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Yang J, Ling C, Zhang H, Hussain Q, Lyu S, Zheng G, Liu Y. A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants. Genes (Basel) 2022; 13:genes13101827. [PMID: 36292711 PMCID: PMC9601400 DOI: 10.3390/genes13101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/01/2022] [Accepted: 10/01/2022] [Indexed: 11/04/2022] Open
Abstract
Actinidiaceae, an economically important plant family, includes the Actinidia, Clematoclethra and Saurauia genus. Kiwifruit, with remarkably high vitamin C content, is an endemic species widely distributed in China with high economic value. Although many Actinidiaceae chloroplast genomes have been reported, few complete mitogenomes of Actinidiaceae have been studied. Here, complete circular mitogenomes of the four kiwifruit species and Saurauia tristyla were assembled. Codon usage, sequence repeats, RNA editing, gene transfers, selective pressure, and phylogenetic relationships in the four kiwifruit species and S. tristyla were comparatively analyzed. This research will contribute to the study of phylogenetic relationships within Actiniaceae and molecular barcoding in kiwifruit.
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Affiliation(s)
- Jun Yang
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Chengcheng Ling
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Huamin Zhang
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China
| | - Shiheng Lyu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou 311300, China
| | - Guohua Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (G.Z.); (Y.L.)
| | - Yongsheng Liu
- College of Horticulture, Anhui Agriculture University, Hefei 350002, China
- Correspondence: (G.Z.); (Y.L.)
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The complete mitochondrial genome of carnivorous Genlisea tuberosa (Lentibulariaceae): Structure and evolutionary aspects. Gene 2022; 824:146391. [PMID: 35259463 DOI: 10.1016/j.gene.2022.146391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022]
Abstract
Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced. The genome comprises 729,765 bp, encoding 80 identified genes of which 36 are protein-coding, 40 tRNA, four rRNA genes, and three pseudogenes. An intronic region from the cox1 gene was identified that encodes an endonuclease enzyme that is present in the other sequenced species of Lentibulariaceae. Chloroplast genes (pseudogene and complete) inserted in the MT genome were identified, showing possible horizontal transfer between organelles. In addition, 50 pairs of long repeats from 94 to 274 bp are present, possibly playing an important role in the maintenance of the MT genome. Phylogenetic analysis carried out with 34 coding mitochondrial genes corroborated the positioning of the species listed here within the family. The molecular dynamism in the mitogenome (e.g. the loss or pseudogenization of genes, insertion of foreign genes, the long repeats as well as accumulated mutations) may be reflections of the carnivorous lifestyle where a significant part of cellular energy was shifted for the adaptation of leaves into traps molding the mitochondrial DNA. The sequence and annotation of G. tuberosa's MT will be useful for further studies and serve as a model for evolutionary and taxonomic clarifications of the group as well as improving our comprehension of MT evolution.
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Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNA Sec). BMC Genomics 2020; 21:804. [PMID: 33213362 PMCID: PMC7678280 DOI: 10.1186/s12864-020-07216-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/08/2020] [Indexed: 12/26/2022] Open
Abstract
Background The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not. Results Therefore, we analysed the tRNAnome of 128 plant species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNAMet has highest (5.039%) whereas GCG anti-codon of tRNAArg has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNALeu (7.808%) has highest abundance followed by tRNASer (7.668%) and tRNAGly (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNASec (0.066%) and tRNAHis (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons (isoacceptor) at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNASec genes undergone losses more frequently than duplication and we found that tRNASec showed anti-codon switch during the course of evolution. Conclusion The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07216-3.
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Cheng N, Lo YS, Ansari MI, Ho KC, Jeng ST, Lin NS, Dai H. Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination. THE NEW PHYTOLOGIST 2017; 213:751-763. [PMID: 27611966 DOI: 10.1111/nph.14158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 07/18/2016] [Indexed: 05/11/2023]
Abstract
The currently accepted model of recombination-dependent replication (RDR) in plant mitochondrial DNA (mtDNA) does not clearly explain how RDR progresses and how highly complex mtDNA develops. This study aimed to investigate the correlation between RDR and mtDNA complexity during mitochondrial development in mung bean (Vigna radiata) seed, and the initiation and processing of RDR in plant mitochondria. Flow cytometry, pulsed-field gel electrophoresis, electron microscopy, real-time PCR and biochemical studies were used in this study. The highly dynamic changes in mtDNA complexity correspond to mtDNA RDR activity throughout mitochondrial development. With in vitro freeze-thaw treatment or prolonged in vivo cold incubation, the mtDNA rosette core disappeared and the rosette structure converted to a much longer linear DNA structure. D-loops, Holliday junctions and putative RDR forks often appeared near the rosette cores. We hypothesize that the rosette core may consist of condensed mtDNA and a replication starting sequence, and play an initial and central role in RDR. The satellite cores in the rosette structure may represent the re-initiation sites of mtDNA RDR in the same parental molecule, thereby forming highly complex and giant mitochondrial molecules, representing the RDR intermediates, in vivo.
