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Saini PK, Dawitz H, Aufschnaiter A, Bondarev S, Thomas J, Amblard A, Stewart J, Thierry-Mieg N, Ott M, Pierrel F. The [PSI +] prion modulates cytochrome c oxidase deficiency caused by deletion of COX12. Mol Biol Cell 2022; 33:ar130. [PMID: 36129767 PMCID: PMC9727813 DOI: 10.1091/mbc.e21-10-0499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 02/04/2023] Open
Abstract
Cytochrome c oxidase (CcO) is a pivotal enzyme of the mitochondrial respiratory chain, which sustains bioenergetics of eukaryotic cells. Cox12, a peripheral subunit of CcO oxidase, is required for full activity of the enzyme, but its exact function is unknown. Here experimental evolution of a Saccharomyces cerevisiae Δcox12 strain for ∼300 generations allowed to restore the activity of CcO oxidase. In one population, the enhanced bioenergetics was caused by a A375V mutation in the cytosolic AAA+ disaggregase Hsp104. Deletion or overexpression of HSP104 also increased respiration of the Δcox12 ancestor strain. This beneficial effect of Hsp104 was related to the loss of the [PSI+] prion, which forms cytosolic amyloid aggregates of the Sup35 protein. Overall, our data demonstrate that cytosolic aggregation of a prion impairs the mitochondrial metabolism of cells defective for Cox12. These findings identify a new functional connection between cytosolic proteostasis and biogenesis of the mitochondrial respiratory chain.
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Affiliation(s)
- Pawan Kumar Saini
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Hannah Dawitz
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Stanislav Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Jinsu Thomas
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Amélie Amblard
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - James Stewart
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Nicolas Thierry-Mieg
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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Czuppon P, Rogers DW. Evolution of mating types in finite populations: The precarious advantage of being rare. J Evol Biol 2019; 32:1290-1299. [PMID: 31479547 DOI: 10.1111/jeb.13528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/28/2019] [Accepted: 08/19/2019] [Indexed: 01/03/2023]
Abstract
Sexually reproducing populations with self-incompatibility bear the cost of limiting potential mates to individuals of a different type. Rare mating types escape this cost since they are unlikely to encounter incompatible partners, leading to the deterministic prediction of continuous invasion by new mutants and an ever-increasing number of types. However, rare types are also at an increased risk of being lost by random drift. Calculating the number of mating types that a population can maintain requires consideration of both the deterministic advantages and the stochastic risks. By comparing the relative importance of selection and drift, we show that a population of size N can maintain a maximum of approximately N1/3 mating types for intermediate population sizes, whereas for large N, we derive a formal estimate. Although the number of mating types in a population is quite stable, the rare-type advantage promotes turnover of types. We derive explicit formulas for both the invasion and turnover probabilities in finite populations.
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Affiliation(s)
- Peter Czuppon
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Centre Interdisciplinaire de Recherche en Biologie, CNRS Collège de France, PSL Research University, Paris, France.,Institut d'Ecologie et des Sciences de l'Environnement (IEES), UPEC, CNRS, IRD, INRA, Sorbonne Université, Paris, France
| | - David W Rogers
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Abstract
The reproductive ecology of Saccharomyces cerevisiae is still largely unknown. Recent evidence of interspecific hybridization, high levels of strain heterozygosity, and prion transmission suggest that outbreeding occurs frequently in yeasts. Nevertheless, the place where yeasts mate and recombine in the wild has not been identified. We found that the intestine of social wasps hosts highly outbred S. cerevisiae strains as well as a rare S. cerevisiae×S. paradoxus hybrid. We show that the intestine of Polistes dominula social wasps favors the mating of S. cerevisiae strains among themselves and with S. paradoxus cells by providing a succession of environmental conditions prompting cell sporulation and spores germination. In addition, we prove that heterospecific mating is the only option for European S. paradoxus strains to survive in the gut. Taken together, these findings unveil the best hidden secret of yeast ecology, introducing the insect gut as an environmental alcove in which crosses occur, maintaining and generating the diversity of the ascomycetes.
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Kiktev DA, Melomed MM, Lu CD, Newnam GP, Chernoff YO. Feedback control of prion formation and propagation by the ribosome-associated chaperone complex. Mol Microbiol 2015; 96:621-32. [PMID: 25649498 DOI: 10.1111/mmi.12960] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2015] [Indexed: 01/01/2023]
Abstract
Cross-beta fibrous protein aggregates (amyloids and amyloid-based prions) are found in mammals (including humans) and fungi (including yeast), and are associated with both diseases and heritable traits. The Hsp104/70/40 chaperone machinery controls propagation of yeast prions. The Hsp70 chaperones Ssa and Ssb show opposite effects on [PSI(+)], a prion form of the translation termination factor Sup35 (eRF3). Ssb is bound to translating ribosomes via ribosome-associated complex (RAC), composed of Hsp40-Zuo1 and Hsp70-Ssz1. Here we demonstrate that RAC disruption increases de novo prion formation in a manner similar to Ssb depletion, but interferes with prion propagation in a manner similar to Ssb overproduction. Release of Ssb into the cytosol in RAC-deficient cells antagonizes binding of Ssa to amyloids. Thus, propagation of an amyloid formed because of lack of ribosome-associated Ssb can be counteracted by cytosolic Ssb, generating a feedback regulatory circuit. Release of Ssb from ribosomes is also observed in wild-type cells during growth in poor synthetic medium. Ssb is, in a significant part, responsible for the prion destabilization in these conditions, underlining the physiological relevance of the Ssb-based regulatory circuit.
