:4167-75. [PMID: 23978223 DOI: 10.1021/pr400498y] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eukaryotic centromere is an essential chromatin region required for accurate segregation of sister chromatids during cell division. Centromere protein B (CENP-B) is a highly conserved protein which can bind to the 17-bp CENP-B box on the centromeric DNA. In this study, we found that CENP-B could be α-N-methylated in human cells. We also showed that the level of the α-N-methylation was stimulated in cells in response to a variety of extracellular stimuli, including increased cell density, heat shock, and arsenite treatment, although the methylation level was not altered upon metaphase arrest. We identified N-terminal RCC1 methyltransferase (NRMT) as a major enzyme required for the CENP-B methylation. Additionally, we found that chromatin-bound CENP-B was primarily trimethylated and α-N-trimethylation could enhance CENP-B's binding to CENP-B box in cells. Our study also expands the function of protein α-N-methylation that has been known for decades and whose function remains largely unexplored.
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Affiliation(s)
- Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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94
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Boex-Fontvieille E, Daventure M, Jossier M, Zivy M, Hodges M, Tcherkez G. Photosynthetic control of Arabidopsis leaf cytoplasmic translation initiation by protein phosphorylation. PLoS One 2013; 8:e70692. [PMID: 23894680 PMCID: PMC3722150 DOI: 10.1371/journal.pone.0070692] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/20/2013] [Indexed: 01/26/2023] Open
Abstract
Photosynthetic CO2 assimilation is the carbon source for plant anabolism, including amino acid production and protein synthesis. The biosynthesis of leaf proteins is known for decades to correlate with photosynthetic activity but the mechanisms controlling this effect are not documented. The cornerstone of the regulation of protein synthesis is believed to be translation initiation, which involves multiple phosphorylation events in Eukaryotes. We took advantage of phosphoproteomic methods applied to Arabidopsis thaliana rosettes harvested under controlled photosynthetic gas-exchange conditions to characterize the phosphorylation pattern of ribosomal proteins (RPs) and eukaryotic initiation factors (eIFs). The analyses detected 14 and 11 new RP and eIF phosphorylation sites, respectively, revealed significant CO2-dependent and/or light/dark phosphorylation patterns and showed concerted changes in 13 eIF phosphorylation sites and 9 ribosomal phosphorylation sites. In addition to the well-recognized role of the ribosomal small subunit protein RPS6, our data indicate the involvement of eIF3, eIF4A, eIF4B, eIF4G and eIF5 phosphorylation in controlling translation initiation when photosynthesis varies. The response of protein biosynthesis to the photosynthetic input thus appears to be the result of a complex regulation network involving both stimulating (e.g. RPS6, eIF4B phosphorylation) and inhibiting (e.g. eIF4G phosphorylation) molecular events.
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Affiliation(s)
- Edouard Boex-Fontvieille
- Institut de Biologie des Plantes, CNRS UMR 8618, Saclay Plant Sciences, Université Paris-Sud, Orsay, France
| | - Marlène Daventure
- Plateforme PAPPSO, UMR de Génétique Végétale, Ferme du Moulon, Gif sur Yvette, France
| | - Mathieu Jossier
- Institut de Biologie des Plantes, CNRS UMR 8618, Saclay Plant Sciences, Université Paris-Sud, Orsay, France
| | - Michel Zivy
- Plateforme PAPPSO, UMR de Génétique Végétale, Ferme du Moulon, Gif sur Yvette, France
| | - Michael Hodges
- Institut de Biologie des Plantes, CNRS UMR 8618, Saclay Plant Sciences, Université Paris-Sud, Orsay, France
| | - Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Saclay Plant Sciences, Université Paris-Sud, Orsay, France
- Institut Universitaire de France, Paris, France
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95
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Roy B, von Arnim AG. Translational Regulation of Cytoplasmic mRNAs. THE ARABIDOPSIS BOOK 2013; 11:e0165. [PMID: 23908601 PMCID: PMC3727577 DOI: 10.1199/tab.0165] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Translation of the coding potential of a messenger RNA into a protein molecule is a fundamental process in all living cells and consumes a large fraction of metabolites and energy resources in growing cells. Moreover, translation has emerged as an important control point in the regulation of gene expression. At the level of gene regulation, translational control is utilized to support the specific life histories of plants, in particular their responses to the abiotic environment and to metabolites. This review summarizes the diversity of translational control mechanisms in the plant cytoplasm, focusing on specific cases where mechanisms of translational control have evolved to complement or eclipse other levels of gene regulation. We begin by introducing essential features of the translation apparatus. We summarize early evidence for translational control from the pre-Arabidopsis era. Next, we review evidence for translation control in response to stress, to metabolites, and in development. The following section emphasizes RNA sequence elements and biochemical processes that regulate translation. We close with a chapter on the role of signaling pathways that impinge on translation.
