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Gao J, Reibetanz U, Venkatraman S, Neu B. Biofunctionalization of Polyelectrolyte Microcapsules with Biotinylated Polyethylene Glycol-Grafted Liposomes. Macromol Biosci 2011; 11:1079-87. [DOI: 10.1002/mabi.201100040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/07/2011] [Indexed: 11/10/2022]
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Iams KP, Sinclair JH. Mapping the mitochondrial DNA of Zea mays: Ribosomal gene localization. Proc Natl Acad Sci U S A 2010; 79:5926-9. [PMID: 16593234 PMCID: PMC347023 DOI: 10.1073/pnas.79.19.5926] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have located the 18S and 26S ribosomal genes on a 32.2-kilobase pair (kb) restriction map of Zea mays mitochondrial DNA. In a BamHI restriction digest of mitochondrial DNA, band 4 carries all of the 26S gene whereas band 2 carries the 18S gene sequence. We have cloned and mapped bands 2 and 4 and show that they are contiguous in the genome. The 26S sequence is at one end of the 13.7-kb fragment 4, immediately adjacent to the junction with fragment 2. The 18S sequence is located at the far end of the 17.5-kb fragment 2, about 15 kb away from the 26S gene. A second region of 18S sequence homology is found on band 40. This region contains sequences that cross-hybridize with those in band 2. The nature of this apparent sequence repetition is unclear.
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Affiliation(s)
- K P Iams
- Biology Department, Indiana University, Bloomington, Indiana 47405
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Bayer EA, Wilchek M. The use of the avidin-biotin complex as a tool in molecular biology. METHODS OF BIOCHEMICAL ANALYSIS 2006; 26:1-45. [PMID: 7392958 DOI: 10.1002/9780470110461.ch1] [Citation(s) in RCA: 346] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Assignment of the chloramphenicol resistance gene to mitochondrial deoxyribonucleic acid and analysis of its expression in cultured human cells. Mol Cell Biol 1997. [PMID: 9279383 DOI: 10.1128/mcb.1.8.697] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial deoxyribonucleic acids (mtDNA's) from human HeLa and HT1080 cells differed in their restriction endonuclease cleavage patterns for HaeII, HaeIII, and HhaI. HaeII digestion yielded a 9-kilobase fragment in HT1080, which was replaced by 4.5-, 2.4-, and 2.1-kilobase fragments in HeLa. HaeIII and HhaI yielded distinctive 1.35- and 0.68-kilobase HeLa fragments. These restriction endonuclease polymorphisms were used as mtDNA markers in HeLa-HT1080 cybrid and hybrid crosses involving the cytoplasmic chloramphenicol resistance mutation was used. mtDNA's were purified and digested with the restriction endonucleases, the fragments were separated on agarose gels, and the bands were detected by ethidium bromide staining and Southern transfer analysis. Three cybrids and four hybrids (four expressing HeLa and three expressing HT1080 chloramphenicol resistance) contained 2- to 10-fold excesses of the mtDNA of the chloramphenicol-resistant parent. One cybrid, which was permitted to segregate chloramphenicol resistance and was then rechallenged with chloramphenicol, had approximately equal proportions of the two mtDNA's. Only one hybrid was discordant. These results indicated that chloramphenicol resistance is encoded in mtDNA and that expression of chloramphenicol resistance is related to the ratio of chloramphenicol-resistant and -sensitive genomes within cells.
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Bock CT, Schwinn S, Zentgraf H. Diheteroduplex formation using gold labeled single-stranded PCR fragments and its application in electron microscopy. Chromosoma 1995; 103:653-7. [PMID: 7587588 DOI: 10.1007/bf00357692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Heteroduplex analysis is commonly used to map homologous sequences in DNA:DNA or DNA:RNA hybrids in spread preparations by electron microscopy. However, the standard procedures are not suitable to detect the orientation of a fragment with a defined sequence in a hybrid molecule. Here, we describe an alternative protocol for the visualization of DNA:DNA "diheteroduplex" structures based on digoxigenin/anti-digoxigenin gold labeling that allows determination of the position and orientation of a fragment. Single-stranded polymerase chain reaction (PCR) generated fragments labeled at their 3' ends are hybridized to double-stranded plasmid DNA. Electron microscopy of spread preparations visualizes the gold label and, in combination with morphometric measurements, it is possible to determine the position and orientation of the fragment with the diheteroduplex molecule.
