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Čáp M, Palková Z. The characteristics of differentiated yeast subpopulations depend on their lifestyle and available nutrients. Sci Rep 2024; 14:3681. [PMID: 38355943 PMCID: PMC10866891 DOI: 10.1038/s41598-024-54300-9] [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: 12/01/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
Yeast populations can undergo diversification during their growth and ageing, leading to the formation of different cell-types. Differentiation into two major subpopulations, differing in cell size and density and exhibiting distinct physiological and metabolic properties, was described in planktonic liquid cultures and in populations of colonies growing on semisolid surfaces. Here, we compare stress resistance, metabolism and expression of marker genes in seven differentiated cell subpopulations emerging during cultivation in liquid fermentative or respiratory media and during colony development on the same type of solid media. The results show that the more-dense cell subpopulations are more stress resistant than the less-dense subpopulations under all cultivation conditions tested. On the other hand, respiratory capacity, enzymatic activities and marker gene expression differed more between subpopulations. These characteristics are more influenced by the lifestyle of the population (colony vs. planktonic cultivation) and the medium composition. Only in the population growing in liquid respiratory medium, two subpopulations do not form as in the other conditions tested, but all cells exhibit a range of characteristics of the more-dense subpopulations. This suggests that signals for cell differentiation may be triggered by prior metabolic reprogramming or by an unknown signal from the structured environment in the colony.
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Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic.
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic.
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2
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Piccirillo S, Honigberg SM. Measuring effect of mutations & conditions on microbial respiratory rates. J Microbiol Methods 2024; 216:106864. [PMID: 38030085 PMCID: PMC10843655 DOI: 10.1016/j.mimet.2023.106864] [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: 08/11/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
Cellular respiration is central to a wide range of cellular processes. In microorganisms, the effect of a mutation or an environmental condition on the rate of respiration is usually determined by measuring oxygen consumption in the media. We describe this method and discuss caveats and controls for the method.
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Affiliation(s)
- Sarah Piccirillo
- Division of Biological and Biomedical Systems, 5007 Rockhill Rd, University of Missouri-Kansas City, Kansas City, MO 64110-1299, United States of America
| | - Saul M Honigberg
- Division of Biological and Biomedical Systems, 5007 Rockhill Rd, University of Missouri-Kansas City, Kansas City, MO 64110-1299, United States of America.
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3
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Mahilkar A, Raj N, Kemkar S, Saini S. Selection in a growing colony biases results of mutation accumulation experiments. Sci Rep 2022; 12:15470. [PMID: 36104390 PMCID: PMC9475022 DOI: 10.1038/s41598-022-19928-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022] Open
Abstract
Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments can be performed with different effective population sizes. In MA experiments with bacteria, a single founder is grown to a size of a colony (~ 108). It is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth. In this work, we simulate colony growth via a mathematical model, and use our model to mimic an MA experiment. We demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over-represented by a factor of almost two, and that the distribution of fitness effects of beneficial and deleterious mutations are inaccurately captured in an MA experiment. Given this, the estimate of mutation rates from MA experiments is non-trivial. We then perform an MA experiment with 160 lines of E. coli, and show that due to the effect of selection in a growing colony, the size and sector of a colony from which the experiment is propagated impacts the results. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.
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Affiliation(s)
- Anjali Mahilkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Namratha Raj
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sharvari Kemkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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4
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Liu ZL. Reasons for 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde resistance in Saccharomyces cerevisiae: current state of knowledge and perspectives for further improvements. Appl Microbiol Biotechnol 2021; 105:2991-3007. [PMID: 33830300 DOI: 10.1007/s00253-021-11256-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022]
Abstract
Common toxic compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) are formed from dehydration of pentose and hexose, respectively, during decomposition of lignocellulosic biomass polymers. Furfural and HMF represent a major class of aldehyde toxic chemicals that inhibit microbial growth and interfere with subsequent fermentation for production of renewable fuels and chemicals. Understanding mechanisms of yeast tolerance aids development of tolerant strains as the most economic means to overcome the toxicity. This review updates current knowledge on yeast resistance to these toxic chemicals obtained from rapid advances in the past few years. Findings are largely exemplified by an adapted strain NRRL Y-50049 compared with its progenitor, the industrial yeast Saccharomyces cerevisiae type strain NRRL Y-12632. Newly characterized molecular phenotypes distinguished acquired resistant components of Y-50049 from innate stress response of its progenitor Y-12632. These findings also raised important questions on how to address more deeply ingrained changes in addition to local renovations for yeast adaptation. An early review on understandings of yeast tolerance to these inhibitory compounds is available and its contents omitted here to avoid redundancy. Controversial and confusing issues on identification of yeast resistance to furfural and HMF are further clarified aiming improved future research. Propositions and perspectives on research understanding molecular mechanisms of yeast resistance and future improvements are also presented. KEY POINTS: • Distinguished adapted resistance from innate stress response in yeast. • Defined pathway-based molecular phenotypes of yeast resistance. • Proposed genomic insight and perspectives on yeast resistance and adaptation.
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Affiliation(s)
- Z Lewis Liu
- National Center for Agricultural Utilization Research, Bioenergy Research Unit, USDA Agricultural Research Service, 1815 N. University Street, Peoria, IL, 61604, USA.
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5
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Fukuda APM, Camandona VDL, Francisco KJM, Rios-Anjos RM, Lucio do Lago C, Ferreira-Junior JR. Simulated microgravity accelerates aging in Saccharomyces cerevisiae. LIFE SCIENCES IN SPACE RESEARCH 2021; 28:32-40. [PMID: 33612178 DOI: 10.1016/j.lssr.2020.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/01/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
The human body experiences physiological changes under microgravity environment that phenocopy aging on Earth. These changes include early onset osteoporosis, skeletal muscle atrophy, cardiac dysfunction, and immunosenescence, and such adaptations to the space environment may pose some risk to crewed missions to Mars. To investigate the effect of microgravity on aging, many model organisms have been used such as the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and mice. Herein we report that the budding yeast Saccharomyces cerevisiae show decreased replicative lifespan (RLS) under simulated microgravity in a clinostat. The reduction of yeast lifespan is not a result of decreased tolerance to heat shock or oxidative stress and could be overcome either by deletion of FOB1 or calorie restriction, two known interventions that extend yeast RLS. Deletion of the sirtuin gene SIR2 worsens the simulated microgravity effect on RLS, and together with the fob1Δ mutant phenotype, it suggests that simulated microgravity augments the formation of extrachromosomal rDNA circles, which accumulate in yeast during aging. We also show that the chronological lifespan in minimal medium was not changed when cells were grown in the clinostat. Our data suggest that the reduction in longevity due to simulated microgravity is conserved in yeast, worms, and flies, and these findings may have potential implications for future crewed missions in space, as well as the use of microgravity as a model for human aging.