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Affiliation(s)
- Ning Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Yih-Shan Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | | | - Kuo-Chieh Ho
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hwa Dai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
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5
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Grienenberger JM. Plant mitochondrial RNA editing: The Strasbourg chapter. IUBMB Life 2009; 61:1110-3. [DOI: 10.1002/iub.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Ohyama K, Takemura M, Oda K, Fukuzawa H, Kohchi T, Nakayama S, Ishizaki K, Fujisawa M, Yamato K. Gene content, organization and molecular evolution of plant organellar genomes and sex chromosomes: insights from the case of the liverwort Marchantia polymorpha. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2009; 85:108-24. [PMID: 19282647 PMCID: PMC3524301 DOI: 10.2183/pjab.85.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The complete nucleotide sequence of chloroplast DNA (121,025 base pairs, bp) from a liverwort, Marchantia polymorpha, has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. We also determined the complete nucleotide sequence of the liverwort mitochondrial DNA and deduced 96 possible genes in the sequence of 186,608 bp. The complete chloroplast genome encodes twenty introns (19 group II and 1 group I) in 18 different genes. One of the chloroplast group II introns separates a ribosomal protein gene in a trans-position. The mitochondrial genome contains thirty-two introns (25 group II and 7 group I) in the coding regions of 17 genes. From the evolutionary point of view, we describe the origin of organellar introns and give evidence for vertical and horizontal intron transfers and their intragenomic propagation. Furthermore, we describe the gene organization of the Y chromosome in the dioecious liverwort M. polymorpha, the first detailed view of a Y chromosome in a haploid organism. On the 10 megabase (Mb) Y chromosome, 64 genes are identified, 14 of which are detected only in the male genome. These 14 genes are expressed in reproductive organs but not in vegetative thalli, suggesting their participation in male reproductive functions. These findings indicate that the Y and X chromosomes share the same ancestral autosome and support the prediction that in a haploid organism essential genes on sex chromosomes are more likely to persist than in a diploid organism.
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Affiliation(s)
- Kanji Ohyama
- Laboratory of Plant Molecular Biology, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan.
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7
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Tada SF, Souza AP. A recombination point is conserved in the mitochondrial genome of higher plant species and located downstream from the cox2 pseudogene in Solanum tuberosum L. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000100017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Oldenburg DJ, Bendich AJ. Mitochondrial DNA from the liverwort Marchantia polymorpha: circularly permuted linear molecules, head-to-tail concatemers, and a 5' protein. J Mol Biol 2001; 310:549-62. [PMID: 11439023 DOI: 10.1006/jmbi.2001.4783] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mapping predicts that the mitochondrial genome of the liverwort Marchantia polymorpha exists as a circular molecule, although nearly all the mitochondrial DNA (mtDNA) is found as genome-sized and multigenomic molecules in linear and branched form. We used restriction enzymes with one recognition site per genome, end-specific exonucleases and pulsed-field gel electrophoresis (PFGE) to analyze the arrangement of genomic units and the terminal structure of the molecules. We find a head-to-tail arrangement in the concatemers and circular permutation in both the monomeric and multigenomic molecules. The termini contain covalently bound protein at the 5' end and an open (unblocked) 3' end. We find that the standard in-gel procedure used to prepare large DNA molecules for PFGE may introduce extraction artifacts leading to erroneous conclusions about the termini. These artifacts can be reduced by omitting high salt (high EDTA) and protease during mitochondrial lysis. Our results suggest that the mtDNA may use a T4 phage-like mechanism of replication and that the linear molecules may be due to strand breaks mediated by type II topoisomerase.
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MESH Headings
- Artifacts
- DNA Replication
- DNA Restriction Enzymes/metabolism
- DNA Topoisomerases, Type II/metabolism
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA-Binding Proteins/metabolism
- Edetic Acid/pharmacology
- Electrophoresis, Gel, Pulsed-Field
- Endopeptidase K/metabolism
- Exodeoxyribonucleases/metabolism
- Genome
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Models, Genetic
- Nucleic Acid Conformation
- Plant Cells
- Plant Proteins/metabolism
- Plants/genetics
- Salts/pharmacology
- Viral Proteins
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Affiliation(s)
- D J Oldenburg
- Department of Botany, University of Washington, Seattle, WA 98195-5325, USA
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9
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Analysis of rice mitochondrial genome organization using pulsed-field gel electrophoresis. J Biosci 1999. [DOI: 10.1007/bf02941203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Oldenburg DJ, Bendich AJ. The structure of mitochondrial DNA from the liverwort, Marchantia polymorpha. J Mol Biol 1998; 276:745-58. [PMID: 9500926 DOI: 10.1006/jmbi.1997.1581] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of mitochondrial DNA (mtDNA) from cultured cells of the liverwort, Marchantia polymorpha, was analyzed by pulsed-field gel electrophoresis (PFGE) and moving pictures of the fluorescently labeled molecules. Previous electron microscopic analysis with this liverwort revealed a unique property among land plants: mtDNA circles of only one size, that of the 186 kb genome, with no subgenomic circles. Most of the mtDNA was immobile in PFGE and contained complex structures, larger than the genome size with a bright fluorescent node and multiple attached fibers. The mobile mtDNA was mostly linear molecules in monomeric to pentameric lengths of the unit genome that increased following mung bean nuclease digestion, with a corresponding decrease in the immobile fraction. From 0 to 5% of the mtDNA was found as circular molecules the size of the genome and its oligomers; no subgenome-sized circles were present. Radiolabeling revealed that mtDNA synthesis began soon after transfer of cells to fresh medium and most newly replicated mtDNA was immobile; the circular form of the genome was not rapidly labeled.