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Affiliation(s)
- C T Bock
- German Cancer Research Center, Heidelberg, Germany
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Affiliation(s)
- M Wilchek
- Department of Biophysics, Weizmann Institute of Science, Rehovot, Israel
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Synthesis and turnover of mitochondrial ribonucleic acid in HeLa cells: the mature ribosomal and messenger ribonucleic acid species are metabolically unstable. Mol Cell Biol 1988. [PMID: 6086013 DOI: 10.1128/mcb.1.6.497] [Citation(s) in RCA: 127] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The synthesis rates and half-lives of the individual mitochondrial ribosomal ribonucleic acid (RNA) and polyadenylic acid-containing RNA species in HeLa cells have been determined by analyzing their kinetics of labeling with [5-3H]-uridine and the changes in specific activity of the mitochondrial nucleotide precursor pools. In one experiment, a novel method for determining the nucleotide precursor pool specific activities, using nascent RNA chains, has been utilized. All mitochondrial RNA species analyzed were found to be metabolically unstable, with half-lives of 2.5 to 3.5 h for the two ribosomal RNA components and between 25 and 90 min for the various putative messenger RNAs. A cordycepin "chase" experiment yielded half-life values for the messenger RNA species which were, in general, larger by a factor of 1.5 to 2.5 than those estimated in the labeling kinetics experiments. On the basis of previous observations, a model is proposed whereby the rate of mitochondrial RNA decay is under feedback control by some mechanism linked to RNA synthesis or processing. A short half-life was determined for five large polyadenylated RNAs, which are probably precursors of mature species. A rate of synthesis of one to two molecules per minute per cell was estimated for the various H-strand-coded messenger RNA species, and a rate of synthesis 50 to 100 times higher was estimated for the ribosomal RNA species. These data indicate that the major portion of the H-strand in each mitochondrial deoxyribonucleic acid molecule is transcribed very infrequently, possibly as rarely as once or twice per cell generation. Furthermore, these results are consistent with a previously proposed model of H-strand transcription in the form of a single polycistronic molecule.
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Mazo AM, Minchenko AG, Avdonina TA, Gause GG, Pusyriov AT. Discrete poly(A)- RNA species from rat liver mitochondria are fragments of 16S mitochondrial rRNA carrying its 5'-termini. Mol Biol Rep 1983; 9:155-61. [PMID: 6195519 DOI: 10.1007/bf00775361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
During electrophoresis in polyacrylamide gels containing 7M urea the major discrete components of preparations of rat liver mitochondrial poly(A)+ and poly(A)- RNA species have similar mobilities. Poly(A)- RNA components hybridize to the 16S rRNA gene of mtDNA. Analysis of 5'-terminal sequences of these components revealed their identity to the 5'-terminal sequence of 16S rRNA. These results show that poly(A)- RNA components are fragmentation products of 16S rRNA. Fragmentation occurs nonrandomly from the 3'-end of the original rRNA molecules and lead to formation of products with electrophoretic mobilities similar to those of poly(A)+ RNA components.
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Abstract
The human mitochondrial genome contains a 23-nucleotide sequence that is homologous to a part of the 5S rRNA's of bacteria. This homology, the structure of the likely transcript, and the location of the sequence relative to the mitochondrial rRNA genes suggest that the sequence represents a fragmentary 5S rRNA gene.
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Abstract
The human mitochondrial genome contains a 23-nucleotide sequence that is homologous to a part of the 5S rRNA's of bacteria. This homology, the structure of the likely transcript, and the location of the sequence relative to the mitochondrial rRNA genes suggest that the sequence represents a fragmentary 5S rRNA gene.