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Affiliation(s)
| | | | | | | | - Claudimir Lucio do Lago
- Departamento de Química Fundamental - Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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6
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The Whi2p-Psr1p/Psr2p complex regulates interference competition and expansion of cells with competitive advantage in yeast colonies. Proc Natl Acad Sci U S A 2020; 117:15123-15131. [PMID: 32541056 DOI: 10.1073/pnas.1922076117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Yeast form complex highly organized colonies in which cells undergo spatiotemporal phenotypic differentiation in response to local gradients of nutrients, metabolites, and specific signaling molecules. Colony fitness depends on cell interactions, cooperation, and the division of labor between differentiated cell subpopulations. Here, we describe the regulation and dynamics of the expansion of papillae that arise during colony aging, which consist of cells that overcome colony regulatory rules and disrupt the synchronized colony structure. We show that papillae specifically expand within the U cell subpopulation in differentiated colonies. Papillae emerge more frequently in some strains than in others. Genomic analyses further revealed that the Whi2p-Psr1p/Psr2p complex (WPPC) plays a key role in papillae expansion. We show that cells lacking a functional WPPC have a sizable interaction-specific fitness advantage attributable to production of and resistance to a diffusible compound that inhibits growth of other cells. Competitive superiority and high relative fitness of whi2 and psr1psr2 strains are particularly pronounced in dense spatially structured colonies and are independent of TORC1 and Msn2p/Msn4p regulators previously associated with the WPPC function. The WPPC function, described here, might be a regulatory mechanism that balances cell competition and cooperation in dense yeast populations and, thus, contributes to cell synchronization, pattern formation, and the expansion of cells with a competitive fitness advantage.
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7
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Liu ZL, Ma M. Pathway-based signature transcriptional profiles as tolerance phenotypes for the adapted industrial yeast Saccharomyces cerevisiae resistant to furfural and HMF. Appl Microbiol Biotechnol 2020; 104:3473-3492. [PMID: 32103314 DOI: 10.1007/s00253-020-10434-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/25/2019] [Accepted: 02/04/2020] [Indexed: 10/24/2022]
Abstract
The industrial yeast Saccharomyces cerevisiae has a plastic genome with a great flexibility in adaptation to varied conditions of nutrition, temperature, chemistry, osmolarity, and pH in diversified applications. A tolerant strain against 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) was successfully obtained previously by adaptation through environmental engineering toward development of the next-generation biocatalyst. Using a time-course comparative transcriptome analysis in response to a synergistic challenge of furfural-HMF, here we report tolerance phenotypes of pathway-based transcriptional profiles as components of the adapted defensive system for the tolerant strain NRRL Y-50049. The newly identified tolerance phenotypes were involved in biosynthesis superpathway of sulfur amino acids, defensive reduction-oxidation reaction process, cell wall response, and endogenous and exogenous cellular detoxification. Key transcription factors closely related to these pathway-based components, such as Yap1, Met4, Met31/32, Msn2/4, and Pdr1/3, were also presented. Many important genes in Y-50049 acquired an enhanced transcription background and showed continued increased expressions during the entire lag phase against furfural-HMF. Such signature expressions distinguished tolerance phenotypes of Y-50049 from the innate stress response of its progenitor NRRL Y-12632, an industrial type strain. The acquired yeast tolerance is believed to be evolved in various mechanisms at the genomic level. Identification of legitimate tolerance phenotypes provides a basis for continued investigations on pathway interactions and dissection of mechanisms of yeast tolerance and adaptation at the genomic level.
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Affiliation(s)
- Z Lewis Liu
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service,U.S. Department of Agriculture, 1815 N University Street, Peoria, IL, 61604, USA.
| | - Menggen Ma
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service,U.S. Department of Agriculture, 1815 N University Street, Peoria, IL, 61604, USA
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8
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Gulli J, Cook E, Kroll E, Rosebrock A, Caudy A, Rosenzweig F. Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan. MICROBIAL CELL 2019; 6:397-413. [PMID: 31528631 PMCID: PMC6717879 DOI: 10.15698/mic2019.09.690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Baker's yeast has a finite lifespan and ages in two ways: a mother cell can only divide so many times (its replicative lifespan), and a non-dividing cell can only live so long (its chronological lifespan). Wild and laboratory yeast strains exhibit natural variation for each type of lifespan, and the genetic basis for this variation has been generalized to other eukaryotes, including metazoans. To date, yeast chronological lifespan has chiefly been studied in relation to the rate and mode of functional decline among non-dividing cells in nutrient-depleted batch culture. However, this culture method does not accurately capture two major classes of long-lived metazoan cells: cells that are terminally differentiated and metabolically active for periods that approximate animal lifespan (e.g. cardiac myocytes), and cells that are pluripotent and metabolically quiescent (e.g. stem cells). Here, we consider alternative ways of cultivating Saccharomyces cerevisiae so that these different metabolic states can be explored in non-dividing cells: (i) yeast cultured as giant colonies on semi-solid agar, (ii) yeast cultured in retentostats and provided sufficient nutrients to meet minimal energy requirements, and (iii) yeast encapsulated in a semisolid matrix and fed ad libitum in bioreactors. We review the physiology of yeast cultured under each of these conditions, and explore their potential to provide unique insights into determinants of chronological lifespan in the cells of higher eukaryotes.
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Affiliation(s)
- Jordan Gulli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Emily Cook
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Eugene Kroll
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Adam Rosebrock
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Present address: Stony Brook School of Medicine, Stony Brook University, Stony Brook, NY 11794
| | - Amy Caudy
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
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9
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Váchová L, Palková Z. How structured yeast multicellular communities live, age and die? FEMS Yeast Res 2019; 18:4950397. [PMID: 29718174 DOI: 10.1093/femsyr/foy033] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/20/2018] [Indexed: 12/28/2022] Open
Abstract
Yeasts, like other microorganisms, create numerous types of multicellular communities, which differ in their complexity, cell differentiation and in the occupation of different niches. Some of the communities, such as colonies and some types of biofilms, develop by division and subsequent differentiation of cells growing on semisolid or solid surfaces to which they are attached or which they can penetrate. Aggregation of individual cells is important for formation of other community types, such as multicellular flocs, which sediment to the bottom or float to the surface of liquid cultures forming flor biofilms, organized at the border between liquid and air under specific circumstances. These examples together with the existence of more obscure communities, such as stalks, demonstrate that multicellularity is widespread in yeast. Despite this fact, identification of mechanisms and regulations involved in complex multicellular behavior still remains one of the challenges of microbiology. Here, we briefly discuss metabolic differences between particular yeast communities as well as the presence and functions of various differentiated cells and provide examples of the ability of these cells to develop different ways to cope with stress during community development and aging.
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Affiliation(s)
- Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 252 50 Vestec, Czech Republic
| | - Zdena Palková
- Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
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10
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Guo H, Huang T, Zhao J, Chen H, Chen G. Fungi short-chain carboxylate transporter: shift from microbe hereditary functional component to metabolic engineering target. Appl Microbiol Biotechnol 2018; 102:4653-4662. [PMID: 29679102 DOI: 10.1007/s00253-018-9010-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/05/2018] [Accepted: 04/10/2018] [Indexed: 11/29/2022]
Abstract
Short-chain carboxylic acids and their derivatives are widely utilized in all aspects of our daily life. Given their specific functional groups, these molecules are also utilized in fine chemical synthesis. The traditional petroleum-based carboxylate production methods are restricted by petrol shortage and environmental pollution. Renowned for their more sustainable processes than traditional methods, biotechnological methods are preferred alternatives and have attracted increasing attention. However, the industrial application of biotechnological methods is currently limited by low factors: low productivity and low yield. Therefore, understanding the regulation of carboxylate accumulation will greatly enhance the industrial biotechnological production of short-chain carboxylate acids. The carboxylate transporter plays a crucial role in transmembrane uptake and secretion of carboxylate; therefore, regulating these transporters is of high academic and application relevance. This review concentrates on the physiological roles, regulation mechanisms, and harnessing strategies of Jen and AcpA orthologs in fungi, which provide potential clues for the biotechnological production of short-chain carboxylic acids with high efficiency.
