1
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Watanabe D. Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation. Biosci Biotechnol Biochem 2024; 88:237-241. [PMID: 38006236 DOI: 10.1093/bbb/zbad167] [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: 09/30/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The yeast Saccharomyces cerevisiae plays a pivotal role in the production of fermented foods by converting sugars in ingredients into ethanol through alcoholic fermentation. However, how accurate is our understanding of its biological significance? Although yeast is essential to produce alcoholic beverages and bioethanol, yeast does not yield ethanol for humankind. Yeast obtains energy in the form of ATP for its own vital processes through alcoholic fermentation, which generates ethanol as a byproduct. The production of ethanol may have more significance for yeast, since many other organisms do not produce ethanol, a highly toxic substance, to obtain energy. The key to address this issue has not been found using conventional microbiology, where yeasts are isolated and cultured in pure form. This review focuses on a possible novel role of yeast alcohol fermentation, which is revealed through our recent studies of microbial interactions.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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2
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Watanabe D, Kumano M, Sugimoto Y, Takagi H. Spontaneous Attenuation of Alcoholic Fermentation via the Dysfunction of Cyc8p in Saccharomyces cerevisiae. Int J Mol Sci 2023; 25:304. [PMID: 38203474 PMCID: PMC10778621 DOI: 10.3390/ijms25010304] [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: 12/03/2023] [Revised: 12/19/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
A cell population characterized by the release of glucose repression and known as [GAR+] emerges spontaneously in the yeast Saccharomyces cerevisiae. This study revealed that the [GAR+] variants exhibit retarded alcoholic fermentation when glucose is the sole carbon source. To identify the key to the altered glucose response, the gene expression profile of [GAR+] cells was examined. Based on RNA-seq data, the [GAR+] status was linked to impaired function of the Cyc8p-Tup1p complex. Loss of Cyc8p led to a decrease in the initial rate of alcoholic fermentation under glucose-rich conditions via the inactivation of pyruvate decarboxylase, an enzyme unique to alcoholic fermentation. These results suggest that Cyc8p can become inactive to attenuate alcoholic fermentation. These findings may contribute to the elucidation of the mechanism of non-genetic heterogeneity in yeast alcoholic fermentation.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Maika Kumano
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan
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3
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Zhouravleva GA, Bondarev SA, Trubitsina NP. How Big Is the Yeast Prion Universe? Int J Mol Sci 2023; 24:11651. [PMID: 37511408 PMCID: PMC10380529 DOI: 10.3390/ijms241411651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The number of yeast prions and prion-like proteins described since 1994 has grown from two to nearly twenty. If in the early years most scientists working with the classic mammalian prion, PrPSc, were skeptical about the possibility of using the term prion to refer to yeast cytoplasmic elements with unusual properties, it is now clear that prion-like phenomena are widespread and that yeast can serve as a convenient model for studying them. Here we give a brief overview of the yeast prions discovered so far and focus our attention to the various approaches used to identify them. The prospects for the discovery of new yeast prions are also discussed.
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Affiliation(s)
- Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
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4
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Jay-Garcia LM, Cornell JL, Howie RL, Faber QL, Salas A, Chernova TA, Chernoff YO. Yeast Chaperone Hsp70-Ssb Modulates a Variety of Protein-Based Heritable Elements. Int J Mol Sci 2023; 24:ijms24108660. [PMID: 37240005 DOI: 10.3390/ijms24108660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Prions are transmissible self-perpetuating protein isoforms associated with diseases and heritable traits. Yeast prions and non-transmissible protein aggregates (mnemons) are frequently based on cross-β ordered fibrous aggregates (amyloids). The formation and propagation of yeast prions are controlled by chaperone machinery. Ribosome-associated chaperone Hsp70-Ssb is known (and confirmed here) to modulate formation and propagation of the prion form of the Sup35 protein [PSI+]. Our new data show that both formation and mitotic transmission of the stress-inducible prion form of the Lsb2 protein ([LSB+]) are also significantly increased in the absence of Ssb. Notably, heat stress leads to a massive accumulation of [LSB+] cells in the absence of Ssb, implicating Ssb as a major downregulator of the [LSB+]-dependent memory of stress. Moreover, the aggregated form of Gγ subunit Ste18, [STE+], behaving as a non-heritable mnemon in the wild-type strain, is generated more efficiently and becomes heritable in the absence of Ssb. Lack of Ssb also facilitates mitotic transmission, while lack of the Ssb cochaperone Hsp40-Zuo1 facilitates both spontaneous formation and mitotic transmission of the Ure2 prion, [URE3]. These results demonstrate that Ssb is a general modulator of cytosolic amyloid aggregation, whose effect is not restricted only to [PSI+].
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Affiliation(s)
- Lina M Jay-Garcia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph L Cornell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rebecca L Howie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Quincy L Faber
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Abigail Salas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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5
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Tanabe K, Maeda N, Okumura H, Shima J. Emergence of [GAR + ] cells in yeast from sake brewing affects the fermentation properties. Yeast 2023; 40:134-142. [PMID: 36755487 DOI: 10.1002/yea.3844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/28/2022] [Accepted: 02/08/2023] [Indexed: 02/10/2023] Open
Abstract
In the traditional (kimoto) method of sake (Japanese rice wine) brewing, Saccharomyces cerevisiae yeast cells are exposed to lactate, which is produced by lactic acid bacteria in the seed mash. Lactate promotes the appearance of glucose-repression-resistant [GAR+ ] cells. Herein, we compared the resistance to glucose repression among kimoto, industrial, and laboratory yeast strains. We observed that the frequencies of the spontaneous emergence of [GAR+ ] cells among the kimoto strains were higher than those among the industrial and laboratory strains. The fermentation ability of a kimoto yeast (strain U44) was lower than that of an industrial strain (K701), as [GAR+ ] cells generally showed slower ethanol production. The addition of lactate decreased the fermentation abilities of the K701 strain by increasing the number of [GAR+ ] cells, but it did not affect those of the U44 strain. These results suggest that lactate controlled fermentation by promoting the appearance of [GAR+ ] cells in the industrial sake strains but not in the kimoto strains.
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Affiliation(s)
- Koichi Tanabe
- Department of Food Science and Human Nutrition, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan.,Research Center for Fermentation and Brewing, Ryukoku University, Otsu, Shiga, Japan
| | - Natsumi Maeda
- Department of Food Science and Human Nutrition, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | - Honoka Okumura
- Department of Plant Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | - Jun Shima
- Research Center for Fermentation and Brewing, Ryukoku University, Otsu, Shiga, Japan.,Department of Plant Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
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6
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Yan J, Zheng D, Gu H, Yu Y, Zeng J, Chen Q, Yu A, Zhang X. In Situ Sprayed Biotherapeutic Gel Containing Stable Microbial Communities for Efficient Anti-Infection Treatment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205480. [PMID: 36479844 PMCID: PMC9896078 DOI: 10.1002/advs.202205480] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/20/2022] [Indexed: 06/09/2023]
Abstract
Systematic administration of antibiotics to treat infections often leads to the rapid evolution and spread of multidrug-resistant bacteria. Here, an in situ-formed biotherapeutic gel that controls multidrug-resistant bacterial infections and accelerates wound healing is reported. This biotherapeutic gel is constructed by incorporating stable microbial communities (kombucha) capable of producing antimicrobial substances and organic acids into thermosensitive Pluronic F127 (polyethylene-polypropylene glycol) solutions. Furthermore, it is found that the stable microbial communities-based biotherapeutic gel possesses a broad antimicrobial spectrum and strong antibacterial effects in diverse pathogenic bacteria-derived xenograft infection models, as well as in patient-derived multidrug-resistant bacterial xenograft infection models. The biotherapeutic gel system considerably outperforms the commercial broad-spectrum antibacterial gel (0.1% polyaminopropyl biguanide) in pathogen removal and infected wound healing. Collectively, this biotherapeutic strategy of exploiting stable symbiotic consortiums to repel pathogens provides a paradigm for developing efficient antibacterial biomaterials and overcomes the failure of antibiotics to treat multidrug-resistant bacterial infections.