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Komm B, Michaels A, Tsokos J, Linton J. Isolation and characterization of the mitochondrial DNA from the florida spiny lobster, Panulirus argus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1982; 73:923-9. [PMID: 6295697 DOI: 10.1016/0305-0491(82)90338-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
1. Mitochondria and mitochondrial DNA were isolated from the digestive gland of Panulirus argus. 2. The mitochondrial DNA has an average contour length of 5.13 microns which corresponds to a molecular weight of 10.10 X 10(6) daltons. 3. The molecular weight based on agarose gel electrophoresis of restricted individual DNA samples ranges from 10.04 to 10.4 X 10(6) daltons. 4. Restriction endonuclease analysis with Bam H1 and Eco R1 demonstrate variation in nucleotide sequence between individual lobsters.
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Ojala D, Crews S, Montoya J, Gelfand R, Attardi G. A small polyadenylated RNA (7 S RNA), containing a putative ribosome attachment site, maps near the origin of human mitochondrial DNA replication. J Mol Biol 1981; 150:303-14. [PMID: 6172590 DOI: 10.1016/0022-2836(81)90454-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Wallace DC. Assignment of the chloramphenicol resistance gene to mitochondrial deoxyribonucleic acid and analysis of its expression in cultured human cells. Mol Cell Biol 1981; 1:697-710. [PMID: 9279383 PMCID: PMC369350 DOI: 10.1128/mcb.1.8.697-710.1981] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The mitochondrial deoxyribonucleic acids (mtDNA's) from human HeLa and HT1080 cells differed in their restriction endonuclease cleavage patterns for HaeII, HaeIII, and HhaI. HaeII digestion yielded a 9-kilobase fragment in HT1080, which was replaced by 4.5-, 2.4-, and 2.1-kilobase fragments in HeLa. HaeIII and HhaI yielded distinctive 1.35- and 0.68-kilobase HeLa fragments. These restriction endonuclease polymorphisms were used as mtDNA markers in HeLa-HT1080 cybrid and hybrid crosses involving the cytoplasmic chloramphenicol resistance mutation was used. mtDNA's were purified and digested with the restriction endonucleases, the fragments were separated on agarose gels, and the bands were detected by ethidium bromide staining and Southern transfer analysis. Three cybrids and four hybrids (four expressing HeLa and three expressing HT1080 chloramphenicol resistance) contained 2- to 10-fold excesses of the mtDNA of the chloramphenicol-resistant parent. One cybrid, which was permitted to segregate chloramphenicol resistance and was then rechallenged with chloramphenicol, had approximately equal proportions of the two mtDNA's. Only one hybrid was discordant. These results indicated that chloramphenicol resistance is encoded in mtDNA and that expression of chloramphenicol resistance is related to the ratio of chloramphenicol-resistant and -sensitive genomes within cells.
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Affiliation(s)
- D C Wallace
- Department of Genetics, School of Medicine, Stanford University, California 94305, USA
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Gelfand R, Attardi G. Synthesis and turnover of mitochondrial ribonucleic acid in HeLa cells: the mature ribosomal and messenger ribonucleic acid species are metabolically unstable. Mol Cell Biol 1981; 1:497-511. [PMID: 6086013 PMCID: PMC369693 DOI: 10.1128/mcb.1.6.497-511.1981] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The synthesis rates and half-lives of the individual mitochondrial ribosomal ribonucleic acid (RNA) and polyadenylic acid-containing RNA species in HeLa cells have been determined by analyzing their kinetics of labeling with [5-3H]-uridine and the changes in specific activity of the mitochondrial nucleotide precursor pools. In one experiment, a novel method for determining the nucleotide precursor pool specific activities, using nascent RNA chains, has been utilized. All mitochondrial RNA species analyzed were found to be metabolically unstable, with half-lives of 2.5 to 3.5 h for the two ribosomal RNA components and between 25 and 90 min for the various putative messenger RNAs. A cordycepin "chase" experiment yielded half-life values for the messenger RNA species which were, in general, larger by a factor of 1.5 to 2.5 than those estimated in the labeling kinetics experiments. On the basis of previous observations, a model is proposed whereby the rate of mitochondrial RNA decay is under feedback control by some mechanism linked to RNA synthesis or processing. A short half-life was determined for five large polyadenylated RNAs, which are probably precursors of mature species. A rate of synthesis of one to two molecules per minute per cell was estimated for the various H-strand-coded messenger RNA species, and a rate of synthesis 50 to 100 times higher was estimated for the ribosomal RNA species. These data indicate that the major portion of the H-strand in each mitochondrial deoxyribonucleic acid molecule is transcribed very infrequently, possibly as rarely as once or twice per cell generation. Furthermore, these results are consistent with a previously proposed model of H-strand transcription in the form of a single polycistronic molecule.
