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Fields O, Hammond MJ, Xu X, O'Neill EC. Advances in euglenoid genomics: unravelling the fascinating biology of a complex clade. Trends Genet 2024:S0168-9525(24)00173-2. [PMID: 39147613 DOI: 10.1016/j.tig.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024]
Abstract
Euglenids have long been studied due to their unique physiology and versatile metabolism, providing underpinnings for much of our understanding of photosynthesis and biochemistry, and a growing opportunity in biotechnology. Until recently there has been a lack of genetic studies due to their large and complex genomes, but recently new technologies have begun to unveil their genetic capabilities. Whilst much research has focused on the model organism Euglena gracilis, other members of the euglenids have now started to receive due attention. Currently only poor nuclear genome assemblies of E. gracilis and Rhabdomonas costata are available, but there are many more plastid genome sequences and an increasing number of transcriptomes. As more assemblies become available, there are great opportunities to understand the fundamental biology of these organisms and to exploit them for biotechnology.
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Affiliation(s)
- Oskar Fields
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; These authors contributed equally
| | - Michael J Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic; These authors contributed equally
| | - Xiao Xu
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; These authors contributed equally
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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2
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Abstract
A complete clone bank representing the chloroplast DNA from Vicia faba has been constructed. A total of 15 fragments (10 Pst1, 1 Pst1-EcoR1 and 4 Sal1 fragments) were inserted into the vector pBR322 and transformed into the E. coli strain HB101. The cloned fragments were used as the main tools in constructing the physical map of Vicia faba for the restriction endonucleases Pst1, Kpn1 and Xho1. The identity of the cloned fragments was demonstrated by restriction analysis and blot hybridization. The information generated was used to construct the map. The 16S and 23S rRNA genes and the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase have been positioned on the map using heterologous probes. The orientation of the gene for the large subunit of RuBP carboxylase has also been determined.
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3
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Spencer DF, Gray MW. Ribosomal RNA genes in Euglena gracilis mitochondrial DNA: fragmented genes in a seemingly fragmented genome. Mol Genet Genomics 2011; 285:19-31. [PMID: 20978909 DOI: 10.1007/s00438-010-0585-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/05/2010] [Indexed: 11/27/2022]
Abstract
Because relatively little information is available about mtDNA in the euglenid protozoa, distant relatives of the kinetoplastid protozoa, we investigated mitochondrial genome structure and expression in Euglena gracilis. We found that isolated E. gracilis mtDNA comprises a heterodisperse collection of short molecules (modal size approximately 4 kbp) and that the mitochondrial large subunit (LSU) and small subunit (SSU) rRNAs are each split into two pieces. For the two halves of the SSU rRNA, we identified separate, non-contiguous coding modules that are flanked by a complex array of (primarily direct) A + T-rich repeats. The potential secondary structure of the bipartite SSU rRNA displays the expected conserved elements implicated in ribosome function. Label from [α-(32)P]GTP was incorporated in the presence of guanylyltransferase into each of the separate SSU and LSU rRNA fragments, confirming that these RNAs are primary transcripts, separately expressed from non-contiguous rRNA modules. In addition to authentic genes for SSU rRNA, we discovered numerous short fragments of protein-coding and rRNA genes dispersed throughout the E. gracilis mitochondrial genome. We propose that antisense transcripts of gene fragments of this type could have been the evolutionary precursors of the guide RNAs that mediate U insertion/deletion editing in the kinetoplastid relatives of the euglenids. To the extent that E. gracilis mtDNA is a representative euglenid mitochondrial genome, it differs radically in structure and organization from that of its kinetoplastid relatives, instead more closely resembling the mitochondrial genome of dinoflagellates in many of its features, an apparent evolutionary convergence.
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Affiliation(s)
- David F Spencer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 1X5, Canada
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4
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Hedberg MF, Huang YS, Hommersand MH. Size of the Chloroplast Genome in Codium fragile. Science 2010; 213:445-7. [PMID: 17760191 DOI: 10.1126/science.213.4506.445] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chloroplasts isolated from the siphonous green alga Codium fragile yield circular DNA molecules averaging 27.3 micrometers in length and 56 x 10(6) daltons in molecular size. This chloroplast genome is 25 to 30 percent smaller than any reported. The small size of the Codium chloroplast genome may represent a primitive evolutionary condition in green plants.