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Affiliation(s)
- Jian‐Hua Yan
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of ChemistryWuhan UniversityWuhan430072P. R. China
| | - Di‐Wei Zheng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of ChemistryWuhan UniversityWuhan430072P. R. China
| | - Hui‐Yun Gu
- Department of Orthopedic Trauma and MicrosurgeryZhongnan Hospital of Wuhan UniversityWuhan430071P. R. China
| | - Yun‐Jian Yu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of ChemistryWuhan UniversityWuhan430072P. R. China
| | - Jin‐Yue Zeng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of ChemistryWuhan UniversityWuhan430072P. R. China
| | - Qi‐Wen Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of ChemistryWuhan UniversityWuhan430072P. R. China
| | - Ai‐Xi Yu
- Department of Orthopedic Trauma and MicrosurgeryZhongnan Hospital of Wuhan UniversityWuhan430071P. R. China
| | - Xian‐Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of ChemistryWuhan UniversityWuhan430072P. R. China
- Department of Orthopedic Trauma and MicrosurgeryZhongnan Hospital of Wuhan UniversityWuhan430071P. R. China
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7
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Vijayraghavan S, Kozmin SG, Xi W, McCusker JH. A novel narnavirus is widespread in Saccharomyces cerevisiae and impacts multiple host phenotypes. G3 (BETHESDA, MD.) 2022; 13:6957440. [PMID: 36560866 PMCID: PMC9911063 DOI: 10.1093/g3journal/jkac337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
RNA viruses are a widespread, biologically diverse group that includes the narnaviridiae, a family of unencapsidated RNA viruses containing a single ORF that encodes an RNA-dependent RNA polymerase. In the yeast Saccharomyces cerevisiae, the 20S and 23S RNA viruses are well-studied members of the narnaviridiae, which are present at low intracellular copy numbers, unless induced by stress or unfavorable growth conditions, and are not known to affect host fitness. In this study, we describe a new S. cerevisiae narnavirus that we designate as N1199. We show that N1199 is uniquely present as a double-stranded RNA at a high level relative to other known members of this family in 1 strain background, YJM1199, and is present as a single-stranded RNA at lower levels in 98 of the remaining 100-genomes strains. Furthermore, we see a strong association between the presence of high level N1199 and host phenotype defects, including greatly reduced sporulation efficiency and growth on multiple carbon sources. Finally, we describe associations between N1199 abundance and host phenotype defects, including autophagy.
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Affiliation(s)
- Sriram Vijayraghavan
- Present address: Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Stanislav G Kozmin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 561 Research Drive 3020, Jones Bldg. Room 239, Durham, NC 27710, USA
| | - Wen Xi
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 561 Research Drive 3020, Jones Bldg. Room 239, Durham, NC 27710, USA
| | - John H McCusker
- Corresponding author: Department of Molecular Genetics and Microbiology, Duke University Medical Center, 561 Research Drive 3020, Jones Bldg. Room 239, Durham, NC 27710, USA.
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8
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Abstract
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.
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Affiliation(s)
- Linda L Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
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9
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Santiago E, Moreno DF, Acar M. Phenotypic plasticity as a facilitator of microbial evolution. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac020. [PMID: 36465837 PMCID: PMC9709823 DOI: 10.1093/eep/dvac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/27/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Tossed about by the tides of history, the inheritance of acquired characteristics has found a safe harbor at last in the rapidly expanding field of epigenetics. The slow pace of genetic variation and high opportunity cost associated with maintaining a diverse genetic pool are well-matched by the flexibility of epigenetic traits, which can enable low-cost exploration of phenotypic space and reactive tuning to environmental pressures. Aiding in the generation of a phenotypically plastic population, epigenetic mechanisms often provide a hotbed of innovation for countering environmental pressures, while the potential for genetic fixation can lead to strong epigenetic-genetic evolutionary synergy. At the level of cells and cellular populations, we begin this review by exploring the breadth of mechanisms for the storage and intergenerational transmission of epigenetic information, followed by a brief review of common and exotic epigenetically regulated phenotypes. We conclude by offering an in-depth coverage of recent papers centered around two critical issues: the evolvability of epigenetic traits through Baldwinian adaptive phenotypic plasticity and the potential for synergy between epigenetic and genetic evolution.
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Affiliation(s)
- Emerson Santiago
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
| | - David F Moreno
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- *Correspondence address. Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA. Tel: +90 (543) 304-0388; E-mail:
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10
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Fermentation of Dairy-Relevant Sugars by Saccharomyces, Kluyveromyces, and Brettanomyces: An Exploratory Study with Implications for the Utilization of Acid Whey, Part II. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In Greek-style yogurt production, every kilogram of product yields 2 to 3 kg of acid whey (YAW); this coproduct’s composition and low pH pose challenges for its proper valorization and reinsertion into the food supply chain. However, 240 mL of YAW contains over 9 g of lactose and represents a good source of minerals; these traits can be leveraged to develop nutritious fermented beverages. The purpose of this study is to investigate the aerobic fermentation of dairy sugars by different yeasts by characterizing these processes and their products. This will determine whether such methods provide viable options for the production of acetic-acid-containing beverages from YAW. To achieve this, yeast nitrogen base was used to prepare four growth media formulations, each supplemented with lactose, glucose, galactose, or a 1:1 mix of glucose and galactose (GLU:GAL), and each adjusted to a pH of 4.20. Fermentations were performed by pure cultures of S. cerevisiae, K. marxianus, B. claussenii, or B. bruxellensis, and were held at 25 °C with agitation at 185 rpm. For each treatment, density, pH, and microbial enumeration were measured over time to obtain process profiles, while ethanol, organic acids, and sugars were analyzed at the beginning and the end of each fermentation via HPLC, to determine resulting products. ANOVA and Tukey’s honest significant difference test at a significance level of 0.05 were used to compare residual sugars and fermentation products. Variable rates of sugar consumption were observed for each species. In GLU:GAL, B. claussenii consumed all of the glucose, left behind most of the galactose, and produced a high concentration of acetic acid. These results suggest the potential to develop versatile processes that target glucose for acetic acid production, while leaving available galactose to confer products with prebiotic properties. The development of processes for the conversion of YAW into beverages with organic acids and other healthful components not only aligns with consumers’ demands for better-for-you products, but also promotes the valorization of this otherwise underutilized dairy coproduct.
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11
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Chen Z, Kheiri S, Young EWK, Kumacheva E. Trends in Droplet Microfluidics: From Droplet Generation to Biomedical Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6233-6248. [PMID: 35561292 DOI: 10.1021/acs.langmuir.2c00491] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the past decade, droplet microfluidics has attracted growing interest in biology, medicine, and engineering. In this feature article, we review the advances in droplet microfluidics, primarily focusing on the research conducted by our group. Starting from the introduction to the mechanisms of microfluidic droplet formation and the strategies for cell encapsulation in droplets, we then focus on droplet transformation into microgels. Furthermore, we review three biomedical applications of droplet microfluidics, that is, 3D cell culture, single-cell analysis, and in vitro organ and disease modeling. We conclude with our perspective on future directions in the development of droplet microfluidics for biomedical applications.