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Affiliation(s)
- R Gelfand
- Division of Biology, California Institute of Technology, Pasadena 91125
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Case JT, Wallace DC. Maternal inheritance of mitochondrial DNA polymorphisms in cultured human fibroblasts. SOMATIC CELL GENETICS 1981; 7:103-8. [PMID: 6261411 DOI: 10.1007/bf01544751] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have isolated the total cellular DNA from the cultured diploid fibroblasts of a six-member, three-generation human family. Using a specific radioactive probe for mitochondrial (mt) sequences we have identified new polymorphic variants in this family for the Hhal restriction endonuclease cleavage pattern of the mtDNA. The inheritance of these cleavage patterns verifies the maternal inheritance of mtDNA through all three generations.
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Abstract
In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).
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Kearsey SE, Flanagan JG, Craig IW. Cloning of mouse mitochondrial DNA in E. coli affects bacterial viability. Gene 1980; 12:249-55. [PMID: 6265318 DOI: 10.1016/0378-1119(80)90107-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Ojala D, Merkel C, Gelfand R, Attardi G. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 1980; 22:393-403. [PMID: 7448867 DOI: 10.1016/0092-8674(80)90350-5] [Citation(s) in RCA: 244] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A detailed transcription map of HeLa cell mitochondrial DNA (mtDNA) has been constructed by using the S1 protection technique to localize precisely the sequences coding for the ribosomal RNA (rRNA) and poly(A)-containing species on the physical map of the DNA. This transcription map has been correlated with the positions of the tRNA genes derived from the mtDNA sequence. It has been shown that, with the exception of the D loop and another small segment near the origin of replication, the mtDNA sequences are completely saturated by the rRNAs, poly(A)-containing RNAs and tRNA coded for by the two strands. No evidence for intervening sequences has been found. The sequences coding for the individual poly(A)-containing RNA and rRNA species appear to be immediately contiguous on one side, and most frequently on both sides, to tRNA coding sequences. Furthermore, the H strand sequences coding for the two rRNAs, the poly(A)-containing RNAs and the tRNAs appear to be adjacent to each other, extending from coordinate 2/100 to coordinate 95/100 of the genome relative to the origin taken as 0/100. The results are consistent with a model of transcription of the H strand in the form of a single molecule which is processed into mature RNA species by precise endonucleolytic cleavages, occurring in almost all cases immediately before and after a tRNA sequence. The tRNA sequences may play an important role as recognition signals in the processing of the primary transcripts.
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Giles RE, Blanc H, Cann HM, Wallace DC. Maternal inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A 1980; 77:6715-9. [PMID: 6256757 PMCID: PMC350359 DOI: 10.1073/pnas.77.11.6715] [Citation(s) in RCA: 778] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Human mitochondrial DNA was obtained from peripheral blood platelets donated by the members of several independent families. The samples were screened for nucleotide sequence polymorphisms between individuals within these families. In each family in which we were able to detect a distinctly different restriction endonuclease cleavage pattern between the parents, the progeny exhibited the maternal cleavage pattern. Informative polymorphisms were detected for Hae II (PuGCGCPy) in a three-generation family composed of 33 members, for HincII (GTPyPuAC) in a two-generation family composed of four members, and for Hae III(GGCC) in a two-generation family composed of four members. The Hae II polymorphism was analyzed through all three generations in both the maternal and paternal lines. The results of this study demonstrate that human mitochondrial DNA is maternally inherited. The techniques described for using peripheral blood platelets as a source of human mitochondrial DNA represent a convenient way to obtain data on mitochondrial DNA variation in both individuals and populations.
