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Delgado-Requerey V, Cejudo FJ, González MC. The Functional Relationship between NADPH Thioredoxin Reductase C, 2-Cys Peroxiredoxins, and m-Type Thioredoxins in the Regulation of Calvin-Benson Cycle and Malate-Valve Enzymes in Arabidopsis. Antioxidants (Basel) 2023; 12:antiox12051041. [PMID: 37237907 DOI: 10.3390/antiox12051041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
The concerted regulation of chloroplast biosynthetic pathways and NADPH extrusion via malate valve depends on f and m thioredoxins (Trxs). The finding that decreased levels of the thiol-peroxidase 2-Cys peroxiredoxin (Prx) suppress the severe phenotype of Arabidopsis mutants lacking NADPH-dependent Trx reductase C (NTRC) and Trxs f uncovered the central function of the NTRC-2-Cys-Prx redox system in chloroplast performance. These results suggest that Trxs m are also regulated by this system; however, the functional relationship between NTRC, 2-Cys Prxs, and m-type Trxs is unknown. To address this issue, we generated Arabidopsis thaliana mutants combining deficiencies in NTRC, 2-Cys Prx B, Trxs m1, and m4. The single trxm1 and trxm4 mutants showed a wild-type phenotype, growth retardation being noticed only in the trxm1m4 double mutant. Moreover, the ntrc-trxm1m4 mutant displayed a more severe phenotype than the ntrc mutant, as shown by the impaired photosynthetic performance, altered chloroplast structure, and defective light-dependent reduction in the Calvin-Benson cycle and malate-valve enzymes. These effects were suppressed by the decreased contents of 2-Cys Prx, since the quadruple ntrc-trxm1m4-2cpb mutant displayed a wild-type-like phenotype. These results show that the activity of m-type Trxs in the light-dependent regulation of biosynthetic enzymes and malate valve is controlled by the NTRC-2-Cys-Prx system.
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Affiliation(s)
- Víctor Delgado-Requerey
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
| | - Francisco Javier Cejudo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain
| | - María-Cruz González
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain
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2
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Latimer S, Keene SA, Stutts LR, Berger A, Bernert AC, Soubeyrand E, Wright J, Clarke CF, Block AK, Colquhoun TA, Elowsky C, Christensen A, Wilson MA, Basset GJ. A dedicated flavin-dependent monooxygenase catalyzes the hydroxylation of demethoxyubiquinone into ubiquinone (coenzyme Q) in Arabidopsis. J Biol Chem 2021; 297:101283. [PMID: 34626646 PMCID: PMC8559556 DOI: 10.1016/j.jbc.2021.101283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 01/08/2023] Open
Abstract
Ubiquinone (Coenzyme Q) is a vital respiratory cofactor and liposoluble antioxidant. In plants, it is not known how the C-6 hydroxylation of demethoxyubiquinone, the penultimate step in ubiquinone biosynthesis, is catalyzed. The combination of cross-species gene network modeling along with mining of embryo-defective mutant databases of Arabidopsis thaliana identified the embryo lethal locus EMB2421 (At1g24340) as a top candidate for the missing plant demethoxyubiquinone hydroxylase. In marked contrast with prototypical eukaryotic demethoxyubiquinone hydroxylases, the catalytic mechanism of which depends on a carboxylate-bridged di-iron domain, At1g24340 is homologous to FAD-dependent oxidoreductases that instead use NAD(P)H as an electron donor. Complementation assays in Saccharomyces cerevisiae and Escherichia coli demonstrated that At1g24340 encodes a functional demethoxyubiquinone hydroxylase and that the enzyme displays strict specificity for the C-6 position of the benzoquinone ring. Laser-scanning confocal microscopy also showed that GFP-tagged At1g24340 is targeted to mitochondria. Silencing of At1g24340 resulted in 40 to 74% decrease in ubiquinone content and de novo ubiquinone biosynthesis. Consistent with the role of At1g24340 as a benzenoid ring modification enzyme, this metabolic blockage could not be bypassed by supplementation with 4-hydroxybenzoate, the immediate precursor of ubiquinone's ring. Unlike in yeast, in Arabidopsis overexpression of demethoxyubiquinone hydroxylase did not boost ubiquinone content. Phylogenetic reconstructions indicated that plant demethoxyubiquinone hydroxylase is most closely related to prokaryotic monooxygenases that act on halogenated aromatics and likely descends from an event of horizontal gene transfer between a green alga and a bacterium.
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Affiliation(s)
- Scott Latimer
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA.
| | - Shea A Keene
- Department of Environmental Horticulture, Plant Innovation Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Lauren R Stutts
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Antoine Berger
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Ann C Bernert
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Eric Soubeyrand
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Janet Wright
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Anna K Block
- Center for Medical, Agricultural and Veterinary Entomology, Chemistry Research Unit, ARS, USDA, Gainesville, Florida, USA
| | - Thomas A Colquhoun
- Department of Environmental Horticulture, Plant Innovation Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Christian Elowsky
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Alan Christensen
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Gilles J Basset
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA.
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3
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Joshi J, Mimura M, Suzuki M, Wu S, Gregory JF, Hanson AD, McCarty DR. The Thiamin-Requiring 3 Mutation of Arabidopsis 5-Deoxyxylulose-Phosphate Synthase 1 Highlights How the Thiamin Economy Impacts the Methylerythritol 4-Phosphate Pathway. FRONTIERS IN PLANT SCIENCE 2021; 12:721391. [PMID: 34421975 PMCID: PMC8377734 DOI: 10.3389/fpls.2021.721391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 06/01/2023]
Abstract
The thiamin-requiring mutants of Arabidopsis have a storied history as a foundational model for biochemical genetics in plants and have illuminated the central role of thiamin in metabolism. Recent integrative genetic and biochemical analyses of thiamin biosynthesis and utilization imply that leaf metabolism normally operates close to thiamin-limiting conditions. Thus, the mechanisms that allocate thiamin-diphosphate (ThDP) cofactor among the diverse thiamin-dependent enzymes localized in plastids, mitochondria, peroxisomes, and the cytosol comprise an intricate thiamin economy. Here, we show that the classical thiamin-requiring 3 (th3) mutant is a point mutation in plastid localized 5-deoxyxylulose synthase 1 (DXS1), a key regulated enzyme in the methylerythritol 4-phosphate (MEP) isoprene biosynthesis pathway. Substitution of a lysine for a highly conserved glutamate residue (E323) located at the subunit interface of the homodimeric enzyme conditions a hypomorphic phenotype that can be rescued by supplying low concentrations of thiamin in the medium. Analysis of leaf thiamin vitamers showed that supplementing the medium with thiamin increased total ThDP content in both wild type and th3 mutant plants, supporting a hypothesis that the mutant DXS1 enzyme has a reduced affinity for the ThDP cofactor. An unexpected upregulation of a suite of biotic-stress-response genes associated with accumulation of downstream MEP intermediate MEcPP suggests that th3 causes mis-regulation of DXS1 activity in thiamin-supplemented plants. Overall, these results highlight that the central role of ThDP availability in regulation of DXS1 activity and flux through the MEP pathway.
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Affiliation(s)
- Jaya Joshi
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Manaki Mimura
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Masaharu Suzuki
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Shan Wu
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jesse F. Gregory
- Department Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
| | - Andrew D. Hanson
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Donald R. McCarty
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
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4
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Bergero R, Ellis P, Haerty W, Larcombe L, Macaulay I, Mehta T, Mogensen M, Murray D, Nash W, Neale MJ, O'Connor R, Ottolini C, Peel N, Ramsey L, Skinner B, Suh A, Summers M, Sun Y, Tidy A, Rahbari R, Rathje C, Immler S. Meiosis and beyond - understanding the mechanistic and evolutionary processes shaping the germline genome. Biol Rev Camb Philos Soc 2021; 96:822-841. [PMID: 33615674 PMCID: PMC8246768 DOI: 10.1111/brv.12680] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.