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5
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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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6
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Kolodner R, Tewari KK. Inverted repeats in chloroplast DNA from higher plants. Proc Natl Acad Sci U S A 2010; 76:41-5. [PMID: 16592612 PMCID: PMC382872 DOI: 10.1073/pnas.76.1.41] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circular chloroplast DNAs from spinach, lettuce, and corn plants have been examined by electron microscopy and shown to contain a large sequence repeated one time in reverse polarity. The inverted sequence in spinach and lettuce chloroplast DNA has been found to be 24,400 base pairs long. The inverted sequence in the corn chloroplast DNA is 22,500 base pairs long. Denaturation mapping studies have shown that the structure of the inverted sequence is highly conserved in these three plants. Pea chloroplast DNA does not contain an inverted repeat. All of the circular dimers of pea chloroplast DNA are found to be in a head-to-tail confirmation. Circular dimers of spinach and lettuce were also found to have head-to-tail conformation. However, approximately 70-80% of the circular dimers in preparations of lettuce and spinach chloroplast DNA were found to be in a head-to-head conformation. We propose that the head-to-head circular dimers are formed by a recombination event between two circular monomers in the inverted sequence.
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Affiliation(s)
- R Kolodner
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92717
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7
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Kuroiwa T. 100 years since the discovery of non-Mendelian plastid phenotypes. JOURNAL OF PLANT RESEARCH 2010; 123:125-9. [PMID: 20135191 DOI: 10.1007/s10265-009-0283-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 10/19/2009] [Indexed: 05/08/2023]
Affiliation(s)
- Tsuneyoshi Kuroiwa
- Research Information Center for Extremophile, Graduate School of Science, Rikkyo University, 3-34-1 Nishiikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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8
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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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9
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Roy J, Faktorová D, Lukes J, Burger G. Unusual Mitochondrial Genome Structures throughout the Euglenozoa. Protist 2007; 158:385-96. [PMID: 17499547 DOI: 10.1016/j.protis.2007.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Accepted: 03/18/2007] [Indexed: 11/28/2022]
Abstract
Mitochondrial DNA of Kinetoplastea is composed of different chromosomes, the maxicircle (bearing 'regular' genes) and numerous minicircles (specifying guide RNAs involved in RNA editing). In trypanosomes [Kinetoplastea], DNA circles are compacted into a single dense body, the kinetoplast. This report addresses the question whether multi-chromosome mitochondrial genomes and compacted chromosome organization are restricted to Kinetoplastea or rather occur throughout Euglenozoa, i.e., Kinetoplastea, Euglenida and Diplonemea. To this end, we investigated the diplonemid Rhynchopus euleeides and the euglenids Petalomonas cantuscygni, Peranema trichophorum and Entosiphon sulcatum, using light and electron microscopy and molecular techniques. Our findings together with previously published data show that multi-chromosome mitochondrial genomes prevail across Euglenozoa, while kinetoplast-like mtDNA packaging is confined to trypanosomes.