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Sanger F, Coulson AR, Barrell BG, Smith AJ, Roe BA. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol 1980; 143:161-78. [PMID: 6260957 DOI: 10.1016/0022-2836(80)90196-5] [Citation(s) in RCA: 2840] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Sekiya T, Kobayashi M, Seki T, Koike K. Nucleotide sequence of a cloned fragment of rat mitochondrial DNA containing the replication origin. Gene X 1980; 11:53-62. [PMID: 6254854 DOI: 10.1016/0378-1119(80)90086-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequence was determined for the 717 bp HapII subfragment (HapEcoA5) of the EcoRI-A fragment of rat mitochondrial DNA, which contains the heavy-strand replication origin. Analysis of the heavy-strand initiation segments released from the D-loop molecules has revealed that some 5'-ends of these initiation segments are linked to ribonucleotide(s) and are heterogeneous. Sequence analysis of the 5'-end portion of the initiation segment indicated that one of the start points of the deoxyribonucleotide polymerization corresponds to the 425th bp on the HapEcoA5. Two-fold rotational symmetry and palindrome structures, and a G-cluster sequence around the start point have been discussed in connection with unidirectional replication.
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Eperon IC, Anderson S, Nierlich DP. Distinctive sequence of human mitochondrial ribosomal RNA genes. Nature 1980; 286:460-7. [PMID: 6157106 DOI: 10.1038/286460a0] [Citation(s) in RCA: 141] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The nucleotide sequence spanning the ribosomal RNA (rRNA) genes of cloned human mitochondrial DNA reveals an extremely compact genome organization wherein the putative tRNA genes are probably 'butt-jointed' around the two rRNA genes. The sequences of the rRNA genes are significantly homologous in some regions to eukaryotic and prokaryotic sequences, but distinctive; the tRNA genes also have unusual nucleotide sequences. It seems that human mitochondria did not originate from recognizable relatives of present day organisms.
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Giles RE, Stroynowski I, Wallace DC. Characterization of mitochondrial DNA in chloramphenicol-resistant interspecific hybrids and a cybrid. SOMATIC CELL GENETICS 1980; 6:543-554. [PMID: 6255617 DOI: 10.1007/bf01539155] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have examined the restriction endonuclease cleavage patterns exhibited by the mitochondrial DNAs (mtDNA) of four chloramphenicol-resistant (CAPR) human x mouse hybrids and one CAPR cybrid derived from CAPR HeLa cells and CAPS mouse RAG cells. Restriction fragments of mtDNAs were separated by electrophoresis and transferred by the Southern technique to diazobenzyloxymethyl paper. The covalently bound DNA fragments were hybridized initially with 32P-labeled complementary RNA (cRNA) prepared from human mtDNA and, after removal of the human probe, hybridized with mouse [32P]cRNA prepared from mouse mtDNA. Three hybrids which preferentially segregated human chromosomes and the cybrid exhibited mtDNA fragments indistinguishable from mouse cells. One hybrid, ROH8A, which exhibited "reverse" chromosome segregation, contained only human mtDNA. The pattern of chromosome and mtDNA segregation observed in these hybrids and the cybrid support the hypothesis that a complete set of human chromosomes must be retained if a human-mouse hybrid is to retain human mitochondrial DNA.