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Affiliation(s)
- Roberta Bergero
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3JTU.K.
| | - Peter Ellis
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | | | - Lee Larcombe
- Applied Exomics LtdStevenage Bioscience CatalystStevenageSG1 2FXU.K.
| | - Iain Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Tarang Mehta
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Mette Mogensen
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - David Murray
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - Will Nash
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexBrightonBN1 9RHU.K.
| | | | | | - Ned Peel
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Luke Ramsey
- The James Hutton InstituteInvergowrieDundeeDD2 5DAU.K.
| | - Ben Skinner
- School of Life SciencesUniversity of EssexColchesterCO4 3SQU.K.
| | - Alexander Suh
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
- Department of Organismal BiologyUppsala UniversityNorbyvägen 18DUppsala752 36Sweden
| | - Michael Summers
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
- The Bridge Centre1 St Thomas Street, London BridgeLondonSE1 9RYU.K.
| | - Yu Sun
- Norwich Medical SchoolUniversity of East AngliaNorwich Research Park, Colney LnNorwichNR4 7UGU.K.
| | - Alison Tidy
- School of BiosciencesUniversity of Nottingham, Plant Science, Sutton Bonington CampusSutton BoningtonLE12 5RDU.K.
| | | | - Claudia Rathje
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | - Simone Immler
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
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5
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Meinke DW. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:306-325. [PMID: 31334862 DOI: 10.1111/nph.16071] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 05/20/2023]
Abstract
With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.
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Affiliation(s)
- David W Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
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6
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Suzuki M, Wu S, Mimura M, Alseekh S, Fernie AR, Hanson AD, McCarty DR. Construction and applications of a B vitamin genetic resource for investigation of vitamin-dependent metabolism in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:442-454. [PMID: 31520508 DOI: 10.1111/tpj.14535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 05/06/2023]
Abstract
The B vitamins provide essential co-factors for central metabolism in all organisms. In plants, B vitamins have surprising emerging roles in development, stress tolerance and pathogen resistance. Hence, there is a paramount interest in understanding the regulation of vitamin biosynthesis as well as the consequences of vitamin deficiency in crop species. To facilitate genetic analysis of B vitamin biosynthesis and functions in maize, we have mined the UniformMu transposon resource to identify insertional mutations in vitamin pathway genes. A screen of 190 insertion lines for seed and seedling phenotypes identified mutations in biotin, pyridoxine and niacin biosynthetic pathways. Importantly, isolation of independent insertion alleles enabled genetic confirmation of genotype-to-phenotype associations. Because B vitamins are essential for survival, null mutations often have embryo lethal phenotypes that prevent elucidation of subtle, but physiologically important, metabolic consequences of sub-optimal (functional) vitamin status. To circumvent this barrier, we demonstrate a strategy for refined genetic manipulation of vitamin status based on construction of heterozygotes that combine strong and hypomorphic mutant alleles. Dosage analysis of pdx2 alleles in endosperm revealed that endosperm supplies pyridoxine to the developing embryo. Similarly, a hypomorphic bio1 allele enabled analysis of transcriptome and metabolome responses to incipient biotin deficiency in seedling leaves. We show that systemic pipecolic acid accumulation is an early metabolic response to sub-optimal biotin status highlighting an intriguing connection between biotin, lysine metabolism and systemic disease resistance signaling. Seed-stocks carrying insertions for vitamin pathway genes are available for free, public distribution via the Maize Genetics Cooperation Stock Center.
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Affiliation(s)
- Masaharu Suzuki
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Manaki Mimura
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology, 4000, Plovdiv, Bulgaria
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
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7
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Zhang Y, Ramming A, Heinke L, Altschmied L, Slotkin RK, Becker JD, Kappel C, Lenhard M. The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:655-672. [PMID: 31009115 DOI: 10.1111/tpj.14348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/21/2019] [Accepted: 04/08/2019] [Indexed: 05/28/2023]
Abstract
RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.
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Affiliation(s)
- Yunming Zhang
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Anna Ramming
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lisa Heinke
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lothar Altschmied
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, D-06466 Seeland, OT, Gatersleben, Germany
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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8
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The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:15297-15306. [PMID: 31296566 PMCID: PMC6660741 DOI: 10.1073/pnas.1908556116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Many mutations that affect plastidial metabolism are embryo-lethal, as expected if the disrupted genes encode enzymes with essential housekeeping functions. However, some mutations that disrupt the plastidial oxidative pentose phosphate pathway (OPPP) cause developmental defects, as well as embryo arrest at the globular stage of development. We show that the OPPP provides the substrate for the pathway of purine synthesis, ribose-5-phosphate, and is thus essential for the generation of nucleic acids during the very early stages of embryo development. Inadequate purine synthesis leads to abnormal patterns of cell division in the embryo and blocks development beyond the globular stage. Therefore, defects in primary metabolic pathways can have profound consequences for development as well as simply reducing growth. Large numbers of genes essential for embryogenesis in Arabidopsis encode enzymes of plastidial metabolism. Disruption of many of these genes results in embryo arrest at the globular stage of development. However, the cause of lethality is obscure. We examined the role of the plastidial oxidative pentose phosphate pathway (OPPP) in embryo development. In nonphotosynthetic plastids the OPPP produces reductant and metabolic intermediates for central biosynthetic processes. Embryos with defects in various steps in the oxidative part of the OPPP had cell division defects and arrested at the globular stage, revealing an absolute requirement for the production via these steps of ribulose-5-phosphate. In the nonoxidative part of the OPPP, ribulose-5-phosphate is converted to ribose-5-phosphate (R5P)—required for purine nucleotide and histidine synthesis—and subsequently to erythrose-4-phosphate, which is required for synthesis of aromatic amino acids. We show that embryo development through the globular stage specifically requires synthesis of R5P rather than erythrose-4-phosphate. Either a failure to convert ribulose-5-phosphate to R5P or a block in purine nucleotide biosynthesis beyond R5P perturbs normal patterning of the embryo, disrupts endosperm development, and causes early developmental arrest. We suggest that seed abortion in mutants unable to synthesize R5P via the oxidative part of the OPPP stems from a lack of substrate for synthesis of purine nucleotides, and hence nucleic acids. Our results show that the plastidial OPPP is essential for normal developmental progression as well as for growth in the embryo.
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9
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Wang W, Zhang X, Niittylä T. OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis. THE PLANT CELL 2019; 31:1446-1465. [PMID: 31023726 PMCID: PMC6635878 DOI: 10.1105/tpc.19.00033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/01/2019] [Accepted: 04/23/2019] [Indexed: 05/19/2023]
Abstract
Currently one-third of the proteins encoded by the Arabidopsis (Arabidopsis thaliana) genome are of unknown function. Some of these unknown proteins are likely to be involved in uncharacterized vital biological processes. Evolutionarily conserved single copy genes in flowering plants have been shown to be enriched in essential housekeeping functions. This together with publicly available gene expression data allows for a focused search for uncharacterized essential genes. Here we identify an essential single copy gene called OPENER (OPNR) in Arabidopsis. We show that OPNR is predominantly expressed in actively dividing cells and performs essential functions in seed development and root meristem maintenance. Cell cycle tracking using 5-ethynyl-2'-deoxyuridine staining and fluorescent cell cycle markers together with the increased size of nucleolus and nucleus in opnr mutants indicate that OPNR is required for cell cycle progression through the S or G2 phases. Intriguingly, OPNR localizes to the nuclear envelope and mitochondria. Furthermore, the nuclear envelope localization of OPNR is dependent on its interaction with nuclear inner membrane Sad1/UNC-84 (SUN) domain proteins SUN1 and SUN2. Taken together our results open a line of investigation into an evolutionarily conserved essential cellular process occurring in both the nuclear envelopes and mitochondria of dividing cells.
