1
|
Ozawa SI, Cavaiuolo M, Jarrige D, Kuras R, Rutgers M, Eberhard S, Drapier D, Wollman FA, Choquet Y. The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo in Chlamydomonas reinhardtii. THE PLANT CELL 2020; 32:1179-1203. [PMID: 31988263 PMCID: PMC7145495 DOI: 10.1105/tpc.19.00770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/02/2020] [Accepted: 01/27/2020] [Indexed: 05/19/2023]
Abstract
In the green alga Chlamydomonas (Chlamydomonas r einhardtii), chloroplast gene expression is tightly regulated posttranscriptionally by gene-specific trans-acting protein factors. Here, we report the identification of the octotricopeptide repeat protein MTHI1, which is critical for the biogenesis of chloroplast ATP synthase oligomycin-sensitive chloroplast coupling factor. Unlike most trans-acting factors characterized so far in Chlamydomonas, which control the expression of a single gene, MTHI1 targets two distinct transcripts: it is required for the accumulation and translation of atpH mRNA, encoding a subunit of the selective proton channel, but it also enhances the translation of atpI mRNA, which encodes the other subunit of the channel. MTHI1 targets the 5' untranslated regions of both the atpH and atpI genes. Coimmunoprecipitation and small RNA sequencing revealed that MTHI1 binds specifically a sequence highly conserved among Chlorophyceae and the Ulvale clade of Ulvophyceae at the 5' end of triphosphorylated atpH mRNA. A very similar sequence, located ∼60 nucleotides upstream of the atpI initiation codon, was also found in some Chlorophyceae and Ulvale algae species and is essential for atpI mRNA translation in Chlamydomonas. Such a dual-targeted trans-acting factor provides a means to coregulate the expression of the two proton hemi-channels.
Collapse
Affiliation(s)
- Shin-Ichiro Ozawa
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Marina Cavaiuolo
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Domitille Jarrige
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Richard Kuras
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Mark Rutgers
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Stephan Eberhard
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Dominique Drapier
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Francis-André Wollman
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Yves Choquet
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| |
Collapse
|
2
|
Yoo BC, Yadav NS, Orozco EM, Sakai H. Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts. PeerJ 2020; 8:e8362. [PMID: 31934513 PMCID: PMC6951285 DOI: 10.7717/peerj.8362] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2019] [Indexed: 11/20/2022] Open
Abstract
We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated "Edit Plasmids," were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ repair system in most bacteria, which are believed to be ancestors of organelles. This is the first demonstration of CRISPR-mediated genome editing in both mitochondria and chloroplasts in two distantly related organisms. The Edit Plasmid approach is expected to open the door to engineer organelle genomes of a wide range of organisms in a precise fashion.
Collapse
|
3
|
Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT. Mitochondrial DNA and temperature tolerance in lager yeasts. SCIENCE ADVANCES 2019; 5:eaav1869. [PMID: 30729163 PMCID: PMC6353617 DOI: 10.1126/sciadv.aav1869] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/03/2019] [Indexed: 06/01/2023]
Abstract
A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces, species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and industrial hybrids (Saccharomyces cerevisiae × Saccharomyces eubayanus or Saccharomyces pastorianus), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world's most commonly fermented beverage.
Collapse
Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Paterna, Valencia, Spain
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Xueying C. Li
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C. Fay
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
| |
Collapse
|
4
|
Abstract
Together, the nuclear and mitochondrial genomes encode the oxidative phosphorylation (OXPHOS) complexes that reside in the mitochondrial inner membrane and enable aerobic life. Mitochondria maintain their own genome that is expressed and regulated by factors distinct from their nuclear counterparts. For optimal function, the cell must ensure proper stoichiometric production of OXPHOS subunits by coordinating two physically separated and evolutionarily distinct gene expression systems. Here, we review our current understanding of mitonuclear coregulation primarily at the levels of transcription and translation. Additionally, we discuss other levels of coregulation that may exist but remain largely unexplored, including mRNA modification and stability and posttranslational protein degradation.