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Affiliation(s)
- Zhengkun Chen
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Sina Kheiri
- Department of Mechanical and Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, Ontario, Canada, M5S 3G8
| | - Edmond W K Young
- Department of Mechanical and Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, Ontario, Canada, M5S 3G8
- Institute of Biomedical Engineering, University of Toronto, Roseburgh Building, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Eugenia Kumacheva
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
- Institute of Biomedical Engineering, University of Toronto, Roseburgh Building, 164 College Street, Toronto, Ontario, Canada M5S 3G9
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
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12
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Morawska LP, Hernandez-Valdes JA, Kuipers OP. Diversity of bet-hedging strategies in microbial communities-Recent cases and insights. WIREs Mech Dis 2022; 14:e1544. [PMID: 35266649 PMCID: PMC9286555 DOI: 10.1002/wsbm.1544] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
Microbial communities are continuously exposed to unpredictable changes in their environment. To thrive in such dynamic habitats, microorganisms have developed the ability to readily switch phenotypes, resulting in a number of differently adapted subpopulations expressing various traits. In evolutionary biology, a particular case of phenotypic heterogeneity that evolved in an unpredictably changing environment has been defined as bet‐hedging. Bet‐hedging is a risk‐spreading strategy where isogenic populations stochastically (randomly) diversify their phenotypes, often resulting in maladapted individuals that suffer lower reproductive success. This fitness trade‐off in a specific environment may have a selective advantage upon the sudden environmental shift. Thus, a bet‐hedging strategy allows populations to persist in very dynamic habitats, but with a particular fitness cost. In recent years, numerous examples of phenotypic heterogeneity in different microorganisms have been observed, some suggesting bet‐hedging. Here, we highlight the latest reports concerning bet‐hedging phenomena in various microorganisms to show how versatile this strategy is within the microbial realms. This article is categorized under:Infectious Diseases > Molecular and Cellular Physiology
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Affiliation(s)
- Luiza P Morawska
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
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13
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Bai FY, Han DY, Duan SF, Wang QM. The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae. Genes (Basel) 2022; 13:genes13020230. [PMID: 35205274 PMCID: PMC8871604 DOI: 10.3390/genes13020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/01/2023] Open
Abstract
The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.
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Affiliation(s)
- Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-6480-7406
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China;
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14
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Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF. A prion accelerates proliferation at the expense of lifespan. eLife 2021; 10:e60917. [PMID: 34545808 PMCID: PMC8455135 DOI: 10.7554/elife.60917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
In fluctuating environments, switching between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Trade-offs arise, however. Mechanisms that aberrantly increase cell size or proliferation-such as mutations or chemicals that interfere with growth regulatory pathways-can also shorten lifespan. Here we report a natural example of how the interplay between growth and lifespan can be epigenetically controlled. We find that a highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation rates at the cost of a shortened lifespan. Cells harboring the prion grow larger and exhibit altered protein synthesis. This epigenetic state, [BIG+] (better in growth), allows cells to heritably yet reversibly alter their translational program, leading to the differential synthesis of dozens of proteins, including many that regulate proliferation and aging. Our data reveal a new role for prion-based control of an RNA-modifying enzyme in driving heritable epigenetic states that transform cell growth and survival.
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Affiliation(s)
- David M Garcia
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Edgar A Campbell
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Christopher M Jakobson
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | - Ethan A Shaw
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Acadia L DiNardo
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Daniel F Jarosz
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
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15
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The information continuum model of evolution. Biosystems 2021; 209:104510. [PMID: 34416317 DOI: 10.1016/j.biosystems.2021.104510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
Most biologists agree that evolution is contingent on inherited information shaped by natural selection. This apparent consensus could be taken to indicate agreement on the forces shaping evolution, but vivid discussions reveal divergences on how evolution is perceived. The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors. This has fueled a demand of a broader evolutionary perspective, for example from the proponents of the Extended Evolutionary Synthesis (EES). Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do - and conclude that information in and of itself is immaterial. We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems.
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16
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Mencher A, Morales P, Tronchoni J, Gonzalez R. Mechanisms Involved in Interspecific Communication between Wine Yeasts. Foods 2021; 10:foods10081734. [PMID: 34441512 PMCID: PMC8394882 DOI: 10.3390/foods10081734] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
In parallel with the development of non-Saccharomyces starter cultures in oenology, a growing interest has developed around the interactions between the microorganisms involved in the transformation of grape must into wine. Nowadays, it is widely accepted that the outcome of a fermentation process involving two or more inoculated yeast species will be different from the weighted average of the corresponding individual cultures. Interspecific interactions between wine yeasts take place on several levels, including interference competition, exploitation competition, exchange of metabolic intermediates, and others. Some interactions could be a simple consequence of each yeast running its own metabolic programme in a context where metabolic intermediates and end products from other yeasts are present. However, there are clear indications, in some cases, of specific recognition between interacting yeasts. In this article we discuss the mechanisms that may be involved in the communication between wine yeasts during alcoholic fermentation.
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Affiliation(s)
- Ana Mencher
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera LO-20, Salida 13, 26007 Logroño, Spain; (A.M.); (P.M.)
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera LO-20, Salida 13, 26007 Logroño, Spain; (A.M.); (P.M.)
| | - Jordi Tronchoni
- Faculty of Health Sciences, Valencian International University (VIU), C/Pintor Sorolla 21, 46002 Valencia, Spain;
| | - Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera LO-20, Salida 13, 26007 Logroño, Spain; (A.M.); (P.M.)
- Correspondence: ; Tel.: +34-941-894-980
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17
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Garai S, Citu, Singla-Pareek SL, Sopory SK, Kaur C, Yadav G. Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:707286. [PMID: 34381483 PMCID: PMC8350573 DOI: 10.3389/fpls.2021.707286] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/29/2021] [Indexed: 08/01/2023]
Abstract
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its "prionome." In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Citu
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sudhir K. Sopory
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Charanpreet Kaur
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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18
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Zajkowski T, Lee MD, Mondal SS, Carbajal A, Dec R, Brennock PD, Piast RW, Snyder JE, Bense NB, Dzwolak W, Jarosz DF, Rothschild LJ. The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. Mol Biol Evol 2021; 38:2088-2103. [PMID: 33480998 DOI: 10.1093/molbev/msab010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Prions, proteins that can convert between structurally and functionally distinct states and serve as non-Mendelian mechanisms of inheritance, were initially discovered and only known in eukaryotes, and consequently considered to likely be a relatively late evolutionary acquisition. However, the recent discovery of prions in bacteria and viruses has intimated a potentially more ancient evolutionary origin. Here, we provide evidence that prion-forming domains exist in the domain archaea, the last domain of life left unexplored with regard to prions. We searched for archaeal candidate prion-forming protein sequences computationally, described their taxonomic distribution and phylogeny, and analyzed their associated functional annotations. Using biophysical in vitro assays, cell-based and microscopic approaches, and dye-binding analyses, we tested select candidate prion-forming domains for prionogenic characteristics. Out of the 16 tested, eight formed amyloids, and six acted as protein-based elements of information transfer driving non-Mendelian patterns of inheritance. We also identified short peptides from our archaeal prion candidates that can form amyloid fibrils independently. Lastly, candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, an observation that may help future archaeal prion predictions. Taken together, our discovery of functional prion-forming domains in archaea provides evidence that multiple archaeal proteins are capable of acting as prions-thus expanding our knowledge of this epigenetic phenomenon to the third and final domain of life and bolstering the possibility that they were present at the time of the last universal common ancestor.
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Affiliation(s)
- Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,University Space Research Association, Mountain View, CA, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Amanda Carbajal
- University Space Research Association, Mountain View, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | - Radoslaw W Piast
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | | | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, USA
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19
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Portz B, Lee BL, Shorter J. FUS and TDP-43 Phases in Health and Disease. Trends Biochem Sci 2021; 46:550-563. [PMID: 33446423 PMCID: PMC8195841 DOI: 10.1016/j.tibs.2020.12.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/24/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022]
Abstract
The distinct prion-like domains (PrLDs) of FUS and TDP-43, modulate phase transitions that result in condensates with a range of material states. These assemblies are implicated in both health and disease. In this review, we examine how sequence, structure, post-translational modifications, and RNA can affect the self-assembly of these RNA-binding proteins (RBPs). We discuss how our emerging understanding of FUS and TDP-43 liquid-liquid phase separation (LLPS) and aggregation, could be leveraged to design new therapies for neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and limbic-predominant age-related TDP-43 encephalopathy (LATE).