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MESH Headings
- Animals
- DNA, Circular/genetics
- DNA, Circular/isolation & purification
- DNA, Circular/ultrastructure
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/isolation & purification
- DNA, Kinetoplast/ultrastructure
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/ultrastructure
- DNA, Protozoan/genetics
- DNA, Protozoan/isolation & purification
- DNA, Protozoan/ultrastructure
- Euglenida/genetics
- Euglenida/ultrastructure
- Microscopy, Electron, Transmission
- Microscopy, Fluorescence
- Mitochondria/diagnostic imaging
- Mitochondria/genetics
- Ultrasonography
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Affiliation(s)
- Joannie Roy
- Centre Robert Cedergren, Bioinformatics & Genomics, Département de biochimie, Université de Montréal, Montréal, QC, Canada, H3 T 1J4
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10
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Santillán Torres JL, Atteia A, Claros MG, González-Halphen D. Cytochrome f and subunit IV, two essential components of the photosynthetic bf complex typically encoded in the chloroplast genome, are nucleus-encoded in Euglena gracilis. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1604:180-9. [PMID: 12837550 DOI: 10.1016/s0005-2728(03)00058-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The photosynthetic protist Euglena gracilis contains chloroplasts surrounded by three membranes which arise from secondary endosymbiosis. The genes petA and petD, encoding cytochrome f and subunit IV of the cytochrome bf complex, normally present in chloroplast genomes, are lacking from the chloroplast DNA (cpDNA) of E. gracilis. The bf complex of E. gracilis was isolated, and the identities of cytochrome f and subunit IV were established immunochemically, by heme-specific staining, and by Edman degradation. Based on N-terminal and conserved internal protein sequences, primers were designed and used for PCR gene amplification and cDNA sequencing. The complete sequence of the petA cDNA and the partial sequence of the petD cDNA from E. gracilis are described. Evidence is provided that in this protist, the petA and petD genes have migrated from the chloroplast to the nucleus. Both genes exhibit a typical nuclear codon usage, clearly distinct from the usage of chloroplast genes. The petA gene encodes an atypical cytochrome f, with a unique insertion of 62 residues not present in other f-type cytochromes. The petA gene also acquired a region that encodes a large tripartite chloroplast transit peptide (CTP), which is thought to allow the import of apocytochrome f through the three-membrane envelope of E. gracilis chloroplasts. This is the first description of petA and petD genes that are nucleus-localized.
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Affiliation(s)
- José Luis Santillán Torres
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, 04510 Mexico City, Mexico
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11
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Herrmann RG, Maier RM, Schmitz-Linneweber C. Eukaryotic genome evolution: rearrangement and coevolution of compartmentalized genetic information. Philos Trans R Soc Lond B Biol Sci 2003; 358:87-97; discussion 97. [PMID: 12594919 PMCID: PMC1693106 DOI: 10.1098/rstb.2002.1177] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The plant cell operates with an integrated, compartmentalized genome consisting of nucleus/cytosol, plastids and mitochondria that, in its entirety, is regulated in time, quantitatively, in multicellular organisms and also in space. This genome, as do genomes of eukaryotes in general, originated in endosymbiotic events, with at least three cells, and was shaped phylogenetically by a massive and highly complex restructuring and intermixing of the genetic potentials of the symbiotic partners and by lateral gene transfer. This was accompanied by fundamental changes in expression signals in the entire system at almost all regulatory levels. The gross genome rearrangements contrast with a highly specific compartmental interplay, which becomes apparent in interspecific nuclear-plastid cybrids or hybrids. Organelle exchanges, even between closely related species, can greatly disturb the intracellular genetic balance ("hybrid bleaching"), which is indicative of compartmental coevolution and is of relevance for speciation processes. The photosynthetic machinery of plastids, which is embedded in that genetic machinery, is an appealing model to probe into genomic and organismic evolution and to develop functional molecular genomics. We have studied the reciprocal Atropa belladonna-Nicotiana tabacum cybrids, which differ markedly in their phenotypes, and found that transcriptional and post-transcriptional processes can contribute to genome/plastome incompatibility. Allopolyploidy can influence this phenomenon by providing an increased, cryptic RNA editing potential and the capacity to maintain the integrity of organelles of different taxonomic origins.
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Affiliation(s)
- Reinhold G Herrmann
- Department für Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 Munich, Germany.
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12
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Abstract
The presence of chloroplast DNA was established in 1963. With the development of recombinant DNA technologies, chloroplast DNA was selected as one of the first candidates for genome sequencing. The first physical map was reported for maize chloroplasts in 1976. As tobacco has been popular as an experimental system, tobacco chloroplast DNA has been extensively analyzed and the complete nucleotide sequence was established in 1986. This sequencing and the availability of tobacco chloroplast transformation techniques and of in vitro expression systems have formed the basis of an ongoing functional genomics program.