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Affiliation(s)
- Denis A Kiktev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
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Abstract
Prions (infectious proteins) cause fatal neurodegenerative diseases in mammals. In the yeast Saccharomyces cerevisiae, many toxic and lethal variants of the [PSI+] and [URE3] prions have been identified in laboratory strains, although some commonly studied variants do not seem to impair cell growth. Phylogenetic analysis has revealed four major clades of S. cerevisiae that share histories of two prion proteins and largely correspond to different ecological niches of yeast. The [PIN+] prion was most prevalent in commercialized niches, infrequent among wine/vineyard strains, and not observed in ancestral isolates. As previously reported, the [PSI+] and [URE3] prions are not found in any of these strains. Patterns of heterozygosity revealed genetic mosaicism and indicated extensive outcrossing among divergent strains in commercialized environments. In contrast, ancestral isolates were all homozygous and wine/vineyard strains were closely related to each other and largely homozygous. Cellular growth patterns were highly variable within and among clades, although ancestral isolates were the most efficient sporulators and domesticated strains showed greater tendencies for flocculation. [PIN+]-infected strains had a significantly higher likelihood of polyploidy, showed a higher propensity for flocculation compared to uninfected strains, and had higher sporulation efficiencies compared to domesticated, uninfected strains. Extensive phenotypic variability among strains from different environments suggests that S. cerevisiae is a niche generalist and that most wild strains are able to switch from asexual to sexual and from unicellular to multicellular growth in response to environmental conditions. Our data suggest that outbreeding and multicellular growth patterns adapted for domesticated environments are ecological risk factors for the [PIN+] prion in wild yeast.
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Byers JS, Jarosz DF. Pernicious pathogens or expedient elements of inheritance: the significance of yeast prions. PLoS Pathog 2014; 10:e1003992. [PMID: 24722628 PMCID: PMC3983059 DOI: 10.1371/journal.ppat.1003992] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- James S Byers
- Departments of Chemical and Systems Biology and of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Daniel F Jarosz
- Departments of Chemical and Systems Biology and of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
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Yeast prions and human prion-like proteins: sequence features and prediction methods. Cell Mol Life Sci 2014; 71:2047-63. [PMID: 24390581 DOI: 10.1007/s00018-013-1543-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/12/2013] [Accepted: 12/16/2013] [Indexed: 11/27/2022]
Abstract
Prions are self-propagating infectious protein isoforms. A growing number of prions have been identified in yeast, each resulting from the conversion of soluble proteins into an insoluble amyloid form. These yeast prions have served as a powerful model system for studying the causes and consequences of prion aggregation. Remarkably, a number of human proteins containing prion-like domains, defined as domains with compositional similarity to yeast prion domains, have recently been linked to various human degenerative diseases, including amyotrophic lateral sclerosis. This suggests that the lessons learned from yeast prions may help in understanding these human diseases. In this review, we examine what has been learned about the amino acid sequence basis for prion aggregation in yeast, and how this information has been used to develop methods to predict aggregation propensity. We then discuss how this information is being applied to understand human disease, and the challenges involved in applying yeast prediction methods to higher organisms.
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Abstract
The capacity to polymerize into amyloid fibrils is common to many proteins. While some proteins naturally form these fibrils to serve functional roles, amyloid is usually associated with pathogenic processes in which specific proteins aberrantly aggregate within cells or tissues. Though the contribution of amyloid fibrils to actual disease pathogenesis is not always clear, one possibility is that the titration of essential proteins from solution into aggregates contributes to the cellular degeneration common to many amyloid diseases. Using mammalian and yeast model systems, we recently showed that the common biophysical properties of amyloid aggregates--including strong resistance to dissolution--enable stringent purification and identification of both amyloid-forming and amyloid-associated proteins directly from cells. Strikingly, many proteins that were previously implicated in formation or clearance of intracellular aggregates, including several stress granule components, were found to co-aggregate with amyloid formed by a polyglutamine-expanded huntingtin fragment. This direct evaluation of proteins within aggregates can help identify new amyloid-forming proteins, as well as proteins that can indirectly contribute to disease mechanisms.
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Affiliation(s)
- Dmitry Kryndushkin
- Department of Pharmacology; Uniformed Services University of the Health Sciences; Bethesda, MD USA
| | - Maggie P Wear
- Department of Pharmacology; Uniformed Services University of the Health Sciences; Bethesda, MD USA
| | - Frank Shewmaker
- Department of Pharmacology; Uniformed Services University of the Health Sciences; Bethesda, MD USA
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