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Velazquez G, Sousa R, Brieba LG. The thumb subdomain of yeast mitochondrial RNA polymerase is involved in processivity, transcript fidelity and mitochondrial transcription factor binding. RNA Biol 2016; 12:514-24. [PMID: 25654332 DOI: 10.1080/15476286.2015.1014283] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Single subunit RNA polymerases have evolved 2 mechanisms to synthesize long transcripts without falling off a DNA template: binding of nascent RNA and interactions with an RNA:DNA hybrid. Mitochondrial RNA polymerases share a common ancestor with T-odd bacteriophage single subunit RNA polymerases. Herein we characterized the role of the thumb subdomain of the yeast mtRNA polymerase gene (RPO41) in complex stability, processivity, and fidelity. We found that deletion and point mutants of the thumb subdomain of yeast mtRNA polymerase increase the synthesis of abortive transcripts and the probability that the polymerase will disengage from the template during the formation of the late initial transcription and elongation complexes. Mutations in the thumb subdomain increase the amount of slippage products from a homopolymeric template and, unexpectedly, thumb subdomain deletions decrease the binding affinity for mitochondrial transcription factor (Mtf1). The latter suggests that the thumb subdomain is part of an extended binding surface area involved in binding Mtf1.
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Affiliation(s)
- Gilberto Velazquez
- a Laboratorio Nacional de Genómica para la Biodiversidad ; Centro de Investigación y de Estudios ; Irapuato , Guanajuato , México
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Sanchez-Sandoval E, Diaz-Quezada C, Velazquez G, Arroyo-Navarro LF, Almanza-Martinez N, Trasviña-Arenas CH, Brieba LG. Yeast mitochondrial RNA polymerase primes mitochondrial DNA polymerase at origins of replication and promoter sequences. Mitochondrion 2015; 24:22-31. [PMID: 26184436 DOI: 10.1016/j.mito.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 11/15/2022]
Abstract
Three proteins phylogenetically grouped with proteins from the T7 replisome localize to yeast mitochondria: DNA polymerase γ (Mip1), mitochondrial RNA polymerase (Rpo41), and a single-stranded binding protein (Rim1). Human and T7 bacteriophage RNA polymerases synthesize primers for their corresponding DNA polymerases. In contrast, DNA replication in yeast mitochondria is explained by two models: a transcription-dependent model in which Rpo41 primes Mip1 and a model in which double stranded breaks create free 3' OHs that are extended by Mip1. Herein we found that Rpo41 transcribes RNAs that can be extended by Mip1 on single and double-stranded DNA. In contrast to human mitochondrial RNA polymerase, which primes DNA polymerase γ using transcripts from the light-strand and heavy-strand origins of replication, Rpo41 primes Mip1 at replication origins and promoter sequences in vitro. Our results suggest that in ori1, short transcripts serve as primers, whereas in ori5 an RNA transcript longer than 29 nucleotides is used as primer.
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Affiliation(s)
- Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Gilberto Velazquez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Luis F Arroyo-Navarro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Norineli Almanza-Martinez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36500 Irapuato, Guanajuato, Mexico.
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Mangus DA, Jaehning JA. Transcription in vitro with Saccharomyces cerevisiae mitochondrial RNA-polymerase. Methods Enzymol 1996; 264:57-66. [PMID: 8965728 DOI: 10.1016/s0076-6879(96)64009-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- D A Mangus
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655, USA
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Sewards R, Wiseman B, Jacobs HT. Apparent functional independence of the mitochondrial and nuclear transcription systems in cultured human cells. MOLECULAR & GENERAL GENETICS : MGG 1994; 245:760-8. [PMID: 7830724 DOI: 10.1007/bf00297283] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have constructed a series of reporter constructs which test the effects of sequence elements from the control region of human mitochondrial DNA on expression in the nucleus, as assayed by transient expression in cultured human cells. The mitochondrial heavy-strand promoter (HSP) was unable to function as a promoter in nuclear DNA. Neither the HSP, nor the binding region for the mitochondrial transcription factor mtTF1 from the light-strand promoter, had any significant or systematic modulatory effects upon transcription from strong or weak RNA polymerase II (pol II) promoters, in three different human cell lines. The same finding held true regardless of orientation with respect to the start site of transcription. Similar results were obtained with a rho 0 derivative of one of these lines, indicating that mitochondrial promoter sequences in the nucleus cannot modulate transcription in response to altered mtDNA copy number. These results support the view that the nuclear and mitochondrial transcription systems in human cells are functionally independent, and do not communicate through factors recognizing shared sequence elements, as suggested by studies in yeast.
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Affiliation(s)
- R Sewards
- Robertson Institute of Biotechnology, Department of Genetics, University of Glasgow, Scotland, UK
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Mangus DA, Jang SH, Jaehning JA. Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)47232-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Dieckmann CL, Staples RR. Regulation of mitochondrial gene expression in Saccharomyces cerevisiae. INTERNATIONAL REVIEW OF CYTOLOGY 1994; 152:145-81. [PMID: 8206703 DOI: 10.1016/s0074-7696(08)62556-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- C L Dieckmann
- Department of Biochemistry, University of Arizona, Tucson 85721
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Affiliation(s)
- G Link
- University of Bochum, Plant Cell Physiology and Molecular Biology, FRG
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Abstract
Despite the striking similarities of RNA polymerases and transcription signals shared by eubacteria, archaebacteria and eukaryotes, there has been little indication that transcription in mitochondria is related to any previously characterized model. Only in yeast has the subunit structure of the mitochondrial RNA polymerase been determined. The yeast enzyme is composed of a core related to polymerases from bacteriophage T7 and T3, and a promoter recognition factor similar to bacterial sigma factors. Soluble systems for studying mitochondrial transcript initiation in vitro have been described from several organisms, and used to determine consensus sequences at or near transcription start sites. Comparison of these sequences from fungi, plants, and amphibians with the T7/T3 promoter suggests some intriguing similarities. Mammalian mitochondrial promoters do not fit this pattern but instead appear to utilize upstream sites, the target of a transcriptional stimulatory factor, to position the RNA polymerase. The recent identification of a possible homologue of the mammalian upstream factor in yeast mitochondria may indicate that a pattern will eventually be revealed relating the transcriptional machineries of all eukaryotic mitochondria.