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Affiliation(s)
- Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bo Lim Lee
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Gonzalez R, Morales P. Truth in wine yeast. Microb Biotechnol 2021; 15:1339-1356. [PMID: 34173338 PMCID: PMC9049622 DOI: 10.1111/1751-7915.13848] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/30/2022] Open
Abstract
Evolutionary history and early association with anthropogenic environments have made Saccharomyces cerevisiae the quintessential wine yeast. This species typically dominates any spontaneous wine fermentation and, until recently, virtually all commercially available wine starters belonged to this species. The Crabtree effect, and the ability to grow under fully anaerobic conditions, contribute decisively to their dominance in this environment. But not all strains of Saccharomyces cerevisiae are equally suitable as starter cultures. In this article, we review the physiological and genetic characteristics of S. cerevisiae wine strains, as well as the biotic and abiotic factors that have shaped them through evolution. Limited genetic diversity of this group of yeasts could be a constraint to solving the new challenges of oenology. However, research in this field has for many years been providing tools to increase this diversity, from genetic engineering and classical genetic tools to the inclusion of other yeast species in the catalogues of wine yeasts. On occasion, these less conventional species may contribute to the generation of interspecific hybrids with S. cerevisiae. Thus, our knowledge about wine strains of S. cerevisiae and other wine yeasts is constantly expanding. Over the last decades, wine yeast research has been a pillar for the modernisation of oenology, and we can be confident that yeast biotechnology will keep contributing to solving any challenges, such as climate change, that we may face in the future.
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Affiliation(s)
- Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera de Burgos, km 6, Logroño, La Rioja, 26071, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera de Burgos, km 6, Logroño, La Rioja, 26071, Spain
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21
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Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p. PLoS One 2021; 16:e0247285. [PMID: 34019539 PMCID: PMC8139511 DOI: 10.1371/journal.pone.0247285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/26/2021] [Indexed: 11/23/2022] Open
Abstract
Across eukaryotes, homopolymeric repeats of amino acids are enriched in regulatory proteins such as transcription factors and chromatin remodelers. These domains play important roles in signaling, binding, prion formation, and functional phase separation. Azf1p is a prion-forming yeast transcription factor that contains two homorepeat domains, a polyglutamine and a polyasparagine domain. In this work, we report a new phenotype for Azf1p and identify a large set of genes that are regulated by Azf1p during growth in glucose. We show that the polyasparagine (polyN) domain plays a subtle role in transcription but is dispensable for Azf1p localization and prion formation. Genes upregulated upon deletion of the polyN domain are enriched in functions related to carbon metabolism and storage. This domain may therefore be a useful target for engineering yeast strains for fermentation applications and small molecule production. We also report that both the polyasparagine and polyglutamine domains vary in length across strains of S. cerevisiae and propose a model for how this variation may impact protein function.
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22
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Chen YR, Ziv I, Swaminathan K, Elias JE, Jarosz DF. Protein aggregation and the evolution of stress resistance in clinical yeast. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200127. [PMID: 33866806 DOI: 10.1098/rstb.2020.0127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Protein aggregation, particularly in its prion-like form, has long been thought to be detrimental. However, recent studies have identified multiple instances where protein aggregation is important for normal physiological functions. Combining mass spectrometry and cell biological approaches, we developed a strategy for the identification of protein aggregates in cell lysates. We used this approach to characterize prion-based traits in pathogenic strains of the yeast Saccharomyces cerevisiae isolated from immunocompromised human patients. The proteins that we found, including the metabolic enzyme Cdc19, the translation elongation factor Yef3 and the fibrillarin homologue Nop1, are known to assemble under certain physiological conditions. Yet, such assemblies have not been reported to be stable or heritable. Our data suggest that some proteins which aggregate in response to stress have the capacity to acquire diverse assembled states, certain ones of which can be propagated across generations in a form of protein-based epigenetics. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Kavya Swaminathan
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.,Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
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23
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Saad S, Jarosz DF. Protein self-assembly: A new frontier in cell signaling. Curr Opin Cell Biol 2021; 69:62-69. [PMID: 33493989 PMCID: PMC8058241 DOI: 10.1016/j.ceb.2020.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022]
Abstract
Long viewed as paradigm-shifting, but rare, prions have recently been discovered in all domains of life. Protein sequences that can drive this form of self-assembly are strikingly common in eukaryotic proteomes, where they are enriched in proteins involved in information flow and signal transduction. Although prions were thought to be a consequence of random errors in protein folding, recent studies suggest that prion formation can be a controlled process initiated by defined cellular signals. Many are present in normal biological contexts, yet are invisible to most technologies used to interrogate the proteome. Here, we review mechanisms by which protein self-assembly can create a stable record of past stimuli, altering adaptive responses, and how prion behavior is controlled by signaling processes. We touch on the diverse implications that this has for normal biological function and regulation, ranging from drug resistance in fungi to the innate immune response in humans. Finally, we discuss the potential for prion domains in transcription factors and RNA-binding proteins to orchestrate heritable gene expression changes in response to transient signals, such as during development.
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Affiliation(s)
- Shady Saad
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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24
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Levkovich SA, Rencus-Lazar S, Gazit E, Laor Bar-Yosef D. Microbial Prions: Dawn of a New Era. Trends Biochem Sci 2021; 46:391-405. [PMID: 33423939 DOI: 10.1016/j.tibs.2020.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Protein misfolding and aggregation are associated with human diseases and aging. However, microorganisms widely exploit the self-propagating properties of misfolded infectious protein particles, prions, as epigenetic information carriers that drive various phenotypic adaptations and encode molecular information. Microbial prion research has faced a paradigm shift in recent years, with breakthroughs that demonstrate the great functional and structural diversity of these agents. Here, we outline unorthodox examples of microbial prions in yeast and other microorganisms, focusing on their noncanonical functions. We discuss novel molecular mechanisms for the inheritance of conformationally-encoded epigenetic information and the evolutionary advantages they confer. Lastly, in light of recent advancements in the field of molecular self-assembly, we present a hypothesis regarding the existence of non-proteinaceous prion-like entities.
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Affiliation(s)
- Shon A Levkovich
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sigal Rencus-Lazar
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel; Sagol Interdisciplinary School of Neurosciences, Tel Aviv University, Tel Aviv, Israel.
| | - Dana Laor Bar-Yosef
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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25
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Ishikawa T. Saccharomyces cerevisiae in neuroscience: how unicellular organism helps to better understand prion protein? Neural Regen Res 2021; 16:489-495. [PMID: 32985470 PMCID: PMC7996030 DOI: 10.4103/1673-5374.293137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The baker’s yeast Saccharomyces (S.) cerevisiae is a single-celled eukaryotic model organism widely used in research on life sciences. Being a unicellular organism, S. cerevisiae has some evident limitations in application to neuroscience. However, yeast prions are extensively studied and they are known to share some hallmarks with mammalian prion protein or other amyloidogenic proteins found in the pathogenesis of Alzheimer’s, Parkinson’s, or Huntington’s diseases. Therefore, the yeast S. cerevisiae has been widely used for basic research on aggregation properties of proteins in cellulo and on their propagation. Recently, a yeast-based study revealed that some regions of mammalian prion protein and amyloid β1–42 are capable of induction and propagation of yeast prions. It is one of the examples showing that evolutionarily distant organisms share common mechanisms underlying the structural conversion of prion proteins making yeast cells a useful system for studying mammalian prion protein. S. cerevisiae has also been used to design novel screening systems for anti-prion compounds from chemical libraries. Yeast-based assays are cheap in maintenance and safe for the researcher, making them a very good choice to perform preliminary screening before further characterization in systems engaging mammalian cells infected with prions. In this review, not only classical red/white colony assay but also yeast-based screening assays developed during last year are discussed. Computational analysis and research carried out using yeast prions force us to expect that prions are widely present in nature. Indeed, the last few years brought us several examples indicating that the mammalian prion protein is no more peculiar protein – it seems that a better understanding of prion proteins nature-wide may aid us with the treatment of prion diseases and other amyloid-related medical conditions.