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MESH Headings
- DNA Replication
- DNA, Circular/biosynthesis
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Mitochondrial/biosynthesis
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Plant/biosynthesis
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Electrophoresis, Gel, Pulsed-Field
- Genome, Plant
- Microscopy, Fluorescence
- Models, Biological
- Molecular Structure
- Plants/chemistry
- Plants/genetics
- Plants/metabolism
- Recombination, Genetic
- Single-Strand Specific DNA and RNA Endonucleases
- Thymidine/metabolism
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Affiliation(s)
- D J Oldenburg
- Department of Botany, University of Washington, Seattle, WA 98195-5325, USA
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11
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Dai H, Lo YS, Wang TS, Chiang KS. Variation in protein and RNA synthesis activity in isolated mitochondria of the developing rice (Oryza sativa L.) panicle. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:1112-1118. [PMID: 24173071 DOI: 10.1007/bf00222930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/1994] [Accepted: 08/18/1994] [Indexed: 06/02/2023]
Abstract
We have studied variation in mitochondrial protein and RNA synthesis during the development of a specialized rice (Oryza sativa L.) reproductive organ in a bacteria-free environment. Mitochondria were prepared from the maturing panicle during microsporogenesis when meiosis occurred and from etiolated seedlings at two growth stages. We found (1) that there was no discernible qualitative difference among the polypeptides synthesized by these three mitochondrial samples; (2) that the quantity of proteins synthesized by panicle mitochondria was approximately 3 times that of the seedling mitochondria, while the two seedling samples exhibited only a minor quantitative difference; (3) that panicle and seedling mitochondria samples synthesized qualitatively the same RNA but at distinctly different rates and that more RNA products were synthesized by panicle than by seedling mitochondria. These results, taken together, suggest that either the regulation of mitochondrial transcription and translation or the copy number of mitochondrial DNA per mitochondrion change discretely in the developing panicle and consequently that the level of mitochondrial gene expression increases considerably during the development of the reproductive structure in rice.
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Affiliation(s)
- H Dai
- Institute of Botany, Academia Sinica, Taipei, Taiwan 11529 ROC
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12
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13
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14
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Benslimane AA, Rode A, Quétier F, Hartmann C. Characterization of two minicircular plasmid-like DNAs isolated from date-palm mitochondria. Curr Genet 1994; 26:535-41. [PMID: 7874749 DOI: 10.1007/bf00309946] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report here the identification and characterization of two minicircular plasmid-like DNAs isolated from mitochondria of a moroccan date-palm variety. Both molecules were cloned and used as probes in Southern analyses of mitochondrial and total-cellular DNA. Evidence was obtained that these plasmid-like DNAs cross-hybridized but did not show any homology to nuclear, chloroplastic, or main mitochondrial genomes. Sequence analysis revealed that both minicircles, 1,346- and 1,160-bp long, share several stretches of homology, the most important consisting of three identical clusters of lengths 42, 47 and 38 bp. In contrast, no major homology was observed with the other higher-plant plasmid-like DNAs reported so far. Sequence analysis also revealed the presence, in the same strand of one of the minicircles, of two open reading frames potentially encoding proteins 89 and 86 amino acids in length. Interestingly, Northern analyses, using single strands of each minicircle as probes, showed the presence of two transcripts hybridizing only with the strand bearing these two open reading frames. However, computer-assisted comparison of the predicted polypeptide sequences with a protein-sequence library failed to detect any significant homology to known sequences.
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MESH Headings
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Cloning, Molecular
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/isolation & purification
- DNA, Plant/biosynthesis
- DNA, Plant/chemistry
- DNA, Plant/isolation & purification
- Fruit/genetics
- Molecular Sequence Data
- Open Reading Frames
- Plasmids/chemistry
- Plasmids/isolation & purification
- RNA, Plant/analysis
- RNA, Plant/biosynthesis
- Restriction Mapping
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- Trees/genetics
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Affiliation(s)
- A A Benslimane
- Département de Biologie, Faculté des Sciences Semlalia, Université Cadi Ayyad, Marrakech, Maroc
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Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T. Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J Mol Biol 1992; 223:1-7. [PMID: 1731062 DOI: 10.1016/0022-2836(92)90708-r] [Citation(s) in RCA: 453] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Analysis of the mitochondrial DNA of a liverwort Marchantia polymorpha by electron microscopy and restriction endonuclease mapping indicated that the liverwort mitochondrial genome was a single circular molecule of about 184,400 base-pairs. We have determined the complete sequence of the liverwort mitochondrial DNA and detected 94 possible genes in the sequence of 186,608 base-pairs. These included genes for three species of ribosomal RNA, 29 genes for 27 species of transfer RNA and 30 open reading frames (ORFs) for functionally known proteins (16 ribosomal proteins, 3 subunits of H(+)-ATPase, 3 subunits of cytochrome c oxidase, apocytochrome b protein and 7 subunits of NADH ubiquinone oxidoreductase). Three ORFs showed similarity to ORFs of unknown function in the mitochondrial genomes of other organisms. Furthermore, 29 ORFs were predicted as possible genes by using the index of G + C content in first, second and third letters of codons (42.0 +/- 10.9%, 37.0 +/- 13.2% and 26.4 +/- 9.4%, respectively) obtained from the codon usages of identified liverwort genes. To date, 32 introns belonging to either group I or group II intron have been found in the coding regions of 17 genes including ribosomal RNA genes (rrn18 and rrn26), a transfer RNA gene (trnS) and a pseudogene (psi nad7). RNA editing was apparently lacking in liverwort mitochondria since the nucleotide sequences of the liverwort mitochondrial DNA were well-conserved at the DNA level.