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Affiliation(s)
- Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya, 467-8501, Japan,
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13
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Bogorad L. Photosynthesis research: advances through molecular biology - the beginnings, 1975-1980s and on... PHOTOSYNTHESIS RESEARCH 2003; 76:13-33. [PMID: 16228563 DOI: 10.1023/a:1024957602990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Restriction endonuclease recognition sites and genes for rRNAs were first mapped on chloroplast chromosomes in 1975-1976. This marked the beginning of the application of molecular biology tools to photosynthesis research. In the first phase, knowledge about proteins involved in photosynthesis was used to identify plastid and nuclear genes encoding these proteins on cloned segments of DNA. Soon afterwards the DNA sequences of the cloned genes revealed the full primary sequences of the proteins. Knowledge of the primary amino acid sequences provided deeper understanding of the functioning of the protein and interactions among proteins of the photosynthetic apparatus. Later, as chloroplast DNA sequencing proceeded, genes were discovered that encoded proteins that had not been known to be part of the photosynthetic apparatus. This more complete knowledge of the composition of reaction centers and of the primary amino acid sequences of individual proteins comprising the reaction centers opened the way to determining the three-dimensional structures of reaction centers. At present, the availability of cloned genes, knowledge of the gene sequences and systems developed to genetically manipulate photosynthetic organisms is permitting experimental inquiries to be made into crucial details of the photosynthetic process.
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Affiliation(s)
- Lawrence Bogorad
- Department of Molecular and Cellular Biology, Harvard University, The Biological Laboratories, 16 Divinity Ave., Cambridge, MA, 02138, USA,
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14
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Abstract
Forty years ago, soon after yeast mitochondrial DNA (mtDNA) was recognized, some animal versions of mtDNA were shown to comprise circular molecules. Supporting an idea that mitochondria had evolved from bacteria, this finding generated a dogmatic belief that yeast mtDNA was also circular, and the endless linear molecules actually observed in yeast were regarded as broken circles. This concept persisted for 30 years and has distorted our understanding of the true nature of the molecule.
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Affiliation(s)
- Don Williamson
- Parasitology Division, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.
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15
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Abstract
The chloroplast genome consists of homogeneous circular DNA molecules. To date, the entire nucleotide sequences (120-190 kbp) of chloroplast genomes have been determined from eight plant species. The chloroplast genomes of land plants and green algae contain about 110 different genes, which can be classified into two main groups: genes involved in gene expression and those related to photosynthesis. The red alga Porphyra chloroplast genome has 70 additional genes, one-third of which are related to biosynthesis of amino acids and other low molecular mass compounds. Chloroplast genes contain at least three structurally distinct promoters and transcribe two or more classes of RNA polymerase. Two chloroplast genes, rps12 of land plants and psaA of Chlamydomonas, are divided into two to three pieces and scattered over the genome. Each portion is transcribed separately, and two to three separate transcripts are joined together to yield a functional mRNA by trans-splicing. RNA editing (C to U base changes) occurs in some of the chloroplast transcripts. Most edited codons are functionally significant, creating start and stop codons and changing codons to retain conserved amino acids.
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Affiliation(s)
- M Sugiura
- Center for Gene Research, Nagoya University, Japan
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16
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Hallick RB, Hong L, Drager RG, Favreau MR, Monfort A, Orsat B, Spielmann A, Stutz E. Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res 1993; 21:3537-44. [PMID: 8346031 PMCID: PMC331456 DOI: 10.1093/nar/21.15.3537] [Citation(s) in RCA: 288] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We report the complete DNA sequence of the Euglena gracilis, Pringsheim strain Z chloroplast genome. This circular DNA is 143,170 bp, counting only one copy of a 54 bp tandem repeat sequence that is present in variable copy number within a single culture. The overall organization of the genome involves a tandem array of three complete and one partial ribosomal RNA operons, and a large single copy region. There are genes for the 16S, 5S, and 23S rRNAs of the 70S chloroplast ribosomes, 27 different tRNA species, 21 ribosomal proteins plus the gene for elongation factor EF-Tu, three RNA polymerase subunits, and 27 known photosynthesis-related polypeptides. Several putative genes of unknown function have also been identified, including five within large introns, and five with amino acid sequence similarity to genes in other organisms. This genome contains at least 149 introns. There are 72 individual group II introns, 46 individual group III introns, 10 group II introns and 18 group III introns that are components of twintrons (introns-within-introns), and three additional introns suspected to be twintrons composed of multiple group II and/or group III introns, but not yet characterized. At least 54,804 bp, or 38.3% of the total DNA content is represented by introns.
