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Veloso Ribeiro Franco L, Barros MH. Biolistic transformation of the yeast Saccharomyces cerevisiae mitochondrial DNA. IUBMB Life 2023; 75:972-982. [PMID: 37470229 DOI: 10.1002/iub.2769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023]
Abstract
The insertion of genes into mitochondria by biolistic transformation is currently only possible in the yeast Saccharomyces cerevisiae and the algae Chlamydomonas reinhardtii. The fact that S. cerevisiae mitochondria can exist with partial (ρ- mutants) or complete deletions (ρ0 mutants) of mitochondrial DNA (mtDNA), without requiring a specific origin of replication, enables the propagation of exogenous sequences. Additionally, mtDNA in this organism undergoes efficient homologous recombination, making it well-suited for genetic manipulation. In this review, we present a summarized historical overview of the development of biolistic transformation and discuss iconic applications of the technique. We also provide a detailed example on how to obtain transformants with recombined foreign DNA in their mitochondrial genome.
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Affiliation(s)
| | - Mario H Barros
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de Sao Paulo, Sao Paulo, Brazil
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2
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Flores-Mireles D, Camacho-Villasana Y, Lutikurti M, García-Guerrero AE, Lozano-Rosas G, Chagoya V, Gutiérrez-Cirlos EB, Brandt U, Cabrera-Orefice A, Pérez-Martínez X. The cytochrome b carboxyl terminal region is necessary for mitochondrial complex III assembly. Life Sci Alliance 2023; 6:e202201858. [PMID: 37094942 PMCID: PMC10132202 DOI: 10.26508/lsa.202201858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
Mitochondrial bc 1 complex from yeast has 10 subunits, but only cytochrome b (Cytb) subunit is encoded in the mitochondrial genome. Cytb has eight transmembrane helices containing two hemes b for electron transfer. Cbp3 and Cbp6 assist Cytb synthesis, and together with Cbp4 induce Cytb hemylation. Subunits Qcr7/Qcr8 participate in the first steps of assembly, and lack of Qcr7 reduces Cytb synthesis through an assembly-feedback mechanism involving Cbp3/Cbp6. Because Qcr7 resides near the Cytb carboxyl region, we wondered whether this region is important for Cytb synthesis/assembly. Although deletion of the Cytb C-region did not abrogate Cytb synthesis, the assembly-feedback regulation was lost, so Cytb synthesis was normal even if Qcr7 was missing. Mutants lacking the Cytb C-terminus were non-respiratory because of the absence of fully assembled bc 1 complex. By performing complexome profiling, we showed the existence of aberrant early-stage subassemblies in the mutant. In this work, we demonstrate that the C-terminal region of Cytb is critical for regulation of Cytb synthesis and bc 1 complex assembly.
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Affiliation(s)
- Daniel Flores-Mireles
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Yolanda Camacho-Villasana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Madhurya Lutikurti
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aldo E García-Guerrero
- Department of Medicine and Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Guadalupe Lozano-Rosas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Victoria Chagoya
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | | | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
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Flores-Mireles D, Camacho-Villasana Y, Pérez-Martínez X. The ARG8 m Reporter for the Study of Yeast Mitochondrial Translation. Methods Mol Biol 2023; 2661:281-301. [PMID: 37166643 DOI: 10.1007/978-1-0716-3171-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitochondrial translation is an intricate process involving both general and mRNA-specific factors. In addition, in the yeast Saccharomyces cerevisiae, translation of mitochondrial mRNAs is coupled to assembly of nascent polypeptides into the membrane. ARG8m is a reporter gene widely used to study the mechanisms of yeast mitochondrial translation. This reporter is a recodified gene that uses the mitochondrial genetic code and is inserted at the desired locus in the mitochondrial genome. After deletion of the endogenous nuclear gene, this reporter produces Arg8, an enzyme necessary for arginine biosynthesis. Since Arg8 is a soluble protein with no relation to oxidative phosphorylation, it is a reliable reporter to study mitochondrial mRNAs translation and dissect translation form assembly processes. In this chapter, we explain how to insert the ARG8m reporter in the desired spot in the mitochondrial DNA, how to analyze Arg8 synthesis inside mitochondria, and how to follow steady-state levels of the protein. We also explain how to use it to find spontaneous suppressors of translation defects.
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Affiliation(s)
- Daniel Flores-Mireles
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yolanda Camacho-Villasana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Zara V, De Blasi G, Ferramosca A. Assembly of the Multi-Subunit Cytochrome bc1 Complex in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:ijms231810537. [PMID: 36142449 PMCID: PMC9502982 DOI: 10.3390/ijms231810537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
The cytochrome bc1 complex is an essential component of the mitochondrial respiratory chain of the yeast Saccharomyces cerevisiae. It is composed of ten protein subunits, three of them playing an important role in electron transfer and proton pumping across the inner mitochondrial membrane. Cytochrome b, the central component of this respiratory complex, is encoded by the mitochondrial genome, whereas all the other subunits are of nuclear origin. The assembly of all these subunits into the mature and functional cytochrome bc1 complex is therefore a complicated process which requires the participation of several chaperone proteins. It has been found that the assembly process of the mitochondrial bc1 complex proceeds through the formation of distinct sub-complexes in an ordered sequence. Most of these sub-complexes have been thoroughly characterized, and their molecular compositions have also been defined. This study critically analyses the results obtained so far and highlights new possible areas of investigation.