Collapse
Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; , ,
| | - Erik McShane
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; , ,
| | - L Stirling Churchman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; , ,
| |
Collapse
|
5
|
Derbikova KS, Levitsky SA, Chicherin IV, Vinogradova EN, Kamenski PA. Activation of Yeast Mitochondrial Translation: Who Is in Charge? BIOCHEMISTRY (MOSCOW) 2018; 83:87-97. [DOI: 10.1134/s0006297918020013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
6
|
Biolistic Transformation for Delivering DNA into the Mitochondria. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
7
|
Horn D, Fontanesi F, Barrientos A. Exploring protein-protein interactions involving newly synthesized mitochondrial DNA-encoded proteins. Methods Mol Biol 2008; 457:125-39. [PMID: 19066023 DOI: 10.1007/978-1-59745-261-8_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biogenesis of the mitochondrial respiratory chain enzymes involves the coordinated action of the mitochondrial and nuclear genomes. As a matter of fact, the structural sub-units forming these multimeric enzymes are encoded in both genomes. In addition, the assistance of nuclear encoded factors, termed assembly factors, is necessary to allow for the expression of the mitochondrial DNA-encoded subunits and to facilitate their maturation, membrane insertion, and further assembly into the corresponding enzymatic complex. These processes involve transient interactions among the newly synthesized mitochondrial products and specific assembly factors. The identification and characterization of these interactions can be achieved by the method described here, consisting of pulling down tagged versions of the assembly factors immediately after radiolabeling the mitochondrial translation products in isolated mitochondria, and analyzing the radiolabeled pulled-down material.
Collapse
Affiliation(s)
- Darryl Horn
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | | |
Collapse
|
8
|
Bonnefoy N, Remacle C, Fox TD. Genetic transformation of Saccharomyces cerevisiae and Chlamydomonas reinhardtii mitochondria. Methods Cell Biol 2007; 80:525-48. [PMID: 17445712 DOI: 10.1016/s0091-679x(06)80026-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nathalie Bonnefoy
- Centre de Génétique Moléculaire, CNRS UPR2167, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | | | | |
Collapse
|
9
|
Bonnefoy N, Fox TD. Directed alteration of Saccharomyces cerevisiae mitochondrial DNA by biolistic transformation and homologous recombination. Methods Mol Biol 2007; 372:153-66. [PMID: 18314724 PMCID: PMC2771616 DOI: 10.1007/978-1-59745-365-3_11] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Saccharomyces cerevisiae is currently the only species in which genetic transformation of mitochondria can be used to generate a wide variety of defined alterations in mitochondrial deoxyribonucleic acid (mtDNA). DNA sequences can be delivered into yeast mitochondria by microprojectile bombardment (biolistic transformation) and subsequently incorporated into mtDNA by the highly active homologous recombination machinery present in the organelle. Although transformation frequencies are relatively low, the availability of strong mitochondrial selectable markers for the yeast system, both natural and synthetic, makes the isolation of transformants routine. The strategies and procedures reviewed here allow the researcher to insert defined mutations into endogenous mitochondrial genes and to insert new genes into mtDNA. These methods provide powerful in vivo tools for the study of mitochondrial biology.
