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Armbrecht L, Eisenhofer R, Utge J, Sibert EC, Rocha F, Ward R, Pierella Karlusich JJ, Tirichine L, Norris R, Summers M, Bowler C. Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. ISME COMMUNICATIONS 2021; 1:66. [PMID: 36755065 PMCID: PMC9723766 DOI: 10.1038/s43705-021-00070-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022]
Abstract
Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.
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Affiliation(s)
- Linda Armbrecht
- Institute for Marine and Antarctic Studies (IMAS), Ecology & Biodiversity Centre, University of Tasmania, Battery Point, TAS, 7004, Australia.
- Australian Centre for Ancient DNA, School of Biological Sciences, Faculty of Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Raphael Eisenhofer
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - José Utge
- UMR 7206, Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, 75016, Paris, France
| | - Elizabeth C Sibert
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, 06511, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06511, USA
| | - Fabio Rocha
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Ryan Ward
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Juan José Pierella Karlusich
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Richard Norris
- GRD, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92093-0244, USA
| | - Mindi Summers
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
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Oldenburg DJ, Bendich AJ. DNA maintenance in plastids and mitochondria of plants. FRONTIERS IN PLANT SCIENCE 2015; 6:883. [PMID: 26579143 PMCID: PMC4624840 DOI: 10.3389/fpls.2015.00883] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/05/2015] [Indexed: 05/02/2023]
Abstract
The DNA molecules in plastids and mitochondria of plants have been studied for over 40 years. Here, we review the data on the circular or linear form, replication, repair, and persistence of the organellar DNA (orgDNA) in plants. The bacterial origin of orgDNA appears to have profoundly influenced ideas about the properties of chromosomal DNA molecules in these organelles to the point of dismissing data inconsistent with ideas from the 1970s. When found at all, circular genome-sized molecules comprise a few percent of orgDNA. In cells active in orgDNA replication, most orgDNA is found as linear and branched-linear forms larger than the size of the genome, likely a consequence of a virus-like DNA replication mechanism. In contrast to the stable chromosomal DNA molecules in bacteria and the plant nucleus, the molecular integrity of orgDNA declines during leaf development at a rate that varies among plant species. This decline is attributed to degradation of damaged-but-not-repaired molecules, with a proposed repair cost-saving benefit most evident in grasses. All orgDNA maintenance activities are proposed to occur on the nucleoid tethered to organellar membranes by developmentally-regulated proteins.
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Raven JA. Implications of mutation of organelle genomes for organelle function and evolution. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5639-50. [PMID: 26077836 DOI: 10.1093/jxb/erv298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK †School of Plant Biology, University of Western Australia, M048, 35 Stirling Highway, Crawley, WA 6009, Australia
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Kumar RA, Oldenburg DJ, Bendich AJ. Changes in DNA damage, molecular integrity, and copy number for plastid DNA and mitochondrial DNA during maize development. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6425-39. [PMID: 25261192 PMCID: PMC4246179 DOI: 10.1093/jxb/eru359] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The amount and structural integrity of organellar DNAs change during plant development, although the mechanisms of change are poorly understood. Using PCR-based methods, we quantified DNA damage, molecular integrity, and genome copy number for plastid and mitochondrial DNAs of maize seedlings. A DNA repair assay was also used to assess DNA impediments. During development, DNA damage increased and molecules with impediments that prevented amplification by Taq DNA polymerase increased, with light causing the greatest change. DNA copy number values depended on the assay method, with standard real-time quantitative PCR (qPCR) values exceeding those determined by long-PCR by 100- to 1000-fold. As the organelles develop, their DNAs may be damaged in oxidative environments created by photo-oxidative reactions and photosynthetic/respiratory electron transfer. Some molecules may be repaired, while molecules with unrepaired damage may be degraded to non-functional fragments measured by standard qPCR but not by long-PCR.