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Affiliation(s)
- Bijoyita Roy
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Current address: University of Massachussetts Medical School, Worcester, MA 01655-0122, USA
| | - Albrecht G. von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
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96
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Zhao L, Zhang N, Ma PF, Liu Q, Li DZ, Guo ZH. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae. PLoS One 2013; 8:e64642. [PMID: 23734211 PMCID: PMC3667173 DOI: 10.1371/journal.pone.0064642] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022] Open
Abstract
BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.
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Affiliation(s)
- Lei Zhao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ning Zhang
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Peng-Fei Ma
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qi Liu
- Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Hua Guo
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Tsukaya H, Byrne ME, Horiguchi G, Sugiyama M, Van Lijsebettens M, Lenhard M. How do 'housekeeping' genes control organogenesis?--Unexpected new findings on the role of housekeeping genes in cell and organ differentiation. JOURNAL OF PLANT RESEARCH 2013; 126:3-15. [PMID: 22922868 DOI: 10.1007/s10265-012-0518-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/31/2012] [Indexed: 05/08/2023]
Abstract
In recent years, an increasing number of mutations in what would appear to be 'housekeeping genes' have been identified as having unexpectedly specific defects in multicellular organogenesis. This is also the case for organogenesis in seed plants. Although it is not surprising that loss-of-function mutations in 'housekeeping' genes result in lethality or growth retardation, it is surprising when (1) the mutant phenotype results from the loss of function of a 'housekeeping' gene and (2) the mutant phenotype is specific. In this review, by defining housekeeping genes as those encoding proteins that work in basic metabolic and cellular functions, we discuss unexpected links between housekeeping genes and specific developmental processes. In a surprising number of cases housekeeping genes coding for enzymes or proteins with functions in basic cellular processes such as transcription, post-transcriptional modification, and translation affect plant development.
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Affiliation(s)
- Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
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98
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Coléno-Costes A, Jang SM, de Vanssay A, Rougeot J, Bouceba T, Randsholt NB, Gibert JM, Le Crom S, Mouchel-Vielh E, Bloyer S, Peronnet F. New partners in regulation of gene expression: the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain. PLoS Genet 2012; 8:e1003006. [PMID: 23071455 PMCID: PMC3469418 DOI: 10.1371/journal.pgen.1003006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/16/2012] [Indexed: 01/24/2023] Open
Abstract
Chromodomains are found in many regulators of chromatin structure, and most of them recognize methylated lysines on histones. Here, we investigate the role of the Drosophila melanogaster protein Corto's chromodomain. The Enhancer of Trithorax and Polycomb Corto is involved in both silencing and activation of gene expression. Over-expression of the Corto chromodomain (CortoCD) in transgenic flies shows that it is a chromatin-targeting module, critical for Corto function. Unexpectedly, mass spectrometry analysis reveals that polypeptides pulled down by CortoCD from nuclear extracts correspond to ribosomal proteins. Furthermore, real-time interaction analyses demonstrate that CortoCD binds with high affinity RPL12 tri-methylated on lysine 3. Corto and RPL12 co-localize with active epigenetic marks on polytene chromosomes, suggesting that both are involved in fine-tuning transcription of genes in open chromatin. RNA-seq based transcriptomes of wing imaginal discs over-expressing either CortoCD or RPL12 reveal that both factors deregulate large sets of common genes, which are enriched in heat-response and ribosomal protein genes, suggesting that they could be implicated in dynamic coordination of ribosome biogenesis. Chromatin immunoprecipitation experiments show that Corto and RPL12 bind hsp70 and are similarly recruited on gene body after heat shock. Hence, Corto and RPL12 could be involved together in regulation of gene transcription. We discuss whether pseudo-ribosomal complexes composed of various ribosomal proteins might participate in regulation of gene expression in connection with chromatin regulators.