Collapse
Affiliation(s)
- Nathalie Bonnefoy
- Centre de Génétique Moléculaire CNRS UPR2167 1, Avenue de la Terrasse, Bât. 26 91198 Gif-sur-Yvette cedex France
| | - Thomas D. Fox
- Department of Molecular Biology and Genetics Cornell University Biotechnology Building Ithaca, New York 14853-2703 USA
| |
Collapse
|
10
|
Barrientos A, Zambrano A, Tzagoloff A. Mss51p and Cox14p jointly regulate mitochondrial Cox1p expression in Saccharomyces cerevisiae. EMBO J 2004; 23:3472-82. [PMID: 15306853 PMCID: PMC516630 DOI: 10.1038/sj.emboj.7600358] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Accepted: 07/19/2004] [Indexed: 11/10/2022] Open
Abstract
Mutations in SURF1, the human homologue of yeast SHY1, are responsible for Leigh's syndrome, a neuropathy associated with cytochrome oxidase (COX) deficiency. Previous studies of the yeast model of this disease showed that mutant forms of Mss51p, a translational activator of COX1 mRNA, partially rescue the COX deficiency of shy1 mutants by restoring normal synthesis of the mitochondrially encoded Cox1p subunit of COX. Here we present evidence showing that Cox1p synthesis is reduced in most COX mutants but is restored to that of wild type by the same mss51 mutation that suppresses shy1 mutants. An important exception is a null mutation in COX14, which by itself or in combination with other COX mutations does not affect Cox1p synthesis. Cox14p and Mss51p are shown to interact with newly synthesized Cox1p and with each other. We propose that the interaction of Mss51p and Cox14p with Cox1p to form a transient Cox14p-Cox1p-Mss51p complex functions to downregulate Cox1p synthesis. The release of Mss51p from the complex occurs at a downstream step in the assembly pathway, probably catalyzed by Shy1p.
Collapse
Affiliation(s)
- Antoni Barrientos
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | | | | |
Collapse
|
11
|
Affiliation(s)
- Nathalie Bonnefoy
- Center for Molecular Genetics, Laboratoire propre du CNRS associé à l'Université Pierre et Marie Curie, 91198 Gif-sur-Yvette, France
| | | |
Collapse
|
12
|
Gurvitz A, Hartig A, Ruis H, Hamilton B, Couet H. Preliminary characterisation ofDML1, an essentialSaccharomyces cerevisiaegene related tomisatoofDrosophila melanogaster. FEMS Yeast Res 2002. [DOI: 10.1111/j.1567-1364.2002.tb00077.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
13
|
Affiliation(s)
- N Bonnefoy
- Centre de Génétique Moléculaire Laboratoire propre du CNRS, l'Université Pierre et Marie Curie 91198 Gif-sur-Yvette, France
| | | |
Collapse
|
14
|
Cohen JS, Fox TD. Expression of green fluorescent protein from a recoded gene inserted into Saccharomyces cerevisiae mitochondrial DNA. Mitochondrion 2001; 1:181-9. [PMID: 16120277 DOI: 10.1016/s1567-7249(01)00012-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2001] [Revised: 04/17/2001] [Accepted: 04/19/2001] [Indexed: 11/22/2022]
Abstract
To generate a visible reporter of mitochondrial gene expression, we have synthesized a DNA fragment that specifies an enhanced variant of the green fluorescent protein (GFP) in the Saccharomyces cerevisiae mitochondrial genetic code. This reporter gene, GFP(m)-3, was inserted into mtDNA at the eighth codon of the COX3 gene. Mitochondria containing this mtDNA could be detected by fluorescence microscopy. Mitochondrially encoded GFP accumulated as soluble matrix protein, whose level could be measured both immunologically and fluorometrically. Quantitation of relative fluorescence by flow cytometry confirmed that cox3 :: GFP(m)-3 expression was affected by carbon source and dependent upon COX3 mRNA-specific translational activation. GFP(m)-3 will be a valuable tool for studying mitochondrial gene regulation and the intracellular fates of mitochondrially synthesized proteins.