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Affiliation(s)
- K Oda
- Department of Agricultural Chemistry Faculty of Agriculture, Kyoto University, Japan
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17
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Affiliation(s)
- M W Gray
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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18
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Abstract
The Texas cytoplasm of maize carries two cytoplasmically inherited traits, male sterility and disease susceptibility, which have been of great interest both for basic research and plant breeding. The two traits are inseparable and are associated with an unusual mitochondrial gene, T-urf13, which encodes a 13-kilodalton polypeptide (URF13). An interaction between fungal toxins and URF13, which results in permeabilization of the inner mitochondrial membrane, accounts for the specific susceptibility to the fungal pathogens.
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19
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Escote-Carlson LJ, Gabay-Laughnan S, Laughnan JR. Nuclear genotype affects mitochondrial genome organization of CMS-S maize. MOLECULAR & GENERAL GENETICS : MGG 1990; 223:457-64. [PMID: 2176716 DOI: 10.1007/bf00264454] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A WF9 strain of maize with the RD subtype of the S male-sterile cytoplasm (CMS-S) was converted to the inbred M825 nuclear background by recurrent backcrossing. The organization of the mitochondrial genomes of the F1 and succeeding backcross progenies was analyzed and compared with the progenitor RD-WF9 using probes derived from the S1 and S2 mitochondrial episomes, and probes containing the genes for cytochrome c oxidase subunit I (coxI), cytochrome c oxidase subunit II (coxII) and apocytochrome b (cob). Changes in mitochondrial DNA (mtDNA) organization were observed for S1-, S2-, and coxI-homologous sequences that involve loss of homologous restriction enzyme fragments present in the RD-WF9 progenitor. With the coxI probe, the loss of certain fragments was accompanied by the appearance of a fragment not detectable in the progenitor. The changes observed indicate the effect of the nuclear genome on the differential replication of specific mitochondrial subgenomic entities.
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Affiliation(s)
- L J Escote-Carlson
- Biotechnology Laboratory, University of British Columbia, Vancouver, Canada
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20
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Kemmerer EC, Wu R. The Pisum sativum mitochondrial gene encoding cytochrome oxidase subunit I has an unusual transcription pattern. Gene 1990; 89:157-62. [PMID: 1695597 DOI: 10.1016/0378-1119(90)90001-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the transcriptional analysis of the mitochondrial (mt) gene encoding cytochrome oxidase subunit I (COXI). A probe made from the protein-coding region of the pea coxI gene hybridized to four RNA transcripts, two of which are much larger than necessary to encode the COXI polypeptide. The RNA hybridization was repeated with a series of sequential probes made from the 5'-untranslated region. The results of these experiments indicated that all four transcripts initiate between 2.8 and 2.1 kb upstream from the protein-coding region. Furthermore, the pattern of hybridization to these sequential probes was unusual, suggesting that introns are spliced out of the 5'-transcribed, but untranslated, region. A sequence located within one of the sequential probes is repeated elsewhere in the pea mt genome. Transcript termini were mapped for the 5' and 3' ends and putative regulatory sequences were located.
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Affiliation(s)
- E C Kemmerer
- Field of Botany, Cornell University, Ithaca, NY 14853
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21
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Saleh NM, Gupta HS, Finch RP, Cocking EC, Mulligan BJ. Stability of mitochondrial DNA in tissue-cultured cells of rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1990; 79:342-346. [PMID: 24226352 DOI: 10.1007/bf01186077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/1989] [Accepted: 10/20/1989] [Indexed: 06/02/2023]
Abstract
Restriction analysis of mitochondrial (mt) DNA from 3-month-old callus cultures of the cytoplasmic male sterile rice, V41A, which contains S2 or "wild abortive" cytoplasm, and its fertile maintainer, V41B, showed the same BamHI restriction profiles as mtDNA from the corresponding leaf material. Similarly, mtDNA of rice (var. Taipei 309) from leaves, a 2-month-old cell suspension (T3MS2/A), a totipotent suspension (T3MS) and a 19-month-old suspension, which had lost its protoplast regeneration ability (LB3), showed indistinguishable BamHI restriction profiles. However, clear differences in mtDNA restriction profiles were observed between LB3 and a 30-month-old suspension culture of Taipei 309 (LB1), which appeared to reflect substantial changes in the relative abundance of specific DNA sequences. Hybridisation of a maizecoxII gene probe to blots of restricted mtDNA confirmed that, while the relative abundance of certain mtDNA sequences was preserved during long-term tissue culture of rice, major changes in abundance were observed with other sequences.
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Affiliation(s)
- N M Saleh
- Department of Botany, University of Nottingham, NG7 2RD, University Park, Nottingham, UK
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22
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Ichikawa H, Tanno-Suenaga L, Imamura J. Mitochondrial genome diversity among cultivars of daucus carota (ssp. sativus) and their wild relatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1989; 77:39-43. [PMID: 24232471 DOI: 10.1007/bf00292313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/1988] [Accepted: 06/28/1988] [Indexed: 06/02/2023]
Abstract
Restriction fragment patterns of mitochondrial DNAs (mtDNAs) from 13 carrot cultivars (Daucus carota ssp. sativus), wild carrot (ssp. carota), ssp. gummifer, and D. capillifolius were compared with each other using four restriction endonucleases. The mtDNAs of the 13 carrot cultivars could be classified into three distinct types - I, II and III - and were also clearly distinguishable from the mtDNAs of wild carrot (type IV), gummifer (V) and D. capillifolius (VI). The proportions of common restriction fragments (F values) shared by two of the three mtDNA types (I, II and III) of carrot cultivars were approximately 0.5-0.6. The F values were 0.4-0.5 for mitochondrial genomes between wild carrot, ssp. gummifer and D. capillifolius. The mitochondrial genomes between wild carrot and the carrot cultivars showed closer homologies those between wild carrot, ssp. gummifer, and D. capillifolius. The diversity of the mitochondrial genomes among the carrot cultivars is too high to presume that it was generated from the cytoplasm of only one common ancestor during the relatively short history of carrot breeding. These results suggested that the three types of cytoplasms found in the carrot cultivars might have existed in a prototype of D. carota in pre-historical times.
