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Haliburton JR, Shao W, Deutschbauer A, Arkin A, Abate AR. Genetic interaction mapping with microfluidic-based single cell sequencing. PLoS One 2017; 12:e0171302. [PMID: 28170417 PMCID: PMC5295688 DOI: 10.1371/journal.pone.0171302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/19/2017] [Indexed: 11/30/2022] Open
Abstract
Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms.
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Affiliation(s)
- John R. Haliburton
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Wenjun Shao
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
| | - Adam Deutschbauer
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
- E.O. Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam Arkin
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
- E.O. Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
- * E-mail:
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2
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Devrekanli A, Kanemaki MT. Conditional Budding Yeast Mutants with Temperature-Sensitive and Auxin-Inducible Degrons for Screening of Suppressor Genes. Methods Mol Biol 2015; 1369:257-78. [PMID: 26519318 DOI: 10.1007/978-1-4939-3145-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The conditional control of protein expression is useful to characterize the function of proteins, especially of those that are essential for cell viability. Two degron-based systems, temperature-sensitive and auxin-inducible degrons, can be used to generate conditional mutants of budding yeast, simply by transforming appropriate cells with PCR-amplified DNA. We describe a protocol for the generation of temperature-sensitive and auxin-inducible degron mutants. We also show that a conditional mutant with few spontaneous revertants was generated by combining two degron systems for the Inn1 protein. Finally, we describe a suppressor screening method that uses the dual degron-Inn1 mutant to identify mutant proteins that suppress Inn1-K31A, which has a defect in cytokinesis.
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Affiliation(s)
- Asli Devrekanli
- Department of Molecular Biology and Genetics, Canik Basari University, Gürgenyatak Köyü, Samsun, 55080, Turkey.
| | - Masato T Kanemaki
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, SOKENDAI, Yata 1111, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, SOKENDAI, Mishima, Shizuoka, Japan. .,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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3
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Thakkar SV, Allegre KM, Joshi SB, Volkin DB, Middaugh CR. An Application of Ultraviolet Spectroscopy to Study Interactions in Proteins Solutions at High Concentrations. J Pharm Sci 2012; 101:3051-61. [DOI: 10.1002/jps.23188] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 04/12/2012] [Accepted: 04/24/2012] [Indexed: 11/11/2022]
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4
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Ng SK, Tan SH. DISCOVERING PROTEIN–PROTEIN INTERACTIONS. J Bioinform Comput Biol 2011; 1:711-41. [PMID: 15290761 DOI: 10.1142/s0219720004000600] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Revised: 12/12/2003] [Accepted: 12/13/2003] [Indexed: 11/18/2022]
Abstract
The ongoing genomics and proteomics efforts have helped identify many new genes and proteins in living organisms. However, simply knowing the existence of genes and proteins does not tell us much about the biological processes in which they participate. Many major biological processes are controlled by protein interaction networks. A comprehensive description of protein–protein interactions is therefore necessary to understand the genetic program of life. In this tutorial, we provide an overview of the various current high-throughput methods for discovering protein–protein interactions, covering both the conventional experimental methods and new computational approaches.
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Affiliation(s)
- See-Kiong Ng
- Knowledge Discovery Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore.
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Perrakis A, Musacchio A, Cusack S, Petosa C. Investigating a macromolecular complex: the toolkit of methods. J Struct Biol 2011; 175:106-12. [PMID: 21620973 DOI: 10.1016/j.jsb.2011.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/11/2011] [Accepted: 05/12/2011] [Indexed: 02/08/2023]
Abstract
Structural biologists studying macromolecular complexes spend considerable effort doing strictly "non-structural" work: investigating the physiological relevance and biochemical properties of a complex, preparing homogeneous samples for structural analysis, and experimentally validating structure-based hypotheses regarding function or mechanism. Familiarity with the diverse perspectives and techniques available for studying complexes helps in the critical assessment of non-structural data, expedites the pre-structural characterization of a complex and facilitates the investigation of function. Here we survey the approaches and techniques used to study macromolecular complexes from various viewpoints, including genetics, cell and molecular biology, biochemistry/biophysics, structural biology, and systems biology/bioinformatics. The aim of this overview is to heighten awareness of the diversity of perspectives and experimental tools available for investigating complexes and of their usefulness for the structural biologist.