Collapse
Affiliation(s)
- J S Cohen
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853-2703, USA
| | | |
Collapse
|
15
|
Green-Willms NS, Butler CA, Dunstan HM, Fox TD. Pet111p, an inner membrane-bound translational activator that limits expression of the Saccharomyces cerevisiae mitochondrial gene COX2. J Biol Chem 2001; 276:6392-7. [PMID: 11106667 DOI: 10.1074/jbc.m009856200] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protein specified by the Saccharomyces cerevisiae nuclear gene PET111 specifically activates translation of the mitochondrially coded mRNA for cytochrome c oxidase subunit II (Cox2p). We found Pet111p specifically in mitochondria of both wild-type cells and cells expressing a chromosomal gene for a functional epitope-tagged form of Pet111p. Pet111p was associated with mitochondrial membranes and was highly resistant to extraction with alkaline carbonate. Pet111p was protected from proteolytic digestion by the mitochondrial inner membrane. Thus, it is exposed only on the matrix side, where it could participate directly in organellar translation and localize Cox2p synthesis by virtue of its functional interaction with the COX2 mRNA 5'-untranslated leader. We also found that Pet111p is present at levels limiting the synthesis of Cox2p by examining the effect of altered PET111 gene dosage in the nucleus on expression of a reporter gene, cox2::ARG8(m), that was inserted into mitochondrial DNA. The level of the reporter protein, Arg8p, was one-half that of wild type in a diploid strain heterozygous for a pet111 deletion mutation, whereas it was increased 2.8-fold in a strain bearing extra copies of PET111 on a high-copy plasmid. Thus, Pet111p could play dual roles in both membrane localization and regulation of Cox2p synthesis within mitochondria.
Collapse
Affiliation(s)
- N S Green-Willms
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
| | | | | | | |
Collapse
|
16
|
Costanzo MC, Bonnefoy N, Williams EH, Clark-Walker GD, Fox TD. Highly diverged homologs of Saccharomyces cerevisiae mitochondrial mRNA-specific translational activators have orthologous functions in other budding yeasts. Genetics 2000; 154:999-1012. [PMID: 10757749 PMCID: PMC1460983 DOI: 10.1093/genetics/154.3.999] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Translation of mitochondrially coded mRNAs in Saccharomyces cerevisiae depends on membrane-bound mRNA-specific activator proteins, whose targets lie in the mRNA 5'-untranslated leaders (5'-UTLs). In at least some cases, the activators function to localize translation of hydrophobic proteins on the inner membrane and are rate limiting for gene expression. We searched unsuccessfully in divergent budding yeasts for orthologs of the COX2- and COX3-specific translational activator genes, PET111, PET54, PET122, and PET494, by direct complementation. However, by screening for complementation of mutations in genes adjacent to the PET genes in S. cerevisiae, we obtained chromosomal segments containing highly diverged homologs of PET111 and PET122 from Saccharomyces kluyveri and of PET111 from Kluyveromyces lactis. All three of these genes failed to function in S. cerevisiae. We also found that the 5'-UTLs of the COX2 and COX3 mRNAs of S. kluyveri and K. lactis have little similarity to each other or to those of S. cerevisiae. To determine whether the PET111 and PET122 homologs carry out orthologous functions, we deleted them from the S. kluyveri genome and deleted PET111 from the K. lactis genome. The pet111 mutations in both species prevented COX2 translation, and the S. kluyveri pet122 mutation prevented COX3 translation. Thus, while the sequences of these translational activator proteins and their 5'-UTL targets are highly diverged, their mRNA-specific functions are orthologous.
Collapse
Affiliation(s)
- M C Costanzo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
| | | | | | | | | |
Collapse
|
17
|
Ellis TP, Lukins HB, Nagley P, Corner BE. Suppression of a nuclear aep2 mutation in Saccharomyces cerevisiae by a base substitution in the 5'-untranslated region of the mitochondrial oli1 gene encoding subunit 9 of ATP synthase. Genetics 1999; 151:1353-63. [PMID: 10101162 PMCID: PMC1460560 DOI: 10.1093/genetics/151.4.1353] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in the nuclear AEP2 gene of Saccharomyces generate greatly reduced levels of the mature form of mitochondrial oli1 mRNA, encoding subunit 9 of mitochondrial ATP synthase. A series of mutants was isolated in which the temperature-sensitive phenotype resulting from the aep2-ts1 mutation was suppressed. Three strains were classified as containing a mitochondrial suppressor: these lost the ability to suppress aep2-ts1 when their mitochondrial genome was replaced with wild-type mitochondrial DNA (mtDNA). Many other isolates were classified as containing dominant nuclear suppressors. The three mitochondrion-encoded suppressors were localized to the oli1 region of mtDNA using rho- genetic mapping techniques coupled with PCR analysis; DNA sequencing revealed, in each case, a T-to-C nucleotide transition in mtDNA 16 nucleotides upstream of the oli1 reading frame. It is inferred that the suppressing mutation in the 5' untranslated region of oli1 mRNA restores subunit 9 biosynthesis by accommodating the modified structure of Aep2p generated by the aep2-ts1 mutation (shown here to cause the substitution of proline for leucine at residue 413 of Aep2p). This mode of mitochondrial suppression is contrasted with that mediated by heteroplasmic rearranged rho- mtDNA genomes bypassing the participation of a nuclear gene product in expression of a particular mitochondrial gene. In the present study, direct RNA-protein interactions are likely to form the basis of suppression.