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Affiliation(s)
- Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
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26
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Extracellular Vesicles-Encapsulated Yeast Prions and What They Can Tell Us about the Physical Nature of Propagons. Int J Mol Sci 2020; 22:ijms22010090. [PMID: 33374854 PMCID: PMC7794690 DOI: 10.3390/ijms22010090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 12/25/2022] Open
Abstract
The yeast Saccharomyces cerevisiae hosts an ensemble of protein-based heritable traits, most of which result from the conversion of structurally and functionally diverse cytoplasmic proteins into prion forms. Among these, [PSI+], [URE3] and [PIN+] are the most well-documented prions and arise from the assembly of Sup35p, Ure2p and Rnq1p, respectively, into insoluble fibrillar assemblies. Yeast prions propagate by molecular chaperone-mediated fragmentation of these aggregates, which generates small self-templating seeds, or propagons. The exact molecular nature of propagons and how they are faithfully transmitted from mother to daughter cells despite spatial protein quality control are not fully understood. In [PSI+] cells, Sup35p forms detergent-resistant assemblies detectable on agarose gels under semi-denaturant conditions and cytosolic fluorescent puncta when the protein is fused to green fluorescent protein (GFP); yet, these macroscopic manifestations of [PSI+] do not fully correlate with the infectivity measured during growth by the mean of protein infection assays. We also discovered that significant amounts of infectious Sup35p particles are exported via extracellular (EV) and periplasmic (PV) vesicles in a growth phase and glucose-dependent manner. In the present review, I discuss how these vesicles may be a source of actual propagons and a suitable vehicle for their transmission to the bud.
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27
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Oamen HP, Lau Y, Caudron F. Prion-like proteins as epigenetic devices of stress adaptation. Exp Cell Res 2020; 396:112262. [DOI: 10.1016/j.yexcr.2020.112262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/26/2020] [Accepted: 08/30/2020] [Indexed: 01/03/2023]
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28
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Walker GA, Henderson CM, Luong P, Block DE, Bisson LF. Downshifting Yeast Dominance: Cell Physiology and Phospholipid Composition Are Altered With Establishment of the [ GAR +] Prion in Saccharomyces cerevisiae. Front Microbiol 2020; 11:2011. [PMID: 32983023 PMCID: PMC7477300 DOI: 10.3389/fmicb.2020.02011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Establishment of the [GAR +] prion in Saccharomyces cerevisiae reduces both transcriptional expression of the HXT3 hexose transporter gene and fermentation capacity in high sugar conditions. We evaluated the impact of deletion of the HXT3 gene on the expression of [GAR +] prion phenotype in a vineyard isolate, UCD932, and found that changes in fermentation capacity were observable even with complete loss of the Hxt3 transporter, suggesting other cellular functions affecting fermentation rate may be impacted in [GAR +] strains. In a comparison of isogenic [GAR +] and [gar -] strains, localization of the Pma1 plasma membrane ATPase showed differences in distribution within the membrane. In addition, plasma membrane lipid composition varied between the two cell types. Oxygen uptake was decreased in prion induced cells suggesting membrane changes affect plasma membrane functionality beyond glucose transport. Thus, multiple cell surface properties are altered upon induction of the [GAR +] prion in addition to changes in expression of the HXT3 gene. We propose a model wherein [GAR +] prion establishment within a yeast population is associated with modulation of plasma membrane functionality, fermentation capacity, niche dominance, and cell physiology to facilitate growth and mitigate cytotoxicity under certain environmental conditions. Down-regulation of expression of the HXT3 hexose transporter gene is only one component of a suite of physiological differences. Our data show the [GAR +] prion state is accompanied by multiple changes in the yeast cell surface that prioritize population survivability over maximizing metabolic capacity and enable progeny to establish an alternative adaptive state while maintaining reversibility.
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Affiliation(s)
- Gordon A Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Clark M Henderson
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Peter Luong
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - David E Block
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Linda F Bisson
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
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29
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Aggregation and Prion-Inducing Properties of the G-Protein Gamma Subunit Ste18 are Regulated by Membrane Association. Int J Mol Sci 2020; 21:ijms21145038. [PMID: 32708832 PMCID: PMC7403958 DOI: 10.3390/ijms21145038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast prions and mnemons are respectively transmissible and non-transmissible self-perpetuating protein assemblies, frequently based on cross-β ordered detergent-resistant aggregates (amyloids). Prions cause devastating diseases in mammals and control heritable traits in yeast. It was shown that the de novo formation of the prion form [PSI+] of yeast release factor Sup35 is facilitated by aggregates of other proteins. Here we explore the mechanism of the promotion of [PSI+] formation by Ste18, an evolutionarily conserved gamma subunit of a G-protein coupled receptor, a key player in responses to extracellular stimuli. Ste18 forms detergent-resistant aggregates, some of which are colocalized with de novo generated Sup35 aggregates. Membrane association of Ste18 is required for both Ste18 aggregation and [PSI+] induction, while functional interactions involved in signal transduction are not essential for these processes. This emphasizes the significance of a specific location for the nucleation of protein aggregation. In contrast to typical prions, Ste18 aggregates do not show a pattern of heritability. Our finding that Ste18 levels are regulated by the ubiquitin-proteasome system, in conjunction with the previously reported increase in Ste18 levels upon the exposure to mating pheromone, suggests that the concentration-dependent Ste18 aggregation may mediate a mnemon-like response to physiological stimuli.
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30
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Abstract
Probabilistic bet hedging is a generalized diversification strategy to maximize fitness in unpredictable environments and has been proposed as an evolutionary basis for herpesvirus latency. However, the molecular mechanisms enabling probabilistic bet hedging have remained elusive. Here, we find that the human herpesvirus cytomegalovirus—a major cause of birth defects and transplant failures—utilizes stochastic variability in the abundance of a protein packaged into individual viral particles to enable probabilistic bet hedging between alternate viral states. Probabilistic bet hedging, a strategy to maximize fitness in unpredictable environments by matching phenotypic variability to environmental variability, is theorized to account for the evolution of various fate-specification decisions, including viral latency. However, the molecular mechanisms underlying bet hedging remain unclear. Here, we report that large variability in protein abundance within individual herpesvirus virion particles enables probabilistic bet hedging between viral replication and latency. Superresolution imaging of individual virions of the human herpesvirus cytomegalovirus (CMV) showed that virion-to-virion levels of pp71 tegument protein—the major viral transactivator protein—exhibit extreme variability. This super-Poissonian tegument variability promoted alternate replicative strategies: high virion pp71 levels enhance viral replicative fitness but, strikingly, impede silencing, whereas low virion pp71 levels reduce fitness but promote silencing. Overall, the results indicate that stochastic tegument packaging provides a mechanism enabling probabilistic bet hedging between viral replication and latency.
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31
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Abstract
The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function.
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Affiliation(s)
- Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Szilvia Kiriakov
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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32
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Harvey ZH, Chakravarty AK, Futia RA, Jarosz DF. A Prion Epigenetic Switch Establishes an Active Chromatin State. Cell 2020; 180:928-940.e14. [PMID: 32109413 PMCID: PMC7195540 DOI: 10.1016/j.cell.2020.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/10/2019] [Accepted: 02/05/2020] [Indexed: 01/24/2023]
Abstract
Covalent modifications to histones are essential for development, establishing distinct and functional chromatin domains from a common genetic sequence. Whereas repressed chromatin is robustly inherited, no mechanism that facilitates inheritance of an activated domain has been described. Here, we report that the Set3C histone deacetylase scaffold Snt1 can act as a prion that drives the emergence and transgenerational inheritance of an activated chromatin state. This prion, which we term [ESI+] for expressed sub-telomeric information, is triggered by transient Snt1 phosphorylation upon cell cycle arrest. Once engaged, the prion reshapes the activity of Snt1 and the Set3C complex, recruiting RNA pol II and interfering with Rap1 binding to activate genes in otherwise repressed sub-telomeric domains. This transcriptional state confers broad resistance to environmental stress, including antifungal drugs. Altogether, our results establish a robust means by which a prion can facilitate inheritance of an activated chromatin state to provide adaptive benefit.