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Affiliation(s)
- Wei Wang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Xueyang Zhang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Totte Niittylä
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
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10
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Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Res 2019. [PMID: 30409771 DOI: 10.1101/gr.242594.118.freely] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Cannabis sativa is widely cultivated for medicinal, food, industrial, and recreational use, but much remains unknown regarding its genetics, including the molecular determinants of cannabinoid content. Here, we describe a combined physical and genetic map derived from a cross between the drug-type strain Purple Kush and the hemp variety "Finola." The map reveals that cannabinoid biosynthesis genes are generally unlinked but that aromatic prenyltransferase (AP), which produces the substrate for THCA and CBDA synthases (THCAS and CBDAS), is tightly linked to a known marker for total cannabinoid content. We further identify the gene encoding CBCA synthase (CBCAS) and characterize its catalytic activity, providing insight into how cannabinoid diversity arises in cannabis. THCAS and CBDAS (which determine the drug vs. hemp chemotype) are contained within large (>250 kb) retrotransposon-rich regions that are highly nonhomologous between drug- and hemp-type alleles and are furthermore embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic and molecular mechanisms in this commercially and medically important plant.
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Affiliation(s)
- Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jake M Stout
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mitchell J Sullivan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Navdeep Gill
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Larry Holbrook
- CanniMed Therapeutics Incorporated, Saskatoon, Saskatchewan S7K 3J8, Canada
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Jonathan E Page
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Anandia Labs, Vancouver, British Columbia V6T 1Z4, Canada
| | - Harm van Bakel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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11
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Qulsum U, Tsukahara T. Tissue-specific alternative splicing of pentatricopeptide repeat (PPR) family genes in Arabidopsis thaliana. Biosci Trends 2018; 12:569-579. [PMID: 30555111 DOI: 10.5582/bst.2018.01178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Alternative splicing is a post- and co-transcriptional regulatory mechanism of gene expression. Pentatricopeptide repeat (PPR) family proteins were recently found to be involved in RNA editing in plants. The aim of this study was to investigate the tissue-specific expression and alternative splicing of PPR family genes and their effects on protein structure and functionality. Of the 27 PPR genes in Arabidopsis thaliana, we selected six PPR genes of the P subfamily that are likely alternatively spliced, which were confirmed by sequencing. Four of these genes show intron retention, and the two remaining genes have 3' alternative-splicing sites. Alternative-splicing events occurred in the coding regions of three genes and in the 3' UTRs of the three remaining genes. We also identified five previously unannotated alternatively spliced isoforms of these PPR genes, which were confirmed by PCR and sequencing. Among these, three contain 3' alternative-splicing sites, one contains a 5' alternative-splicing site, and the remaining gene contains a 3'-5' alternative-splicing site. The new isoforms of two genes affect protein structure, and three other alternative-splicing sites are located in 3' UTRs. These findings suggest that tissue-specific expression of different alternatively spliced transcripts occurs in Arabidopsis, even at different developmental stages.
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Affiliation(s)
- Umme Qulsum
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST)
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST).,Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST).,Division of Transdisciplinary Science, Japan Advanced Institute of Science and Technology (JAIST)
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12
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Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Res 2018; 29:146-156. [PMID: 30409771 PMCID: PMC6314170 DOI: 10.1101/gr.242594.118] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/07/2018] [Indexed: 01/19/2023]
Abstract
Cannabis sativa is widely cultivated for medicinal, food, industrial, and recreational use, but much remains unknown regarding its genetics, including the molecular determinants of cannabinoid content. Here, we describe a combined physical and genetic map derived from a cross between the drug-type strain Purple Kush and the hemp variety “Finola.” The map reveals that cannabinoid biosynthesis genes are generally unlinked but that aromatic prenyltransferase (AP), which produces the substrate for THCA and CBDA synthases (THCAS and CBDAS), is tightly linked to a known marker for total cannabinoid content. We further identify the gene encoding CBCA synthase (CBCAS) and characterize its catalytic activity, providing insight into how cannabinoid diversity arises in cannabis. THCAS and CBDAS (which determine the drug vs. hemp chemotype) are contained within large (>250 kb) retrotransposon-rich regions that are highly nonhomologous between drug- and hemp-type alleles and are furthermore embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic and molecular mechanisms in this commercially and medically important plant.
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Affiliation(s)
- Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jake M Stout
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mitchell J Sullivan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Navdeep Gill
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Larry Holbrook
- CanniMed Therapeutics Incorporated, Saskatoon, Saskatchewan S7K 3J8, Canada
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Jonathan E Page
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Anandia Labs, Vancouver, British Columbia V6T 1Z4, Canada
| | - Harm van Bakel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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13
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Meng LS, Xu MK, Li D, Zhou MM, Jiang JH. Soluble Sugar Accumulation Can Influence Seed Size via AN3-YDA Gene Cascade. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4121-4132. [PMID: 28489361 DOI: 10.1021/acs.jafc.7b00228] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In higher plants, seed size is central to many aspects in evolutionary fitness and is a crucial agricultural trait. In this study, Arabidopsis an3 (angustifolia3) mutants present with increased seed size. Target-gene analysis revealed that YDA, which encodes a mitogen-activated protein kinase kinase kinase, is a target gene of AN3. Indeed, the loss of YDA function decreases seed size. Furthermore, AN3 and YDA mutations both disrupt normal sucrose and glucose contents and cause altered seed size in an3 or yda mutants. With these results, we provide a molecular model in which soluble sugar accumulation might affect seed size regulation via the AN3-YDA gene cascade. Our findings guide the synthesis of a model that predicts the integration of soluble sugar accumulation at AN3 to control the establishment of seed size.
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Affiliation(s)
- Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University , Xuzhou, Jiangsu 221116, People's Republic of China
| | - Meng-Ke Xu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University , Xuzhou, Jiangsu 221116, People's Republic of China
| | - Dan Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University , Xuzhou, Jiangsu 221116, People's Republic of China
| | - Ming-Ming Zhou
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University , Xuzhou, Jiangsu 221116, People's Republic of China
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University , Xuzhou, Jiangsu 221116, People's Republic of China
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14
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Parker N, Wang Y, Meinke D. Analysis of Arabidopsis Accessions Hypersensitive to a Loss of Chloroplast Translation. PLANT PHYSIOLOGY 2016; 172:1862-1875. [PMID: 27707889 PMCID: PMC5100756 DOI: 10.1104/pp.16.01291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
Natural accessions of Arabidopsis (Arabidopsis thaliana) differ in their ability to tolerate a loss of chloroplast translation. These differences can be attributed in part to variation in a duplicated nuclear gene (ACC2) that targets homomeric acetyl-coenzyme A carboxylase (ACCase) to plastids. This functional redundancy allows limited fatty acid biosynthesis to occur in the absence of heteromeric ACCase, which is encoded in part by the plastid genome. In the presence of functional ACC2, tolerant alleles of several nuclear genes, not yet identified, enhance the growth of seedlings and embryos disrupted in chloroplast translation. ACC2 knockout mutants, by contrast, are hypersensitive. Here we describe an expanded search for hypersensitive accessions of Arabidopsis, evaluate whether all of these accessions are defective in ACC2, and characterize genotype-to-phenotype relationships for homomeric ACCase variants identified among 855 accessions with sequenced genomes. Null alleles with ACC2 nonsense mutations, frameshift mutations, small deletions, genomic rearrangements, and defects in RNA splicing are included among the most sensitive accessions examined. By contrast, most missense mutations affecting highly conserved residues failed to eliminate ACC2 function. Several accessions were identified where sensitivity could not be attributed to a defect in either ACC2 or Tic20-IV, the chloroplast membrane channel required for ACC2 uptake. Overall, these results underscore the central role of ACC2 in mediating Arabidopsis response to a loss of chloroplast translation, highlight future applications of this system to analyzing chloroplast protein import, and provide valuable insights into the mutational landscape of an important metabolic enzyme that is highly conserved throughout eukaryotes.
