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Basu U, Bostwick AM, Das K, Dittenhafer-Reed KE, Patel SS. Structure, mechanism, and regulation of mitochondrial DNA transcription initiation. J Biol Chem 2020; 295:18406-18425. [PMID: 33127643 PMCID: PMC7939475 DOI: 10.1074/jbc.rev120.011202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
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Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA; Graduate School of Biomedical Sciences, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | | | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA.
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Paul MF, Alushin GM, Barros MH, Rak M, Tzagoloff A. The putative GTPase encoded by MTG3 functions in a novel pathway for regulating assembly of the small subunit of yeast mitochondrial ribosomes. J Biol Chem 2012; 287:24346-55. [PMID: 22621929 PMCID: PMC3397861 DOI: 10.1074/jbc.m112.363309] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/22/2012] [Indexed: 11/06/2022] Open
Abstract
Very little is known about biogenesis of mitochondrial ribosomes. The GTPases encoded by the nuclear MTG1 and MTG2 genes of Saccharomyces cerevisiae have been reported to play a role in assembly of the ribosomal 54 S subunit. In the present study biochemical screens of a collection of respiratory deficient yeast mutants have enabled us to identify a third gene essential for expression of mitochondrial ribosomes. This gene codes for a member of the YqeH family of GTPases, which we have named MTG3 in keeping with the earlier convention. Mutations in MTG3 cause the accumulation of the 15 S rRNA precursor, previously shown to have an 80-nucleotide 5' extension. Sucrose gradient sedimentation of mitochondrial ribosomes from temperature-sensitive mtg3 mutants grown at the permissive and restrictive temperatures, combined with immunobloting with subunit-specific antibodies, indicate that Mtg3p is required for assembly of the 30 S but not 54 S ribosomal subunit. The respiratory deficient growth phenotype of an mtg3 null mutant is partially rescued by overexpression of the Mrpl4p constituent located at the peptide exit site of the 54 S subunit. The rescue is accompanied by an increase in processed 15 S rRNA. This suggests that Mtg3p and Mrpl4p jointly regulate assembly of the small subunit by modulating processing of the 15 S rRNA precursor.
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Affiliation(s)
- Marie-Françoise Paul
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Gregory M. Alushin
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Mario H. Barros
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Malgorzata Rak
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Alexander Tzagoloff
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
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DMR1 (CCM1/YGR150C) of Saccharomyces cerevisiae encodes an RNA-binding protein from the pentatricopeptide repeat family required for the maintenance of the mitochondrial 15S ribosomal RNA. Genetics 2010; 184:959-73. [PMID: 20124025 DOI: 10.1534/genetics.110.113969] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins form the largest known RNA-binding protein family and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly in mitochondria and chloroplasts, where they modulate organellar genome expression on the post-transcriptional level. The Saccharomyces cerevisiae DMR1 (CCM1, YGR150C) encodes a PPR protein that localizes to mitochondria. Deletion of DMR1 results in a complete and irreversible loss of respiratory capacity and loss of wild-type mtDNA by conversion to rho(-)/rho(0) petites, regardless of the presence of introns in mtDNA. The phenotype of the dmr1Delta mitochondria is characterized by fragmentation of the small subunit mitochondrial rRNA (15S rRNA), that can be reversed by wild-type Dmr1p. Other mitochondrial transcripts, including the large subunit mitochondrial rRNA (21S rRNA), are not affected by the lack of Dmr1p. The purified Dmr1 protein specifically binds to different regions of 15S rRNA in vitro, consistent with the deletion phenotype. Dmr1p is therefore the first yeast PPR protein, which has an rRNA target and is probably involved in the biogenesis of mitochondrial ribosomes and translation.
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Stepien PP, Kokot L, Leski T, Bartnik E. The suv3 nuclear gene product is required for the in vivo processing of the yeast mitochondrial 21s rRNA transcripts containing the r1 intron. Curr Genet 1995; 27:234-8. [PMID: 7736607 DOI: 10.1007/bf00326154] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have constructed a yeast mitochondrial genome containing only one group-I intron, r1, from the 21s rRNA gene and introduced this genome into a strain bearing a disruption of the suv3 gene. The presence of the r1 intron alone causes a block in respiration, while the isogenic strain containing the intronless genome is respiratory competent. Northern analysis indicates that the functional suv3 protein is necessary for the yeast cell in order to process the r1-containing transcripts: in the absence of the suv3 protein the hybridization pattern of the excised r1 intron is altered and the amount of mature 21s rRNA is 50-fold lower. We suggest that the multifunctional suv3 protein, which displays motifs of ATP-dependent RNA helicases, is necessary for the in vivo pathway leading to formation of mature 21s rRNA from the transcripts containing the r1 intron in mitochondria of Saccharomyces cerevisiae.