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Nass MM. Analysis of the two heavy and light strand origins and the direction of replication of mitochondrial DNA within a detailed physical map of this genome in transformed hamster cells. J Mol Biol 1980; 140:231-56. [PMID: 7431392 DOI: 10.1016/0022-2836(80)90104-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Cantatore P, Attardi G. Mapping of nascent light and heavy strand transcripts on the physical map of HeLa cell mitochondrial DNA. Nucleic Acids Res 1980; 8:2605-25. [PMID: 6159578 PMCID: PMC324109 DOI: 10.1093/nar/8.12.2605] [Citation(s) in RCA: 81] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The sequences complementary to the nascent RNA molecules isolated from transcription complexes of HeLa cell mtDNA have been mapped on the H and L strands of mtDNA by the S1 protection technique. The distribution of these sequences among different Hpa II restriction fragments was found to reflect the position of these fragments in the Hpa II map of mtDNA. Thus, the S1-resistant hybrids formed with the L strand corresponded almost exclusively to the right half of the genome past the origin of replication in the direction of L strand transcription, and were especially concentrated in the region immediately adjacent to the origin. By contrast, the hybrid duplexes involving the H strand appeared to be localized in the left half of the genome, and in particular in the quadrant of the map adjacent to the origin in the direction of H strand transcription. These results strongly suggest that the region of mtDNA around the origin of replication contains an initiation site for L strand transcription and an initiation site for H strand transcription.
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Barrell BG, Anderson S, Bankier AT, de Bruijn MH, Chen E, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc Natl Acad Sci U S A 1980; 77:3164-6. [PMID: 6932013 PMCID: PMC349574 DOI: 10.1073/pnas.77.6.3164] [Citation(s) in RCA: 231] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Analysis of an almost complete mammalian mitochondrial DNA sequence has identified 23 possible tRNA genes and we speculate here that these are sufficient to translate all the codons of the mitochondrial genetic code. This number is much smaller than the minimum of 31 required by the wobble hypothesis. For each of the eight genetic code boxes with four codons for one amino acid we find a single specific tRNA gene with T in the first (wobble) position of the anticodon. We suggest that these tRNAs with U in the wobble position can recognize all four codons in these genetic code boxes either by a "two out of three" base interaction or by U.N wobble.
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Heckman JE, Sarnoff J, Alzner-DeWeerd B, Yin S, RajBhandary UL. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc Natl Acad Sci U S A 1980; 77:3159-63. [PMID: 6447871 PMCID: PMC349573 DOI: 10.1073/pnas.77.6.3159] [Citation(s) in RCA: 192] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We report the sequences of Neurospora crassa mitochondrial alanine, leucine(1), leucine(2), threonine, tryptophan, and valine tRNAs. On the basis of the anticodon sequences of these tRNAs and of a glutamine tRNA, whose sequence analysis is nearly complete, we infer the following: (i) The N. crassa mitochondrial tRNA species for alanine, leucine(2), threonine, and valine, amino acids that belong to four-codon families (GCN, CUN, ACN, and GUN, respectively; N = U, C, A, or G) all contain an unmodified U in the first position of the anticodon. In contrast, tRNA species for glutamine, leucine(1), and tryptophan, amino acids that use codons ending in purines (CA(G) (A), UU(G) (A), and UG(G) (A), respectively) contain a modified U derivative in the same position. These findings and the fact that we have not detected any other isoacceptor tRNAs for these amino acids suggest that N. crassa mitochondrial tRNAs containing U in the first position of the anticodon are capable of reading all four codons of a four-codon family whereas those containing a modified U are restricted to reading codons ending in A or G. Such an expanded codon-reading ability of certain mitochondrial tRNAs will explain how the mitochondrial protein-synthesizing system operates with a much lower number of tRNA species than do systems present in prokaryotes or in eukaryotic cytoplasm. (ii) The anticodon sequence of the N. crassa mitochondrial tryptophan tRNA is U(*)CA and not CCA or CmCA as is the case with tryptophan tRNAs from prokaryotes or from eukaryotic cytoplasm. Because a tRNA with U(*)CA in the anti-codon would be expected to read the codon UGA, as well as the normal tryptophan codon UGG, this suggests that in N. crassa mitochondria, as in yeast and in human mitochondria, UGA is a codon for tryptophan and not a signal for chain termination. (iii) The anticodon sequences of the two leucine tRNAs indicate that N. crassa mitochondria use both families of leucine codons (UU(A) (G) and CUN; N = U, C, A, or G) for leucine, in contrast to yeast mitochondria [Li, M. & Tzagoloff, A. (1979) Cell 18, 47-53] in which the CUA leucine codon and possibly the entire CUN family of leucine codons may be translated as threonine.