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Affiliation(s)
- Nicole Parker
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Yixing Wang
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
| | - David Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
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15
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Mimura M, Zallot R, Niehaus TD, Hasnain G, Gidda SK, Nguyen TND, Anderson EM, Mullen RT, Brown G, Yakunin AF, de Crécy-Lagard V, Gregory JF, McCarty DR, Hanson AD. Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase. THE PLANT CELL 2016; 28:2683-2696. [PMID: 27677881 PMCID: PMC5134987 DOI: 10.1105/tpc.16.00600] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
To synthesize the cofactor thiamin diphosphate (ThDP), plants must first hydrolyze thiamin monophosphate (ThMP) to thiamin, but dedicated enzymes for this hydrolysis step were unknown and widely doubted to exist. The classical thiamin-requiring th2-1 mutation in Arabidopsis thaliana was shown to reduce ThDP levels by half and to increase ThMP levels 5-fold, implying that the THIAMIN REQUIRING2 (TH2) gene product could be a dedicated ThMP phosphatase. Genomic and transcriptomic data indicated that TH2 corresponds to At5g32470, encoding a HAD (haloacid dehalogenase) family phosphatase fused to a TenA (thiamin salvage) family protein. Like the th2-1 mutant, an insertional mutant of At5g32470 accumulated ThMP, and the thiamin requirement of the th2-1 mutant was complemented by wild-type At5g32470 Complementation tests in Escherichia coli and enzyme assays with recombinant proteins confirmed that At5g32470 and its maize (Zea mays) orthologs GRMZM2G148896 and GRMZM2G078283 are ThMP-selective phosphatases whose activity resides in the HAD domain and that the At5g32470 TenA domain has the expected thiamin salvage activity. In vitro and in vivo experiments showed that alternative translation start sites direct the At5g32470 protein to the cytosol and potentially also to mitochondria. Our findings establish that plants have a dedicated ThMP phosphatase and indicate that modest (50%) ThDP depletion can produce severe deficiency symptoms.
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Affiliation(s)
- Manaki Mimura
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Thuy N D Nguyen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Erin M Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | | | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, Florida 32611
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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16
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Meng LS, Li YQ, Liu MQ, Jiang JH. The Arabidopsis ANGUSTIFOLIA3- YODA Gene Cascade Induces Anthocyanin Accumulation by Regulating Sucrose Levels. FRONTIERS IN PLANT SCIENCE 2016; 7:1728. [PMID: 27920784 PMCID: PMC5118565 DOI: 10.3389/fpls.2016.01728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/02/2016] [Indexed: 05/09/2023]
Abstract
Anthocyanin accumulation specifically depends on sucrose (Suc) signaling/levels. However, the gene cascades specifically involved in the Suc signaling/level-mediated anthocyanin biosynthetic pathway are still unknown. Arabidopsis ANGUSTIFOLIA3 (AN3), a transcription coactivator, is involved in the regulation of leaf shape and drought tolerance. Recently, an AN3-CONSTITUTIVE PHOTOMORPHOGENIC 1 gene cascade has been reported to regulate the light signaling-mediated anthocyanin accumulation. Target gene analysis indicates that AN3 is associated with the YODA (YDA) promoter, a mitogen-activated protein kinase kinase kinase, in vivo for inducing anthocyanin accumulation. Indeed, loss-of-function mutants of YDA showed significantly increased anthocyanin accumulation. YDA mutation can also suppress the decrease in an3-4 anthocyanin accumulation. Further analysis indicates that the mutations of AN3 and YDA disrupt the normal Suc levels because of the changes of invertase activity in mutants of an3 or yda, which in turn induces the alterations of anthocyanin accumulation in mutants of an3 or yda via unknown regulatory mechanisms.
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Affiliation(s)
- Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
- *Correspondence: Lai-Sheng Meng, Ji-Hong, Jiang
| | - Ying-Qiu Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
| | - Meng-Qian Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
- Centre for Transformational Biotechnology of Medicinal and Food Plants, Jiangsu Normal University – Edinburgh UniversityXuzhou, China
- *Correspondence: Lai-Sheng Meng, Ji-Hong, Jiang
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17
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Narsai R, Edwards JM, Roberts TH, Whelan J, Joss GH, Atwell BJ. Mechanisms of growth and patterns of gene expression in oxygen-deprived rice coleoptiles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:25-40. [PMID: 25650041 DOI: 10.1111/tpj.12786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 01/21/2015] [Accepted: 01/22/2015] [Indexed: 05/04/2023]
Abstract
Coleoptiles of rice (Oryza sativa) seedlings grown under water commonly elongate by up to 1 mm h(-1) to reach the atmosphere. We initially analysed this highly specialized phenomenon by measuring epidermal cell lengths along the coleoptile axis to determine elongation rates. This revealed a cohort of cells in the basal zone that elongated rapidly following emergence from the embryo, reaching 200 μm within 12 h. After filming coleoptiles in vivo for a day, kinematic analysis was applied. Eight time-sliced 'segments' were defined by their emergence from the embryo at four-hourly intervals, revealing a mathematically simple growth model. Each segment entering the coleoptile from the embryo elongated at a constant velocity, resulting in accelerating growth for the entire organ. Consistent with the epidermal cell lengths, relative rates of elongation (mm mm(-1) h(-1)) were tenfold greater in the small, newly emerged basal segments than the older distal tip segments. This steep axial gradient defined two contrasting growth zones (bases versus tips) in which we measured ATP production and protein, RNA and DNA content, and analysed the global transcriptome under steady-state normoxia, hypoxia (3% O2) and anoxia. Determination of the transcriptome revealed tip-specific induction of genes encoding TCP [Teosinte Branched1 (Tb1) of maize, Cycloidea (Cyc), and Proliferating Cell Factor (Pcf)] transcription factors, RNA helicases, ribosomal proteins and proteins involved in protein folding, whilst expression of F-box domain-containing proteins in the ubiquitin E3-SCF complex (Skp, Cullin, F-box containing complex) was induced specifically in bases under low oxygen conditions. We ascribed the sustained elongation under hypoxia to hypoxia-specific responses such as controlled suppression of photosystem components and induction of RNA binding/splicing functions, indicating preferential allocation of energy to cell extension.
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Affiliation(s)
- Reena Narsai
- Department of Botany, School of Life Science, La Trobe University, Melbourne, Victoria, 3086, Australia
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18
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Parker N, Wang Y, Meinke D. Natural variation in sensitivity to a loss of chloroplast translation in Arabidopsis. PLANT PHYSIOLOGY 2014; 166:2013-27. [PMID: 25336520 PMCID: PMC4256881 DOI: 10.1104/pp.114.249052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mutations that eliminate chloroplast translation in Arabidopsis (Arabidopsis thaliana) result in embryo lethality. The stage of embryo arrest, however, can be influenced by genetic background. To identify genes responsible for improved growth in the absence of chloroplast translation, we examined seedling responses of different Arabidopsis accessions on spectinomycin, an inhibitor of chloroplast translation, and crossed the most tolerant accessions with embryo-defective mutants disrupted in chloroplast ribosomal proteins generated in a sensitive background. The results indicate that tolerance is mediated by ACC2, a duplicated nuclear gene that targets homomeric acetyl-coenzyme A carboxylase to plastids, where the multidomain protein can participate in fatty acid biosynthesis. In the presence of functional ACC2, tolerance is enhanced by a second locus that maps to chromosome 5 and heightened by additional genetic modifiers present in the most tolerant accessions. Notably, some of the most sensitive accessions contain nonsense mutations in ACC2, including the "Nossen" line used to generate several of the mutants studied here. Functional ACC2 protein is therefore not required for survival in natural environments, where heteromeric acetyl-coenzyme A carboxylase encoded in part by the chloroplast genome can function instead. This work highlights an interesting example of a tandem gene duplication in Arabidopsis, helps to explain the range of embryo phenotypes found in Arabidopsis mutants disrupted in essential chloroplast functions, addresses the nature of essential proteins encoded by the chloroplast genome, and underscores the value of using natural variation to study the relationship between chloroplast translation, plant metabolism, protein import, and plant development.