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Affiliation(s)
- Hongwei Guo
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biochemical Technology, National Huaqiao University, 668 Jimei Road, Amoy, 361021, Fujian, China.
| | - Tianqiu Huang
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biochemical Technology, National Huaqiao University, 668 Jimei Road, Amoy, 361021, Fujian, China
| | - Jun Zhao
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biochemical Technology, National Huaqiao University, 668 Jimei Road, Amoy, 361021, Fujian, China
| | - Hongwen Chen
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biochemical Technology, National Huaqiao University, 668 Jimei Road, Amoy, 361021, Fujian, China
| | - Guo Chen
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biochemical Technology, National Huaqiao University, 668 Jimei Road, Amoy, 361021, Fujian, China
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11
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Transcriptome Remodeling of Differentiated Cells during Chronological Ageing of Yeast Colonies: New Insights into Metabolic Differentiation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4932905. [PMID: 29576850 PMCID: PMC5821948 DOI: 10.1155/2018/4932905] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/08/2017] [Accepted: 11/13/2017] [Indexed: 11/17/2022]
Abstract
We present the spatiotemporal metabolic differentiation of yeast cell subpopulations from upper, lower, and margin regions of colonies of different ages, based on comprehensive transcriptomic analysis. Furthermore, the analysis was extended to include smaller cell subpopulations identified previously by microscopy within fully differentiated U and L cells of aged colonies. New data from RNA-seq provides both spatial and temporal information on cell metabolic reprogramming during colony ageing and shows that cells at marginal positions are similar to upper cells, but both these cell types are metabolically distinct from cells localized to lower colony regions. As colonies age, dramatic metabolic reprogramming occurs in cells of upper regions, while changes in margin and lower cells are less prominent. Interestingly, whereas clear expression differences were identified between two L cell subpopulations, U cells (which adopt metabolic profiles, similar to those of tumor cells) form a more homogeneous cell population. The data identified crucial metabolic reprogramming events that arise de novo during colony ageing and are linked to U and L cell colony differentiation and support a role for mitochondria in this differentiation process.
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12
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Carmona-Gutierrez D, Bauer MA, Zimmermann A, Aguilera A, Austriaco N, Ayscough K, Balzan R, Bar-Nun S, Barrientos A, Belenky P, Blondel M, Braun RJ, Breitenbach M, Burhans WC, Büttner S, Cavalieri D, Chang M, Cooper KF, Côrte-Real M, Costa V, Cullin C, Dawes I, Dengjel J, Dickman MB, Eisenberg T, Fahrenkrog B, Fasel N, Fröhlich KU, Gargouri A, Giannattasio S, Goffrini P, Gourlay CW, Grant CM, Greenwood MT, Guaragnella N, Heger T, Heinisch J, Herker E, Herrmann JM, Hofer S, Jiménez-Ruiz A, Jungwirth H, Kainz K, Kontoyiannis DP, Ludovico P, Manon S, Martegani E, Mazzoni C, Megeney LA, Meisinger C, Nielsen J, Nyström T, Osiewacz HD, Outeiro TF, Park HO, Pendl T, Petranovic D, Picot S, Polčic P, Powers T, Ramsdale M, Rinnerthaler M, Rockenfeller P, Ruckenstuhl C, Schaffrath R, Segovia M, Severin FF, Sharon A, Sigrist SJ, Sommer-Ruck C, Sousa MJ, Thevelein JM, Thevissen K, Titorenko V, Toledano MB, Tuite M, Vögtle FN, Westermann B, Winderickx J, Wissing S, Wölfl S, Zhang ZJ, Zhao RY, Zhou B, Galluzzi L, Kroemer G, Madeo F. Guidelines and recommendations on yeast cell death nomenclature. MICROBIAL CELL (GRAZ, AUSTRIA) 2018; 5:4-31. [PMID: 29354647 PMCID: PMC5772036 DOI: 10.15698/mic2018.01.607] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 12/29/2017] [Indexed: 12/18/2022]
Abstract
Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cel-lular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the defi-nition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differ-ential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death rou-tines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the au-thors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the pro-gress of this vibrant field of research.
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Affiliation(s)
| | - Maria Anna Bauer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Andrés Aguilera
- Centro Andaluz de Biología, Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Sevilla, Spain
| | | | - Kathryn Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Rena Balzan
- Department of Physiology and Biochemistry, University of Malta, Msida, Malta
| | - Shoshana Bar-Nun
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Antonio Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, USA
- Department of Neurology, University of Miami Miller School of Medi-cine, Miami, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, USA
| | - Marc Blondel
- Institut National de la Santé et de la Recherche Médicale UMR1078, Université de Bretagne Occidentale, Etablissement Français du Sang Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Ralf J. Braun
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | | | - William C. Burhans
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Sabrina Büttner
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Michael Chang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katrina F. Cooper
- Dept. Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, USA
| | - Manuela Côrte-Real
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Vítor Costa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | | | - Ian Dawes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Martin B. Dickman
- Institute for Plant Genomics and Biotechnology, Texas A&M University, Texas, USA
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Birthe Fahrenkrog
- Laboratory Biology of the Nucleus, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
| | - Nicolas Fasel
- Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Kai-Uwe Fröhlich
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Ali Gargouri
- Laboratoire de Biotechnologie Moléculaire des Eucaryotes, Center de Biotechnologie de Sfax, Sfax, Tunisia
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Campbell W. Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Chris M. Grant
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Michael T. Greenwood
- Department of Chemistry and Chemical Engineering, Royal Military College, Kingston, Ontario, Canada
| | - Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | | | - Jürgen Heinisch
- Department of Biology and Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Eva Herker
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Sebastian Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | | | - Helmut Jungwirth
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Dimitrios P. Kontoyiannis
- Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Minho, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Stéphen Manon
- Institut de Biochimie et de Génétique Cellulaires, UMR5095, CNRS & Université de Bordeaux, Bordeaux, France
| | - Enzo Martegani
- Department of Biotechnolgy and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Cristina Mazzoni
- Instituto Pasteur-Fondazione Cenci Bolognetti - Department of Biology and Biotechnology "C. Darwin", La Sapienza University of Rome, Rome, Italy
| | - Lynn A. Megeney