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Liang C, Zhang S, Robinson D, Ploeg MV, Wilson R, Nah J, Taylor D, Beh S, Lim R, Sun L, Muoio DM, Stroud DA, Ho L. Mitochondrial microproteins link metabolic cues to respiratory chain biogenesis. Cell Rep 2022; 40:111204. [PMID: 35977508 DOI: 10.1016/j.celrep.2022.111204] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/25/2022] [Accepted: 07/21/2022] [Indexed: 11/28/2022] Open
Abstract
Electron transport chain (ETC) biogenesis is tightly coupled to energy levels and availability of ETC subunits. Complex III (CIII), controlling ubiquinol:ubiquinone ratio in ETC, is an attractive node for modulating ETC levels during metabolic stress. Here, we report the discovery of mammalian Co-ordinator of mitochondrial CYTB (COM) complexes that regulate the stepwise CIII biogenesis in response to nutrient and nuclear-encoded ETC subunit availability. The COMA complex, consisting of UQCC1/2 and membrane anchor C16ORF91, facilitates translation of CIII enzymatic core subunit CYTB. Subsequently, microproteins SMIM4 and BRAWNIN together with COMA subunits form the COMB complex to stabilize nascent CYTB. Finally, UQCC3-containing COMC facilitates CYTB hemylation and association with downstream CIII subunits. Furthermore, when nuclear CIII subunits are limiting, COMB is required to chaperone nascent CYTB to prevent OXPHOS collapse. Our studies highlight CYTB synthesis as a key regulatory node of ETC biogenesis and uncover the roles of microproteins in maintaining mitochondrial homeostasis.
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Affiliation(s)
- Chao Liang
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Shan Zhang
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore; Department of Biochemistry, Department of Cardiology of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - David Robinson
- Department of Biochemistry and Pharmacology, the Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC 3052, Australia
| | - Matthew Vander Ploeg
- Departments of Medicine and Pharmacology and Cancer Biology, Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Rebecca Wilson
- Departments of Medicine and Pharmacology and Cancer Biology, Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Jiemin Nah
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Dale Taylor
- Department of Biochemistry and Pharmacology, the Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC 3052, Australia
| | - Sheryl Beh
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Radiance Lim
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Lei Sun
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore
| | - Deborah M Muoio
- Departments of Medicine and Pharmacology and Cancer Biology, Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - David A Stroud
- Department of Biochemistry and Pharmacology, the Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, the Royal Children's Hospital, 50 Flemington Road, Parkville, VIC 3052, Australia
| | - Lena Ho
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, 169857 Singapore, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, 61 Biopolis Dr, 138673 Singapore, Singapore.
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Herbert CJ, Labarre-Mariotte S, Cornu D, Sophie C, Panozzo C, Michel T, Dujardin G, Bonnefoy N. Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria. Nucleic Acids Res 2021; 49:11145-11166. [PMID: 34634819 PMCID: PMC8565316 DOI: 10.1093/nar/gkab789] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/24/2021] [Accepted: 10/05/2021] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles the human system by its mitochondrial DNA structure and physiology, most translational activators appear to be either lacking, or recruited for post-translational functions. By combining bioinformatics, genetic and biochemical approaches we identified two interacting factors, Cbp7 and Cbp8, controlling Cytb production in S. pombe. We show that their absence affects cytb mRNA stability and impairs the detection of the Cytb protein. We further identified two classes of Cbp7/Cbp8 partners and showed that they modulated Cytb or Cox1 synthesis. First, two isoforms of bS1m, a protein of the small mitoribosomal subunit, that appear mutually exclusive and confer translational specificity. Second, a complex of four proteins dedicated to Cox1 synthesis, which includes an RNA helicase that interacts with the mitochondrial ribosome. Our results suggest that S. pombe contains, in addition to complexes of translational activators, a heterogeneous population of mitochondrial ribosomes that could specifically modulate translation depending on the mRNA translated, in order to optimally balance the production of different respiratory complex subunits.
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Affiliation(s)
- Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sylvie Labarre-Mariotte
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - David Cornu
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyrielle Sophie
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Thomas Michel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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Abstract
Mitochondria contain their own genome that encodes for a small number of proteins, while the vast majority of mitochondrial proteins is produced on cytosolic ribosomes. The formation of respiratory chain complexes depends on the coordinated biogenesis of mitochondrially encoded and nuclear-encoded subunits. In this review, we describe pathways that adjust mitochondrial protein synthesis and import of nuclear-encoded subunits to the assembly of respiratory chain complexes. Furthermore, we outline how defects in protein import into mitochondria affect nuclear gene expression to maintain protein homeostasis under physiological and stress conditions.
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Affiliation(s)
- Chantal Priesnitz
- Institute of Biochemistry and Molecular Biology, Center for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Center for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
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