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Affiliation(s)
- Nicole Parker
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Yixing Wang
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
| | - David Meinke
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078
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19
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Morphological and proteomic analysis reveal the role of pistil under pollination in Liriodendron chinense (Hemsl.) Sarg. PLoS One 2014; 9:e99970. [PMID: 24924488 PMCID: PMC4055720 DOI: 10.1371/journal.pone.0099970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/21/2014] [Indexed: 11/19/2022] Open
Abstract
Pollination is an important physiological process during which interaction between pollen and pistil occurs. This interaction could determine whether or not fertilization will occur and hence the ratio of plant seed setting. Liriodendron chinense (Hemsl.) Sarg. (L. chinense) exhibits a distinct phenomenon where seed setting ratio is not more than 10% in natural environment. To explore the origin of this phenomenon, we conducted a comparative morphological and proteomic analysis on L. chinense pistils upon pollination. The morphological analysis showed that pollen grows well in vitro, but much slower on pistil or nutrient medium containing pistil extract. Proteomic analysis showed that 493 proteins had changed the expression after pollination. Among them, 468 and 51 proteins were identified by isobaric tags for relative and absolute quantitation and two-dimensional gel electrophoresis respectively, and 26 proteins were common in the two methods. After proteins functional categorization, 66 differentially expressed proteins that are involved in reproduction process were found. Further analysis showed that among the reproductive process related proteins, protein disulfide-isomerase A6 and four embryo-defective proteins showed closer relations with the low seed setting phenomenon. The results indicated that the element from pistil might be the main reason leading to low seed setting in L. chinense, which will provide new insights in the mechanisms underlying L. chinense reproduction process.
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20
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Wijnen CL, Keurentjes JJB. Genetic resources for quantitative trait analysis: novelty and efficiency in design from an Arabidopsis perspective. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:103-9. [PMID: 24657834 DOI: 10.1016/j.pbi.2014.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 05/11/2023]
Abstract
The use of genetic resources for the analysis of quantitative traits finds its roots in crop breeding but has seen a rejuvenation in Arabidopsis thaliana thanks to specific tools and genomic approaches. Although widely used in numerous crop and natural species, many approaches were first developed in this reference plant. We will discuss the scientific background and historical use of mapping populations in Arabidopsis and highlight the technological innovations that drove the development of novel strategies. We will especially lay emphasis on the methodologies used to generate the diverse population types and designate possible applications. Finally we highlight some of the most recent developments in generating genetic mapping resources and suggest specific usage for these novel tools and concepts.
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Affiliation(s)
- Cris L Wijnen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, Amsterdam 1098 XH, The Netherlands.
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21
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Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo MC. Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Funct Integr Genomics 2014; 14:59-73. [PMID: 24610029 PMCID: PMC4273598 DOI: 10.1007/s10142-014-0363-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/27/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
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Affiliation(s)
- Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Reyazul Rouf Mir
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Yuqin Hu
- University of California, Davis, USA
| | - Sarwar Azam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Canada
| | | | - Oscar Riera-Lizarazu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Dow AgroSciences, Pullman, USA
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22
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López-Bucio JS, Dubrovsky JG, Raya-González J, Ugartechea-Chirino Y, López-Bucio J, de Luna-Valdez LA, Ramos-Vega M, León P, Guevara-García AA. Arabidopsis thaliana mitogen-activated protein kinase 6 is involved in seed formation and modulation of primary and lateral root development. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:169-83. [PMID: 24218326 PMCID: PMC3883294 DOI: 10.1093/jxb/ert368] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Mitogen-activated protein kinase (MAPKs) cascades are signal transduction modules highly conserved in all eukaryotes regulating various aspects of plant biology, including stress responses and developmental programmes. In this study, we characterized the role of MAPK 6 (MPK6) in Arabidopsis embryo development and in post-embryonic root system architecture. We found that the mpk6 mutation caused altered embryo development giving rise to three seed phenotypes that, post-germination, correlated with alterations in root architecture. In the smaller seed class, mutant seedlings failed to develop the primary root, possibly as a result of an earlier defect in the division of the hypophysis cell during embryo development, but they had the capacity to develop adventitious roots to complete their life cycle. In the larger class, the MPK6 loss of function did not cause any evident alteration in seed morphology, but the embryo and the mature seed were bigger than the wild type. Seedlings developed from these bigger seeds were characterized by a primary root longer than that of the wild type, accompanied by significantly increased lateral root initiation and more and longer root hairs. Apparently, the increment in primary root growth resulted from an enhanced cell production and cell elongation. Our data demonstrated that MPK6 plays an important role during embryo development and acts as a repressor of primary and lateral root development.
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Affiliation(s)
- J. S. López-Bucio
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - J. G. Dubrovsky
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - J. Raya-González
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio A-1′, CP 58030 Morelia, Michoacán, México
| | - Y. Ugartechea-Chirino
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 3er circuito exterior SN, Del. Coyoacán, México D.F. 04510, México
| | - J. López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio A-1′, CP 58030 Morelia, Michoacán, México
| | - L. A. de Luna-Valdez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - M. Ramos-Vega
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - P. León
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - A. A. Guevara-García
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
- * To whom correspondence should be addressed. E-mail:
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23
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Kim J, Olinares PD, Oh SH, Ghisaura S, Poliakov A, Ponnala L, van Wijk KJ. Modified Clp protease complex in the ClpP3 null mutant and consequences for chloroplast development and function in Arabidopsis. PLANT PHYSIOLOGY 2013; 162:157-79. [PMID: 23548781 PMCID: PMC3641200 DOI: 10.1104/pp.113.215699] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/27/2013] [Indexed: 05/18/2023]
Abstract
The plastid ClpPRT protease consists of two heptameric rings of ClpP1/ClpR1/ClpR2/ClpR3/ClpR4 (the R-ring) and ClpP3/ClpP4/ClpP5/ClpP6 (the P-ring) and peripherally associated ClpT1/ClpT2 subunits. Here, we address the contributions of ClpP3 and ClpP4 to ClpPRT core organization and function in Arabidopsis (Arabidopsis thaliana). ClpP4 is strictly required for embryogenesis, similar to ClpP5. In contrast, loss of ClpP3 (clpp3-1) leads to arrest at the hypocotyl stage; this developmental arrest can be removed by supplementation with sucrose or glucose. Heterotrophically grown clpp3-1 can be transferred to soil and generate viable seed, which is surprising, since we previously showed that CLPR2 and CLPR4 null alleles are always sterile and die on soil. Based on native gels and mass spectrometry-based quantification, we show that despite the loss of ClpP3, modified ClpPR core(s) could be formed, albeit at strongly reduced levels. A large portion of ClpPR subunits accumulated in heptameric rings, with overaccumulation of ClpP1/ClpP5/ClpP6 and ClpR3. Remarkably, the association of ClpT1 to the modified Clp core was unchanged. Large-scale quantitative proteomics assays of clpp3-1 showed a 50% loss of photosynthetic capacity and the up-regulation of plastoglobules and all chloroplast stromal chaperone systems. Specific chloroplast proteases were significantly up-regulated, whereas the major thylakoid protease (FtsH1/FtsH2/FtsH5/FtsH8) was clearly unchanged, indicating a controlled protease network response. clpp3-1 showed a systematic decrease of chloroplast-encoded proteins that are part of the photosynthetic apparatus but not of chloroplast-encoded proteins with other functions. Candidate substrates and an explanation for the differential phenotypes between the CLPP3, CLPP4, and CLPP5 null mutants are discussed.