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Affiliation(s)
- Anastassis Perrakis
- Department of Biochemistry, NKI, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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Sarkar S, Haldar S, Hajra S, Sinha P. The budding yeast protein Sum1 functions independently of its binding partners Hst1 and Sir2 histone deacetylases to regulate microtubule assembly. FEMS Yeast Res 2010; 10:660-73. [PMID: 20608984 DOI: 10.1111/j.1567-1364.2010.00655.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The budding yeast protein Sum1 is a transcription factor that associates with the histone deacetylase Hst1p or, in its absence, with Sir2p to form repressed chromatin. In this study, SUM1 has been identified as an allele-specific dosage suppressor of mutations in the major alpha-tubulin-coding gene TUB1. When cloned in a 2mu vector, SUM1 suppressed the cold-sensitive and benomyl-hypersensitive phenotypes associated with the tub1-1 mutation. The suppression was Hst1p- and Sir2p-independent, suggesting that it was not mediated by deacetylation events associated with Sum1p when it functions along with its known partner histone deacetylases. This protein was confined to the nucleus, but did not colocalize with the microtubules nor did it bind to alpha- or beta-tubulin. Cells deleted of SUM1 showed hypersensitivity to benomyl and cold-sensitive growth, phenotypes exhibited by mutants defective in microtubule function and cytoskeletal defects. These observations suggest that Sum1p is a novel regulator of microtubule function. We propose that as a dosage suppressor, Sum1p promotes the formation of microtubules by increasing the availability of the alphabeta-heterodimer containing the mutant alpha-tubulin subunit.
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Affiliation(s)
- Sourav Sarkar
- Department of Biochemistry, Bose Institute, Kolkata, India
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Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C. Systematic Mapping of Genetic Interaction Networks. Annu Rev Genet 2009; 43:601-25. [DOI: 10.1146/annurev.genet.39.073003.114751] [Citation(s) in RCA: 216] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Scott J. Dixon
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Michael Costanzo
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
| | - Anastasia Baryshnikova
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
| | - Brenda Andrews
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
| | - Charles Boone
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
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Rigel NW, Gibbons HS, McCann JR, McDonough JA, Kurtz S, Braunstein M. The Accessory SecA2 System of Mycobacteria Requires ATP Binding and the Canonical SecA1. J Biol Chem 2009; 284:9927-36. [PMID: 19240020 DOI: 10.1074/jbc.m900325200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In bacteria, the majority of exported proteins are transported by the general Sec pathway from their site of synthesis in the cytoplasm across the cytoplasmic membrane. The essential SecA ATPase powers this Sec-mediated export. Mycobacteria possess two nonredundant SecA homologs: SecA1 and SecA2. In pathogenic Mycobacterium tuberculosis and the nonpathogenic model mycobacterium Mycobacterium smegmatis, SecA1 is essential for protein export and is the "housekeeping" SecA, whereas SecA2 is an accessory SecA that exports a specific subset of proteins. In M. tuberculosis the accessory SecA2 pathway plays a role in virulence. In this study, we uncovered basic properties of the mycobacterial SecA2 protein and its pathway for exporting select proteins. By constructing secA2 mutant alleles that encode proteins defective in ATP binding, we showed that ATP binding is required for SecA2 function. SecA2 mutant proteins unable to bind ATP were nonfunctional and dominant negative. By evaluating the subcellular distribution of each SecA, SecA1 was shown to be equally divided between cytosolic and cell envelope fractions, whereas SecA2 was predominantly localized to the cytosol. Finally, we showed that the canonical SecA1 has a role in the process of SecA2-dependent export. The accessory SecA2 export system is important to the physiology and virulence of mycobacteria. These studies help establish the mechanism of this new type of specialized protein export pathway.