Collapse
Affiliation(s)
- T P Ellis
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168, Australia
| | | | | | | |
Collapse
|
18
|
Grossman LI, Seelan RS, Jaradat SA. Transcriptional regulation of mammalian cytochrome c oxidase genes. Electrophoresis 1998; 19:1254-9. [PMID: 9694260 DOI: 10.1002/elps.1150190805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cytochrome c oxidase (COX) holoenzyme is a 13-subunit complex that carries out the terminal step in the electron transport chain. Three of the subunits, which contain the electron transfer function, are coded by mitochondrial DNA and the other ten subunits by nuclear DNA. Since the holoenzyme contains equivalent amounts of each subunit, we and others have examined transcriptional regulation of COX nuclear subunits to explore whether there is a common basis for co-regulation. Each gene is seen to have a unique pattern of recognition by regulatory factors; although some factors bind to more than one gene, not all COX genes seem to be regulated by the same set of factors. Current information about the COX promoters that have been examined is summarized, and the relation of promoter regulation to coordinate gene expression is discussed.
Collapse
Affiliation(s)
- L I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | | | | |
Collapse
|
19
|
Higgs DC, Kuras R, Kindle KL, Wollman FA, Stern DB. Inversions in the Chlamydomonas chloroplast genome suppress a petD 5' untranslated region deletion by creating functional chimeric mRNAs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 14:663-671. [PMID: 9681031 DOI: 10.1046/j.1365-313x.1998.00165.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
FUD6 is a non-photosynthetic Chlamydomonas mutant that lacks the cytochrome b6/f complex, due to a 236 bp deletion that removes the promoter and part of the 5' untranslated region (UTR) of the chloroplast petD gene, which encodes subunit IV of the complex. Two photosynthetic revertants of FUD6 that synthesized wild-type levels of subunit IV were found to contain related inversions of the chloroplast genome that resulted from recombination between small inverted repeats. These inversions created a functional chimeric petD gene that includes the promoter and part of the 5' UTR of the newly identified ycf9-psbM transciption unit, fused to the petD 5' UTR upstream of the FUD6 deletion. Accumulation of the ycf9-psbM dicistronic transcript was disrupted in the revertants, but monocistronic psbM mRNA accumulated normally. The FUD6 revertants demonstrate the ability of the Chlamydomonas chloroplast genome to undergo a large inversion without a deleterious effect on chloroplast function, reminiscent of events that have led to the evolutionary divergence of chloroplast genomes.