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24
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Bohne AV, Schwarz C, Schottkowski M, Lidschreiber M, Piotrowski M, Zerges W, Nickelsen J. Reciprocal regulation of protein synthesis and carbon metabolism for thylakoid membrane biogenesis. PLoS Biol 2013; 11:e1001482. [PMID: 23424285 PMCID: PMC3570535 DOI: 10.1371/journal.pbio.1001482] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/04/2013] [Indexed: 11/19/2022] Open
Abstract
A subunit of the chloroplast pyruvate dehydrogenase complex, which serves as a metabolic enzyme, also has a dual function as an RNA-binding protein and influences mRNA translation. Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities. This control can be exerted by metabolites acting as regulatory signals and/or a class of metabolic enzymes with dual functions as regulators of gene expression. However, little is known about how metabolic signals affect the balance between enzymatic and regulatory roles of these dual functional proteins. We previously described the RNA binding activity of a 63 kDa chloroplast protein from Chlamydomonas reinhardtii, which has been implicated in expression of the psbA mRNA, encoding the D1 protein of photosystem II. Here, we identify this factor as dihydrolipoamide acetyltransferase (DLA2), a subunit of the chloroplast pyruvate dehydrogenase complex (cpPDC), which is known to provide acetyl-CoA for fatty acid synthesis. Analyses of RNAi lines revealed that DLA2 is involved in the synthesis of both D1 and acetyl-CoA. Gel filtration analyses demonstrated an RNP complex containing DLA2 and the chloroplast psbA mRNA specifically in cells metabolizing acetate. An intrinsic RNA binding activity of DLA2 was confirmed by in vitro RNA binding assays. Results of fluorescence microscopy and subcellular fractionation experiments support a role of DLA2 in acetate-dependent localization of the psbA mRNA to a translation zone within the chloroplast. Reciprocally, the activity of the cpPDC was specifically affected by binding of psbA mRNA. Beyond that, in silico analysis and in vitro RNA binding studies using recombinant proteins support the possibility that RNA binding is an ancient feature of dihydrolipoamide acetyltransferases. Our results suggest a regulatory function of DLA2 in response to growth on reduced carbon energy sources. This raises the intriguing possibility that this regulation functions to coordinate the synthesis of lipids and proteins for the biogenesis of photosynthetic membranes. Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities. This control can be exerted by metabolites acting as regulatory signals on a class of metabolic enzymes with dual functions as regulators of gene expression. However, little is known about how metabolic signals affect the balance between enzymatic and regulatory roles of these proteins. Here, we report an example of a protein with dual functions in gene expression and carbon metabolism. The chloroplast pyruvate dehydrogenase complex is well-known to produce activated di-carbon precursors for fatty acid, which is required for lipid synthesis. Our results show that a subunit of this enzyme forms ribonucleoprotein particles and influences chloroplast mRNA translation. Conversely, RNA binding affects pyruvate dehydrogenase (metabolic) activity. These findings offer insight into how intracellular metabolic signaling and gene expression are reciprocally regulated during membrane biogenesis. In addition, our results suggest that these dual roles of the protein might exist in evolutionary distant organisms ranging from cyanobacteria to humans.
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Affiliation(s)
- Alexandra-Viola Bohne
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Christian Schwarz
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Marco Schottkowski
- Biology Department and Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Michael Lidschreiber
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Markus Piotrowski
- Department of Plant Physiology, Ruhr-University Bochum, Bochum, Germany
| | - William Zerges
- Biology Department and Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Jörg Nickelsen
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
- * E-mail:
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25
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Zhou Y, Tan B, Luo M, Li Y, Liu C, Chen C, Yu CW, Yang S, Dong S, Ruan J, Yuan L, Zhang Z, Zhao L, Li C, Chen H, Cui Y, Wu K, Huang S. HISTONE DEACETYLASE19 interacts with HSL1 and participates in the repression of seed maturation genes in Arabidopsis seedlings. THE PLANT CELL 2013; 25:134-48. [PMID: 23362207 PMCID: PMC3584530 DOI: 10.1105/tpc.112.096313] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 12/21/2012] [Accepted: 12/30/2012] [Indexed: 05/18/2023]
Abstract
The seed maturation genes are specifically and highly expressed during late embryogenesis. In this work, yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays revealed that HISTONE DEACETYLASE19 (HDA19) interacted with the HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2-LIKE1 (HSL1), and the zinc-finger CW [conserved Cys (C) and Trp (W) residues] domain of HSL1 was responsible for the interaction. Furthermore, we found that mutations in HDA19 resulted in the ectopic expression of seed maturation genes in seedlings, which was associated with increased levels of gene activation marks, such as Histone H3 acetylation (H3ac), Histone H4 acetylation (H4ac), and Histone H3 Lys 4 tri-methylation (H3K4me3), but decreased levels of the gene repression mark Histone H3 Lys 27 tri-methylation (H3K27me3) in the promoter and/or coding regions. In addition, elevated transcription of certain seed maturation genes was also found in the hsl1 mutant seedlings, which was also accompanied by the enrichment of gene activation marks but decreased levels of the gene repression mark. Chromatin immunoprecipitation assays showed that HDA19 could directly bind to the chromatin of the seed maturation genes. These results suggest that HDA19 and HSL1 may act together to repress seed maturation gene expression during germination. Further genetic analyses revealed that the homozygous hsl1 hda19 double mutants are embryonic lethal, suggesting that HDA19 and HSL1 may play a vital role during embryogenesis.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Bin Tan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ming Luo
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chen Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chen Chen
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Chun-Wei Yu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Songguang Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shuai Dong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbin Yuan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhou Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Linmao Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chenlong Li
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Huhui Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Address correspondences to
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26
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Sosso D, Canut M, Gendrot G, Dedieu A, Chambrier P, Barkan A, Consonni G, M. Rogowsky P. PPR8522 encodes a chloroplast-targeted pentatricopeptide repeat protein necessary for maize embryogenesis and vegetative development. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5843-57. [PMID: 22945943 PMCID: PMC3467297 DOI: 10.1093/jxb/ers232] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The pentatricopeptide repeat (PPR) domain is an RNA binding domain allowing members of the PPR superfamily to participate in post-transcriptional processing of organellar RNA. Loss of PPR8522 from maize (Zea mays) confers an embryo-specific (emb) phenotype. The emb8522 mutation was isolated in an active Mutator (Mu) population and co-segregation analysis revealed that it was tightly linked to a MuDR insertion in the first exon of PPR8522. Independent evidence that disruption of PPR8522 caused the emb phenotype was provided by fine mapping to a region of 116kb containing no other gene than PPR8522 and complementation of the emb8522 mutant by a PPR8522 cDNA. The deduced PPR8522 amino acid sequence of 832 amino acids contains 10 PPR repeats and a chloroplast target peptide, the function of which was experimentally demonstrated by transient expression in Nicotiana benthamiana. Whereas mutant endosperm is apparently normal, mutant embryos deviate from normal development as early as 3 days after pollination, are reduced in size, exhibit more or less severe morphological aberrations depending on the genetic background, and generally do not germinate. The emb8522 mutation is the first to associate the loss of a PPR gene with an embryo-lethal phenotype in maize. Analyses of mutant plantlets generated by embryo-rescue experiments indicate that emb8522 also affects vegetative plant growth and chloroplast development. The loss of chloroplast transcription dependent on plastid-encoded RNA polymerase is the likely cause for the lack of an organized thylakoid network and an albino, seedling-lethal phenotype.
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Affiliation(s)
- Davide Sosso
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
- Dipartimento di Produzione Vegetale, Università degli Studi di
Milano,20133 Milan,Italy
| | - Matthieu Canut
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Ghislaine Gendrot
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Annick Dedieu
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Pierre Chambrier
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, EugeneOR 97403,USA
| | - Gabriella Consonni
- Dipartimento di Produzione Vegetale, Università degli Studi di
Milano,20133 Milan,Italy
| | - Peter M. Rogowsky
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
- To whom correspondence should be addressed: E-mail:
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Yin T, Pan G, Liu H, Wu J, Li Y, Zhao Z, Fu T, Zhou Y. The chloroplast ribosomal protein L21 gene is essential for plastid development and embryogenesis in Arabidopsis. PLANTA 2012; 235:907-21. [PMID: 22105802 DOI: 10.1007/s00425-011-1547-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/31/2011] [Indexed: 05/22/2023]
Abstract
Embryogenesis in higher plants is controlled by a complex gene network. Identification and characterization of genes essential for embryogenesis will provide insights into the early events in embryo development. In this study, a novel mutant with aborted seed development (asd) was identified in Arabidopsis. The asd mutant produced about 25% of albino seeds at the early stage of silique development. The segregation of normal and albino seeds was inherited as a single recessive embryo-lethal trait. The gene disrupted in the asd mutant was isolated through map-based cloning. The mutated gene contains a single base change (A to C) in the coding region of RPL21C (At1g35680) that is predicted to encode the chloroplast 50S ribosomal protein L21. Allele test with other two T-DNA insertion lines in RPL21C and a complementation test demonstrated that the mutation in RPL21C was responsible for the asd phenotype. RPL21C exhibits higher expression in leaves and flowers compared with expression levels in roots and developing seeds. The RPL21C-GFP fusion protein was localized in chloroplasts. Cytological observations showed that the asd embryo development was arrested at the globular stage. There were no plastids with normal thylakoids and as a result no normal chloroplasts formed in mutant cells, indicating an indispensable role of the ASD gene in chloroplasts biogenesis. Our studies suggest that the chloroplast ribosomal protein L21 gene is required for chloroplast development and embryogenesis in Arabidopsis.
