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Broz AK, Sloan DB, Johnston IG. Stochastic organelle genome segregation through Arabidopsis development and reproduction. THE NEW PHYTOLOGIST 2024; 241:896-910. [PMID: 37925790 PMCID: PMC10841260 DOI: 10.1111/nph.19288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023]
Abstract
Organelle DNA (oDNA) in mitochondria and plastids is vital for plant (and eukaryotic) life. Selection against damaged oDNA is mediated in part by segregation - sorting different oDNA types into different cells in the germline. Plants segregate oDNA very rapidly, with oDNA recombination protein MSH1 a key driver of this segregation, but we have limited knowledge of the dynamics of this segregation within plants and between generations. Here, we reveal how oDNA evolves through Arabidopsis thaliana development and reproduction. We combine stochastic modelling, Bayesian inference, and model selection with new and existing tissue-specific oDNA measurements from heteroplasmic Arabidopsis plant lines through development and between generations. Segregation proceeds gradually but continually during plant development, with a more rapid increase between inflorescence formation and the next generation. When MSH1 is compromised, the majority of observed segregation can be achieved through partitioning at cell divisions. When MSH1 is functional, mtDNA segregation is far more rapid; we show that increased oDNA gene conversion is a plausible mechanism quantitatively explaining this acceleration. These findings reveal the quantitative, time-dependent details of oDNA segregation in Arabidopsis. We also discuss the support for different models of the plant germline provided by these observations.
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Affiliation(s)
- Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, 5007, Norway
- Computational Biology Unit, University of Bergen, Bergen, 5007, Norway
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2
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Mao L, Zou Q, Sun Z, Dong Q, Cao X. Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae). Sci Rep 2023; 13:87. [PMID: 36596857 PMCID: PMC9810647 DOI: 10.1038/s41598-022-27163-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Species from the flowering plant genus Cyclamen are popular amongst consumers. In particular Cyclamen persicum Mill. has been significantly used commercially, and certain small flowering species such as Cyclamen hederifolium and Cyclamen coum are gradually growing in popularity in the potted flower market. Here, the chloroplast genomes of nine Cyclamen samples including four Cyclamen species and five varieties of C. hederifolium were sequenced for genome structure comparison, White green septal striped leaves related gene screening and DNA molecular markers were developed for phylogenetic analysis. In comparing Cyclamen species' chloroplast genomes, gene content and gene order were found to be highly similar with the length of genomes ranging from 151,626 to 153,058 bp. The chloroplast genome of Cyclamen has 128 genes, including 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Based on intraspecific variation, seven hotspots, including three genes and four intergenic regions, were identified as variable markers for downstream species delimitation and interspecific relationship analyses. Moreover, a phylogenetic tree constructed with complete chloroplast genomes, revealed that Cyclamen are monophyletic with Lysimachia as the closest neighbor. Phylogenetic analyses of the 14 Cyclamen species with the seven variable regions showed five distinct clades within this genus. The highly supported topologies showed these seven regions may be used as candidate DNA barcode sequences to distinguish Cyclamen species. White green septal striped leaves is common in C. hederifolium, however the molecular mechanism of this has not yet been described. Here, we find that the intergenic region rps4-trnT-UGU seems related to white green septal striped leaves.
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Affiliation(s)
- Lihui Mao
- Zhejiang Instiute of Landscape Plants and Flowers, Hangzhou, 311251 Zhejiang China
| | - Qingcheng Zou
- Zhejiang Instiute of Landscape Plants and Flowers, Hangzhou, 311251 Zhejiang China
| | - Zhongshuai Sun
- grid.440657.40000 0004 1762 5832Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000 Zhejiang China
| | - Qing Dong
- Zhejiang Instiute of Landscape Plants and Flowers, Hangzhou, 311251 Zhejiang China
| | - Xuerui Cao
- Zhejiang Instiute of Landscape Plants and Flowers, Hangzhou, 311251 Zhejiang China
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3
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Broz AK, Keene A, Fernandes Gyorfy M, Hodous M, Johnston IG, Sloan DB. Sorting of mitochondrial and plastid heteroplasmy in Arabidopsis is extremely rapid and depends on MSH1 activity. Proc Natl Acad Sci U S A 2022; 119:e2206973119. [PMID: 35969753 PMCID: PMC9407294 DOI: 10.1073/pnas.2206973119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 12/16/2022] Open
Abstract
The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell (heteroplasmy). The extent to which heteroplasmies are transmitted across generations or eliminated through genetic bottlenecks is not well understood in plants, in part because their low mutation rates make these variants so infrequent. Disruption of MutS Homolog 1 (MSH1), a gene involved in plant organellar DNA repair, results in numerous de novo point mutations, which we used to quantitatively track the inheritance of single nucleotide variants in mitochondrial and plastid genomes in Arabidopsis. We found that heteroplasmic sorting (the fixation or loss of a variant) was rapid for both organelles, greatly exceeding rates observed in animals. In msh1 mutants, plastid variants sorted faster than those in mitochondria and were typically fixed or lost within a single generation. Effective transmission bottleneck sizes (N) for plastids and mitochondria were N ∼ 1 and 4, respectively. Restoring MSH1 function further increased the rate of heteroplasmic sorting in mitochondria (N ∼ 1.3), potentially because of its hypothesized role in promoting gene conversion as a mechanism of DNA repair, which is expected to homogenize genome copies within a cell. Heteroplasmic sorting also favored GC base pairs. Therefore, recombinational repair and gene conversion in plant organellar genomes can potentially accelerate the elimination of heteroplasmies and bias the outcome of this sorting process.