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Department of Medicine, Division of Cardiology, University of Ottawa, Ottawa, Canada
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Heinz D. Osiewacz
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Tiago F. Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
- Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, United Kingdom
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Hay-Oak Park
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Tobias Pendl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Dina Petranovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Stephane Picot
- Malaria Research Unit, SMITh, ICBMS, UMR 5246 CNRS-INSA-CPE-University Lyon, Lyon, France
- Institut of Parasitology and Medical Mycology, Hospices Civils de Lyon, Lyon, France
| | - Peter Polčic
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Ted Powers
- Department of Molecular and Cellular Biology, College of Biological Sciences, UC Davis, Davis, California, USA
| | - Mark Ramsdale
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Mark Rinnerthaler
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Patrick Rockenfeller
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Raffael Schaffrath
- Institute of Biology, Division of Microbiology, University of Kassel, Kassel, Germany
| | - Maria Segovia
- Department of Ecology, Faculty of Sciences, University of Malaga, Malaga, Spain
| | - Fedor F. Severin
- A.N. Belozersky Institute of physico-chemical biology, Moscow State University, Moscow, Russia
| | - Amir Sharon
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Stephan J. Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Cornelia Sommer-Ruck
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | | | - Michel B. Toledano
- Institute for Integrative Biology of the Cell (I2BC), SBIGEM, CEA-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mick Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - F.-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, Leuven-Heverlee, Belgium
| | | | - Stefan Wölfl
- Institute of Pharmacy and Molecu-lar Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Zhaojie J. Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, USA
| | - Bing Zhou
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Université Paris Descartes/Paris V, Paris, France
| | - Guido Kroemer
- Université Paris Descartes/Paris V, Paris, France
- Equipe 11 Labellisée Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Cell Biology and Metabolomics Platforms, Gustave Roussy Comprehensive Cancer Center, Villejuif, France
- INSERM, U1138, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, Paris, France
- Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, Stockholm, Sweden
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
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13
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Hammond TG, Allen PL, Gunter MA, Chiang J, Giaever G, Nislow C, Birdsall HH. Physical Forces Modulate Oxidative Status and Stress Defense Meditated Metabolic Adaptation of Yeast Colonies: Spaceflight and Microgravity Simulations. MICROGRAVITY SCIENCE AND TECHNOLOGY 2017; 30:195-208. [PMID: 31258252 PMCID: PMC6560652 DOI: 10.1007/s12217-017-9588-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/19/2017] [Indexed: 06/09/2023]
Abstract
Baker's yeast (Saccharomyces cerevisiae) has broad genetic homology to human cells. Although typically grown as 1-2mm diameter colonies under certain conditions yeast can form very large (10 + mm in diameter) or 'giant' colonies on agar. Giant yeast colonies have been used to study diverse biomedical processes such as cell survival, aging, and the response to cancer pharmacogenomics. Such colonies evolve dynamically into complex stratified structures that respond differentially to environmental cues. Ammonia production, gravity driven ammonia convection, and shear defense responses are key differentiation signals for cell death and reactive oxygen system pathways in these colonies. The response to these signals can be modulated by experimental interventions such as agar composition, gene deletion and application of pharmaceuticals. In this study we used physical factors including colony rotation and microgravity to modify ammonia convection and shear stress as environmental cues and observed differences in the responses of both ammonia dependent and stress response dependent pathways We found that the effects of random positioning are distinct from rotation. Furthermore, both true and simulated microgravity exacerbated both cellular redox responses and apoptosis. These changes were largely shear-response dependent but each model had a unique response signature as measured by shear stress genes and the promoter set which regulates them These physical techniques permitted a graded manipulation of both convection and ammonia signaling and are primed to substantially contribute to our understanding of the mechanisms of drug action, cell aging, and colony differentiation.
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Affiliation(s)
- Timothy G. Hammond
- Durham VA Medical Center, Medicine Service Line, 508 Fulton Street, Durham, NC 27705 USA
- Nephrology Division, Department of Medicine, Duke University School of Medicine, Durham, NC 27710 USA
- Space Policy Institute, Elliott School of International Affairs, George Washington University, Washington, DC 20052 USA
| | - Patricia L. Allen
- Durham VA Medical Center, Medicine Service Line, 508 Fulton Street, Durham, NC 27705 USA
| | | | - Jennifer Chiang
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Holly H. Birdsall
- Space Policy Institute, Elliott School of International Affairs, George Washington University, Washington, DC 20052 USA
- Department of Veterans Affairs, Veterans Healthcare Administration, Office of Research, Washington, DC 20420 USA
- Departments of Otorhinolaryngology, Immunology, and Psychiatry, Baylor College of Medicine, Houston, TX 77030 USA
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Podholová K, Plocek V, Rešetárová S, Kučerová H, Hlaváček O, Váchová L, Palková Z. Divergent branches of mitochondrial signaling regulate specific genes and the viability of specialized cell types of differentiated yeast colonies. Oncotarget 2017; 7:15299-314. [PMID: 26992228 PMCID: PMC4941242 DOI: 10.18632/oncotarget.8084] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/23/2016] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial retrograde signaling mediates communication from altered mitochondria to the nucleus and is involved in many normal and pathophysiological changes, including cell metabolic reprogramming linked to cancer development and progression in mammals. The major mitochondrial retrograde pathway described in yeast includes three activators, Rtg1p, Rtg2p and Rtg3p, and repressors, Mks1p and Bmh1p/Bmh2p. Using differentiated yeast colonies, we show that Mks1p-Rtg pathway regulation is complex and includes three branches that divergently regulate the properties and fate of three specifically localized cell subpopulations via signals from differently altered mitochondria. The newly identified RTG pathway-regulated genes ATO1/ATO2 are expressed in colonial upper (U) cells, the cells with active TORC1 that metabolically resemble tumor cells, while CIT2 is a typical target induced in one subpopulation of starving lower (L) cells. The viability of the second L cell subpopulation is strictly dependent on RTG signaling. Additional co-activators of Rtg1p-Rtg3p specific to particular gene targets of each branch are required to regulate cell differentiation.