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Affiliation(s)
- H Ichikawa
- Plantech Research Institute, 1000, Kamoshida-cho, Midori-ku, 227, Yokohama, Japan
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23
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Abstract
Rearrangements in the mitochondrial genome of the longlife mutant ex1 of the ascomycete Podospora anserina have led to a heterogeneous population of subgenomic molecules. The restriction maps of individual subcircles were established using overlapping recombinant lambda phages isolated from an ex 1 mtDNA/EMBL3 library. The formation of the subcircles and the resulting multipartite organization of the ex1 mtDNA are discussed.
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Affiliation(s)
- E Schulte
- Lehrstuhl für Allgemeine Botanik, Ruhr-Universität, Bochum, Federal Republic of Germany
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24
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Markowicz Y, Loiseaux-de Goër S, Mache R. Presence of a 16S rRNA pseudogene in the bi-molecular plastid genome of the primitive brown alga Pylaiella littoralis. Evolutionary implications. Curr Genet 1988; 14:599-608. [PMID: 3242867 DOI: 10.1007/bf00434086] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The plastid genome of the brown alga Pylaiella littoralis (L.) Kjellm. is composed of two different circular DNA molecules: the largest carries two rrn operons, and the smallest, only one copy of both 16S and 23S rDNAs. 16S rDNA copies located on both molecules have been cloned and their nucleotide sequences determined: they are 65% homologous to one another. The expression of these genes was assayed by hybridizing in vivo labelled P. littoralis rRNAs to both clones, and specific oligonucleotides to total RNA from P. littoralis. Results indicate that the 16S rDNA copy located on the small molecule is a pseudogene. Comparisons of the functional gene with other 16S rRNA genes shows that chloroplasts from green plants emerged earlier from the cyanobacterial lineage than Euglena gracilis and Pylaiella littoralis plastids.
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Affiliation(s)
- Y Markowicz
- Laboratoire de Biologie Moléculaire Végétale, CNRS UA 1178, Université J. Fourier, Grenoble, France
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25
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Dudareva NA, Kiseleva EV, Boyarintseva AE, Maystrenko AG, Khristolyubova NB, Salganik RI. Structure of the mitochondrial genome of Beta vulgaris L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1988; 76:753-759. [PMID: 24232354 DOI: 10.1007/bf00303522] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/1987] [Accepted: 02/29/1988] [Indexed: 06/02/2023]
Abstract
The structure of mitochondrial DNA (mt-DNA) from sugarbeet (Beta vulgaris L.) has been studied by biochemical methods and electron microscopy. It was found to be complex multipartite consisting of two main classes of molecules: high molecules weight (HMW) mtDNA and low molecular weight (LMW) mtDNA. The HMW mtDNA consists of rosette-like structures and globules resembling chromomeres (150-200nm). A typical rosette has a protein core and radially stemming closed DNA loops (from 0.6-1.5 μm). The number of loops in a rosette varies from 16-30. The bulk of HMW mtDNAs are represented by interconnected rosettes (total contour length about 130-160 μm, 403-496 kbp). Such large circular DNAs may be evidence of the master chromosome arrangement of the sugarbeet genome. Globules and rosettes are interconnected by thick and thin DNA fibrils, along which nucleosome- and nucleomere-like structures are distributed. The LWM mtDNA is composed of two groups of supercoiled circular molecules, 0,2-1.5 μm and 0.02-0.05 μm in size. Electrophoretic analysis demonstrated that LWM mtDNA is represented by minicircle plasmid-like DNA molecules of 1.3, 1.4 and 1.6 kbp.
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Affiliation(s)
- N A Dudareva
- Siberian Department, Institute of Cytology and Genetics, Academy of Sciences of the USSR, SU-630090, Novosibirsk, USSR
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26
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Joyce PB, Spencer DF, Gray MW. Multiple sequence rearrangements accompanying the duplication of a tRNA(Pro) gene in wheat mitochondrial DNA. PLANT MOLECULAR BIOLOGY 1988; 11:833-843. [PMID: 24272633 DOI: 10.1007/bf00019523] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/1988] [Accepted: 09/21/1988] [Indexed: 06/02/2023]
Abstract
In the course of isolating tRNA genes from wheat mtDNA, we have found the same tRNA(Pro) gene in two different Hind III restriction fragments, H-P1 (0.7 kbp) and H-P2 (1.7 kbp). Sequences immediately flanking these duplicate genes are closely related, although not identical; sequence comparisons suggest that multiple rearrangements have occurred in the vicinity of the H-P2 tRNA(Pro) gene, relative to the H-P1 version. The chimeric nature of H-P2 is emphasized by the presence of sequences that are also found upstream of the wheat mitochondrial 26S rRNA gene, as well as sequences derived from chloroplast DNA. Comparison of H-P2 with H-P1 plus upstream sequences provides some insight into possible molecular events that might have generated H-P2. In particular, such comparisons suggest a model in which the homologous sequences in H-P2 are seen to be derived from H-P1 plus upstream sequences as a result of an intragenomic, site-specific rearrangement event, followed by amplification of the product, its fixation in the mitochondrial genome, and subsequent sequence divergence (single base changes as well as insertions/deletions of up to 50 nucleotides). The results reported here implicate particular primary sequence motifs in certain of the rearrangements that characterize H-P2.