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Affiliation(s)
- Zachary H Harvey
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anupam K Chakravarty
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Raymond A Futia
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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33
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Brimacombe CA, Sierocinski T, Dahabieh MS. A white-to-opaque-like phenotypic switch in the yeast Torulaspora microellipsoides. Commun Biol 2020; 3:86. [PMID: 32111968 PMCID: PMC7048803 DOI: 10.1038/s42003-020-0815-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Torulaspora microellipsoides is an under-characterized budding yeast of the Saccharomycetaceae family that is primarily associated with viticulture. Here we report for the first time to our knowledge that T. microellipsoides undergoes a low-frequency morphological switch from small budding haploid (white) yeast to larger, higher ploidy (opaque) yeast. Comparison of transcriptomes by mRNA-seq revealed 511 differentially regulated genes, with white cells having greater expression of genes involved in stress resistance and complex carbohydrate utilization, and opaque cells up-regulating genes involved in ribosome biogenesis. Growth assays showed that white cells are physiologically more resistant to stationary-phase conditions and oxidative stress, whereas opaque cells exhibited greater cold tolerance. We propose that phenotypic switching in T. microellipsoides is an ecological adaptation, as has been suggested for similar morphological switching in distantly related species like Candida albicans, and we propose that this switching is a more broadly utilized biological strategy among yeasts than previously thought.
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Affiliation(s)
- Cedric A Brimacombe
- Renaissance BioScience Corporation, 410-2389 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.,Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Thomas Sierocinski
- Renaissance BioScience Corporation, 410-2389 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Matthew S Dahabieh
- Renaissance BioScience Corporation, 410-2389 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
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34
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Holec SA, Block AJ, Bartz JC. The role of prion strain diversity in the development of successful therapeutic treatments. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 175:77-119. [PMID: 32958242 PMCID: PMC8939712 DOI: 10.1016/bs.pmbts.2020.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prions are a self-propagating misfolded conformation of a cellular protein. Prions are found in several eukaryotic organisms with mammalian prion diseases encompassing a wide range of disorders. The first recognized prion disease, the transmissible spongiform encephalopathies (TSEs), affect several species including humans. Alzheimer's disease, synucleinopathies, and tauopathies share a similar mechanism of self-propagation of the prion form of the disease-specific protein reminiscent of the infection process of TSEs. Strain diversity in prion disease is characterized by differences in the phenotype of disease that is hypothesized to be encoded by strain-specific conformations of the prion form of the disease-specific protein. Prion therapeutics that target the prion form of the disease-specific protein can lead to the emergence of drug-resistant strains of prions, consistent with the hypothesis that prion strains exist as a dynamic mixture of a dominant strain in combination with minor substrains. To overcome this obstacle, therapies that reduce or eliminate the template of conversion are efficacious, may reverse neuropathology, and do not result in the emergence of drug resistance. Recent advancements in preclinical diagnosis of prion infection may allow for a combinational approach that treats the prion form and the precursor protein to effectively treat prion diseases.
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Affiliation(s)
- Sara A.M. Holec
- Institute for Applied Life Sciences and Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States,Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, United States
| | - Alyssa J. Block
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, United States
| | - Jason C. Bartz
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, United States,Corresponding author:
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35
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Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. Mol Cell 2019; 77:266-278.e6. [PMID: 31757756 DOI: 10.1016/j.molcel.2019.10.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/29/2019] [Accepted: 10/17/2019] [Indexed: 02/08/2023]
Abstract
Theory and experiments suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors, but the mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.
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36
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Liberman N, Wang SY, Greer EL. Transgenerational epigenetic inheritance: from phenomena to molecular mechanisms. Curr Opin Neurobiol 2019; 59:189-206. [PMID: 31634674 DOI: 10.1016/j.conb.2019.09.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 09/11/2019] [Indexed: 02/07/2023]
Abstract
Inherited information not encoded in the DNA sequence can regulate a variety of complex phenotypes. However, how this epigenetic information escapes the typical epigenetic erasure that occurs upon fertilization and how it regulates behavior is still unclear. Here we review recent examples of brain related transgenerational epigenetic inheritance and delineate potential molecular mechanisms that could regulate how non-genetic information could be transmitted.
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Affiliation(s)
- Noa Liberman
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston MA 02115, USA
| | - Simon Yuan Wang
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston MA 02115, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston MA 02115, USA.
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37
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Yeast Models for Amyloids and Prions: Environmental Modulation and Drug Discovery. Molecules 2019; 24:molecules24183388. [PMID: 31540362 PMCID: PMC6767215 DOI: 10.3390/molecules24183388] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 12/11/2022] Open
Abstract
Amyloids are self-perpetuating protein aggregates causing neurodegenerative diseases in mammals. Prions are transmissible protein isoforms (usually of amyloid nature). Prion features were recently reported for various proteins involved in amyloid and neural inclusion disorders. Heritable yeast prions share molecular properties (and in the case of polyglutamines, amino acid composition) with human disease-related amyloids. Fundamental protein quality control pathways, including chaperones, the ubiquitin proteasome system and autophagy are highly conserved between yeast and human cells. Crucial cellular proteins and conditions influencing amyloids and prions were uncovered in the yeast model. The treatments available for neurodegenerative amyloid-associated diseases are few and their efficiency is limited. Yeast models of amyloid-related neurodegenerative diseases have become powerful tools for high-throughput screening for chemical compounds and FDA-approved drugs that reduce aggregation and toxicity of amyloids. Although some environmental agents have been linked to certain amyloid diseases, the molecular basis of their action remains unclear. Environmental stresses trigger amyloid formation and loss, acting either via influencing intracellular concentrations of the amyloidogenic proteins or via heterologous inducers of prions. Studies of environmental and physiological regulation of yeast prions open new possibilities for pharmacological intervention and/or prophylactic procedures aiming on common cellular systems rather than the properties of specific amyloids.
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38
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Yeast prion-based metabolic reprogramming induced by bacteria in fermented foods. FEMS Yeast Res 2019; 19:5553466. [DOI: 10.1093/femsyr/foz061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT
Microbial communities of yeast and bacterial cells are often observed in the manufacturing processes of fermented foods and drinks, such as sourdough bread, cheese, kefir, wine and sake. Community interactions and dynamics among microorganisms, as well as their significance during the manufacturing processes, are central issues in modern food microbiology. Recent studies demonstrated that the emergence of a yeast prion termed [GAR+] in Saccharomyces cerevisiae is induced by coculturing with bacterial cells, resulting in the switching of the carbon metabolism. In order to facilitate mutualistic symbiosis among microorganisms, this mode of microbial interaction is induced between yeasts and lactic acid bacteria species used in traditional sake making. Thus, yeast prions have attracted much attention as novel platforms that govern the metabolic adaptation of cross-kingdom ecosystems. Our minireview focuses on the plausible linkage between fermented-food microbial communication and yeast prion-mediated metabolic reprogramming.
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39
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Manjrekar J, Shah H. Protein-based inheritance. Semin Cell Dev Biol 2019; 97:138-155. [PMID: 31344459 DOI: 10.1016/j.semcdb.2019.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/08/2019] [Indexed: 01/17/2023]
Abstract
Epigenetic mechanisms of inheritance have come to occupy a prominent place in our understanding of living systems, primarily eukaryotes. There has been considerable and lively discussion of the possible evolutionary significance of transgenerational epigenetic inheritance. One particular type of epigenetic inheritance that has not figured much in general discussions is that based on conformational changes in proteins, where proteins with altered conformations can act as templates to propagate their own structure. An increasing number of such proteins - prions and prion-like - are being discovered. Phenotypes due to the structurally altered proteins are transmitted along with their structures. This review discusses the properties and implications of "classical" amyloid-forming prions, as well as the broader class of proteins with intrinsically disordered domains, which are proving to have fascinating properties that appear to play important roles in cell organisation and function, especially during stress responses.