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Affiliation(s)
- Amanda K. Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Alexandra Keene
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | | | - Mychaela Hodous
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, 5007, Norway
- Computational Biology Unit, University of Bergen, Bergen, 5007, Norway
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
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Malinova I, Zupok A, Massouh A, Schöttler MA, Meyer EH, Yaneva-Roder L, Szymanski W, Rößner M, Ruf S, Bock R, Greiner S. Correction of frameshift mutations in the atpB gene by translational recoding in chloroplasts of Oenothera and tobacco. THE PLANT CELL 2021; 33:1682-1705. [PMID: 33561268 PMCID: PMC8254509 DOI: 10.1093/plcell/koab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/02/2021] [Indexed: 05/10/2023]
Abstract
Translational recoding, also known as ribosomal frameshifting, is a process that causes ribosome slippage along the messenger RNA, thereby changing the amino acid sequence of the synthesized protein. Whether the chloroplast employs recoding is unknown. I-iota, a plastome mutant of Oenothera (evening primrose), carries a single adenine insertion in an oligoA stretch [11A] of the atpB coding region (encoding the β-subunit of the ATP synthase). The mutation is expected to cause synthesis of a truncated, nonfunctional protein. We report that a full-length AtpB protein is detectable in I-iota leaves, suggesting operation of a recoding mechanism. To characterize the phenomenon, we generated transplastomic tobacco lines in which the atpB reading frame was altered by insertions or deletions in the oligoA motif. We observed that insertion of two adenines was more efficiently corrected than insertion of a single adenine, or deletion of one or two adenines. We further show that homopolymeric composition of the oligoA stretch is essential for recoding, as an additional replacement of AAA lysine codon by AAG resulted in an albino phenotype. Our work provides evidence for the operation of translational recoding in chloroplasts. Recoding enables correction of frameshift mutations and can restore photoautotrophic growth in the presence of a mutation that otherwise would be lethal.
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Affiliation(s)
- Irina Malinova
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Arkadiusz Zupok
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Amid Massouh
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Etienne H Meyer
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Liliya Yaneva-Roder
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Witold Szymanski
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Margit Rößner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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5
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Edwards DM, Røyrvik EC, Chustecki JM, Giannakis K, Glastad RC, Radzvilavicius AL, Johnston IG. Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck. PLoS Biol 2021; 19:e3001153. [PMID: 33891583 PMCID: PMC8064548 DOI: 10.1371/journal.pbio.3001153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes. A comprehensive model for mitochondrial and plasmid DNA segregation, supported by with genomic, transcriptomic, and single-cell data, shows how the attritional effects of Muller’s ratchet can be avoided in the organelles of diverse eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Norway
- Computational Biology Unit, University of Bergen, Norway
- * E-mail:
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6
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Ji J, Day A. Construction of a highly error-prone DNA polymerase for developing organelle mutation systems. Nucleic Acids Res 2020; 48:11868-11879. [PMID: 33135056 PMCID: PMC7708058 DOI: 10.1093/nar/gkaa929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
A novel family of DNA polymerases replicates organelle genomes in a wide distribution of taxa encompassing plants and protozoans. Making error-prone mutator versions of gamma DNA polymerases revolutionised our understanding of animal mitochondrial genomes but similar advances have not been made for the organelle DNA polymerases present in plant mitochondria and chloroplasts. We tested the fidelities of error prone tobacco organelle DNA polymerases using a novel positive selection method involving replication of the phage lambda cI repressor gene. Unlike gamma DNA polymerases, ablation of 3'-5' exonuclease function resulted in a modest 5-8-fold error rate increase. Combining exonuclease deficiency with a polymerisation domain substitution raised the organelle DNA polymerase error rate by 140-fold relative to the wild type enzyme. This high error rate compares favourably with error-rates of mutator versions of animal gamma DNA polymerases. The error prone organelle DNA polymerase introduced mutations at multiple locations ranging from two to seven sites in half of the mutant cI genes studied. Single base substitutions predominated including frequent A:A (template: dNMP) mispairings. High error rate and semi-dominance to the wild type enzyme in vitro make the error prone organelle DNA polymerase suitable for elevating mutation rates in chloroplasts and mitochondria.