Collapse
Affiliation(s)
- D C Higgs
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | | | | | | | | |
Collapse
|
20
|
Dunstan HM, Green-Willms NS, Fox TD. In vivo analysis of Saccharomyces cerevisiae COX2 mRNA 5'-untranslated leader functions in mitochondrial translation initiation and translational activation. Genetics 1997; 147:87-100. [PMID: 9286670 PMCID: PMC1208125 DOI: 10.1093/genetics/147.1.87] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have used mutational and revertant analysis to study the elements of the 54-nucleotide COX2 5'-untranslated leader involved in translation initiation in yeast mitochondria and in activation by the COX2 translational activator. Pet111p. We generated a collection of mutants with substitutions spanning the entire COX2 5'-UTL by in vitro mutagenesis followed by mitochondrial transformation and gene replacement. The phenotypes of these mutants delimit a 31-nucleotide segment, from -16 to -46, that contains several short sequence elements necessary for COX2 5'-UTL function in translation. The sequences from -16 to -47 were shown to be partially sufficient to promote translation in a foreign context. Analysis of revertants of both the series of linker-scanning alleles and two short deletion/ insertion alleles has refined the positions of several possible functional elements of the COX2 5'-untranslated leader, including a putative RNA stem-loop structure that functionally interacts with Pet111p and an octanucleotide sequence present in all S. cerevisiae mitochondrial mRNA 5'-UTLs that is a potential rRNA binding site.
Collapse
Affiliation(s)
- H M Dunstan
- Section of Genetics and Development, Cornell University, Ithaca, New York 14853-2703, USA
| | | | | |
Collapse
|
21
|
Fox TD. Translational control of endogenous and recoded nuclear genes in yeast mitochondria: regulation and membrane targeting. EXPERIENTIA 1996; 52:1130-5. [PMID: 8988256 DOI: 10.1007/bf01952112] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mitochondrial gene expression in yeast, Saccharomyces cerevisiae, depends on translational activation of individual mRNAs by distinct proteins encoded in the nucleus. These unclearly coded mRNA-specific translational activators are bound to the inner membrane and function to mediate the interaction between mRNAs and mitochondrial ribosomes. This complex system, found to date only in organelles, appears to be an adaptation for targeting the synthesis of mitochondrially coded integral membrane proteins to the membrane. In addition, mRNA-specific translational activation is a rate-limiting step used to modulate expression of at least one mitochondrial gene in response to environmental conditions. Direct study of mitochondrial gene regulation and the targeting of mitochondrially coded proteins in vivo will now be possible using synthetic genes inserted into mtDNA that encode soluble reporter/passenger proteins.
Collapse
Affiliation(s)
- T D Fox
- Section of Genetics and Development, Cornell University, Ithaca, New York 14853-2703, USA.
| |
Collapse
|
22
|
Fox TD. Genetic strategies for identification of mitochondrial translation factors in Saccharomyces cerevisiae. Methods Enzymol 1996; 264:228-37. [PMID: 8965696 DOI: 10.1016/s0076-6879(96)64023-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- T D Fox
- Section of Genetics and Development, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
23
|
Boynton JE, Gillham NW. Genetics and transformation of mitochondria in the green alga Chlamydomonas. Methods Enzymol 1996; 264:279-96. [PMID: 8965701 DOI: 10.1016/s0076-6879(96)64027-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- J E Boynton
- Department of Botany, Duke University, Durham, North Carolina 27708, USA
| | | |
Collapse
|
24
|
Butow RA, Henke RM, Moran JV, Belcher SM, Perlman PS. Transformation of Saccharomyces cerevisiae mitochondria using the biolistic gun. Methods Enzymol 1996; 264:265-78. [PMID: 8965700 DOI: 10.1016/s0076-6879(96)64026-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- R A Butow
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235, USA
| | | | | | | | | |
Collapse
|
25
|
Costanzo MC, Fox TD. A point mutation in the 5'-untranslated leader that affects translational activation of the mitochondrial COX3 mRNA. Curr Genet 1995; 28:60-6. [PMID: 8536314 DOI: 10.1007/bf00311882] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The 613-base 5'-untranslated leader (5'-UTL) of the Saccharomyces cerevisiae mitochondrial COX3 mRNA contains the target of an mRNA-specific translational activator complex composed of at least three nuclearly encoded proteins. We have genetically mapped a collection of cox3 point mutations, using a set of defined COX3 deletions, and found one to be located in the region coding the 5'-UTL. The strain carrying this allele was specifically defective in translation of the COX3 mRNA. Nucleotide-sequence analysis showed that the allele was in fact a double mutation comprised of a single-base insertion in the 5'-UTL (T inserted between bases -428 and -427 with respect to the start of translation) and a G to A substitution at +3 that changed the ATG initiation codon to ATA. Both mutations were required to block translation completely. The effects of the ATG to ATA mutation alone (cox3-1) had previously been analyzed in this laboratory: it reduces, but does not eliminate, translation, causing a slow respiratory growth phenotype. The T insertion in the 5'-UTL had no detectable respiratory growth phenotype as a single mutation. However, the 5'-UTL insertion mutation enhanced the respiratory defective phenotype of missense mutations in pet54, one of the COX3-specific translational-activator genes. This phenotypic enhancement suggests that the -400 region of the 5'-UTL, where the mutation is located, is important for Pet54p-COX3 mRNA interaction.