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Affiliation(s)
- Nathan W Rigel
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7290, USA
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Frigieri MC, João Luiz MVS, Apponi LH, Zanelli CF, Valentini SR. Synthetic lethality between eIF5A and Ypt1 reveals a connection between translation and the secretory pathway in yeast. Mol Genet Genomics 2008; 280:211-21. [PMID: 18568365 DOI: 10.1007/s00438-008-0357-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 06/03/2008] [Indexed: 12/27/2022]
Abstract
The putative translation initiation factor 5A (eIF5A) is a small protein, highly conserved and essential in all organisms from archaea to mammals. Although the involvement of eIF5A in translation initiation has been questioned, new evidence reestablished the connection between eIF5A and this cellular process. In order to better understand the function of elF5A, a screen for synthetic lethal gene using the tif51A-3 mutant was carried out and a new mutation (G80D) was found in the essential gene YPT1, encoding a protein involved in vesicular trafficking. The precursor form of the vacuolar protein CPY is accumulated in the ypt1-G80D mutant at the nonpermissive temperature, but this defect in vesicular trafficking did not occur in the tif51A mutants tested. Overexpression of eIF5A suppresses the growth defect of a series of ypt1 mutants, but this suppression does not restore correct CPY sorting. On the other hand, overexpression of YPT1 does not suppress the growth defect of tif51A mutants. Further, it was revealed that eIF-5A is present in both soluble and membrane fractions, and its membrane association is ribosome-dependent. Finally, we demonstrated that the ypt1 and other secretion pathway mutants are sensitive to paromomycin. These results confirm the link between translation and vesicular trafficking and reinforce the implication of eIF5A in protein synthesis.
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Affiliation(s)
- Mariana C Frigieri
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University, UNESP, Rod Araraquara-Jaú, km 1, Araraquara, SP, Brazil
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Zhang X, Grey PH, Krishnakumar S, Oppenheimer DG. The IRREGULAR TRICHOME BRANCH loci regulate trichome elongation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2005; 46:1549-60. [PMID: 16043432 DOI: 10.1093/pcp/pci168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The proper control of cell expansion is vital to plant development. It is responsible for shaping individual cells and, together with cell division, it plays a lead role in shaping plant organs. Much of the underlying mechanism by which plant cells expand anisotropically is not understood. We are taking a genetic approach to cell expansion by isolating mutants that affect the branching pattern of Arabidopsis trichomes. Here we report the identification of four new loci that control trichome morphogenesis. These loci were named the IRREGULAR TRICHOME BRANCH (ITB) loci because of the deleterious effects on branch position and length in the mutants. Our analysis of branch expansion in itb mutants shows that the ITB genes act as positive regulators of branch elongation, and that the branch position defects are caused by altered expansion of the trichome stalk. The itb mutations display synergistic effects in double mutant combinations with certain branch number mutations, suggesting that the ITB genes also play key roles in branch initiation. These results demonstrate that the ITB genes are key regulators of anisotropic cell expansion in trichomes.
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Affiliation(s)
- Xiaoguo Zhang
- Department of Botany, University of Florida Genetics Institute, and the Plant Molecular and Cellular Biology Program, University of Florida, 220 Bartram Hall, PO Box 118526, Gainesville, FL 32611-8526, USA
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11
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Singer RA, Johnston GC. The FACT chromatin modulator: genetic and structure/function relationships. Biochem Cell Biol 2005; 82:419-27. [PMID: 15284894 DOI: 10.1139/o04-050] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The chromatin configuration of DNA inhibits access by enzymes such as RNA polymerase II. This inhibition is alleviated by FACT, a conserved transcription elongation factor that has been found to reconfigure nucleosomes to allow transit along the DNA by RNA polymerase II, thus facilitating transcription. FACT also reorganizes nucleosomes after the passage of RNA polymerase II, as indicated by the effects of certain FACT mutations. The larger of the two subunits of FACT is Spt16/Cdc68, while the smaller is termed SSRP1 (vertebrates) or Pob3 (budding yeast). The HMG-box domain at the C terminus of SSRP1 is absent from Pob3; the function of this domain for yeast FACT is supplied by the small HMG-box protein Nhp6. In yeast, this "detachable" HMG domain is a general chromatin component, unlike FACT, which is found only in transcribed regions and associated with RNA polymerase II. The several domains of the larger FACT subunit are also likely to have different functions. Genetic studies suggest that FACT mediates nucleosome reorganization along several pathways, and reinforce the notion that protein unfolding and (or) refolding is involved in FACT activity for transcription.
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Affiliation(s)
- Richard A Singer
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.