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Affiliation(s)
- Rachana A Kumar
- Department of Biology, University of Washington, Seattle, WA 98195-5325, USA
| | - Delene J Oldenburg
- Department of Biology, University of Washington, Seattle, WA 98195-5325, USA
| | - Arnold J Bendich
- Department of Biology, University of Washington, Seattle, WA 98195-5325, USA
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Bendich AJ. DNA abandonment and the mechanisms of uniparental inheritance of mitochondria and chloroplasts. Chromosome Res 2014; 21:287-96. [PMID: 23681660 DOI: 10.1007/s10577-013-9349-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
For most eukaryotic organisms, the nuclear genomes of both parents are transmitted to the progeny following biparental inheritance. For mitochondria and chloroplasts, however, uniparental inheritance (UPI) is frequently observed. The maternal mode of inheritance for mitochondria in animals can be nearly absolute, suggesting an adaptive advantage for UPI. In other organisms, however, the mode of inheritance for mitochondria and chloroplasts can vary greatly even among strains of a species. Here, I review the data on the transmission of organellar DNA (orgDNA) from parent to progeny and the structure, copy number, and stability of orgDNA molecules. I propose that UPI is an incidental by-product of DNA abandonment, a process that lowers the metabolic cost of orgDNA repair.
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Affiliation(s)
- Arnold J Bendich
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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Schlunegger B, Stutz E. The Euglena gracilis chloroplast genome: structural features of a DNA region possibly carrying the single origin of DNA replication. Curr Genet 2013; 8:629-34. [PMID: 24178003 DOI: 10.1007/bf00395709] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/1984] [Indexed: 10/26/2022]
Abstract
We sequenced a Bg1II-HindIII DNA fragment of the Euglena gracilis chloroplast genome which most likely carries the single origin of DNA replication according to recent electronmicroscopic mapping studies (Koller and Delius 1982a; Ravel-Chapuis et al. 1982). This DNA fragment contains a polymorphic region (Schlunegger et al. 1983) which is composed, as will be shown, of multiple tandem repeats (54 bp, 87% A+T). Furthermore we located on this DNA fragment a short inverted repeat element (96 positions) observed in the electronmicroscopic studies (Koller and Delius 1982b). Between the borders of the polymorphic region and the nearby inverted repeat (distance of 179 positions) we retrieved an exact copy of parts of the rDNA leader (105 positions) including 49 positions of the chloroplast trnW gene. A computer search for bacterial type Ori-regions did not reveal any significant sequence homology. However, the polymorphic region and its immediate vicinity have the capacity to form multiple stem and loop structures which may be involved in DNA replication initiation.
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Affiliation(s)
- B Schlunegger
- Laboratoire de Biochimie, Université de Neuchâtel, Chantemerle 18, CH-2000, Neuchâtel, Switzerland
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Rawson JR, Boerma C. Influence of growth conditions upon the number of chloroplast DNA molecules in Euglena gracilis. Proc Natl Acad Sci U S A 2010; 73:2401-4. [PMID: 16592334 PMCID: PMC430584 DOI: 10.1073/pnas.73.7.2401] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The number of chloroplast DNA molecules in Euglena gracilis cells was measured by determining the shift in the observed second-order rate constant for the reassociation of (125)I-labeled chloroplast DNA in the presence of unlabeled total cell DNA. Cells grown to stationary phase in the dark contained 217 molecules of chloroplast DNA. Cells grown to stationary phase in the light in either heterotrophic or autotrophic medium contained 590 and 1014 chloroplast DNA molecules, respectively. The observed second-order rate constant for the reassociation of (125)I-labeled chloroplast DNA was not significantly altered in the presence of total cell DNA from a heat-bleached mutant, ZHB, which lacks chloroplast DNA. This evidence suggests that there is less than 0.3 of a chloroplast DNA molecule present in the nucleus of Euglena.