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MESH Headings
- Amino Acid Sequence
- Bacterial Outer Membrane Proteins/chemistry
- Bacterial Outer Membrane Proteins/genetics
- Bacterial Outer Membrane Proteins/metabolism
- Binding Sites
- Chloroplasts/genetics
- Chloroplasts/metabolism
- Cloning, Molecular
- DNA Polymerase gamma/chemistry
- DNA Polymerase gamma/genetics
- DNA Polymerase gamma/metabolism
- DNA Replication
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Models, Molecular
- Mutation
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Polymorphism, Single Nucleotide
- Porins/chemistry
- Porins/genetics
- Porins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Selection, Genetic
- Sequence Alignment
- Sequence Homology, Amino Acid
- Nicotiana/classification
- Nicotiana/genetics
- Nicotiana/metabolism
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Affiliation(s)
- Junwei Ji
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Anil Day
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
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7
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Lencina F, Landau AM, Petterson ME, Pacheco MG, Kobayashi K, Prina AR. The rpl23 gene and pseudogene are hotspots of illegitimate recombination in barley chloroplast mutator seedlings. Sci Rep 2019; 9:9960. [PMID: 31292475 PMCID: PMC6620283 DOI: 10.1038/s41598-019-46321-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/26/2019] [Indexed: 11/23/2022] Open
Abstract
Previously, through a TILLING (Targeting Induced Local Lesions in Genomes) approach applied on barley chloroplast mutator (cpm) seedlings a high frequency of polymorphisms in the rpl23 gene was detected. All the polymorphisms corresponded to five differences already known to exist in nature between the rpl23 gene located in the inverted repeats (IRs) and the rpl23 pseudogene located in the large single copy region (LSC). In this investigation, polymorphisms in the rpl23 gene were verified and besides, a similar situation was found for the pseudogene in cpm seedlings. On the other hand, no polymorphisms were found in any of those loci in 40 wild type barley seedlings. Those facts and the independent occurrence of polymorphisms in the gene and pseudogene in individual seedlings suggest that the detected polymorphisms initially arose from gene conversion between gene and pseudogene. Moreover, an additional recombination process involving small recombinant segments seems to occur between the two gene copies as a consequence of their location in the IRs. These and previous results support the hypothesis that the CPM protein is a component of the plastome mismatch repair (MMR) system, whose failure of the anti-recombination activity results in increased illegitimate recombination between the rpl23 gene and pseudogene.
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Affiliation(s)
- F Lencina
- Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), INTA (Instituto Nacional de Tecnología Agropecuaria), Nicolás Repetto y de los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
| | - A M Landau
- Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), INTA (Instituto Nacional de Tecnología Agropecuaria), Nicolás Repetto y de los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
| | - M E Petterson
- Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), INTA (Instituto Nacional de Tecnología Agropecuaria), Nicolás Repetto y de los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
| | - M G Pacheco
- Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), INTA (Instituto Nacional de Tecnología Agropecuaria), Nicolás Repetto y de los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
| | - K Kobayashi
- Laboratorio de Agrobiotecnología, Grupo Biología Molecular Vegetal Aplicada, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA, CONICET-UBA), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - A R Prina
- Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), INTA (Instituto Nacional de Tecnología Agropecuaria), Nicolás Repetto y de los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina.