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Affiliation(s)
- Johannes Manjrekar
- Microbiology Department and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India.
| | - Hiral Shah
- Microbiology Department and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India
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40
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Duan SF, Shi JY, Yin Q, Zhang RP, Han PJ, Wang QM, Bai FY. Reverse Evolution of a Classic Gene Network in Yeast Offers a Competitive Advantage. Curr Biol 2019; 29:1126-1136.e5. [PMID: 30905601 DOI: 10.1016/j.cub.2019.02.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/04/2019] [Accepted: 02/15/2019] [Indexed: 11/26/2022]
Abstract
Glucose repression is a central regulatory system in yeast that ensures the utilization of carbon sources in a highly economical manner. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that a Saccharomyces cerevisiae (S. cerevisiae) lineage in spontaneously fermented milk has swapped all its structural GAL genes (GAL2 and the GAL7-10-1 cluster) with early diverged versions through introgression. The rewired GAL network has abolished glucose repression and conversed from a strictly inducible to a constitutive system through polygenic changes in the regulatory components of the network, including a thymine (T) to cytosine (C) and a guanine (G) to adenine (A) transition in the upstream repressing sequence (URS) sites of GAL1 and GAL4, respectively, which impair Mig1p-mediated repression, loss of function of the repressor Gal80p through a T146I substitution in the protein, and subsequent futility of GAL3. Furthermore, the milk lineage of S. cerevisiae has achieved galactose-utilization rate elevation and galactose-over-glucose preference switch through the duplication of the introgressed GAL2 and the loss of function of the main glucose transporter genes HXT6 and HXT7. In addition, we demonstrate that GAL2 requires GAL7 or GAL10 for its expression, and Gal2p likely requires Gal1p for its transportation function in the milk lineage of S. cerevisiae. We show a clear case of reverse evolution of a classic gene network for ecological adaptation and provide new insights into the regulatory model of the canonical GAL network.
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Affiliation(s)
- Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jun-Yan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Qi Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China.
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41
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Gonzalez R, Tronchoni J, Mencher A, Curiel JA, Rodrigues AJ, López-Berges L, Juez C, Patil KR, Jouhten P, Gallego N, Omarini A, Fernández-Preisegger M, Morales P. Low Phenotypic Penetrance and Technological Impact of Yeast [ GAR +] Prion-Like Elements on Winemaking. Front Microbiol 2019; 9:3311. [PMID: 30687288 PMCID: PMC6333647 DOI: 10.3389/fmicb.2018.03311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
[GAR+] prion-like elements partially relieve carbon catabolite repression in Saccharomyces cerevisiae. They have been hypothesized to contribute to wine yeast survival and alcohol level reduction, as well as communication with bacteria and stuck fermentation. In this work, we selected [GAR+] derivatives from several genetic backgrounds. They were characterized for phenotypic penetrance, heritability and confirmed as prion-like through curing by desiccation. In terms of fermentation kinetics, the impact of the prion on anaerobic wine fermentation (natural grape juice) was either neutral or negative, depending on the genetic background. Likewise, residual sugars were higher or similar for [GAR+] as compared to the cognate [gar-] strains. The prions had little or no impact on glycerol and ethanol yields; while acetic acid yields experienced the highest variations between [GAR+] and [gar-] strains. Strains analyzed under aerobic conditions followed the same pattern, with either little or no impact on fermentation kinetics, ethanol or glycerol yield; and a clearer influence on volatile acidity. Although no clear winemaking advantages were found for [GAR+] strains in this work, they might eventually show interest for some combinations of genetic background or winemaking conditions, e.g., for reducing acetic acid yield under aerated fermentation.
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Affiliation(s)
- Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Jordi Tronchoni
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Ana Mencher
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - José Antonio Curiel
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Alda Joao Rodrigues
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Laura López-Berges
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Cristina Juez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Kiran Raosaheb Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paula Jouhten
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Industrial Biotechnology and Food Solutions, VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Noelia Gallego
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - Alejandra Omarini
- INCITAP Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de La Pampa, Santa Rosa, Argentina
| | - Mariana Fernández-Preisegger
- Consejo Nacional de Investigaciones Científicas y Técnicas - UNER Universidad Nacional de Entre Ríos - Centro de Investigaciones Científicas y Transferencia de Tecnología a la Produccion, Diamante, Argentina
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
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42
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Abstract
Fungi are prone to phenotypic instability, that is, the vegetative phase of these organisms, be they yeasts or molds, undergoes frequent switching between two or more behaviors, often with different morphologies, but also sometime having different physiologies without any obvious morphological outcome. In the context of industrial utilization of fungi, this can have a negative impact on the maintenance of strains and/or on their productivity. Instabilities have been shown to result from various mechanisms, either genetic or epigenetic. This chapter will review different types of instabilities and discuss some lesser-known ones, mostly in filamentous fungi, while it will direct readers to additional literature in the case of well-known phenomena such as the amyloid prions or fungal senescence. It will present in depth the "white/opaque" switch of Candida albicans and the "crippled growth" degeneration of the model fungus Podospora anserina. These are two of the most thoroughly studied epigenetic phenotypic switches. I will also discuss the "sectors" presented by many filamentous ascomycetes, for which a prion-based model exists but is not demonstrated. Finally, I will also describe intriguing examples of phenotypic instability for which an explanation has yet to be provided.
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43
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Metabolic switching of sake yeast by kimoto lactic acid bacteria through the [GAR] non-genetic element. J Biosci Bioeng 2018; 126:624-629. [DOI: 10.1016/j.jbiosc.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 12/11/2022]
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44
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Cereghetti G, Saad S, Dechant R, Peter M. Reversible, functional amyloids: towards an understanding of their regulation in yeast and humans. Cell Cycle 2018; 17:1545-1558. [PMID: 29963943 DOI: 10.1080/15384101.2018.1480220] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein aggregates, and in particular amyloids, are generally considered to be inherently irreversible aberrant clumps, and are often associated with pathologies, such as Alzheimer's disease, Parkinson's disease, or systemic amyloidosis. However, recent evidence demonstrates that some aggregates are not only fully reversible, but also perform essential physiological functions. Despite these new findings, very little is known about how these functional protein aggregates are regulated in a physiological context. Here, we take the yeast pyruvate kinase Cdc19 as an example of a protein forming functional, reversible, solid, amyloid-like aggregates in response to stress conditions. Cdc19 aggregation is regulated via an aggregation-prone low complexity region (LCR). In favorable growth conditions, this LCR is prevented from aggregating by phosphorylation or oligomerization, while upon glucose starvation it becomes exposed and allows aggregation. We suggest that LCR phosphorylation, oligomerization or partner-binding may be general and widespread mechanisms regulating LCR-mediated reversible protein aggregation. Moreover, we show that, as predicted by computational tools, Cdc19 forms amyloid-like aggregates in vitro. Interestingly, we also observe striking similarities between Cdc19 and its mammalian counterpart, PKM2. Indeed, also PKM2 harbors a LCR and contains several peptides with high amyloidogenic propensity, which coincide with known phosphorylation sites. Thus, we speculate that the formation of reversible, amyloid-like aggregates may be a general physiological mechanism for cells to adapt to stress conditions, and that the underlying regulatory mechanisms may be conserved from yeast to humans.
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Affiliation(s)
- Gea Cereghetti
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland.,b Life Science Zürich , Molecular Life Sciences , Zürich , Switzerland
| | - Shady Saad
- c Department of Chemical and Systems Biology , Stanford University , Stanford, CA , USA
| | - Reinhard Dechant
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
| | - Matthias Peter
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
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45
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Newby GA, Kayatekin C. Microbial specialization by prions. Prion 2018; 12:1-5. [PMID: 29923447 PMCID: PMC6277177 DOI: 10.1080/19336896.2018.1469945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/01/2018] [Accepted: 04/24/2018] [Indexed: 01/10/2023] Open
Abstract
Microbial prions facilitate a variety of phenotypic switches. Recently-developed tools that can directly interrogate, in the living cell, the aggregation state of a protein have enabled a wider range of experiments for prion-mediated behaviors. With such tools, the roles of the yeast prion [SWI+] in migration and mating were studied. Although [SWI+] cells were consistently less fit than their [swi-] counterparts under traditional laboratory conditions, in these new phenotypic paradigms [SWI+] cells demonstrated a distinct advantage. [SWI+] cells dispersed over a larger area under conditions resembling rainfall and outcrossed more frequently. We postulate that many behaviors in microorganisms may be modulated by stochastic prion switching. In diverse and changing natural environments, prion switching at low frequency may promote greater fitness of the population by specializing a small number of individuals with altered responses to their environments.