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Affiliation(s)
- P B Joyce
- Department of Biochemistry, Dalhousie University, B3H 4H7, Halifax, Nova Scotia, Canada
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27
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Chowdhury MK, Schaeffer GW, Smith RL, Matthews BF. Molecular analysis of organelle DNA of different subspecies of rice and the genomic stability of mtDNA in tissue cultured cells of rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1988; 76:533-539. [PMID: 24232271 DOI: 10.1007/bf00260903] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/1987] [Accepted: 03/15/1988] [Indexed: 06/02/2023]
Abstract
Chloroplast (ct) and mitochondrial (mt) DNAs were isolated from two subspecies of rice (Oryza sativa), japonica (Calrose 76) and indica (PI353705) and compared by restriction endonuclease fragment pattern analysis. Similarly, PI353705 (A5) mtDNA was also compared with the mtDNA of its long term tissue cultured line, BL2. Variation in the ctDNA of the 2 subspecies was detected with two (AvaI and BglI) of the 11 restriction endonucleases tested, whereas their mtDNAs showed considerable variation when restricted by PstI, BamHI, HindIII and XhoI endonucleases. Thus, the chloroplast DNA was more highly conserved than the mtDNA in the subspecies comparisons. Only minor variation was observed between the restriction endonuclease patterns of the mtDNAs of BL2 and A5. Southern blots of mtDNA were hybridized with heterologous probes from maize and spinach organelle genes. Differences were found in the hybridization patterns of the two subspecies for six of the eight (mitochondrial and chloroplast) probes tested. Two of the seven (mitochondrial) probes (coxII and 26S rRNA) detected tissue culture generated variation in mtDNA. The relative values of restriction endonuclease and hybridization patterns for studying phylogenetic and genetic relationships in rice are discussed.
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Affiliation(s)
- M K Chowdhury
- Department of Agronomy, University of Florida, 32611, Gainesville, FL, USA
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28
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Influence of nuclear background on transcription of a maize mitochondrial region associated with Texas male sterile cytoplasm. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf00327189] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Gwynn B, Dewey RE, Sederoff RR, Timothy DH, Levjngs CS. Sequence of the 18S-5S ribosomal gene region and the cytochrome oxidase II gene from mtDNA of Zea diploperennis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1987; 74:781-788. [PMID: 24240340 DOI: 10.1007/bf00247557] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/1986] [Accepted: 05/27/1987] [Indexed: 06/02/2023]
Abstract
The coding and flanking sequences of the 18S-5S ribosomal RNA genes and the cytochrome oxidase subunit II gene of Zea diploperennis mitochondrial DNA have been determined and compared to the corresponding sequences of normal maize (Zea mays L.) Both length and substitution mutations are found in the coding region of the 18S rRNA gene, whereas only one substitution mutation is found in the coding region of cytochrome oxidase II. Sequence divergence between maize and Zea diploperennis is about one-tenth of that between wheat and maize. The rate of nucleotide divergence by base substitution is less for plant mitochrondrial genes than for comparable genes in animal mitochondria.
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Affiliation(s)
- B Gwynn
- Department of Genetics, North Carolina State University, 27695, Raleigh, NC, USA
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30
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Mignouna H, Virmani SS, Briquet M. Mitochondrial DNA modifications associated with cytoplasmic male sterility in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1987; 74:666-669. [PMID: 24240225 DOI: 10.1007/bf00288868] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/1987] [Accepted: 04/28/1987] [Indexed: 06/02/2023]
Abstract
Mitochondrial DNA was isolated from fertile and cytoplasmic male sterile lines of rice. Restriction analysis showed specific modifications in the male sterile cytoplasm. In addition to the major mitochondrial DNA, three small plasmid-like DNA molecules were detected by agarose gel electrophoresis in both cytoplasms. An additional molecule was specifically found in the sterile cytoplasm. These mitochondrial DNA modifications support the hypothesis of the mitochondrial inheritance of the cytoplasmic male sterility in rice.
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Affiliation(s)
- H Mignouna
- Laboratoire d'Etude de l'Hérédité Cytoplasmique, Faculté des Sciences Agronomiques, Université Catholique de Louvain, Place Croix du Sud, 1, B-1348, Louvain-la-Neuve, Belgium
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31
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Smith RL, Chowdhury MK, Pring DR. Mitochondrial DNA rearrangements in Pennisetum associated with reversion from cytoplasmic male sterility to fertility. PLANT MOLECULAR BIOLOGY 1987; 9:277-286. [PMID: 24276975 DOI: 10.1007/bf00166463] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/1987] [Accepted: 05/21/1987] [Indexed: 06/02/2023]
Abstract
Endonuclease restriction fragment patterns of Pennisetum americanum L. mitochondrial DNAs (mtDNAs) from a cytoplasmic male-sterile (CMS-A1), fertile revertants and a normal fertile cytoplasm were variable, while chloroplast DNA from those lines lacked variation. Comparisons between mtDNAs of CMS-A1 (parental) and fertile revertant lines revealed the presence of a unique 4.7 kbp PstI fragment in the sterile line that was not detected in any of the revertant lines. A 9.7 kbp PstI fragment was found in all of the revertants, but not in the CMS-A1. Neither of those fragments was found in the normal cytoplasm mtDNA. Hybridization studies revealed two sets of multiple homologies: 1) the 4.7 kbp fragment had homology with a 10.9 kbp and a 13.6 kbp fragment; and 2) the 9.7 kbp fragment was homologous with the 13.6 kbp fragment. The presence of those two repeated mitochondrial sequences on the altered fragments suggests that they may be involved in the recombinational associated events with reversion from CMS to fertility in P. americanum.