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Affiliation(s)
- J R Rawson
- Department of Botany, University of Georgia, Athens, Ga. 30602
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Bendich AJ. Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organisms. Biol Direct 2010; 5:42. [PMID: 20587059 PMCID: PMC2907347 DOI: 10.1186/1745-6150-5-42] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 06/29/2010] [Indexed: 01/12/2023] Open
Abstract
Background Several proposals have been made to explain the rise of multicellular life forms. An internal environment can be created and controlled, germ cells can be protected in novel structures, and increased organismal size allows a "division of labor" among cell types. These proposals describe advantages of multicellular versus unicellular organisms at levels of organization at or above the individual cell. I focus on a subsequent phase of evolution, when multicellular organisms initiated the process of development that later became the more complex embryonic development found in animals and plants. The advantage here is realized at the level of the mitochondrion and chloroplast. Hypothesis The extreme instability of DNA in mitochondria and chloroplasts has not been widely appreciated even though it was first reported four decades ago. Here, I show that the evolutionary success of multicellular animals and plants can be traced to the protection of organellar DNA. Three stages are envisioned. Sequestration allowed mitochondria and chloroplasts to be placed in "quiet" germ line cells so that their DNA is not exposed to the oxidative stress produced by these organelles in "active" somatic cells. This advantage then provided Opportunity, a period of time during which novel processes arose for signaling within and between cells and (in animals) for cell-cell recognition molecules to evolve. Development then led to the enormous diversity of animals and plants. Implications The potency of a somatic stem cell is its potential to generate cell types other than itself, and this is a systems property. One of the biochemical properties required for stemness to emerge from a population of cells might be the metabolic quiescence that protects organellar DNA from oxidative stress. Reviewers This article was reviewed by John Logsdon, Arcady Mushegian, and Patrick Forterre.
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Affiliation(s)
- Arnold J Bendich
- Department of Biology, University of Washington, Seattle, WA 98195-5325, USA.
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Roberts TM, Lauer GD, Klotz LC, Zimm BH. Physical Studies on DNA From “Primitive” Eucaryote. ACTA ACUST UNITED AC 2008. [DOI: 10.3109/10409237609105455] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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10
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11
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Genetic Organization of the Chloroplast. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/s0074-7696(08)61372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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12
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Schlunegger B, Fasnacht M, Stutz E, Koller B, Delius H. Analysis of a polymorphic region of the Euglena gracilis chloroplast genome. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0167-4781(83)90051-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Heizmann P, Ravel-Chapuis P, Nigon V. Minicircular DNA having sequence homologies with chloroplast DNA in a bleached mutant of Euglena gracilis. Curr Genet 1982; 6:119-22. [DOI: 10.1007/bf00435210] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/1982] [Indexed: 10/26/2022]
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Hussein Y, Heizmann P, Nicolas P, Nigon V. Quantitative estimations of chloroplast DNA in bleached mutants of Euglena gracilis. Curr Genet 1982; 6:111-7. [DOI: 10.1007/bf00435209] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/1982] [Indexed: 11/28/2022]
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15
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Ravel-Chapuis P, Heizmann P, Nigon V. Electron microscopic localization of the replication origin of Euglena gracilis chloroplast DNA. Nature 1982. [DOI: 10.1038/300078a0] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Keller SJ, Ho C. Chloroplast DNA Replication in Chlamydomonas reinhardtii. ACTA ACUST UNITED AC 1981. [DOI: 10.1016/s0074-7696(08)62322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Nicolas P, Hussein Y, Heizmann P, Nigon V. Comparative studies of chloroplastic and nuclear DNA repair abilities after ultraviolet irradiation of Euglena gracilis. MOLECULAR & GENERAL GENETICS : MGG 1980; 178:567-72. [PMID: 6930537 DOI: 10.1007/bf00337862] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Studies of nuclear and chloroplastic-DNA repair after ultraviolet irradiation of Euglena gracilis show that photoreactivation is very efficient at both the nuclear and chloroplastic level. Liquid-holding or split-dose experiments and treatment with caffeine reveal, furthermore, that dark-repair is very efficient in nuclear DNA but not in chloroplastic DNA (ctDNA). The possibility of a chloroplastic dark-repair of restricted efficiency is discussed. Determination of chloroplastic DNA content by reassociation kinetics indicates that an important degradation follows UV irradiation during liquid holding in the dark.
