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Sanchirico M, Tzellas A, Fox TD, Conrad-Webb H, Periman PS, Mason TL. Relocation of the unusual VAR1 gene from the mitochondrion to the nucleus. Biochem Cell Biol 1995; 73:987-95. [PMID: 8722014 DOI: 10.1139/o95-106] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Var1 protein (Var1p) is an essential, stoichiometric component of the yeast mitochondrial small ribosomal subunit, and it is the only major protein product of the mitochondrial genetic system that is not part of an energy transducing complex of the inner membrane. Interestingly, no mutations have been reported that affect the function of Var1p, presumably because loss of a functional mitochondrial translation system leads to an instability of mtDNA. To study the structure, function and synthesis of Var1p, we have engineered yeast strains for the expression of this protein from a nuclear gene, VAR1U, in which 39 nonstandard mitochondrial codons were converted to the universal code. Immunoblot analysis using an epitope-tagged form of Var1Up showed that the nuclear-encoded protein was expressed and imported into the mitochondria. VAR1U was tested for its ability to complement a mutation in mtDNA, PZ206, which disrupts '3-end processing of the VARI mRNA, causing greatly reduced synthesis of Var1p and a respiratory-deficient phenotype. Respiratory growth was restored in PZ206 mutants by transformation with a centromere plasmid carrying VAR1U under ADH1 promoter control, thus proving that VAR1 function can be relocated from the mitochondrion to the nucleus. Moreover, epitope-tagged Var1Up co-sedimented specifically with small ribosomal subunits in high salt sucrose gradients. The relocation of VAR1 from the mitochondrion to the nucleus provides an excellent system for the molecular genetic analysis of structure-function relationships in the unusual Var1 protein.
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Affiliation(s)
- M Sanchirico
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003-4505, USA
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Abstract
The var1 gene specifies the only mitochondrial ribosomal protein known to be encoded by yeast mitochondrial DNA. The gene is unusual in that its base composition is nearly 90 percent adenine plus thymine. It and its expression product show a strain-dependent variation in size of up to 7 percent; this variation does not detectably interfere with function. Furthermore, var1 is an expandable gene that participates in a novel recombinational event resembling gene conversion whereby shorter alleles are preferentially converted to longer ones. The remarkable features of var1 indicate that it may have evolved by a mechanism analogous to exon shuffling, although no introns are actually present.
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3
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Ainley WM, Hensley P, Butow RA. Expression of GC clusters in the yeast mitochondrial var 1 gene. Translation and secondary structure implications. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)39748-x] [Citation(s) in RCA: 8] [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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4
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Affiliation(s)
- R R Sederoff
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27650, USA
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Transcriptional analysis of the Saccharomyces cerevisiae mitochondrial var1 gene: anomalous hybridization of RNA from AT-rich regions. Mol Cell Biol 1983. [PMID: 6355829 DOI: 10.1128/mcb.3.9.1615] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A family of mitochondrial RNAs hybridizes specifically to the var1 region on Saccharomyces cerevisiae mitochondrial DNA (Farrelly et al., J. Biol. Chem. 257:6581-6587, 1982). We constructed a fine-structure transcription map of this region by hybridizing DNA probes containing different portions of the var1 region and some flanking sequences to mitochondrial RNAs isolated from var1-containing petites. We also report the nucleotide sequence of more than 1.2 kilobases of DNA flanking the var1 gene. Our primary findings are: (i) The family of RNAs we detect with homology to var1 DNA is colinear with the var1 gene. Their direction of transcription is olil to cap, as it is for most other mitochondrial genes. (ii) Extensive hybridization anomalies are present, most likely due to the high A-T (A-U) content of the hybridizing species and to the asymmetric distribution of their G-C residues. An important conclusion is that failure to detect transcripts from A-T-rich regions of the yeast mitochondrial genome by standard blot transfer hybridizations cannot be interpreted to mean that such sequences, which are commonly supposed to be spacer DNA, are noncoding or lack direct function in the expression of mitochondrial genes.
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6
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Zassenhaus HP, Farrelly F, Hudspeth ME, Grossman LI, Butow RA. Transcriptional analysis of the Saccharomyces cerevisiae mitochondrial var1 gene: anomalous hybridization of RNA from AT-rich regions. Mol Cell Biol 1983; 3:1615-24. [PMID: 6355829 PMCID: PMC370015 DOI: 10.1128/mcb.3.9.1615-1624.1983] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A family of mitochondrial RNAs hybridizes specifically to the var1 region on Saccharomyces cerevisiae mitochondrial DNA (Farrelly et al., J. Biol. Chem. 257:6581-6587, 1982). We constructed a fine-structure transcription map of this region by hybridizing DNA probes containing different portions of the var1 region and some flanking sequences to mitochondrial RNAs isolated from var1-containing petites. We also report the nucleotide sequence of more than 1.2 kilobases of DNA flanking the var1 gene. Our primary findings are: (i) The family of RNAs we detect with homology to var1 DNA is colinear with the var1 gene. Their direction of transcription is olil to cap, as it is for most other mitochondrial genes. (ii) Extensive hybridization anomalies are present, most likely due to the high A-T (A-U) content of the hybridizing species and to the asymmetric distribution of their G-C residues. An important conclusion is that failure to detect transcripts from A-T-rich regions of the yeast mitochondrial genome by standard blot transfer hybridizations cannot be interpreted to mean that such sequences, which are commonly supposed to be spacer DNA, are noncoding or lack direct function in the expression of mitochondrial genes.