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de Francesco L, Attardi G. Analysis of sequence homology between human and mouse mitochondrial DNA. J Mol Biol 1980; 139:85-93. [PMID: 7265196 DOI: 10.1016/0022-2836(80)90117-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Bonen L, Gray MW. Organization and expression of the mitochondrial genome of plants I. The genes for wheat mitochondrial ribosomal and transfer RNA: evidence for an unusual arrangement. Nucleic Acids Res 1980; 8:319-35. [PMID: 6252544 PMCID: PMC327269 DOI: 10.1093/nar/8.2.319] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We show here that mitochondrial-specific ribosomal and transfer RNAs of wheat (Triticum vulgare Vill. [Triticum aestivum L.] var. Thatcher) are encoded by the mitochondrial DNA (mtDNA). Individual wheat mitochondrial rRNA species (26S, 18S, 5S) each hybridized with several mtDNA fragments in a particular restriction digest (Eco RI, Xho I, or Sal I). In each case, the DNA fragments to which 18S and 5S rRNAs hybridized were the same, but different from those to which 26S rRNA hybridized. From these results, we conclude that the structural genes for wheat mitochondrial 18S and 5S rRNAs are closely linked, but are physically distant from the genes for wheat mitochondrial 26S rRNA. This arrangement of rRNA genes is clearly different from that in prokaryotes and chloroplasts, where 23S, 16S and 5S rRNA genes are closely linked, even though wheat mitochondrial 18S rRNA has previously been shown to be prokaryotic in nature. The mixed population of wheat mitochondrial 4S RNAs (tRNAs) hybridized with many large restriction fragments, indicating that the tRNA genes are broadly distributed throughout the mitochondrial genome, with some apparent clustering in regions containing 18S and 5S rRNA genes.
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Poyton RO. Cooperative interaction between mitochondrial and nuclear genomes: cytochrome c oxidase assembly as a model. CURRENT TOPICS IN CELLULAR REGULATION 1980; 17:231-95. [PMID: 6254730 DOI: 10.1016/b978-0-12-152817-1.50012-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Hauswirth WW, Laipis PJ, Gilman ME, O'Brien TW, Michaels GS, Rayfield MA. Genetic mapping of bovine mitochondrial DNA from a single animal. Gene X 1980; 8:193-209. [PMID: 7358273 DOI: 10.1016/0378-1119(80)90037-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Using a physical map of bovine mitochondrial DNA derived from the liver of a single Holstein cow, we have determined the location of the genes specifying the large and small ribosomal RNAs by hybridization analysis and electron microscopic observations of R-loop forms. Also, the position of the origin of DNA replication (D-loop) has been located by electron microscopy. Additionally, the direction of D-loop expansion and the polarity of the large and small ribosomal RNA genes were determined.
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Singhal RP, Fallis PA. Structure, function, and evolution of transfer RNAs (with appendix giving complete sequences of 178 tRNAs). PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1980; 23:227-90. [PMID: 549104 DOI: 10.1016/s0079-6603(08)60135-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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45
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Melton DA, Cortese R. Transcription of cloned tRNA genes and the nuclear partitioning of a tRNA precursor. Cell 1979; 18:1165-72. [PMID: 391407 DOI: 10.1016/0092-8674(79)90229-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The transcription of transfer RNA genes (tDNAs) and processing of the transcripts have been studied by injecting cloned tDNAs into Xenopus oocyte nuclei. Three main conclusions can be drawn. First, eucaryotic nuclear tRNA genes, but neither procaryotic nor mitochondrial tRNA genes, are expressed in injected oocytes. While both nematode and yeast tDNAS direct the synthesis of authentic tRNAs, neither E. coli tDNA nor human mitochondrial tDNAs support the synthesis of defined tRNAs when injected into oocytes. Second, competition experiments with co-injected 5S genes and inhibition experiments with alpha-amanitin show that injected tDNAs are transcribed by RNA polymerase III. Third, oocytes injected with a nematode tDNA synthesize a tRNA precursor which is processed post-transcriptionally by removal of a 5' leader sequence. This precursor is found exclusively in the nucleus and is processed in the nucleus before the mature tRNA enters the cytoplasm.