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Affiliation(s)
- Gregory A. Newby
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
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Chakravarty AK, Jarosz DF. More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change. J Mol Biol 2018; 430:4607-4618. [PMID: 30031007 DOI: 10.1016/j.jmb.2018.07.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 12/11/2022]
Abstract
A central tenet of molecular biology is that heritable information is stored in nucleic acids. However, this paradigm has been overturned by a group of proteins called "prions." Prion proteins, many of which are intrinsically disordered, can adopt multiple conformations, at least one of which has the capacity to self-template. This unusual folding landscape drives a form of extreme epigenetic inheritance that can be stable through both mitotic and meiotic cell divisions. Although the first prion discovered-mammalian PrP-is the causative agent of debilitating neuropathies, many additional prions have now been identified that are not obviously detrimental and can even be adaptive. Intrinsically disordered regions, which endow proteins with the bulk property of "phase-separation," can also be drivers of prion formation. Indeed, many protein domains that promote phase separation have been described as prion-like. In this review, we describe how prions lie at the crossroads of phase separation, epigenetic inheritance, and evolutionary adaptation.
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Affiliation(s)
- Anupam K Chakravarty
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States; Department of Developmental Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305, United States.
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47
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Tikhodeyev ON. The mechanisms of epigenetic inheritance: how diverse are they? Biol Rev Camb Philos Soc 2018; 93:1987-2005. [PMID: 29790249 DOI: 10.1111/brv.12429] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 12/18/2022]
Abstract
Although epigenetic inheritance (EI) is a rapidly growing field of modern biology, it still has no clear place in fundamental genetic concepts which are traditionally based on the hereditary role of DNA. Moreover, not all mechanisms of EI attract the same attention, with most studies focused on DNA methylation, histone modification, RNA interference and amyloid prionization, but relatively few considering other mechanisms such as stable inhibition of plastid translation. Herein, we discuss all known and some hypothetical mechanisms that can underlie the stable inheritance of phenotypically distinct hereditary factors that lack differences in DNA sequence. These mechanisms include (i) regulation of transcription by DNA methylation, histone modifications, and transcription factors, (ii) RNA splicing, (iii) RNA-mediated post-transcriptional silencing, (iv) organellar translation, (v) protein processing by truncation, (vi) post-translational chemical modifications, (vii) protein folding, and (viii) homologous and non-homologous protein interactions. The breadth of this list suggests that any or almost any regulatory mechanism that participates in gene expression or gene-product functioning, under certain circumstances, may produce EI. Although the modes of EI are highly variable, in many epigenetic systems, stable allelic variants can be distinguished. Irrespective of their nature, all such alleles have an underlying similarity: each is a bimodular hereditary unit, whose features depend on (i) a certain epigenetic mark (epigenetic determinant) in the DNA sequence or its product, and (ii) the DNA sequence itself (DNA determinant; if this is absent, the epigenetic allele fails to perpetuate). Thus, stable allelic epigenetic inheritance (SAEI) does not contradict the hereditary role of DNA, but involves additional molecular mechanisms with no or almost no limitations to their variety.
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Affiliation(s)
- Oleg N Tikhodeyev
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
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48
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Zhou N, Bottagisi S, Katz M, Schacherer J, Friedrich A, Gojkovic Z, Swamy KBS, Knecht W, Compagno C, Piškur J. Yeast-bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri. FEMS Yeast Res 2018; 17:4064365. [PMID: 28910985 DOI: 10.1093/femsyr/fox060] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/03/2017] [Indexed: 12/28/2022] Open
Abstract
Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations. We described a long-term cross-kingdom competition experiment between Lachancea kluyveri and five species of bacteria. Now, we report how we further subjected the same yeast to a sixth species of bacteria, Pseudomonas fluorescens, resulting in the appearance of a fixed and stably inherited large-scale genomic rearrangement in two out of three parallel evolution lines. The 'extra-banded' karyotype, characterized by a higher fitness and an elevated fermentative capacity, conferred the emergence of new metabolic traits in most carbon sources and osmolytes. We tracked down the event to a duplication and translocation event involving a 261-kb segment. Such an experimental setup described here is an attractive method for developing industrial strains without genetic engineering strategies.
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Affiliation(s)
- Nerve Zhou
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, P Bag 16, 00267 Palapye, Botswana
| | - Samuele Bottagisi
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.,Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Michael Katz
- Carlsberg Laboratories, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS UMR7156, 67083 Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS UMR7156, 67083 Strasbourg, France
| | - Zoran Gojkovic
- Carlsberg Laboratories, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
| | - Krishna B S Swamy
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wolfgang Knecht
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.,Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via Giovanni Celoria 2, 20133 Milan, Italy
| | - Jure Piškur
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden
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49
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Jakobson CM, Jarosz DF. Organizing biochemistry in space and time using prion-like self-assembly. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 8:16-24. [PMID: 29725624 PMCID: PMC5926789 DOI: 10.1016/j.coisb.2017.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prion-like proteins have the capacity to adopt multiple stable conformations, at least one of which can recruit proteins from the native conformation into the alternative fold. Although classically associated with disease, prion-like assembly has recently been proposed to organize a range of normal biochemical processes in space and time. Organisms from bacteria to mammals use prion-like mechanisms to (re)organize their proteome in response to intracellular and extracellular stimuli. Prion-like behavior is an economical means to control biochemistry and gene regulation at the systems level, and prions can act as protein-based genes to facilitate quasi-Lamarckian inheritance of induced traits. These mechanisms allow individual cells to express distinct heritable traits using the same complement of polypeptides. Understanding and controlling prion-like behavior is therefore a promising strategy to combat diverse pathologies and organize engineered biological systems.
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Affiliation(s)
- Christopher M. Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
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50
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Lane S, Xu H, Oh EJ, Kim H, Lesmana A, Jeong D, Zhang G, Tsai CS, Jin YS, Kim SR. Glucose repression can be alleviated by reducing glucose phosphorylation rate in Saccharomyces cerevisiae. Sci Rep 2018; 8:2613. [PMID: 29422502 PMCID: PMC5805702 DOI: 10.1038/s41598-018-20804-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/19/2018] [Indexed: 01/06/2023] Open
Abstract
Microorganisms commonly exhibit preferential glucose consumption and diauxic growth when cultured in mixtures of glucose and other sugars. Although various genetic perturbations have alleviated the effects of glucose repression on consumption of specific sugars, a broadly applicable mechanism remains unknown. Here, we report that a reduction in the rate of glucose phosphorylation alleviates the effects of glucose repression in Saccharomyces cerevisiae. Through adaptive evolution under a mixture of xylose and the glucose analog 2-deoxyglucose, we isolated a mutant strain capable of simultaneously consuming glucose and xylose. Genome sequencing of the evolved mutant followed by CRISPR/Cas9-based reverse engineering revealed that mutations in the glucose phosphorylating enzymes (Hxk1, Hxk2, Glk1) were sufficient to confer simultaneous glucose and xylose utilization. We then found that varying hexokinase expression with an inducible promoter led to the simultaneous utilization of glucose and xylose. Interestingly, no mutations in sugar transporters occurred during the evolution, and no specific transporter played an indispensable role in simultaneous sugar utilization. Additionally, we demonstrated that slowing glucose consumption also enabled simultaneous utilization of glucose and galactose. These results suggest that the rate of intracellular glucose phosphorylation is a decisive factor for metabolic regulations of mixed sugars.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haiqing Xu
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eun Joong Oh
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anastashia Lesmana
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Guochang Zhang
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ching-Sung Tsai
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. .,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea. .,Institute of Agricultural Science & Technology, Kyungpook National University, Daegu, Republic of Korea.
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