Collapse
Affiliation(s)
- M C Costanzo
- Section of Genetics and Development, Cornell University, Ithaca, NY 14853-2703, USA
| | | |
Collapse
|
26
|
Abstract
All proteins encoded by mitochondrial DNA (mtDNA) are dependent on proteins encoded by nuclear genes for their synthesis and function. Recent developments in the identification of these genes and the elucidation of the roles their products play at various stages of mitochondrial gene expression are covered in this review, which focuses mainly on work with the yeast Saccharomyces cerevisiae. The high degree of evolutionary conservation of many cellular processes between this yeast and higher eukaryotes, the ease with which mitochondrial biogenesis can be manipulated both genetically and physiologically, and the fact that it will be the first organism for which a complete genomic sequence will be available within the next 2 to 3 years makes it the organism of choice for drawing up an inventory of all nuclear genes involved in mitochondrial biogenesis and for the identification of their counterparts in other organisms.
Collapse
Affiliation(s)
- L A Grivell
- Department of Molecular Cell Biology, University of Amsterdam, Netherlands
| |
Collapse
|
27
|
Affiliation(s)
- H J Pel
- Department of Molecular Cell Biology, University of Amsterdam, The Netherlands
| | | |
Collapse
|
28
|
Mulero JJ, Fox TD. Reduced but accurate translation from a mutant AUA initiation codon in the mitochondrial COX2 mRNA of Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:383-90. [PMID: 7510017 DOI: 10.1007/bf00281787] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We have changed the translation initiation codon of the COX2 mRNA of Saccharomyces cerevisiae from AUG to AUA, generating a mutation termed cox2-10. This mutation reduced translation of the COX2 mRNA at least five-fold without affecting the steady-state level of the mRNA, and produced a leaky nonrespiratory growth phenotype. To address the question of whether residual translation of the cox2-10 mRNA was initiating at the altered initiation codon or at the next AUG codon downstream (at position 14), we took advantage of the fact that the mature coxII protein is generated from the electrophoretically distinguishable coxII precursor by removal of the amino-terminal 15 residues, and that this processing can be blocked by a mutation in the nuclear gene PET2858. We constructed a pet2858, cox2-10 double mutant strain using a pet2858 allele from our mutant collection. The double mutant accumulated low levels of a polypeptide which comigrated with the coxII precursor protein, not the mature species, providing strong evidence that residual initiation was occurring at the mutant AUA codon. Residual translation of the mutant mRNA required the COX2 mRNA-specific activator PET111. Furthermore, growth of cox2-10 mutant strains was sensitive to alterations in PET111 gene dosage: the respiratory-defective growth phenotype was partially suppressed in haploid strains containing PET111 on a high-copy-number vector, but became more severe in diploid strains containing only one functional copy of PET111.
Collapse
Affiliation(s)
- J J Mulero
- Section of Biochemistry, Molecular and Cell Biology Cornell University, Ithaca, NY 14853-2703
| | | |
Collapse
|
29
|
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: 2.3] [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
| | | |
Collapse
|