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Heckman J, Yin S, Alzner-DeWeerd B, RajBhandary U. Mapping and cloning of Neurospora crassa mitochondrial transfer RNA genes. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86369-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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47
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Abstract
Comparison of the human mitochrondial DNA sequence of the cytochrome oxidase subunit II gene and the sequence of the corresponding beef heart protein shows that UGA is used as a tryptophan codon and not as a termination codon and suggests that AUA may be a methionine and not an isoleucine codon. The cytochrome oxidase II gene is contiguous at its 5' end with a tRNAAsp gene and there are only 25 bases at its 3' end before a tRNALys gene. These tRNA'S are different from all other known tRNA sequences.
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Abstract
The twelve most abundant transcripts in X. laevis mitochondria were characterized, and their coding regions were mapped on the mitochondrial DNA (mtDNA) by R loop mapping in the electron microscope and by RNA gel transfer hybridization. The transcripts map in nonoverlapping positions with one exception, and they account for about 80% of the coding capacity of mtDNA. Ten of the twelve RNA molecules contain poly(A): the two poly(A)-lacking transcripts are the rRNAs. Analysis withe single-strand-specific nucleases clearly demonstrated the absence of intervening sequences from the coding regions for seven RNAs. For two RNAs, uninterrupted coding sequences are strongly suggested and one RNA could not be analyzed. Eight transcripts of low abundance and high molecular weight were characterized, and their coding regions were mapped approximately. They overlap the coding regions of the abundant mitochondrial RNAs and could be precursors of these RNAs. Most of the RNA molecules characterized were shown to be transcribed from the heavy strand of mtDNA. No abundant discrete light-strand transcript was found.
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Driesel AJ, Crouse EJ, Gordon K, Bohnert HJ, Herrmann RG, Steinmetz A, Mubumbila M, Keller M, Burkard G, Weil JH. Fractionation and identification of spinach chloroplast transfer RNAs and mapping of their genes on the restriction map of chloroplast DNA. Gene 1979; 6:285-306. [PMID: 499808 DOI: 10.1016/0378-1119(79)90070-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spinach chloroplast 4S RNAs has been separated by two-dimensional polyacrylamide gel electrophoresis into about 35 species. After extraction from the gel, 27 of these RNA species were identified by aminoacylation as tRNAs specific for 16 amino acids. Individual tRNAs were labeled in vitro with 125I and hybridized to DNA fragments obtained by digestion of spinach chloroplast DNA with KpnI, PstI, SalI and XmaI restriction endonucleases. A minimum of 21 genes corresponding to tRNAs for 14 different amino acids have been localized on the restriction endonuclease cleavage site map of the DNA molecule. Of these, 15 genes corresponding to tRNAs for 12 amino acids are located in the larger of the two single-copy regions which separate the two inverted copies of the repeat region. Each copy of this repeat region contains a set of genes for the ribosomal RNAs and a gene for tRNA2Ile in the "spacer" sequence between the 16S and 23S ribosomal RNAs. The genes for tRNA1Ile, tRNA2Leu and tRNA3Leu also map in the repeat region, but outside the ribosomal DNA unit. At present, two more chloroplast tRNAs (for Pro and Lys) have been identified, but not mapped, while 4 unidentified 4S RNAs have been mapped in the large single-copy region of the DNA molecule. Evidence is presented that isoaccepting tRNA species can be transcripts from different loci.
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Bohnert HJ, Driesel AJ, Crouse EJ, Gordon K, Herrmann RG, Steinmetz A, Mubumbila M, Keller M, Burkard G, Weil JH. Presence of a transfer RNA gene in the spacer sequence between the 16 S and 23 S rRNA genes of spinach chloroplast DNA. FEBS Lett 1979; 103:52-6. [PMID: 467653 DOI: 10.1016/0014-5793(79)81248-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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