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Wurtz EA, Sears BB, Rabert DK, Shepherd HS, Gillham NW, Boynton JE. A specific increase in chloroplast gene mutations following growth of Chlamydomonas in 5-fluorodeoxyuridine. MOLECULAR & GENERAL GENETICS : MGG 1979; 170:235-42. [PMID: 156870 DOI: 10.1007/bf00267056] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Verdier G. Poly(adenylic acid)-containing RNA of Euglena gracilis during chloroplast development. I. Analysis of their complexity by hybridization to complementary DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:573-80. [PMID: 105904 DOI: 10.1111/j.1432-1033.1979.tb12857.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Verdier G. Poly(adenylic acid)-containing RNA of Euglena gracilis during chloroplast development. 2. Transcriptional origin of the different RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:581-6. [PMID: 105905 DOI: 10.1111/j.1432-1033.1979.tb12858.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
The mechanism for the turnover-synthesis of chloroplast DNA in the absence of net synthesis during the chloroplast maturation in Euglena gracilis was determined. DNA synthesis was measured by incorporation of32Pi into chloroplast DNA. The density label, 15N, was incorporated to examine the mechanism of turnover-synthesis. The newly synthesized segments represent a replacement of segments in the DNA containing 1.5 X 10(3) to 6.1 X 10(3) nucleotides. Twenty-three fragments of chloroplast DNA, generated by digestion with the restriction endonuclease EcoRI, became labeled with 32Pi. Turnover-synthesis, therefore, replaces segments throughout the molecule of chloroplast DNA.
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Nigon V, Heizmann P. Morphology, Biochemistry, and Genetics of Plastid Development in Euglena gracilis. INTERNATIONAL REVIEW OF CYTOLOGY 1978. [DOI: 10.1016/s0074-7696(08)62243-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Small GD, Greimann CS. Photoreactivation and dark repair of ultraviolet light-induced pyrimidine dimers in chloroplast DNA. Nucleic Acids Res 1977; 4:2893-902. [PMID: 909795 PMCID: PMC342617 DOI: 10.1093/nar/4.8.2893] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A UV-specific endonuclease was used to detect ultraviolet light-induced pyrimidine dimers in chloroplast DNA of Chlamydomonas reinhardi that was specifically labeled with tritiated thymidine. All of the dimers induced by 100 J/m2 of 254 nm light are removed by photoreaction. Wild-type cells exposed to 50 J/m2 of UF light removed over 80% of the dimers from chloroplast DNA after 24 h of incubation in growth medium in the dark. A UV- sensitive mutant, UVS1, defective in the excision of pyrimidine dimers from nuclear DNA is capable of removing pyrimidine dimers from chloroplast DNA nearly as well as wild-type, suggesting that nuclear and chloroplast DNA dark-repair systems are under separate genetic control.
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Manning JE, Wolstenholme DR. Replication of kinetoplast DNA of Crithidia acanthocephali. I. Density shift experiments using deuterium oxide. J Cell Biol 1976; 70:406-18. [PMID: 939783 PMCID: PMC2109834 DOI: 10.1083/jcb.70.2.406] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The protozoan Crithidia acanthocephali contains, within a modified region of a mitochondrion, a mass of DNA known as kinetoplast DNA (kDNA). This DNA consists mainly of an association of approximately 27,000 covalently closed 0.8-mum circular molecules which are apparently held together in a definite ordered manner by topological interlocking. After culturing of C. acanthocephali cells for 25 generations in medium containing 75% deuterium oxide, both nuclear DNA (rhonative, nondeuterated=1.717 g/cm3) and kDNA (rhonative, nondeuterated=1.702 g/cm3) increased in buoyant density by 0.012 g/cm3. The replication of the two DNAs was studied by cesium chloride buoyant density analysis of DNAs from exponentially growing cells taken at 1.0, 1.4, 2.0, 3.0, and 4.0 cell doublings after transfer of cells from D2O-containing medium into medium containing only normal water. The results obtained from analysis of both native and denatured nuclear DNAs indicate that this DNA replicates semiconservatively. From an analysis of intact associations of kDNA, it appears that this DNA doubles once per generation and that the newly synthesized DNA does not segregate from parental DNA. Fractions of covalently closed single circular molecules and of open circular and unit length linear molecules were obtained from associations of kDNA by sonication, sucrose sedimentation, and cesium chloride-ethidium bromide equilibrium gradient centrifugation. Buoyant density profiles obtained from these fractions indicate that: (a) doubling of the kDNA results from the replication of each circular molecule rather than from repeated replication of a small fraction of the circular molecules; (b) replication of kDNA is semiconservative rather than conservative, but there is recombination between the circles at an undefined time during the cell cycle.