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Affiliation(s)
- Kristýna Podholová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Vítězslav Plocek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | - Helena Kučerová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Otakar Hlaváček
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Libuše Váchová
- Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Maršíková J, Wilkinson D, Hlaváček O, Gilfillan GD, Mizeranschi A, Hughes T, Begany M, Rešetárová S, Váchová L, Palková Z. Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling. BMC Genomics 2017; 18:814. [PMID: 29061122 PMCID: PMC5654107 DOI: 10.1186/s12864-017-4214-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/16/2017] [Indexed: 12/19/2022] Open
Abstract
Background Yeast infections are often connected with formation of biofilms that are extremely difficult to eradicate. An excellent model system for deciphering multifactorial determinants of yeast biofilm development is the colony biofilm, composed of surface (“aerial”) and invasive (“root”) cells. While surface cells have been partially analyzed before, we know little about invasive root cells. In particular, information on the metabolic, chemical and morphogenetic properties of invasive versus surface cells is lacking. In this study, we used a new strategy to isolate invasive cells from agar and extracellular matrix, and employed it to perform genome wide expression profiling and biochemical analyses of surface and invasive cells. Results RNA sequencing revealed expression differences in 1245 genes with high statistical significance, indicating large genetically regulated metabolic differences between surface and invasive cells. Functional annotation analyses implicated genes involved in stress defense, peroxisomal fatty acid β-oxidation, autophagy, protein degradation, storage compound metabolism and meiosis as being important in surface cells. In contrast, numerous genes with functions in nutrient transport and diverse synthetic metabolic reactions, including genes involved in ribosome biogenesis, biosynthesis and translation, were found to be important in invasive cells. Variation in gene expression correlated significantly with cell-type specific processes such as autophagy and storage compound accumulation as identified by microscopic and biochemical analyses. Expression profiling also provided indications of cell-specific regulations. Subsequent knockout strain analyses identified Gip2p, a regulatory subunit of type 1 protein phosphatase Glc7p, to be essential for glycogen accumulation in surface cells. Conclusions This is the first study reporting genome wide differences between surface and invasive cells of yeast colony biofilms. New findings show that surface and invasive cells display very different physiology, adapting to different conditions in different colony areas and contributing to development and survival of the colony biofilm as a whole. Notably, surface and invasive cells of colony biofilms differ significantly from upper and lower cells of smooth colonies adapted to plentiful laboratory conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4214-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jana Maršíková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Derek Wilkinson
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Otakar Hlaváček
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 252 50, Vestec, Czech Republic
| | | | - Alexandru Mizeranschi
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Timothy Hughes
- Oslo University Hospital and University of Oslo, 0450, Oslo, Norway.,NORMENT, Institute of Clinical Medicine, University of Oslo, 0450, Oslo, Norway
| | - Markéta Begany
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 252 50, Vestec, Czech Republic
| | - Stanislava Rešetárová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 252 50, Vestec, Czech Republic
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 252 50, Vestec, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 252 50, Vestec, Czech Republic.
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Adaptive Roles of SSY1 and SIR3 During Cycles of Growth and Starvation in Saccharomyces cerevisiae Populations Enriched for Quiescent or Nonquiescent Cells. G3-GENES GENOMES GENETICS 2017; 7:1899-1911. [PMID: 28450371 PMCID: PMC5473767 DOI: 10.1534/g3.117.041749] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over its evolutionary history, Saccharomyces cerevisiae has evolved to be well-adapted to fluctuating nutrient availability. In the presence of sufficient nutrients, yeast cells continue to proliferate, but upon starvation haploid yeast cells enter stationary phase and differentiate into nonquiescent (NQ) and quiescent (Q) cells. Q cells survive stress better than NQ cells and show greater viability when nutrient-rich conditions are restored. To investigate the genes that may be involved in the differentiation of Q and NQ cells, we serially propagated yeast populations that were enriched for either only Q or only NQ cell types over many repeated growth–starvation cycles. After 30 cycles (equivalent to 300 generations), each enriched population produced a higher proportion of the enriched cell type compared to the starting population, suggestive of adaptive change. We also observed differences in each population’s fitness suggesting possible tradeoffs: clones from NQ lines were better adapted to logarithmic growth, while clones from Q lines were better adapted to starvation. Whole-genome sequencing of clones from Q- and NQ-enriched lines revealed mutations in genes involved in the stress response and survival in limiting nutrients (ECM21, RSP5, MSN1, SIR4, and IRA2) in both Q and NQ lines, but also differences between the two lines: NQ line clones had recurrent independent mutations affecting the Ssy1p-Ptr3p-Ssy5p (SPS) amino acid sensing pathway, while Q line clones had recurrent, independent mutations in SIR3 and FAS1. Our results suggest that both sets of enriched-cell type lines responded to common, as well as distinct, selective pressures.
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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18
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Liu TY, Dodson AE, Terhorst J, Song YS, Rine J. Riches of phenotype computationally extracted from microbial colonies. Proc Natl Acad Sci U S A 2016; 113:E2822-31. [PMID: 27140647 PMCID: PMC4878510 DOI: 10.1073/pnas.1523295113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic, epigenetic, and physiological differences among cells in clonal microbial colonies are underexplored opportunities for discovery. A recently developed genetic assay reveals that transient losses of heterochromatic repression, a heritable form of gene silencing, occur throughout the growth of Saccharomyces colonies. This assay requires analyzing two-color fluorescence patterns in yeast colonies, which is qualitatively appealing but quantitatively challenging. In this paper, we developed a suite of automated image processing, visualization, and classification algorithms (MORPHE) that facilitated the analysis of heterochromatin dynamics in the context of colonial growth and that can be broadly adapted to many colony-based assays in Saccharomyces and other microbes. Using the features that were automatically extracted from fluorescence images, our classification method distinguished loss-of-silencing patterns between mutants and wild type with unprecedented precision. Application of MORPHE revealed subtle but significant differences in the stability of heterochromatic repression between various environmental conditions, revealed that haploid cells experienced higher rates of silencing loss than diploids, and uncovered the unexpected contribution of a sirtuin to heterochromatin dynamics.
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Affiliation(s)
- Tzu-Yu Liu
- Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720
| | - Anne E Dodson
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Jonathan Terhorst
- Department of Statistics, University of California, Berkeley, CA 94720
| | - Yun S Song
- Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720; Department of Statistics, University of California, Berkeley, CA 94720; Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720;
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Svenkrtova A, Belicova L, Volejnikova A, Sigler K, Jazwinski SM, Pichova A. Stratification of yeast cells during chronological aging by size points to the role of trehalose in cell vitality. Biogerontology 2016; 17:395-408. [PMID: 26614086 PMCID: PMC4808460 DOI: 10.1007/s10522-015-9625-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/23/2015] [Indexed: 02/06/2023]
Abstract
Cells of the budding yeast Saccharomyces cerevisiae undergo a process akin to differentiation during prolonged culture without medium replenishment. Various methods have been used to separate and determine the potential role and fate of the different cell species. We have stratified chronologically-aged yeast cultures into cells of different sizes, using centrifugal elutriation, and characterized these subpopulations physiologically. We distinguish two extreme cell types, very small (XS) and very large (L) cells. L cells display higher viability based on two separate criteria. They respire much more actively, but produce lower levels of reactive oxygen species (ROS). L cells are capable of dividing, albeit slowly, giving rise to XS cells which do not divide. L cells are more resistant to osmotic stress and they have higher trehalose content, a storage carbohydrate often connected to stress resistance. Depletion of trehalose by deletion of TPS2 does not affect the vital characteristics of L cells, but it improves some of these characteristics in XS cells. Therefore, we propose that the response of L and XS cells to the trehalose produced in the former differs in a way that lowers the vitality of the latter. We compare our XS- and L-fraction cell characteristics with those of cells isolated from stationary cultures by others based on density. This comparison suggests that the cells have some similarities but also differences that may prove useful in addressing whether it is the segregation or the response to trehalose that may play the predominant role in cell division from stationary culture.
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Abstract
Next-generation sequencing approaches have considerably advanced our understanding of genome function and regulation. However, the knowledge of gene function and complex cellular processes remains a challenge and bottleneck in biological research. Phenomics is a rapidly emerging area, which seeks to rigorously characterize all phenotypes associated with genes or gene variants. Such high-throughput phenotyping under different conditions can be a potent approach toward gene function. The fission yeast Schizosaccharomyces pombe (S. pombe) is a proven eukaryotic model organism that is increasingly used for genomewide screens and phenomic assays. In this review, we highlight current large-scale, cell-based approaches used with S. pombe, including computational colony-growth measurements, genetic interaction screens, parallel profiling using barcodes, microscopy-based cell profiling, metabolomic methods and transposon mutagenesis. These diverse methods are starting to offer rich insights into the relationship between genotypes and phenotypes.