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Affiliation(s)
- Anne Coléno-Costes
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Suk Min Jang
- Institut Pasteur, Département de Biologie du Développement, Unité de Régulation Epigénétique, Paris, France
- Centre National de la Recherche Scientifique, URA2578, Paris, France
- INSERM Avenir, Paris, France
| | - Augustin de Vanssay
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Répression Épigénétique et Éléments Transposables, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Répression Épigénétique et Éléments Transposables, Paris, France
| | - Julien Rougeot
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Tahar Bouceba
- Plateforme d'Ingénierie des Protéines, Service d'Interaction des Biomolécules, IFR83, Université Pierre et Marie Curie-Paris 6, UMR7622, Paris, France
| | - Neel B. Randsholt
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Jean-Michel Gibert
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Stéphane Le Crom
- École Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Plateforme Génomique, Paris, France
- INSERM, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Analyse des Données à Haut Débit en Génomique Fonctionnelle, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Analyse des Données à Haut Débit en Génomique Fonctionnelle, Paris, France
| | - Emmanuèle Mouchel-Vielh
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Sébastien Bloyer
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
| | - Frédérique Peronnet
- Université Pierre et Marie Curie-Paris 6, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
- Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Equipe Chromatine et Développement, Paris, France
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Hummel M, Cordewener JHG, de Groot JCM, Smeekens S, America AHP, Hanson J. Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics. Proteomics 2012; 12:1024-38. [PMID: 22522809 DOI: 10.1002/pmic.201100413] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cytosolic ribosomes are among the largest multisubunit cellular complexes. Arabidopsis thaliana ribosomes consist of 79 different ribosomal proteins (r-proteins) that each are encoded by two to six (paralogous) genes. It is unknown whether the paralogs are incorporated into the ribosome and whether the relative incorporation of r-protein paralogs varies in response to environmental cues. Immunopurified ribosomes were isolated from A. thaliana rosette leaves fed with sucrose. Trypsin digested samples were analyzed by qTOF-LC-MS using both MS(E) and classical MS/MS. Peptide features obtained by using these two methods were identified using MASCOT and Proteinlynx Global Server searching the theoretical sequences of A. thaliana proteins. The A. thaliana genome encodes 237 r-proteins and 69% of these were identified with proteotypic peptides for most of the identified proteins. These r-proteins were identified with average protein sequence coverage of 32% observed by MS(E) . Interestingly, the analysis shows that the abundance of r-protein paralogs in the ribosome changes in response to sucrose feeding. This is particularly evident for paralogous RPS3aA, RPS5A, RPL8B, and RACK1 proteins. These results show that protein synthesis in the A. thaliana cytosol involves a heterogeneous ribosomal population. The implications of these findings in the regulation of translation are discussed.
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Affiliation(s)
- Maureen Hummel
- Molecular Plant Physiology, Utrecht University, Utrecht, The Netherlands
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Horiguchi G, Van Lijsebettens M, Candela H, Micol JL, Tsukaya H. Ribosomes and translation in plant developmental control. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:24-34. [PMID: 22682562 DOI: 10.1016/j.plantsci.2012.04.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/16/2012] [Accepted: 04/16/2012] [Indexed: 05/06/2023]
Abstract
Ribosomes play a basic housekeeping role in global translation. However, a number of ribosomal-protein-defective mutants show common and rare developmental phenotypes including growth defects, changes in leaf development, and auxin-related phenotypes. This suggests that translational regulation may be occurring during development. In addition, proteomic and bioinformatic analyses have demonstrated a high heterogeneity in ribosome composition. Although this might be a sign of unequal roles of individual ribosomal proteins, it does not explain every ribosomal-protein-defective phenotype. Moreover, comprehensive interpretations concerning the relationship between ribosomal-protein-defective phenotypes and molecular changes in ribosome status are lacking. In this review, we address these phenotypes based on three models, ribosome insufficiency, heterogeneity, and aberrancy, to consider how ribosomes play developmental roles. We propose that the three models are not mutually exclusive, and ribosomal-protein-defective phenotypes can be explained with one or more of these models. The three models with reference to genetic, biochemical, and bioinformatic knowledge will serve as a foundation for future studies of translational regulation.
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Affiliation(s)
- Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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