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Affiliation(s)
- P P Stepien
- Department of Genetics, University of Warsaw, Poland
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Lisowsky T. A high copy number of yeast gamma-glutamylcysteine synthetase suppresses a nuclear mutation affecting mitochondrial translation. Curr Genet 1993; 23:408-13. [PMID: 8100487 DOI: 10.1007/bf00312627] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A new temperature-sensitive nuclear mutant affecting the biogenesis of functional mitochondria has been identified. This pet mutant was formerly characterized by a complete block of mitochondrial translation at the restrictive temperature. The analysis of mitochondrial transcripts demonstrates the accumulation of precursors for the small ribosomal RNA. Transformation of the mutant with plasmids from gene banks identified a chromosomal DNA fragment which can restore growth at the restrictive temperature. A reading frame of 2034 base pairs was found to be responsible for complementation of the mutant phenotype. Sequence analysis identified this gene as the gamma-glutamylcysteine synthetase of yeast. This enzyme catalyses the first reaction in the gamma-glutamyl cycle for the synthesis of glutathione. Disruption of yeast gamma-glutamylcysteine synthetase causes a drastic reduction of growth on glucose medium. The insertion mutants were not able to grow on plates with glycerol as the sole carbon source indicating the special dependence of mitochondria on this substance. Crosses between the pet-ts mutant and the disruption mutant produced diploid cells with a complementation of all their genetic defects indicating that the pet-ts mutation and the insertion mutation are located in different genes. This finding demonstrates that the cloned yeast gene acts as an extragenic suppressor when present on a high-copy-number plasmid inside the pet mutant.
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Affiliation(s)
- T Lisowsky
- Botanisches Institut, Heinrich-Heine-Universität Düsseldorf, Germany
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Wolf K, Del Giudice L. The variable mitochondrial genome of ascomycetes: organization, mutational alterations, and expression. ADVANCES IN GENETICS 1988; 25:185-308. [PMID: 3057820 DOI: 10.1016/s0065-2660(08)60460-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- K Wolf
- Institut für Genetik und Mikrobiologie, Universität München, Munich, Federal Republic of Germany
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Doersen CJ, Guerrier-Takada C, Altman S, Attardi G. Characterization of an RNase P activity from HeLa cell mitochondria. Comparison with the cytosol RNase P activity. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)88920-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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9
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Martin NC, Miller DL, Underbrink K, Ming X. Structure of a precursor to the yeast mitochondrial tRNAMetf. Implications for the function of the tRNA synthesis locus. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89617-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Maheshwari KK, Marzuki S. The formation of a defective small subunit of the mitochondrial ribosomes in petite mutants of Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 781:153-64. [PMID: 6365167 DOI: 10.1016/0167-4781(84)90133-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The involvement of mitochondrial protein synthesis in the assembly of the mitochondrial ribosomes was investigated by studying the extent to which the assembly process can proceed in petite mutants of Saccharomyces cerevisiae which lack mitochondrial protein synthetic activity due to the deletion of some tRNA genes and/or one of the rRNA genes on the mtDNA. Petite strains which retain the 15-S rRNA gene can synthesize this rRNA species, but do not contain any detectable amounts of the small mitochondrial ribosomal subunit. Instead, a ribonucleoparticle with a sedimentation coefficient of 30 S (instead of 37 S) was observed. This ribonucleoparticle contained all the small ribosomal subunit proteins with the exception of the var1 and three to five other proteins, which indicates that the 30-S ribonucleoparticle is related to the small mitochondrial ribosomal subunit (37 S). Reconstitution experiments using the 30-S particle and the large mitochondrial ribosomal subunit from a wild-type yeast strain indicate that the 30-S particle is not active in translating the artificial message poly(U). The large mitochondrial ribosomal subunit was present in petite strains retaining the 21-S rRNA gene. The petite 54-S subunit is biologically active in the translation of poly(U) when reconstituted with the small subunit (37 S) from a wild-type strain. The above results indicate that mitochondrial protein synthetic activity is essential for the assembly of the mature small ribosomal subunit, but not for the large subunit. Since the var1 protein is the only mitochondrial translation product known to date to be associated with the mitochondrial ribosomes, the results suggest that this protein is essential for the assembly of the mature small subunit.