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Affiliation(s)
- R B Hallick
- Department of Biochemistry, University of Arizona, Tucson 85721
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17
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Affiliation(s)
- M Sugiura
- Center for Gene Research, Nagoya University, Japan
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18
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Ohyama K. Organization and Expression of Genes of Plastid Chromosomes from Non-Angiospermous Land Plants and Green Algae. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/978-3-7091-9138-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
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19
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20
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Affiliation(s)
- R R Sederoff
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27650, USA
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21
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Karabin GD, Narita JO, Dodd JR, Hallick RB. Euglena gracilis chloroplast ribosomal RNA transcription units. Nucleotide sequence polymorphism in 5 S rRNA genes and 5 S rRNAs. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)43730-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Karabin GD, Hallick RB. Euglena gracilis chloroplast transfer RNA transcription units. Nucleotide sequence analysis of a tRNAThr-tRNAGly-tRNAMet-tRNASer-tRNAGln gene cluster. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(20)81920-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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23
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Orozco EM, Hallick RB. Euglena gracilis chloroplast transfer RNA transcription units. I. Physical map of the transfer RNA gene loci. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)81104-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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24
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PHOTOCONTROL OF CHLOROPLAST DEVELOPMENT IN EUGLENA. Physiology (Bethesda) 1982. [DOI: 10.1016/b978-0-12-139903-0.50015-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
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25
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Ersland DR, Cattolico RA. Nuclear deoxyribonucleic acid characterization of the marine chromophyte Olisthodiscus luteus. Biochemistry 1981; 20:6886-93. [PMID: 7317360 DOI: 10.1021/bi00527a023] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nuclear DNA of the marine chromophytic alga Olisthodiscus luteus was analyzed in this study. Reassociation kinetics analysis has shown that 440-nucleotide DNA fragments from the genome of this alga contain 4% foldback, 58% repetitive, and 34% single-copy sequences. Precise analysis using isolated single-copy DNA revealed that Olisthodiscus has a large haploid DNA content of 1.66 x 10(-12) g/cell. For determination of the organization of single-copy and repetitive sequences within this genome, DNA fragments 3000 nucleotides in length were reassociated to C0t= 100 M . s. At this low C0t value 89% of the DNA bound to hydroxylapatite, suggesting that single-copy and repetitive elements are interspersed. The lengths of the duplexed repetitive DNA on these 3000-nucleotide fragments were measured by electron microscopy after digestion with S1 nuclease which removed the unreassociated single-copy DNA regions. Of these repetitive sequences, 68% were shorter than 1200 nucleotide pairs in length and had a modal length of 350 nucleotide pairs. A minor class of longer (to 4000 nucleotide pairs) repetitive sequences was also observed.
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Aldrich J, Cattolico RA. Isolation and Characterization of Chloroplast DNA from the Marine Chromophyte, Olisthodiscus luteus: Electron Microscopic Visualization of Isomeric Molecular Forms. PLANT PHYSIOLOGY 1981; 68:641-7. [PMID: 16661972 PMCID: PMC425954 DOI: 10.1104/pp.68.3.641] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Chloroplast DNA (ctDNA) from the marine chromophytic alga, Olisthodiscus luteus, has been isolated using a whole cell lysis method followed by CsCl-Hoechst 33258 dye gradient centrifugation. This DNA, which has a buoyant density of 1.691 grams per cubic centimeter was identified as plastidic in origin by enrichment experiments. Inclusion of the nuclease inhibitor aurintricarboxylic acid in all lysis buffers was mandatory for isolation of high molecular weight DNA. Long linear molecules (40 to 48 micrometers) with considerable internal organization comprised the majority of the ctDNA isolated, whereas supertwisted ctDNA and open circular molecules averaging 46 micrometers were occasionally present. Also observed in this study were folded ctDNA molecules with electron dense centers ("rosettes") and plastid DNA molecules which have a tightly wound "key-ring" center. The ctDNA of Olisthodiscus has a contour length that is median to the size range reported for chlorophytic plants.A minor component of the total cellular DNA, which originates from a DNase insensitive cellular structure, has a buoyant density of 1.694 grams per cubic centimeter. This DNA consists predominantly of linear molecules, but open circles 11.5 micrometers in length and rare 22-micrometer dimers were also present.This study represents the first analysis of the extranuclear DNA of a chromophytic alga.