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7
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Abstract
We have found a contiguous DNA sequence in the yeast nuclear genome with extensive homology to non-contiguous yeast mitochondrial DNA sequences. Closely linked to this nuclear sequence in some, but not all, yeast strains is a tandem pair of transposable (Ty) elements. Certain features of the content and organization of this nuclear DNA sequence suggest that it may have originated from petite mitochondrial DNA which integrated into the nuclear genome.
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8
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Collins RA, Lambowitz AM. Structural variations and optional introns in the mitochondrial DNAs of Neurospora strains isolated from nature. Plasmid 1983; 9:53-70. [PMID: 6300945 DOI: 10.1016/0147-619x(83)90031-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mitochondrial DNAs from ten wild-type Neurospora crassa, Neurospora intermedia, and Neurospora sitophila strains collected from different geographical areas were screened for structural variations by restriction enzyme analysis. The different mtDNAs show much greater structural diversity, both within and among species, than had been apparent from previous studies of mtDNA from laboratory N. crassa strains. The mtDNAs range in size from 60 to 73 kb, and both the smallest and largest mtDNAs are found in N. crassa strains. In addition, four strains contain intramitochondrial plasmid DNAs that do not hybridize with the standard mtDNA. All of the mtDNA species have a basically similar organization. A 25-kb region that includes the rRNA genes and most tRNA genes shows very strong conservation of restriction sites in all strains. The 2.3-kb intron found in the large rRNA gene in standard N. crassa mtDNAs is present in all strains examined, including N. intermedia and N. sitophila strains. The size differences between the different mtDNAs are due to insertions or deletions that occur outside of the rRNA-tRNA region. Restriction enzyme and heteroduplex mapping suggest that four of these insertions are optional introns in the gene encoding cytochrome oxidase subunit I. Mitochondrial DNAs from different wild-type strains contain zero, one, three, or four of these introns.
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9
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Zassenhaus HP, Perlman PS. Respiration deficient mutants in the A+T-rich region on yeast mitochondrial DNA containing the var1 gene. Curr Genet 1982; 6:179-88. [DOI: 10.1007/bf00390336] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/1982] [Indexed: 10/26/2022]
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10
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Ching E, Attardi G. High-resolution electrophoretic fractionation and partial characterization of the mitochondrial translation products from HeLa cells. Biochemistry 1982; 21:3188-95. [PMID: 6285960 DOI: 10.1021/bi00256a024] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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11
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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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12
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Subík J, Goffeau A. Mitochondrial translation products of yeast mutants resistant to mucidin. Folia Microbiol (Praha) 1981; 26:300-2. [PMID: 7026393 DOI: 10.1007/bf02927255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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13
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Lopez I, Farrelly F, Butow R. Trans action and the var1 determinant region on yeast mitochondrial DNA. Specific labeling of mitochondrial translation products in zygotes. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69193-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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15
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Yatscoff RW, Mason JR, Belbeck LW, Freeman KB. The maternal inheritance of proteins synthesized in mammalian mitochondria. Exp Cell Res 1981; 131:417-9. [PMID: 7202542 DOI: 10.1016/0014-4827(81)90247-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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16
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Strausberg RL, Butow RA. Gene conversion at the var1 locus on yeast mitochondrial DNA. Proc Natl Acad Sci U S A 1981; 78:494-8. [PMID: 7017717 PMCID: PMC319080 DOI: 10.1073/pnas.78.1.494] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Alleles of the var1 locus on yeast mtDNA determine the apparent size of the mitochondrial translation product, var1 polypeptide. We have analyzed most of the different var1 alleles in our collection, which number at least 15, and have developed procedures and a genetic rationale for determining their origin and predicting their behavior in crosses. The var1 alleles are characterized by two genetically defined segments, designated a and b, which can move from one var1 allele to another by asymmetric gene conversion. We show that the a segment behaves as an entity in recombination; it is either present in or absent from different var1 alleles. The b segment usually, but not always, recombines as an entity; in some cases, only portions of the b segment recombine by gene conversion. Thus, the total number of electrophoretically resolvable var1 species we observe is explained by the assortment of a, b, and partial b segments. Each segment recombines at a characteristic frequency; however, one example is presented which shows that the recipient can modulate the frequency of gene conversion. Finally, we show that, like the 21S rDNA region (omega), there is polarity of gene conversion within var1.