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Affiliation(s)
- Tuanzhang Yin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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28
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Lloyd J, Meinke D. A comprehensive dataset of genes with a loss-of-function mutant phenotype in Arabidopsis. PLANT PHYSIOLOGY 2012; 158:1115-29. [PMID: 22247268 PMCID: PMC3291275 DOI: 10.1104/pp.111.192393] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 01/12/2012] [Indexed: 05/18/2023]
Abstract
Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms.
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29
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Lu P, Han X, Qi J, Yang J, Wijeratne AJ, Li T, Ma H. Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis. Genome Res 2012; 22:508-18. [PMID: 22106370 PMCID: PMC3290786 DOI: 10.1101/gr.127522.111] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 11/17/2011] [Indexed: 11/24/2022]
Abstract
Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two sets of all four meiotic products from a Columbia (Col)/Ler hybrid to investigate genome-wide variation and meiotic recombination at nucleotide resolution. Comparing Ler and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs, and small indels. A total of 443 genes have at least 10 nonsynonymous substitutions in protein-coding regions, with enrichment for disease-resistance genes. Another 316 genes are affected by large indels, including 130 genes with complete deletion of coding regions in Ler. Using the Arabidopsis qrt1 mutant, two sets of four meiotic products were generated and analyzed by sequencing for meiotic recombination, representing the first tetrad analysis with whole-genome sequencing in a nonfungal species. We detected 18 COs, six of which had an associated GC event, and four GCs without COs (NCOs), and revealed that Arabidopsis GCs are likely fewer and with shorter tracts than those in yeast. Meiotic recombination and chromosome assortment events dramatically redistributed genome variation in meiotic products, contributing to population diversity. In particular, meiosis provides a rapid mechanism to generate copy-number variation (CNV) of sequences that have different chromosomal positions in Col and Ler.
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Affiliation(s)
- Pingli Lu
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Xinwei Han
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Program in Genetics, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jiange Yang
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Asela J. Wijeratne
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Program in Plant Biology, the Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tao Li
- Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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30
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Kumar S, Yoshizumi T, Hongo H, Yoneda A, Hara H, Hamasaki H, Takahashi N, Nagata N, Shimada H, Matsui M. Arabidopsis mitochondrial protein TIM50 affects hypocotyl cell elongation through intracellular ATP level. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 183:212-7. [PMID: 22195596 DOI: 10.1016/j.plantsci.2011.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 08/31/2011] [Accepted: 08/31/2011] [Indexed: 05/08/2023]
Abstract
The plant hypocotyl is an excellent model for the analysis of cell elongation. We have characterized a knockout mutant of the Arabidopsis TIM50 gene that showed a reduction in the hypocotyls length of etiolated seedlings. We also found that a knockout of TIM50 caused enlargement and deformation of the mitochondrial structure and a reduction in intracellular ATP levels. TIM50 is a component of the mitochondrial TIM23 inner membrane protein complex and is involved in the import of mitochondrial proteins. The short hypocotyl phenotype was recovered by the addition of Compound C, an inhibitor of AMPK. Thus, the mitochondrial ATP level controls cell elongation in Arabidopsis hypocotyls through possible signaling via AMPK.
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Affiliation(s)
- Shailesh Kumar
- Plant Synthetic Genomics Research Division, Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama 244-0813, Japan
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Muralla R, Lloyd J, Meinke D. Molecular foundations of reproductive lethality in Arabidopsis thaliana. PLoS One 2011; 6:e28398. [PMID: 22164284 PMCID: PMC3229588 DOI: 10.1371/journal.pone.0028398] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/07/2011] [Indexed: 11/23/2022] Open
Abstract
The SeedGenes database (www.seedgenes.org) contains information on more than 400 genes required for embryo development in Arabidopsis. Many of these EMBRYO-DEFECTIVE (EMB) genes encode proteins with an essential function required throughout the life cycle. This raises a fundamental question. Why does elimination of an essential gene in Arabidopsis often result in embryo lethality rather than gametophyte lethality? In other words, how do mutant (emb) gametophytes survive and participate in fertilization when an essential cellular function is disrupted? Furthermore, why do some mutant embryos proceed further in development than others? To address these questions, we first established a curated dataset of genes required for gametophyte development in Arabidopsis based on information extracted from the literature. This provided a basis for comparison with EMB genes obtained from the SeedGenes dataset. We also identified genes that exhibited both embryo and gametophyte defects when disrupted by a loss-of-function mutation. We then evaluated the relationship between mutant phenotype, gene redundancy, mutant allele strength, gene expression pattern, protein function, and intracellular protein localization to determine what factors influence the phenotypes of lethal mutants in Arabidopsis. After removing cases where continued development potentially resulted from gene redundancy or residual function of a weak mutant allele, we identified numerous examples of viable mutant (emb) gametophytes that required further explanation. We propose that the presence of gene products derived from transcription in diploid (heterozygous) sporocytes often enables mutant gametophytes to survive the loss of an essential gene in Arabidopsis. Whether gene disruption results in embryo or gametophyte lethality therefore depends in part on the ability of residual, parental gene products to support gametophyte development. We also highlight here 70 preglobular embryo mutants with a zygotic pattern of inheritance, which provide valuable insights into the maternal-to-zygotic transition in Arabidopsis and the timing of paternal gene activation during embryo development.
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Affiliation(s)
- Rosanna Muralla
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Johnny Lloyd
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - David Meinke
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail:
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Schmidt A, Wuest SE, Vijverberg K, Baroux C, Kleen D, Grossniklaus U. Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development. PLoS Biol 2011; 9:e1001155. [PMID: 21949639 PMCID: PMC3176755 DOI: 10.1371/journal.pbio.1001155] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 08/05/2011] [Indexed: 01/23/2023] Open
Abstract
Germ line specification is a crucial step in the life cycle of all organisms. For sexual plant reproduction, the megaspore mother cell (MMC) is of crucial importance: it marks the first cell of the plant "germline" lineage that gets committed to undergo meiosis. One of the meiotic products, the functional megaspore, subsequently gives rise to the haploid, multicellular female gametophyte that harbours the female gametes. The MMC is formed by selection and differentiation of a single somatic, sub-epidermal cell in the ovule. The transcriptional network underlying MMC specification and differentiation is largely unknown. We provide the first transcriptome analysis of an MMC using the model plant Arabidopsis thaliana with a combination of laser-assisted microdissection and microarray hybridizations. Statistical analyses identified an over-representation of translational regulation control pathways and a significant enrichment of DEAD/DEAH-box helicases in the MMC transcriptome, paralleling important features of the animal germline. Analysis of two independent T-DNA insertion lines suggests an important role of an enriched helicase, MNEME (MEM), in MMC differentiation and the restriction of the germline fate to only one cell per ovule primordium. In heterozygous mem mutants, additional enlarged MMC-like cells, which sometimes initiate female gametophyte development, were observed at higher frequencies than in the wild type. This closely resembles the phenotype of mutants affected in the small RNA and DNA-methylation pathways important for epigenetic regulation. Importantly, the mem phenotype shows features of apospory, as female gametophytes initiate from two non-sister cells in these mutants. Moreover, in mem gametophytic nuclei, both higher order chromatin structure and the distribution of LIKE HETEROCHROMATIN PROTEIN1 were affected, indicating epigenetic perturbations. In summary, the MMC transcriptome sets the stage for future functional characterization as illustrated by the identification of MEM, a novel gene involved in the restriction of germline fate.