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Affiliation(s)
- R L Smith
- Agronomy Department, University of Florida, 32611, Gainesville, FL, USA
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32
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Aviv D, Galun E. Chondriome analysis in sexual progenies of Nicotiana cybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1987; 73:821-826. [PMID: 24241290 DOI: 10.1007/bf00289385] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/1986] [Accepted: 11/25/1986] [Indexed: 06/02/2023]
Abstract
We studied the chondriomes (the mitochondrial genomes) of sexual-progeny plants derived from eleven Nicotiana cybrids which resulted from donor-recipient protoplast fusions. The recipients were either N. tabacum or N. sylvestris and the donor (of the cytoplasm) was N. bigelovii. The chondriomes were characterized by the mitochondrial DNA (mtDNA) restriction-patterns. The differences in mtDNA restriction patterns were revealed after Sal I digestions and probing the respective Southern-blots with three mtDNA fragments. The hybridization patterns of mtDNAs from 35 second-generation plants (i.e. the sexual progeny derived from the cybrid plants) indicated only minor variations between plants derived from the same cybrid but pronounced variations among sibs derived from different cybrids. The mtDNA of 32 second-generation plants varied from both original fusion partners but the mtDNA of one (male-sterile) plant was apparently identical with the mtDNA of one of the original donor (N. bigelovii) and the mtDNA of two other (male-fertile) plants was apparently identical to the mtDNA of an original recipient (N. sylvestris). Generally, the mtDNAs of male-fertile, second-generation plants were similar to the mtDNAs of the original recipients while the mtDNAs of the male-sterile second-generation plants were similar to the mtDNA of the donor (N. begelovii). The analyses of mtDNAs from the thirdgeneration plants indicated stabilization of the chondriomes; no variations were detected between the mtDNAs of plants derived from a given second-generation plant.
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Affiliation(s)
- D Aviv
- Department of Plant Genetics, Weizmann Institute of Science, 76100, Rehovot, Israel
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33
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Brendel V, Segel LA. On modes of recombination, replication, and segregation of the higher plant mitochondrial genome. J Theor Biol 1987. [DOI: 10.1016/s0022-5193(87)80038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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34
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Grabau EA. Cytochrome oxidase subunit II gene is adjacent to an initiator methionine tRNA gene in soybean mitochondrial DNA. Curr Genet 1987; 11:287-93. [PMID: 2834094 DOI: 10.1007/bf00355402] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nucleotide sequence of the cytochrome oxidase subunit II (COII) gene from soybean mitochondria reveals a high degree of sequence conservation to other plant COII sequences. The greatest homology is to pea (97.9%) and the homology extends for some distance both 5' and 3' from the gene. Upstream from the breakpoint in homology with the pea sequence there is a tRNA gene identified as the initiator methionine by homology to known plant tRNA genes. The COII coding sequence appears to be present at a single location in the soybean mitochondrial genome, however some portion of the 5' flanking region is repeated at other sites in the genome. The transcription from the cloned region is complex and is complicated by the presence of the repeated sequence.
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Affiliation(s)
- E A Grabau
- Howard Hughes Medical Institute, University of Utah, Salt Lake City 84132
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35
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Tudzynski P, Rogmann P, Geiger HH. Molecular analysis of mitochondrial DNA from rye (Secale cereale L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1986; 72:695-699. [PMID: 24248083 DOI: 10.1007/bf00289011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/1986] [Accepted: 03/26/1986] [Indexed: 06/02/2023]
Abstract
Molecular characterization of mitochondrial (mt) DNA of rye (Secale cereale L.), free of significant amounts of contaminating chloroplast (cp) DNA, was initiated using the open-pollinated cultivar 'Halo' as a source of mtDNA. Based on the compilation of data from restriction patterns, the molecular size of the mtDNA was estimated to be 410 Kb and its buoyant density was determined as 1.705 g/ml. Southern hybridization, using labelled cp genes (P700 and ribulosebiphosphate-carboxylase large subunit), indicated the presence of cpDNA-homologous regions on putative mtDNA fragments. Mt DNAs of inbred lines with fertile and cytoplasmic male sterile (CMS) 'Pampa' cytoplasm were also analysed. Whereas the restriction patterns of mtDNAs of 'Halors and the fertile line turned out to be identical, 'Pampa' mtDNA showed a unique restriction pattern, indicating (as in most other CMS systems) the involvement of mtDNA rearrangements in the expression of male sterility in rye. All 3 mtDNAs investigated contain regions homologous to the plasmid S1 of the CMS-S cytoplasm of Maize (Zea mays), as indicated by hybridization experiments. In 'Pampa' cytoplasm the S-homologous sequence is located within a rearranged region of mtDNA.