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Affiliation(s)
- J Aldrich
- Department of Botany, AJ-10, University of Washington, Seattle, Washington 98195
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27
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Orozco E, Gray P, Hallick R. Euglena gracilis chloroplast ribosomal RNA transcription units. I. The location of transfer RNA, 5 S, 16 S, and 23 S ribosomal RNA genes. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70405-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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28
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van Ee JH, Veld WA, Planta RJ. Isolation and Characterization of Chloroplast DNA from the Duckweed Spirodela oligorrhiza. PLANT PHYSIOLOGY 1980; 66:572-5. [PMID: 16661479 PMCID: PMC440680 DOI: 10.1104/pp.66.4.572] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Chloroplast DNA of the duckweed Spirodela oligorrhiza, isolated by CsCl gradient centrifugation, was characterized by its buoyant density, guanine + cytosine content, melting behavior, circularity, and contour length. In all these characteristics, chloroplast DNA of S. oligorrhiza is similar to the chloroplast genomes of other higher plants, except that it has a significantly larger size.
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Affiliation(s)
- J H van Ee
- Biochemisch Laboratorium der Vrije Universiteit, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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29
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Jurgenson JE, Bourque DP. Mapping of rRNA genes in an inverted repeat in Nicotiana tabacum chloroplast DNA. Nucleic Acids Res 1980; 8:3505-16. [PMID: 6253903 PMCID: PMC324171 DOI: 10.1093/nar/8.16.3505] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Nicotiana tabacum chloroplast DNA contains two copies each of 16S and 23S rRNA genes. These genes are located in an inverted order as determined from restriction fragment mapping and Southern hybridization to restriction fragments. The position of these genes on the N. tabacum chloroplast DNA molecule has been established relative to a complete map of SalI and SMaI restriction enzyme cleavage sites.
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30
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Rushlow K, Orozco E, Lipper C, Hallick R. Selective in vitro transcription of Euglena chloroplast ribosomal RNA genes by a transcriptionally active chromosome. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)85773-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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32
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Murray MG, Palmer JD, Cuellar RE, Thompson WF. Deoxyribonucleic acid sequence organization in the mung bean genome. Biochemistry 1979; 18:5259-66. [PMID: 497181 DOI: 10.1021/bi00590a034] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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33
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34
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Estève J, Nicolas P, Nigon V. Fitting survival curves with theoretical models; goodness-of-fit tests and parameter estimation. application to the clonal survival of Chlorella and the chloroplastic survival of Euglena gracilis after irradiation. Math Biosci 1978. [DOI: 10.1016/0025-5564(78)90101-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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36
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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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37
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Nicolas P, Innocent JP, Nigon V. Somatic segregation and rate of greening after ultraviolet irradiation of Euglena gracilis. MOLECULAR & GENERAL GENETICS : MGG 1977; 155:123-9. [PMID: 412054 DOI: 10.1007/bf00393150] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
1. During multiplication of irradiated cells, a segregation may take place between bleached cells, whose progeny is unable to green, and green ones. Some of the green cells give progenies exclusively made of green cells; the progeny of others is partly composed of bleached cells. 2. If one assumes that greening results from the activity of functional units endowed with genetic continuity (Plastidial Segregating Units = PSU), segregation of these units seems to occur according to a model involving random sorting out during the three first divisions. During the following divisions, functional units seem to multiply faster than those impaired by irradiation. 3. The greening rate of colonies issued from irradiated cells seems to be conditioned mostly by the number of functional PSU remaining in the mother cell of the colony.