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12
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Goeke S, Greene EA, Grant PK, Gates MA, Crowner D, Aigaki T, Giniger E. Alternative splicing of lola generates 19 transcription factors controlling axon guidance in Drosophila. Nat Neurosci 2003; 6:917-24. [PMID: 12897787 DOI: 10.1038/nn1105] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2003] [Accepted: 05/16/2003] [Indexed: 11/08/2022]
Abstract
The Drosophila melanogaster transcription factor Lola (longitudinals lacking) is a pivotal regulator of neural wiring that sets the precise expression levels of proteins that execute specific axon guidance decisions. Lola has a zinc finger DNA binding domain and a BTB (for Broad-complex, Tramtrack and Bric a brac) dimerization motif. We now show that alternative splicing of the lola gene creates a family of 19 transcription factors. All lola isoforms share a common dimerization domain, but 17 have their own unique DNA-binding domains. Seven of these 17 isoforms are present in the distantly-related Dipteran Anopheles gambiae, suggesting that the properties of specific isoforms are likely to be critical to lola function. Analysis of the expression patterns of individual splice variants and of the phenotypes of mutants lacking single isoforms supports this idea and establishes that the alternative forms of lola are responsible for different functions of this gene. Thus, in this system, the alternative splicing of a key transcription factor helps to explain how a small genome encodes all the information that is necessary to specify the enormous diversity of axonal trajectories.
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Affiliation(s)
- Scott Goeke
- Division of Basic Sciences and Program in Developmental Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
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Veselovsky AV, Ivanov YD, Ivanov AS, Archakov AI, Lewi P, Janssen P. Protein-protein interactions: mechanisms and modification by drugs. J Mol Recognit 2002; 15:405-22. [PMID: 12501160 DOI: 10.1002/jmr.597] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein-protein interactions form the proteinaceous network, which plays a central role in numerous processes in the cell. This review highlights the main structures, properties of contact surfaces, and forces involved in protein-protein interactions. The properties of protein contact surfaces depend on their functions. The characteristics of contact surfaces of short-lived protein complexes share some similarities with the active sites of enzymes. The contact surfaces of permanent complexes resemble domain contacts or the protein core. It is reasonable to consider protein-protein complex formation as a continuation of protein folding. The contact surfaces of the protein complexes have unique structure and properties, so they represent prospective targets for a new generation of drugs. During the last decade, numerous investigations have been undertaken to find or design small molecules that block protein dimerization or protein(peptide)-receptor interaction, or on the other hand, induce protein dimerization.
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14
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Davis TN. Genetic analysis of yeast spindle pole bodies. Methods Cell Biol 2002; 67:95-111. [PMID: 11550483 DOI: 10.1016/s0091-679x(01)67007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- T N Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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Vélot C, Srere PA. Reversible transdominant inhibition of a metabolic pathway. In vivo evidence of interaction between two sequential tricarboxylic acid cycle enzymes in yeast. J Biol Chem 2000; 275:12926-33. [PMID: 10777592 DOI: 10.1074/jbc.275.17.12926] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzymes of the Krebs tricarboxylic acid cycle in mitochondria are proposed to form a supramolecular complex, in which there is channeling of intermediates between enzyme active sites. While interactions have been demonstrated in vitro between most of the sequential tricarboxylic acid cycle enzymes, no direct evidence has been obtained in vivo for such interactions. We have isolated, in the Saccharomyces cerevisiae gene encoding the tricarboxylic acid cycle enzyme citrate synthase Cit1p, an "assembly mutation," i.e. a mutation that causes a tricarboxylic acid cycle deficiency without affecting the citrate synthase activity. We have shown that a 15-amino acid peptide from wild type Cit1p encompassing the mutation point inhibits the tricarboxylic acid cycle in a dominant manner, and that the inhibitory phenotype is overcome by a co-overexpression of Mdh1p, the mitochondrial malate dehydrogenase. These data provide the first direct in vivo evidence of interaction between two sequential tricarboxylic acid cycle enzymes, Cit1p and Mdh1p, and indicate that the characterization of assembly mutations by the reversible transdominant inhibition method may be a powerful way to study multienzyme complexes in their physiological context.
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Affiliation(s)
- C Vélot
- Research Service of the Department of Veterans Affairs Medical Center, Dallas, Texas 75216, USA.
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