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8
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Sobanski J, Giavalisco P, Fischer A, Kreiner JM, Walther D, Schöttler MA, Pellizzer T, Golczyk H, Obata T, Bock R, Sears BB, Greiner S. Chloroplast competition is controlled by lipid biosynthesis in evening primroses. Proc Natl Acad Sci U S A 2019; 116:5665-5674. [PMID: 30833407 PMCID: PMC6431223 DOI: 10.1073/pnas.1811661116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In most eukaryotes, organellar genomes are transmitted preferentially by the mother, but molecular mechanisms and evolutionary forces underlying this fundamental biological principle are far from understood. It is believed that biparental inheritance promotes competition between the cytoplasmic organelles and allows the spread of so-called selfish cytoplasmic elements. Those can be, for example, fast-replicating or aggressive chloroplasts (plastids) that are incompatible with the hybrid nuclear genome and therefore maladaptive. Here we show that the ability of plastids to compete against each other is a metabolic phenotype determined by extremely rapidly evolving genes in the plastid genome of the evening primrose Oenothera Repeats in the regulatory region of accD (the plastid-encoded subunit of the acetyl-CoA carboxylase, which catalyzes the first and rate-limiting step of lipid biosynthesis), as well as in ycf2 (a giant reading frame of still unknown function), are responsible for the differences in competitive behavior of plastid genotypes. Polymorphisms in these genes influence lipid synthesis and most likely profiles of the plastid envelope membrane. These in turn determine plastid division and/or turnover rates and hence competitiveness. This work uncovers cytoplasmic drive loci controlling the outcome of biparental chloroplast transmission. Here, they define the mode of chloroplast inheritance, as plastid competitiveness can result in uniparental inheritance (through elimination of the "weak" plastid) or biparental inheritance (when two similarly "strong" plastids are transmitted).
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Affiliation(s)
- Johanna Sobanski
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Department Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Axel Fischer
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Julia M Kreiner
- Department of Ecology & Evolutionary Biology, University of Toronto, ON M5S 3B2, Canada
| | - Dirk Walther
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Tommaso Pellizzer
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Hieronim Golczyk
- Department of Molecular Biology, Institute of Biotechnology, John Paul II Catholic University of Lublin, Konstantynów 1I, 20-708, Poland
| | - Toshihiro Obata
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Ralph Bock
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Barbara B Sears
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312
| | - Stephan Greiner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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9
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Tang X, Wang Y, Zhang Y, Huang S, Liu Z, Fei D, Feng H. A missense mutation of plastid RPS4 is associated with chlorophyll deficiency in Chinese cabbage (Brassica campestris ssp. pekinensis). BMC PLANT BIOLOGY 2018; 18:130. [PMID: 29940850 PMCID: PMC6019835 DOI: 10.1186/s12870-018-1353-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 06/17/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plastome mutants are ideal resources for elucidating the functions of plastid genes. Numerous studies have been conducted for the function of plastid genes in barley and tobacco; however, related information is limited in Chinese cabbage. RESULTS A chlorophyll-deficient mutant of Chinese cabbage that was derived by ethyl methanesulfonate treatment on isolated microspores showed uniformly pale green inner leaves and slow growth compared with that shown by the wild type "Fukuda 50' ('FT'). Genetic analysis revealed that cdm was cytoplasmically inherited. Physiological and ultrastructural analyses of cdm showed impaired photosynthesis and abnormal chloroplast development. Utilizing next generation sequencing, the complete plastomes of cdm and 'FT' were respectively re-mapped to the reference genome of Chinese cabbage, and an A-to-C base substitution with a mutation ratio higher than 99% was detected. The missense mutation of plastid ribosomal protein S4 led to valine substitution for glycine at residue 193. The expression level of rps4 was analyzed using quantitative real-time PCR and found lower in than in 'FT'. RNA gel-blot assays showed that the abundance of mature 23S rRNA, 16S rRNA, 5S rRNA, and 4.5S rRNA significantly decreased and that the processing of 23S, 16S rRNA, and 4.5S rRNA was seriously impaired, affecting the ribosomal function in cdm. CONCLUSIONS These findings indicated that cdm was a plastome mutant and that chlorophyll deficiency might be due to an A-to-C base substitution of the plastome-encoded rps4 that impaired the rRNA processing and affected the ribosomal function.