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38
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Isolation of a Transcription-active RNA Polymerase — DNA Complex from Euglena Chloroplasts. ACTA ACUST UNITED AC 1977. [DOI: 10.1016/s0015-3796(17)30337-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Liedvogel B. DNA content and ploidy of chromoplasts. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1976; 63:248. [PMID: 958500 DOI: 10.1007/bf00610922] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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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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41
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Kolodner RD, Tewari KK. Chloroplast DNA from higher plants replicates by both the Cairns and the rolling circle mechanism. Nature 1975; 256:708-11. [PMID: 1153007 DOI: 10.1038/256708a0] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The chloroplast DNA (ctDNA) from pea and corn plants contains both Cairns type and rolling circle replicative intermediates. Denaturation mapping studies with pea ctDNA molecules have shown that the rolling circles initiate replication at or near the site where the Cairns replicative intermediates terminate replication. These results suggest that the rolling circles are initiated by a Cairns round of replication. A model for the replication of the chloroplast DNA is based on these results.
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42
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Kolodner RD, Tewari KK. Denaturation mapping studies on the circular chloroplast deoxyribonucleic acid from pea leaves. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41252-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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43
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Fonty G, Crouse EJ, Stutz E, Bernardi G. The mitochondrial genome of Euglena gracilis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 54:367-72. [PMID: 809268 DOI: 10.1111/j.1432-1033.1975.tb04147.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mitochondrial DNA from Euglena gracilis has been investigated in its chemical and physical properties. Its G + C content is equal to 25%; its buoyant density in a CsCl density gradient (1.690 g/cm3) is higher, by 5 mg/cm3, than expected for a bacterial DNA having the same base composition. The buoyant densities of denatured and renatured DNA are higher than that of native DNA by 10-12 mg/cm3 and 6 mg/cm3, respectively. The melting temperature, Tm, is 77 degrees C in standard saline citrate; the first derivative of the melting curve shows a striking multimodality. Degradation of the DNA by micrococcal nuclease indicates that about 40% of the DNA is formed by stretches lower than 10% in G + C. In all its properties the mitochondrial DNA from Euglena gracilis is strikingly similar to that of Saccharomyces cerevisiae.
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44
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Brandt P. [Two peaks of plastidial DNA-synthesis with different light-dependency in the cell cycle of Euglena gracilis]. PLANTA 1975; 124:105-107. [PMID: 24435180 DOI: 10.1007/bf00390074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/1975] [Accepted: 03/17/1975] [Indexed: 06/03/2023]
Abstract
In the course of the life cycle of synchronized Euglena gracilis (14: 10 h light-dark cycles) two separate peaks of plastidial DNA synthesis appear. A first maximum (stage I) occurs 1 to 2 hours, after initiation of the light period, the second maximum (stage II) 9 to 10 hours after beginning of the light period. The second maximum of plastidial DNA synthesis precedes the nucleic DNA synthesis by approximately 4 hours. DNA synthesis during stage I also takes place when previously synchronized cells are cultivated in darkness, whereas no DNA synthesis occurs during stage II in the dark.
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Affiliation(s)
- P Brandt
- Abt. Exp. Phykologie, Pflanzenphysiologisches Institut der Universität, Untere Karspüle 2, D-34, Göttingen, Federal Republic of Germany
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45
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Hettiarachchy NS, Jones IG. Isolation and characterization of mitochondrial deoxyribonucleic acid of Acanthamoeba castellanii. Biochem J 1974; 141:159-64. [PMID: 4455199 PMCID: PMC1168062 DOI: 10.1042/bj1410159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA was prepared from isolated mitochondria of Acanthamoeba castellanii and was shown to behave as a single component in density gradients, on ;melting' and on renaturation. From measurements of renaturation kinetics, sedimentation coefficient and electron micrographs the genome size of the mitochondrial DNA was calculated to be about 3.4x10(7) daltons. A small proportion of the preparations could be isolated as relaxed circular molecules of mean contour length 16.2mum.
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46
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47
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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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48
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Sprey B, Gietz N. Isolierung von etioplasten und elektronenmikroskopische abbildung membranassoziierter etioplasten-DNA. ACTA ACUST UNITED AC 1973. [DOI: 10.1016/s0044-328x(73)80107-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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49
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Schiff JA. The development, inheritance, and origin of the plastid in Euglena. ADVANCES IN MORPHOGENESIS 1973; 10:265-312. [PMID: 4581329 DOI: 10.1016/b978-0-12-028610-2.50010-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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50
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Kolodner R, Tewari K. Molecular Size and Conformation of Chloroplast Deoxyribonucleic Acid from Pea Leaves. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)44804-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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