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Affiliation(s)
- Anja Schmidt
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Samuel E. Wuest
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Kitty Vijverberg
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Célia Baroux
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Daniela Kleen
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- * E-mail:
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Hsu SC, Belmonte MF, Harada JJ, Inoue K. Indispensable Roles of Plastids in Arabidopsis thaliana Embryogenesis. Curr Genomics 2011; 11:338-49. [PMID: 21286311 PMCID: PMC2944999 DOI: 10.2174/138920210791616716] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/18/2010] [Accepted: 05/25/2010] [Indexed: 11/22/2022] Open
Abstract
The plastid is an organelle vital to all photosynthetic and some non-photosynthetic eukaryotes. In the model plant Arabidopsis thaliana, a number of nuclear genes encoding plastid proteins have been found to be necessary for embryo development. However, the exact roles of plastids in this process remain largely unknown. Here we use publicly available datasets to obtain insights into the relevance of plastid activities to A. thaliana embryogenesis. By searching the SeedGenes database (http://www.seedgenes.org) and recent literature, we found that, of the 339 non-redundant genes required for proper embryo formation, 108 genes likely encode plastid-targeted proteins. Nineteen of these genes are necessary for development of preglobular embryos and/or their conversion to globular embryos, of which 13 genes encode proteins involved in non-photosynthetic metabolism. By contrast, among 38 genes which are dispensable for globular embryo formation but necessary for further development, only one codes for a protein involved in metabolism. Products of 21 of the 38 genes play roles in plastid gene expression and maintenance. Examination of RNA profiles of embryos at distinct growth stages obtained in laser-capture microdissection coupled with DNA microarray experiments revealed that most of the identified genes are expressed throughout embryo morphogenesis and maturation. These findings suggest that metabolic activities are required at preglobular and throughout all stages of embryo development, whereas plastid gene expression becomes necessary during and/or after the globular stage to sustain various activities of the organelle including photosynthetic electron transport.
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Affiliation(s)
- Shih-Chi Hsu
- Department of Plant Sciences, University of California, Davis, CA, USA
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Bryant N, Lloyd J, Sweeney C, Myouga F, Meinke D. Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis. PLANT PHYSIOLOGY 2011; 155:1678-89. [PMID: 21139083 PMCID: PMC3091104 DOI: 10.1104/pp.110.168120] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 11/29/2010] [Indexed: 05/18/2023]
Abstract
We describe here the diversity of chloroplast proteins required for embryo development in Arabidopsis (Arabidopsis thaliana). Interfering with certain chloroplast functions has long been known to result in embryo lethality. What has not been reported before is a comprehensive screen for embryo-defective (emb) mutants altered in chloroplast proteins. From a collection of transposon and T-DNA insertion lines at the RIKEN chloroplast function database (http://rarge.psc.riken.jp/chloroplast/) that initially appeared to lack homozygotes and segregate for defective seeds, we identified 23 additional examples of EMB genes that likely encode chloroplast-localized proteins. Fourteen gene identities were confirmed with allelism tests involving duplicate mutant alleles. We then queried journal publications and the SeedGenes database (www.seedgenes.org) to establish a comprehensive dataset of 381 nuclear genes encoding chloroplast proteins of Arabidopsis associated with embryo-defective (119 genes), plant pigment (121 genes), gametophyte (three genes), and alternate (138 genes) phenotypes. Loci were ranked based on the level of certainty that the gene responsible for the phenotype had been identified and the protein product localized to chloroplasts. Embryo development is frequently arrested when amino acid, vitamin, or nucleotide biosynthesis is disrupted but proceeds when photosynthesis is compromised and when levels of chlorophyll, carotenoids, or terpenoids are reduced. Chloroplast translation is also required for embryo development, with genes encoding chloroplast ribosomal and pentatricopeptide repeat proteins well represented among EMB datasets. The chloroplast accD locus, which is necessary for fatty acid biosynthesis, is essential in Arabidopsis but not in Brassica napus or maize (Zea mays), where duplicated nuclear genes compensate for its absence or loss of function.
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Olinares PDB, Ponnala L, van Wijk KJ. Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering. Mol Cell Proteomics 2010; 9:1594-615. [PMID: 20423899 DOI: 10.1074/mcp.m000038-mcp201] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To characterize MDa-sized macromolecular chloroplast stroma protein assemblies and to extend coverage of the chloroplast stroma proteome, we fractionated soluble chloroplast stroma in the non-denatured state by size exclusion chromatography with a size separation range up to approximately 5 MDa. To maximize protein complex stability and resolution of megadalton complexes, ionic strength and composition were optimized. Subsequent high accuracy tandem mass spectrometry analysis (LTQ-Orbitrap) identified 1081 proteins across the complete native mass range. Protein complexes and assembly states above 0.8 MDa were resolved using hierarchical clustering, and protein heat maps were generated from normalized protein spectral counts for each of the size exclusion chromatography fractions; this complemented previous analysis of stromal complexes up to 0.8 MDa (Peltier, J. B., Cai, Y., Sun, Q., Zabrouskov, V., Giacomelli, L., Rudella, A., Ytterberg, A. J., Rutschow, H., and van Wijk, K. J. (2006) The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Mol. Cell. Proteomics 5, 114-133). This combined experimental and bioinformatics analyses resolved chloroplast ribosomes in different assembly and functional states (e.g. 30, 50, and 70 S), which enabled the identification of plastid homologues of prokaryotic ribosome assembly factors as well as proteins involved in co-translational modifications, targeting, and folding. The roles of these ribosome-associating proteins will be discussed. Known RNA splice factors (e.g. CAF1/WTF1/RNC1) as well as uncharacterized proteins with RNA-binding domains (pentatricopeptide repeat, RNA recognition motif, and chloroplast ribosome maturation), RNases, and DEAD box helicases were found in various sized complexes. Chloroplast DNA (>3 MDa) was found in association with the complete heteromeric plastid-encoded DNA polymerase complex, and a dozen other DNA-binding proteins, e.g. DNA gyrase, topoisomerase, and various DNA repair enzymes. The heteromeric >or=5-MDa pyruvate dehydrogenase complex and the 0.8-1-MDa acetyl-CoA carboxylase complex associated with uncharacterized biotin carboxyl carrier domain proteins constitute the entry point to fatty acid metabolism in leaves; we suggest that their large size relates to the need for metabolic channeling. Protein annotations and identification data are available through the Plant Proteomics Database, and mass spectrometry data are available through Proteomics Identifications database.
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Koornneef M, Meinke D. The development of Arabidopsis as a model plant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:909-21. [PMID: 20409266 DOI: 10.1111/j.1365-313x.2009.04086.x] [Citation(s) in RCA: 220] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom.
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Affiliation(s)
- Maarten Koornneef
- Department of Plant Breeding and Genetics at the Max Planck Institute for Plant Breeding Research, Carl-von Linné Weg 10, Cologne, Germany.
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De Smet I, Lau S, Mayer U, Jürgens G. Embryogenesis - the humble beginnings of plant life. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:959-70. [PMID: 20409270 DOI: 10.1111/j.1365-313x.2010.04143.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Each plant starts life from the zygote formed by the fusion of an egg and a sperm cell. The zygote gives rise to a multicellular embryo that displays a basic plant body organization and is surrounded by nutritive endosperm and maternal tissue. How the body organization is generated had already been studied before the genome sequence of Arabidopsis thaliana was completed 10 years ago, but several regulatory mechanisms of embryo development have since been discovered or analysed in more detail. Although this progress did not strictly depend on the availability of the genome sequence itself, several advances were considerably facilitated. In this review, we mainly address early embryo development, highlighting general mechanisms and crucial regulators, including phytohormones, that are involved in patterning the embryo and were mainly analysed in the post-genome decade. We also highlight some unsolved problems, provide a brief outlook on the future of Arabidopsis embryo research, and discuss how the knowledge gained from Arabidopsis could be translated to crop species.
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Affiliation(s)
- Ive De Smet
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 3, Tübingen, Germany
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