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17
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Murphy M, Choo KB, Macreadie I, Marzuki S, Lukins HB, Nagley P, Linnane AW. Biogenesis of mitochondria: a temperature sensitivity mutation affecting the mitochondrially synthesized var1 protein of Saccharomyces cerevisiae. Arch Biochem Biophys 1980; 203:260-70. [PMID: 6250484 DOI: 10.1016/0003-9861(80)90176-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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18
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Vincent RD, Perlman PS, Strausberg RL, Butow RA. Physical mapping of genetic determinants on yeast mitochondrial DNA affecting the apparent size of the Var 1 polypeptide. Curr Genet 1980; 2:27-38. [DOI: 10.1007/bf00445691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/1980] [Indexed: 10/26/2022]
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19
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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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20
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Beattie DS, Clejan L. Aggregates of yeast mitochondrial cytochrome b observed after electrophoresis. J Bioenerg Biomembr 1980; 12:35-45. [PMID: 7410343 DOI: 10.1007/bf00745011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mitochondrial translation produces obtained from yeast cells labeled in vivo in the presence of cycloheximide were separated by dodecylsulfate polyacrylamide gel electrophoresis. The labeled band, with a molecular weight of 30,000 corresponding to cytochrome b, was excised and subsequently transferred to a second gel. After electrophoretic separation, two labeled polypetides with apparent molecular weights of 67,000 and 27,000 became visible in addition to the cytochrome b band of 30,000 molecular weight. Heating of the cytochrome b band prior to transfer resulted in an increase in the amount of the labeled polypeptides migrating with a molecular weight of 67,000. Longer exposure during autoradiography of the gels of mitochondrial translation products resulted in the appearance of a double band with an apparent molecular weight of 67,000. Limited proteolysis of this 67,000 dalton protein with Staphylococcus aureus V8 protease revealed a peptide map similar to that obtained after proteolysis of cytochrome b. These results suggest that the polypeptide with an apparent molecular weight of 67,000 represents an aggregate of cytochrome b that is either present as such in the membrane or is formed in vitro during the experimental manipulation to prepare mitochondria for gel electrophoresis.
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22
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24
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Martin N, Miller D, Donelson J. Cloning of yeast mitochondrial DNA in the Escherichia coli plasmid pBR322. Identification of tRNA genes. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86543-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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25
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Mahler HR, Johnson J. Specific effects of nalidixic acid on mitochondrial gene expression in Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1979; 176:25-31. [PMID: 396447 DOI: 10.1007/bf00334291] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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Lewin AS, Morimoto R, Rabinowitz M. Stable heterogeneity of mitochondrial DNA in grande and petite strains of S. cerevisiae. Plasmid 1979; 2:474-84. [PMID: 384424 DOI: 10.1016/0147-619x(79)90031-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Regulatory interactions between mitochondrial genes. I. Genetic and biochemical characterization of some mutant types affecting apocytochrome b and cytochrome oxidase. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)30247-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Koch H, Friesen JD. Individual messenger RNA half lives in Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1979; 170:129-35. [PMID: 372757 DOI: 10.1007/bf00337787] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have measured the decay half-life of functional messenger RNA (mRNA) for some thirty different proteins in the yeast Saccharomyces cerevisiae. Production of newly synthesized mRNA was halted by raising the temperature of a culture of a temperature-sensitive mutant, ts 136. Aliquots of this culture were pulsed-labelled with [35S]-methionine at various times after the temperature shift and the radioactive proteins separated on the two-dimensional gel electrophoresis system of O'Farrell. We find a range in the decay half lives of individual mRNA species which varies from 3.5 min to greater than 70 min. We find three general classes of decay curves, (a) simple exponential (first order); some of these showed a shoulder before onset of exponential decay; (b) bi-component or multi-component concave upward; (c) initial stimulation of rate of mRNA synthesis, followed by virtually undetectable decay.
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29
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Strausberg RL, Vincent RD, Perlman PS, Butow RA. Asymmetric gene conversion at inserted segments on yeast mitochondrial DNA. Nature 1978; 276:577-83. [PMID: 364319 DOI: 10.1038/276577a0] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Different molecular weight forms of the protein product of the yeast mitochondrial gene var 1 are shown at arise by a process of asymmetric gene conversion. These different forms can be accounted by two DNA segments, 36 and 57 base pairs long, present in one allelic form of the var 1 structural gene, which can be inserted independently and at different frequencies into other var 1 alleles.
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30
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Yatscoff RW, Goldstein S, Freeman KB. Conservation of genes coding for proteins synthesized in human mitochondria. SOMATIC CELL GENETICS 1978; 4:633-45. [PMID: 741350 DOI: 10.1007/bf01543155] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Proteins synthesized in mitochondria of 27 different human cell lines, identified by labeling with [35S]methionine in the presence of cycloheximide, have been enumerated and their electrophoretic mobilities determined by sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis and fluorography. Twelve bands were observed in all cell lines. In 24 cell lines, the electrophoretic mobilities of the proteins were the same regardless of race, sex, tissue of origin, cell type, viral transformation, or premature biological aging syndromes. The patterns obtained for the remaining cell lines, HeLa, KB, and Hep-2 were identical. These cell lines showed one protein component that was absent in the 24 others, and lacked a component present in these cell lines. Since it has been previously asserted that KB and Hep-2 are HeLa cells, the data indicate that one basic pattern exists in human cells with a variant of unknown origin occurring in HeLa cells.
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