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Affiliation(s)
- Charalampos Rallis
- a Research Department of Genetics , Evolution and Environment and UCL Institute of Healthy Ageing, University College London , London , UK
| | - Jürg Bähler
- a Research Department of Genetics , Evolution and Environment and UCL Institute of Healthy Ageing, University College London , London , UK
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21
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Medkour Y, Svistkova V, Titorenko VI. Cell-Nonautonomous Mechanisms Underlying Cellular and Organismal Aging. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 321:259-97. [PMID: 26811290 DOI: 10.1016/bs.ircmb.2015.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cell-autonomous mechanisms underlying cellular and organismal aging in evolutionarily distant eukaryotes have been established; these mechanisms regulate longevity-defining processes within a single eukaryotic cell. Recent findings have provided valuable insight into cell-nonautonomous mechanisms modulating cellular and organismal aging in eukaryotes across phyla; these mechanisms involve a transmission of various longevity factors between different cells, tissues, and organisms. Herein, we review such cell-nonautonomous mechanisms of aging in eukaryotes. We discuss the following: (1) how low molecular weight transmissible longevity factors modulate aging and define longevity of cells in yeast populations cultured in liquid media or on solid surfaces, (2) how communications between proteostasis stress networks operating in neurons and nonneuronal somatic tissues define longevity of the nematode Caenorhabditis elegans by modulating the rates of aging in different tissues, and (3) how different bacterial species colonizing the gut lumen of C. elegans define nematode longevity by modulating the rate of organismal aging.
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Affiliation(s)
- Younes Medkour
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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22
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Arlia-Ciommo A, Piano A, Leonov A, Svistkova V, Titorenko VI. Quasi-programmed aging of budding yeast: a trade-off between programmed processes of cell proliferation, differentiation, stress response, survival and death defines yeast lifespan. Cell Cycle 2015; 13:3336-49. [PMID: 25485579 PMCID: PMC4614525 DOI: 10.4161/15384101.2014.965063] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent findings suggest that evolutionarily distant organisms share the key features of the aging process and exhibit similar mechanisms of its modulation by certain genetic, dietary and pharmacological interventions. The scope of this review is to analyze mechanisms that in the yeast Saccharomyces cerevisiae underlie: (1) the replicative and chronological modes of aging; (2) the convergence of these 2 modes of aging into a single aging process; (3) a programmed differentiation of aging cell communities in liquid media and on solid surfaces; and (4) longevity-defining responses of cells to some chemical compounds released to an ecosystem by other organisms populating it. Based on such analysis, we conclude that all these mechanisms are programs for upholding the long-term survival of the entire yeast population inhabiting an ecological niche; however, none of these mechanisms is a ʺprogram of agingʺ - i.e., a program for progressing through consecutive steps of the aging process.
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Key Words
- D, diauxic growth phase
- ERCs, extrachromosomal rDNA circles
- IPOD, insoluble protein deposit
- JUNQ, juxtanuclear quality control compartment
- L, logarithmic growth phase
- MBS, the mitochondrial back-signaling pathway
- MTC, the mitochondrial translation control signaling pathway
- NPCs, nuclear pore complexes
- NQ, non-quiescent cells
- PD, post-diauxic growth phase
- Q, quiescent cells
- ROS, reactive oxygen species
- RTG, the mitochondrial retrograde signaling pathway
- Ras/cAMP/PKA, the Ras family GTPase/cAMP/protein kinase A signaling pathway
- ST, stationary growth phase
- TOR/Sch9, the target of rapamycin/serine-threonine protein kinase Sch9 signaling pathway
- UPRER, the unfolded protein response pathway in the endoplasmic reticulum
- UPRmt, the unfolded protein response pathway in mitochondria
- cell growth and proliferation
- cell survival
- cellular aging
- ecosystems
- evolution
- longevity
- programmed cell death
- yeast
- yeast colony
- yeast replicative and chronological aging
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Faria-Oliveira F, Carvalho J, Belmiro CLR, Martinez-Gomariz M, Hernaez ML, Pavão M, Gil C, Lucas C, Ferreira C. Methodologies to generate, extract, purify and fractionate yeast ECM for analytical use in proteomics and glycomics. BMC Microbiol 2014; 14:244. [PMID: 25344425 PMCID: PMC4219020 DOI: 10.1186/s12866-014-0244-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/09/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND In a multicellular organism, the extracellular matrix (ECM) provides a cell-supporting scaffold and helps maintaining the biophysical integrity of tissues and organs. At the same time it plays crucial roles in cellular communication and signalling, with implications in spatial organisation, motility and differentiation. Similarly, the presence of an ECM-like extracellular polymeric substance is known to support and protect bacterial and fungal multicellular aggregates, such as biofilms or colonies. However, the roles and composition of this microbial ECM are still poorly understood. RESULTS This work presents a protocol to produce S. cerevisiae and C. albicans ECM in an equally highly reproducible manner. Additionally, methodologies for the extraction and fractionation into protein and glycosidic analytical pure fractions were improved. These were subjected to analytical procedures, respectively SDS-PAGE, 2-DE, MALDI-TOF-MS and LC-MS/MS, and DAE and FPLC. Additional chemical methods were also used to test for uronic acids and sulphation. CONCLUSIONS The methodologies hereby presented were equally efficiently applied to extract high amounts of ECM material from S. cerevisiae and C. albicans mats, therefore showing their robustness and reproducibility for yECM molecular and structural characterization. yECM from S. cerevisiae and C. albicans displayed a different proteome and glycoside fractions. S. cerevisiae yECM presented two well-defined polysaccharides with different mass/charge, and C. albicans ECM presented a single different one. The chemical methods further suggested the presence of uronic acids, and chemical modification, possibly through sulphate substitution. All taken, the procedures herein described present the first sensible and concise approach to the molecular and chemical characterisation of the yeast ECM, opening the way to the in-depth study of the microbe multicellular aggregates structure and life-style.
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Affiliation(s)
- Fábio Faria-Oliveira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Joana Carvalho
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Celso L R Belmiro
- Institute of Medical Biochemistry, Laboratory of Glycoconjugates Biochemistry and Cellular Biology, Federal University of Rio de Janeiro/ Polo de Macaé, Macaé, Brazil.
| | - Montserrat Martinez-Gomariz
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid UCM-PCM), Madrid, Spain.
| | - Maria Luisa Hernaez
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid UCM-PCM), Madrid, Spain.
| | - Mauro Pavão
- Institute of Medical Biochemistry, Laboratory of Glycoconjugates Biochemistry and Cellular Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Concha Gil
- Unidad de Proteómica, Universidad Complutense de Madrid - Parque Científico de Madrid UCM-PCM), Madrid, Spain. .,Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.
| | - Cândida Lucas
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Célia Ferreira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
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Carmona-Gutierrez D, Büttner S. The many ways to age for a single yeast cell. Yeast 2014; 31:289-98. [PMID: 24842537 PMCID: PMC4140606 DOI: 10.1002/yea.3020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/07/2014] [Accepted: 05/09/2014] [Indexed: 12/17/2022] Open
Abstract
The identification and characterization of the molecular determinants governing ageing represents the key to counteracting age-related diseases and eventually prolonging our health span. A large number of fundamental insights into the ageing process have been provided by research into the budding yeast Saccharomyces cerevisiae, which couples a wide array of technical advantages with a high degree of genetic, proteomic and mechanistic conservation. Indeed, this unicellular organism harbours regulatory pathways, such as those related to programmed cell death or nutrient signalling, that are crucial for ageing control and are reminiscent of other eukaryotes, including mammals. Here, we summarize and discuss three different paradigms of yeast ageing: replicative, chronological and colony ageing. We address their physiological relevance as well as the specific and common characteristics and regulators involved, providing an overview of the network underlying ageing in one of the most important eukaryotic model organisms.