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Affiliation(s)
- P Tudzynski
- Lehrstuhl für Allgemeine Botanik, Ruhr-Universität, D-4630, Bochum, FRG
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36
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Schuster W, Brennicke A. Pseudocopies of the ATPase α-subunit gene in Oenothera mitochondria are present on different circular molecules. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf00330183] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Negruk VI, Eisner GI, Redichkina TD, Dumanskaya NN, Cherny DI, Alexandrov AA, Shemyakin MF, Butenko RG. Diversity of Vicia faba circular mtDNA in whole plants and suspension cultures. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1986; 72:541-547. [PMID: 24248029 DOI: 10.1007/bf00289538] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/1986] [Indexed: 06/02/2023]
Abstract
A comparative analysis of the Vicia faba mitochondrial genome in whole plants and in longterm suspension culture has been conducted. Restriction fragment patterns of the mtDNA isolated from these two sources were notably different. Electronmicroscopic analysis also revealed significant differences. Large circular mtDNA patterns shifted from a 37-80 kb subpopulation, which was predominant in whole plants, to 18-34 kb subpopulations although in both classes notable quantities of circular molecules of 80 to 120 kb and more were also found. Both in whole plant and suspension culture cells very large circular DNAs were observed. Some of them had lengths nearly 290 kb and could be considered as evidence of the existence of master chromosomes. The minicircular DNA population was also altered. In the suspension culture we observed a notable increase of percentage of minicircles with sizes near 1 kb. Simultaneously, the percentage of minicircles with sizes near 3.5-10 kb significantly increased in suspension culture cells. In addition, a new peak (10-12 kb) of minicircles appeared. Copy number alterations for some sequences homologous to CCC1A, CCC1B and CCC2 (Negruk et al. 1982, 1985) were shown. Southern hybridization revealed the existence of a family of minicircles having sizes 1.4-2 kb with predominance of CCC1A, CCC1B and CCC2. The copy numbers of CCC1B and some minor minicircles was changed in the suspension culture when compared with the whole plants.
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Affiliation(s)
- V I Negruk
- Institute of Plant Physiology, USSR Academy of Science, Botanicheskaya 35, 127273, Moscow, USSR
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38
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Site-specific circularisation at an intragenic sequence in Oenothera mitochondria. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf00422060] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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O'Connell MA, Hanson MR. Regeneration of somatic hybrid plants formed between Lycopersicon esculentum and Solatium rickii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1986; 72:59-65. [PMID: 24247772 DOI: 10.1007/bf00261455] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/1985] [Accepted: 11/14/1985] [Indexed: 06/02/2023]
Abstract
A single somatic hybrid callus clone was identified following the fusion of Lycopersicon esculentum protoplasts and Solanum rickii suspension culture protoplasts. The hybrid nature of the callus and the plants regenerating from it was determined by assaying phosphoglucomutase-2 isozyme expression. The chloroplast genome present in four somatic hybrid plants was characterized by probing digests of total DNA with nick translated L. esculentum chloroplast DNA(cpDNA). All four somatic hybrid plants had inherited S. rickii cpDNA. Two clones of plant mitochondrial DNA (mtDNA), soybean 18S and 5S rDNA and maize cytochrome oxidase subunit II were used to characterize the mtDNA present in total DNA digests of four somatic hybrid plants. In both cases, the somatic hybrid plants had inherited most but not all of the S. rickii specific fragments, but none of the L. esculentum specific fragments.
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Affiliation(s)
- M A O'Connell
- Plant Genetic Engineering Laboratory and Department of Horticulture, New Mexico State University, 88003, Las Cruces, NM, USA
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40
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Analysis of the genome structure of plant mitochondria. Methods Enzymol 1986. [DOI: 10.1016/0076-6879(86)18092-x] [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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41
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Oro AE, Newton KJ, Walbot V. Molecular analysis of the inheritance and stability of the mitochondrial genome of an inbred line of maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1985; 70:287-293. [PMID: 24252923 DOI: 10.1007/bf00304913] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/1984] [Accepted: 10/24/1984] [Indexed: 06/02/2023]
Abstract
We have investigated the inheritance of the mitochondrial DNA (mtDNA) restriction endonuclease digestion patterns of maize inbred line B37N in individual plants and pooled siblings in lineages derived from five separate plants in the third generation following successive self-pollinations. The restriction fragment patterns of the different mtDNA samples were compared after digestion with five endonucleases. No differences were visible in the mobilities of the 199 fragments scored per sample. Hybridization analysis with two different cloned mtDNA probes, one of which contains homologies to a portion of the S2 plasmid characteristic of cms-S maize, failed to reveal cryptic variation. The apparent rate of genomic change in maize mtDNA from inbred plants appears to be very slow, compared with the faster rates of change seen in maize tissue cultures and with the documented rapid rate of inter- and intraspecific variation for mammalian mtDNA.
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Affiliation(s)
- A E Oro
- Department of Biological Sciences, Stanford University, 94305, Stanford, CA, USA
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42
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Hanson MR, Conde MF. Functioning and Variation of Cytoplasmic Genomes: Lessons from Cytoplasmic–Nuclear Interactions Affecting Male Fertility in Plants. INTERNATIONAL REVIEW OF CYTOLOGY 1985. [DOI: 10.1016/s0074-7696(08)60398-8] [Citation(s) in RCA: 142] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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43
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Ludwig SR, Pohlman RF, Vieira J, Smith AG, Messing J. The nucleotide sequence of a mitochondrial replicon from maize. Gene 1985; 38:131-8. [PMID: 4065571 DOI: 10.1016/0378-1119(85)90211-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 1913-bp maize mitochondrial (mt) plasmid was isolated from a suspension culture of a Black Mexican Sweet maize strain, cloned into M13mp vectors, and sequenced by a unidirectional progressive deletion method. The 1.9-kb extrachromosomal double-stranded circular DNA plasmid was found to contain regions of sequence which in other systems are known to be part of origins of replication (ori). This plasmid could be used as a carrier for chimeric genes and a molecular probe for replication.
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44
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