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Affiliation(s)
- J A Jaehning
- Department of Biology, Indiana University, Bloomington 47405
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Bolotin-Fukuhara M, Grivell LA. Genetic approaches to the study of mitochondrial biogenesis in yeast. Antonie Van Leeuwenhoek 1992; 62:131-53. [PMID: 1444332 DOI: 10.1007/bf00584467] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In contrast to most other organisms, the yeast Saccharomyces cerevisiae can survive without functional mitochondria. This ability has been exploited in genetic approaches to the study of mitochondrial biogenesis. In the last two decades, mitochondrial genetics have made major contributions to the identification of genes on the mitochondrial genome, the mapping of these genes and the establishment of structure-function relationships in the products they encode. In parallel, more than 200 complementation groups, corresponding to as many nuclear genes necessary for mitochondrial function or biogenesis have been described. Many of the latter are required for post-transcriptional events in mitochondrial gene expression, including the processing of mitochondrial pre-RNAs, the translation of mitochondrial mRNAs, or the assembly of mitochondrial translation products into the membrane. The aim of this review is to describe the genetic approaches used to unravel the intricacies of mitochondrial biogenesis and to summarize recent insights gained from their application.
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Affiliation(s)
- M Bolotin-Fukuhara
- Laboratoire de Génétique Moléculaire, Université Paris-Sud, Orsay, France
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Sauer B. Identification of cryptic lox sites in the yeast genome by selection for Cre-mediated chromosome translocations that confer multiple drug resistance. J Mol Biol 1992; 223:911-28. [PMID: 1554399 DOI: 10.1016/0022-2836(92)90252-f] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Cre recombinase efficiently causes site-specific DNA recombination at loxP sites placed into the eukaryotic genome. Since the loxP site of phage P1 is 34 base-pairs in size, the natural occurrence of this exact sequence is unlikely in any eukaryotic genome. However, related sequences may exist in eukaryotic genomes that could recombine at low efficiency with an authentic loxP site. This work identifies such cryptic lox sites in the yeast genome using a positive selection procedure that allows the detection of events occurring at a frequency of less than 1 x 10(-7). The selection is based on the disruption/reconstruction of the yeast gene YGL022. Disruption of YGL022 confers multiple drug sensitivity. Recombination events at a loxP site 5' to the structural gene restore expression of YGL022 and result in a multiple drug resistant phenotype. These drug resistant mutants all display chromosomal rearrangements resulting from low-frequency Cre-mediated recombination with an endogenous cryptic lox site. Ten such sites have been found and they have been mapped physically to a number of different yeast chromosomes. Although the efficiency of Cre-mediated recombination between loxP and such endogenous sites is quite low, it may be possible to redesign recombination substrates to improve recombination efficiency. Because of the greater complexity of the human and mouse genomes compared with yeast, an analogous situation is likely to exist in these organisms. The availability of such sites would be quite useful in the development of alternative strategies for gene therapy and in the generation of transgenic animals.
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Affiliation(s)
- B Sauer
- DuPont-Merck Pharmaceutical Company, Wilmington, DE 19880-0328
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Ulery TL, Mangus DA, Jaehning JA. The yeast IMP1 gene is allelic to GAL2. MOLECULAR & GENERAL GENETICS : MGG 1991; 230:129-35. [PMID: 1745225 DOI: 10.1007/bf00290660] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have found that many laboratory strains of yeast are defective in galactose metabolism owing to a recessive mutation in the previously characterized nuclear gene, IMP1. This defect leads to a requirement for mitochondrial function for growth on, and metabolism of, galactose. Genetic background affects the degree to which cells are defective. In particular, alleles of GAL3 affect the ability to score the Imp phenotype. We have found that in imp1 strains, transcriptional induction of the galactose inducible genes (GAL1, 2, 7 + 10, MEL1) is normal, but galactose transport is reduced in both rho+ and rho0 cells. This phenotype is normally associated with mutations in GAL2, the galactose permease. Although the growth phenotypes of gal2 and imp1 mutants are distinct, we found that the transformation of imp1 rho0 strains with a plasmid containing the GAL2 gene allows these strains to grow on galactose. Initial genetic analyses did not demonstrate linkage between the GAL2 and IMP1 genes owing to the effects of an unlinked gene on the Imp phenotype. By disrupting the GAL2 gene in an Imp+ background, we have shown that IMP1 and GAL2 segregate as tightly linked genes. Based on these data, we believe that imp1 is a partially defective allele of the GAL2 gene.
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Affiliation(s)
- T L Ulery
- Department of Biology, Indiana University, Bloomington 47405
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Riggs DL, Nomura M. Specific transcription of Saccharomyces cerevisiae 35 S rDNA by RNA polymerase I in vitro. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39156-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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