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Affiliation(s)
- Xiaoyan Tang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Yiheng Wang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Yun Zhang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Shengnan Huang
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Zhiyong Liu
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Danli Fei
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
| | - Hui Feng
- College of Horticulture, Liaoning Key Lab of Genetics and Breeding for Cruciferous Vegetable Crops, Shenyang Agricultural University, Shenyang, Liaoning 110866 People’s Republic of China
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10
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Landau A, Lencina F, Pacheco MG, Prina AR. Plastome Mutations and Recombination Events in Barley Chloroplast Mutator Seedlings. J Hered 2016; 107:266-73. [PMID: 26774059 PMCID: PMC4885237 DOI: 10.1093/jhered/esw003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/04/2016] [Indexed: 11/12/2022] Open
Abstract
The barley chloroplast mutator (cpm) is an allele of a nuclear gene that when homozygous induces several types of cytoplasmically inherited chlorophyll deficiencies. In this work, a plastome Targeting Induced Local Lesions in Genomes (TILLING) strategy based on mismatch digestion was used on families that carried the cpm genotype through many generations. Extensive scanning of 33 plastome genes and a few intergenic regions was conducted. Numerous polymorphisms were detected on both genic and intergenic regions. The detected polymorphisms can be accounted for by at least 61 independent mutational events. The vast majority of the polymorphisms originated in substitutions and small indels (insertions/deletions) in microsatellites. The rpl23 and the rps16 genes were the most polymorphic. Interestingly, the variation observed in the rpl23 gene consisted of several combinations of 5 different one nucleotide polymorphisms. Besides, 4 large indels that have direct repeats at both ends were also observed, which appear to be originated from recombinational events. The cpm mutation spectrum suggests that the CPM gene product is probably involved in plastome mismatch repair. The numerous subtle molecular changes that were localized in a wide range of plastome sites show the cpm as a valuable source of plastome variability for plant research and/or plant breeding. Moreover, the cpm mutant appears to be an interesting experimental material for investigating the mechanisms responsible for maintaining the stability of plant organelle DNA.
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Affiliation(s)
- Alejandra Landau
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina)
| | - Franco Lencina
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina)
| | - María G Pacheco
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina)
| | - Alberto R Prina
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina).
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Abstract
Why the DNA-containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall-back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode.
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Affiliation(s)
- Stephan Greiner
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Johanna Sobanski
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
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12
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Bock DG, Andrew RL, Rieseberg LH. On the adaptive value of cytoplasmic genomes in plants. Mol Ecol 2014; 23:4899-911. [PMID: 25223488 DOI: 10.1111/mec.12920] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 01/30/2023]
Abstract
Is DNA variation maintained in organelle genomes selectively neutral? The answer to this question has important implications for many aspects of ecology and evolution. While traditionally the answer has been 'yes', recent studies in animals have shown that, on the contrary, mitochondrial DNA polymorphism is frequently adaptive. In plants, however, the neutrality assumption has not been strongly challenged. Here, we begin with a critical evaluation of arguments in favour of this long-held view. We then discuss the latest empirical evidence for the opposing prediction that sequence variation in plant cytoplasmic genomes is frequently adaptive. While outstanding research progress is being made towards understanding this fundamental topic, we highlight the need for studies that combine information ranging from field experiments to physiology to molecular evolutionary biology. Such an interdisciplinary approach provides a means for determining the frequency, drivers and evolutionary significance of adaptive organelle DNA variation.
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Affiliation(s)
- Dan G Bock
- Department of Botany, Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, Canada, V6T 1Z4
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Greiner S, Köhl K. Growing evening primroses (Oenothera). FRONTIERS IN PLANT SCIENCE 2014; 5:38. [PMID: 24592268 PMCID: PMC3923160 DOI: 10.3389/fpls.2014.00038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/27/2014] [Indexed: 05/10/2023]
Abstract
The model plant Oenothera has contributed significantly to the biological sciences and it dominated the early development of plant genetics, cytogenetics, and evolutionary biology. The great advantage of using Oenothera as a model system is a large body of genetic, cytological, morphological, and ecological information collected over more than a century. The Oenothera system offers a well-studied taxonomy, population structure, and ecology. Cytogenetics and formal genetics at the population level are extensively developed, providing an excellent basis to study evolutionary questions. Further, Oenothera is grown as an oil seed crop for the production of essential fatty acids (gamma-linoleic acid) and is considered to be a medicinal plant due to its many pharmaceutically active secondary metabolites, such as ellagitannins. Although Oenothera has been cultivated as a laboratory organism since the end of the 19th century, there is a substantial lack of literature dealing with modern greenhouse techniques for the genus. This review compiles an overview about the growth requirements for the genus Oenothera, with a special focus on its genetically best-studied subsections Oenothera and Munzia. Requirements for greenhouse, field, and agronomic cultures are presented, together with information on substrate types, pest control, as well as vegetative and seed propagation, cross pollination, harvest, and seed storage. Particular aspects like germination, bolting, and flowering induction in taxonomically diverse material are reviewed. Methods recommended are supported by ecological and experimental data. An overview of the possibilities for wide hybridization and polyploidy induction in the genus is given. Germplasm resources are referenced. In summary, a comprehensive guideline for successful laboratory cultivation of Oenothera species is provided.
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Affiliation(s)
- Stephan Greiner
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
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Greiner S, Bock R. Tuning a ménage à trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants. Bioessays 2013; 35:354-65. [DOI: 10.1002/bies.201200137] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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