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25
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The transport of carboxylic acids and important role of the Jen1p transporter during the development of yeast colonies. Biochem J 2013; 454:551-8. [PMID: 23790185 DOI: 10.1042/bj20120312] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
On solid substrates, yeast colonies pass through distinct developmental phases characterized by the changes in pH of their surroundings from acidic to nearly alkaline and vice versa. At the beginning of the alkali phase colonies start to produce ammonia, which functions as a quorum-sensing molecule inducing the reprogramming of cell metabolism. Such reprogramming includes, among others, the activation of several plasma membrane transporters and is connected with colony differentiation. In the present study, we show that colony cells can use two transport mechanisms to import lactic acid: a 'saturable' component of the transport, which requires the presence of a functional Jen1p transporter, and a 'non-saturable' component (diffusion) that is independent of Jen1p. During colony development, the efficiency of both transport components changes similarly in central and outer colonial cells. Although the lactate uptake capacity of central cells gradually decreases during colony development, the lactate uptake capacity of outer cells peaks during the alkali phase and is also kept relatively high in the second acidic phase. This lactate uptake profile correlates with the localization of the Jen1p transporter to the plasma membrane of colony cells. Both lactic acid uptake mechanisms are diminished in sok2 colonies where JEN1 expression is decreased. The Sok2p transcription factor may therefore be involved in the regulation of non-saturable lactic acid uptake in yeast colonies.
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26
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Palková Z, Wilkinson D, Váchová L. Aging and differentiation in yeast populations: elders with different properties and functions. FEMS Yeast Res 2013; 14:96-108. [PMID: 24119061 DOI: 10.1111/1567-1364.12103] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 09/23/2013] [Accepted: 09/26/2013] [Indexed: 01/08/2023] Open
Abstract
Over the past decade, it has become evident that similarly to cells forming metazoan tissues, yeast cells have the ability to differentiate and form specialized cell types. Examples of yeast cellular differentiation have been identified both in yeast liquid cultures and within multicellular structures occupying solid surfaces. Most current knowledge on different cell types comes from studies of the spatiotemporal internal architecture of colonies developing on various media. With a few exceptions, yeast cell differentiation often concerns nongrowing, stationary-phase cells and leads to the formation of cell subpopulations differing in stress resistance, cell metabolism, respiration, ROS production, and others. These differences can affect longevity of particular subpopulations. In contrast to liquid cultures, where various cell types are dispersed within stationary-phase populations, cellular differentiation depends on the specific position of particular cells within multicellular colonies. Differentiated colonies, thus, resemble primitive multicellular organisms, in which the gradients of certain compounds and the position of cells within the structure affect cellular differentiation. In this review, we summarize and compare the properties of diverse types of differentiated chronologically aging yeast cells that have been identified in colonies growing on different media, as well as of those found in liquid cultures.
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Affiliation(s)
- Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
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27
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Rapidly developing yeast microcolonies differentiate in a similar way to aging giant colonies. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:102485. [PMID: 23970946 PMCID: PMC3736409 DOI: 10.1155/2013/102485] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/25/2013] [Indexed: 12/28/2022]
Abstract
During their development and aging on solid substrates, yeast giant colonies produce ammonia, which acts as a quorum sensing molecule. Ammonia production is connected with alkalization of the surrounding medium and with extensive reprogramming of cell metabolism. In addition, ammonia signaling is important for both horizontal (colony centre versus colony margin) and vertical (upper versus lower cell layers) colony differentiations. The centre of an aging differentiated giant colony is thus composed of two major cell subpopulations, the subpopulation of long-living, metabolically active and stress-resistant cells that form the upper layers of the colony and the subpopulation of stress-sensitive starving cells in the colony interior. Here, we show that microcolonies originating from one cell pass through similar developmental phases as giant colonies. Microcolony differentiation is linked to ammonia signaling, and cells similar to the upper and lower cells of aged giant colonies are formed even in relatively young microcolonies. A comparison of the properties of these cells revealed a number of features that are similar in microcolonies and giant colonies as well as a few that are only typical of chronologically aged giant colonies. These findings show that colony age per se is not crucial for colony differentiation.
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28
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Liu J, Qi Z, Huang Q, Wei X, Ke Z, Fang Y, Tian Y, Yu Z. Study of energetic-particle-irradiation induced biological effect on Rhizopus oryzae through synchrotron-FTIR micro-spectroscopy. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Baron JA, Laws KM, Chen JS, Culotta VC. Superoxide triggers an acid burst in Saccharomyces cerevisiae to condition the environment of glucose-starved cells. J Biol Chem 2012; 288:4557-66. [PMID: 23281478 DOI: 10.1074/jbc.m112.409508] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although yeast cells grown in abundant glucose tend to acidify their extracellular environment, they raise the pH of the environment when starved for glucose or when grown strictly with non-fermentable carbon sources. Following prolonged periods in this alkaline phase, Saccharomyces cerevisiae cells will switch to producing acid. The mechanisms and rationale for this "acid burst" were unknown. Herein we provide strong evidence for the role of mitochondrial superoxide in initiating the acid burst. Yeast mutants lacking the mitochondrial matrix superoxide dismutase (SOD2) enzyme, but not the cytosolic Cu,Zn-SOD1 enzyme, exhibited marked acceleration in production of acid on non-fermentable carbon sources. Acid production is also dramatically enhanced by the superoxide-producing agent, paraquat. Conversely, the acid burst is eliminated by boosting cellular levels of Mn-antioxidant mimics of SOD. We demonstrate that the acid burst is dependent on the mitochondrial aldehyde dehydrogenase Ald4p. Our data are consistent with a model in which mitochondrial superoxide damage to Fe-S enzymes in the tricarboxylic acid (TCA) cycle leads to acetate buildup by Ald4p. The resultant expulsion of acetate into the extracellular environment can provide a new carbon source to glucose-starved cells and enhance growth of yeast. By triggering production of organic acids, mitochondrial superoxide has the potential to promote cell population growth under nutrient depravation stress.