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Stolarsky L, Walfield AM, Birch RA, Hershberger CL. Light-stimulated synthesis of chloroplast DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 425:438-50. [PMID: 816375 DOI: 10.1016/0005-2787(76)90008-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Light-stimulated chloroplast DNA synthesis was studied during chloroplast development in the absence of cell division and nuclear DNA synthesis. Incorporation of 32Pi was stimulated 10-15 fold, however, the ratio of chloroplast DNA to nuclear DNA remained constant. Isotope dilution experiments suggested that stimulated labeling of chloroplast DNA represented more efficient utilization of exogenously supplied Pi rather than stimulated turnover of chloroplast DNA. The low level of DNA synthesis and chloroplast development were resistant to nalidixic acid which inhibits semiconservative replication of chloroplast DNA.
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27
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Presence of displacement loops in the covalently closed circular chloroplast deoxyribonucleic acid from higher plants. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)40750-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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28
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Pienkos P, Walfield A, Hershberger CL. Effect of nalidixic acid on Euglena gracilis: induced loss of chloroplast deoxyribonucleic acid. Arch Biochem Biophys 1974; 165:548-53. [PMID: 4216299 DOI: 10.1016/0003-9861(74)90281-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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29
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Crouse EJ, Vandrey JP, Stutz E. Hybridization studies with RNA and DNA isolated from Euglena gracilis chloroplasts and mitochondria. FEBS Lett 1974; 42:262-6. [PMID: 4212058 DOI: 10.1016/0014-5793(74)80741-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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30
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Mielenz JR, Hershberger CL. Are segments of chloroplast DNA differentially amplified? Biochem Biophys Res Commun 1974; 58:769-77. [PMID: 4209285 DOI: 10.1016/s0006-291x(74)80484-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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31
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32
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33
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Gibbs SP, Poole RJ. Autoradiographic evidence for many segregating DNA molecules in the chloroplast of Ochromonas danica. J Cell Biol 1973; 59:318-28. [PMID: 4805002 PMCID: PMC2109101 DOI: 10.1083/jcb.59.2.318] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Light-grown cells of Ochromonas danica, which contain a single chloroplast per cell, were labeled with [methyl-(3)H]thymidine for 3 h (0.36 generations) and the distribution of labeled DNA among the progeny chloroplasts was followed during exponential growth in unlabeled medium for a further 3.3 generations using light microscope autoradiography of serial sections of entire chloroplasts. Thymidine was specifically incorporated into DNA in both nuclei and chloroplasts. Essentially all the chloroplasts incorporated label in the 3-h labeling period, indicating that chloroplast DNA is synthesized throughout the cell cycle. Nuclear DNA has a more limited S period. Both chloroplast DNA and nuclear DNA are conserved during 3.3 generations. After 3.3 generations in unlabeled medium, grains per chloroplast followed a Poisson distribution indicating essentially equal labeling of all progeny chloroplasts. It is concluded that the average chloroplast in cells of Ochromonas growing exponentially in the light contains at least 10 segregating DNA molecules.
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Rawson JR, Haselkorn R. Chloroplast ribosomal RNA genes in the chloroplast DNA of Euglena gracilis. J Mol Biol 1973; 77:125-32. [PMID: 4203658 DOI: 10.1016/0022-2836(73)90366-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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