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Christianson T, Rabinowitz M. Identification of multiple transcriptional initiation sites on the yeast mitochondrial genome by in vitro capping with guanylyltransferase. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44019-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Underbrink-Lyon K, Miller DL, Ross NA, Fukuhara H, Martin NC. Characterization of a yeast mitochondrial locus necessary for tRNA biosynthesis. Deletion mapping and restriction mapping studies. MOLECULAR & GENERAL GENETICS : MGG 1983; 191:512-8. [PMID: 6355772 DOI: 10.1007/bf00425771] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Yeast mitochondrial DNA codes for a complete set of tRNAs. Although most components necessary for the biosynthesis of mitochondrial tRNA are coded by nuclear genes, there is one genetic locus on mitochondrial DNA necessary for the synthesis of mitochondrial tRNAs other than the mitochondrial tRNA genes themselves. Characterization of mutants by deletion mapping and restriction enzyme mapping studies has provided a precise location of this yeast mitochondrial tRNA synthesis locus. Deletion mutants retaining various segments of mitochondrial DNA were examined for their ability to synthesize tRNAs from the genes they retain. A subset of these strains was also tested for the ability to provide the tRNA synthesis function in complementation tests with deletion mutants unable to synthesize mature mitochondrial tRNAs. By correlating the tRNA synthetic ability with the presence or absence of certain wild-type restriction fragments, we have confined the locus to within 780 base pairs of DNA located between the tRNAMetf gene and tRNAPro gene, at 29 units on the wild-type map. Heretofore, no genetic function or gene product had been localized in this area of the yeast mitochondrial genome.
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Tabak HF, Grivell LA, Borst P. Transcription of mitochondrial DNA. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1983; 14:297-317. [PMID: 6196153 DOI: 10.3109/10409238309102797] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
While mitochondrial DNA (mtDNA) is the simplest DNA in nature, coding for rRNAs and tRNAs, results of DNA sequence, and transcript analysis have demonstrated that both the synthesis and processing of mitochondrial RNAs involve remarkably intricate events. At one extreme, genes in animal mtDNAs are tightly packed, both DNA strands are completely transcribed (symmetric transcription), and the appearance of specific mRNAs is entirely dependent on processing at sites signalled by the sequences of the tRNAs, which abut virtually every gene. At the other extreme, gene organization in yeast (Saccharomyces) is anything but compact, with long stretches of AT-rich DNA interspaced between coding sequences and no obvious logic to the order of genes. Transcription is asymmetric and several RNAs are initiated de novo. Nevertheless, extensive RNA processing occurs due largely to the presence of split genes. RNA splicing is complex, is controlled by both mitochondrial and nuclear genes, and in some cases is accompanied by the formation of RNAs that behave as covalently closed circles. The present article reviews current knowledge of mitochondrial transcription and RNA processing in relation to possible mechanisms for the regulation of mitochondrial gene expression.
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Cobon GS, Beilharz MW, Linnane AW, Nagley P. Biogenesis of mitochondria: Mapping of transcripts from the oli2 region of mitochondrial DNA in two grande strains of Saccharomyces cerevisiae. Curr Genet 1982; 5:97-107. [DOI: 10.1007/bf00365700] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/1982] [Indexed: 12/01/2022]
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16
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Farrelly F, Zassenhaus HP, Butow RA. Characterization of transcripts from the Var1 region on mitochondrial DNA of Saccharomyces cerevisiae. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(20)65182-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Christianson T, Edwards J, Levens D, Locker J, Rabinowitz M. Transcriptional initiation and processing of the small ribosomal RNA of yeast mitochondria. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(20)65169-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Wright RM, Laping JL, Horrum MA, Cummings DJ. Mitochondrial DNA from Podospora anserina. ACTA ACUST UNITED AC 1982. [DOI: 10.1007/bf00333790] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Locker J, Rabinowitz M. Transcription in yeast mitochondria: analysis of the 21 S rRNA region and its transcripts. Plasmid 1981; 6:302-14. [PMID: 6273949 DOI: 10.1016/0147-619x(81)90038-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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21
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Levens D, Ticho B, Ackerman E, Rabinowitz M. Transcriptional initiation and 5' termini of yeast mitochondrial RNA. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69391-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Locker J, Synenki RM, Merten S, Rabinowitz M. EUKARYOTIC FEATURES OF MITOCHONDRIAL TRANSCRIPTION AND GENE STRUCTURE IN YEAST. Ann N Y Acad Sci 1981. [DOI: 10.1111/j.1749-6632.1981.tb46514.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Transcripts and processing patterns for the ribosomal RNA and transfer RNA region of Neurospora crassa mitochondrial DNA. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69911-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Levens D, Morimoto R, Rabinowitz M. Mitochondrial transcription complex from Saccharomyces cerevisiae. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69986-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Levens D, Lustig A, Rabinowitz M. Purification of mitochondrial RNA polymerase from Saccharomyces cerevisiae. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69987-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70224-5] [Citation(s) in RCA: 301] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Steinkeler JA, Mahler HR. Regulatory interactions between mitochondrial genes: exon and intron phenotypes observed in vivo can be expressed in vitro. Plasmid 1980; 4:17-33. [PMID: 6765560 DOI: 10.1016/0147-619x(80)90080-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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28
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Analysis of mitochondrial RNA in Saccharomyces cerevisiae. Curr Genet 1980; 1:163-72. [DOI: 10.1007/bf00446962] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/1979] [Indexed: 11/26/2022]
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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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