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Affiliation(s)
- J Allen Baron
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
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30
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Ramsdale M. Programmed cell death in the cellular differentiation of microbial eukaryotes. Curr Opin Microbiol 2012; 15:646-52. [DOI: 10.1016/j.mib.2012.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/21/2012] [Accepted: 09/25/2012] [Indexed: 01/22/2023]
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31
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Yeast colonies: a model for studies of aging, environmental adaptation, and longevity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:601836. [PMID: 22928081 PMCID: PMC3425895 DOI: 10.1155/2012/601836] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
Abstract
When growing on solid surfaces, yeast, like other microorganisms, develops organized multicellular populations (colonies and biofilms) that are composed of differentiated cells with specialized functions. Life within these populations is a prevalent form of microbial existence in natural settings that provides the cells with capabilities to effectively defend against environmental attacks as well as efficiently adapt and survive long periods of starvation and other stresses. Under such circumstances, the fate of an individual yeast cell is subordinated to the profit of the whole population. In the past decade, yeast colonies, with their complicated structure and high complexity that are also developed under laboratory conditions, have become an excellent model for studies of various basic cellular processes such as cell interaction, signaling, and differentiation. In this paper, we summarize current knowledge on the processes related to chronological aging, adaptation, and longevity of a colony cell population and of its differentiated cell constituents. These processes contribute to the colony ability to survive long periods of starvation and mostly differ from the survival strategies of individual yeast cells.
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32
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Goswami AV, Samaddar M, Sinha D, Purushotham J, D'Silva P. Enhanced J-protein interaction and compromised protein stability of mtHsp70 variants lead to mitochondrial dysfunction in Parkinson's disease. Hum Mol Genet 2012; 21:3317-32. [PMID: 22544056 PMCID: PMC3392108 DOI: 10.1093/hmg/dds162] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 04/13/2012] [Accepted: 04/20/2012] [Indexed: 12/31/2022] Open
Abstract
Parkinson's disease (PD) is the second most prevalent progressive neurological disorder commonly associated with impaired mitochondrial function in dopaminergic neurons. Although familial PD is multifactorial in nature, a recent genetic screen involving PD patients identified two mitochondrial Hsp70 variants (P509S and R126W) that are suggested in PD pathogenesis. However, molecular mechanisms underlying how mtHsp70 PD variants are centrally involved in PD progression is totally elusive. In this article, we provide mechanistic insights into the mitochondrial dysfunction associated with human mtHsp70 PD variants. Biochemically, the R126W variant showed severely compromised protein stability and was found highly susceptible to aggregation at physiological conditions. Strikingly, on the other hand, the P509S variant exhibits significantly enhanced interaction with J-protein cochaperones involved in folding and import machinery, thus altering the overall regulation of chaperone-mediated folding cycle and protein homeostasis. To assess the impact of mtHsp70 PD mutations at the cellular level, we developed yeast as a model system by making analogous mutations in Ssc1 ortholog. Interestingly, PD mutations in yeast (R103W and P486S) exhibit multiple in vivo phenotypes, which are associated with 'mitochondrial dysfunction', including compromised growth, impairment in protein translocation, reduced functional mitochondrial mass, mitochondrial DNA loss, respiratory incompetency and increased susceptibility to oxidative stress. In addition to that, R103W protein is prone to aggregate in vivo due to reduced stability, whereas P486S showed enhanced interaction with J-proteins, thus remarkably recapitulating the cellular defects that are observed in human PD variants. Taken together, our findings provide evidence in favor of direct involvement of mtHsp70 as a susceptibility factor in PD.
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Affiliation(s)
| | | | | | | | - Patrick D'Silva
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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33
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Reactive oxygen species in the signaling and adaptation of multicellular microbial communities. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:976753. [PMID: 22829965 PMCID: PMC3395218 DOI: 10.1155/2012/976753] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 05/24/2012] [Indexed: 02/07/2023]
Abstract
One of the universal traits of microorganisms is their ability to form multicellular structures, the cells of which differentiate and communicate via various signaling molecules. Reactive oxygen species (ROS), and hydrogen peroxide in particular, have recently become well-established signaling molecules in higher eukaryotes, but still little is known about the regulatory functions of ROS in microbial structures. Here we summarize current knowledge on the possible roles of ROS during the development of colonies and biofilms, representatives of microbial multicellularity. In Saccharomyces cerevisiae colonies, ROS are predicted to participate in regulatory events involved in the induction of ammonia signaling and later on in programmed cell death in the colony center. While the latter process seems to be induced by the total ROS, the former event is likely to be regulated by ROS-homeostasis, possibly H2O2-homeostasis between the cytosol and mitochondria. In Candida albicans biofilms, the predicted signaling role of ROS is linked with quorum sensing molecule farnesol that significantly affects biofilm formation. In bacterial biofilms, ROS induce genetic variability, promote cell death in specific biofilm regions, and possibly regulate biofilm development. Thus, the number of examples suggesting ROS as signaling molecules and effectors in the development of microbial multicellularity is rapidly increasing.
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34
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Cáp M, Stěpánek L, Harant K, Váchová L, Palková Z. Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism. Mol Cell 2012; 46:436-48. [PMID: 22560924 DOI: 10.1016/j.molcel.2012.04.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 12/16/2011] [Accepted: 03/23/2012] [Indexed: 12/30/2022]
Abstract
Nutrient sensing and metabolic reprogramming are crucial for metazoan cell aging and tumor growth. Here, we identify metabolic and regulatory parallels between a layered, multicellular yeast colony and a tumor-affected organism. During development, a yeast colony stratifies into U and L cells occupying the upper and lower colony regions, respectively. U cells activate a unique metabolism controlled by the glutamine-induced TOR pathway, amino acid-sensing systems (SPS and Gcn4p) and signaling from mitochondria with lowered respiration. These systems jointly modulate U cell physiology, which adapts to nutrient limitations and utilize the nutrients released from L cells. Stress-resistant U cells share metabolic pathways and other similar characteristics with tumor cells, including the ability to proliferate. L cells behave similarly to stressed and starving cells, which activate degradative mechanisms to provide nutrients to U cells. Our data suggest a nutrient flow between both cell types, resembling the Cori cycle and glutamine-NH(4)(+) shuttle between tumor and healthy metazoan cells.
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Affiliation(s)
- Michal Cáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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35
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Aging and longevity of yeast colony populations: metabolic adaptation and differentiation. Biochem Soc Trans 2012; 39:1471-5. [PMID: 21936836 DOI: 10.1042/bst0391471] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Yeast multicellular colonies possess several traits that are absent from individual yeasts. These include the ability to synchronize colony population development and adapt its metabolism to different environmental changes, such as nutrient depletion. This, together with cell diversification to cell variants with distinct metabolic and other properties, contributes to the main goal of the colony population: to achieve longevity. In this respect, a benefit to individual cells is subordinated to the benefit to the whole population, exhibiting a kind of altruistic behaviour. For example, some colony cells located at particular positions undergo regulated cell dying and provide components to other cells located in more propitious areas. The enhancement of techniques that enable the in vivo investigation of three-dimensional spatiotemporal colony development may lead to new discoveries on metabolic differentiation and regulation in the near future.
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36
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Cell signals, cell contacts, and the organization of yeast communities. EUKARYOTIC CELL 2011; 10:466-73. [PMID: 21296916 DOI: 10.1128/ec.00313-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Even relatively simple species have evolved mechanisms to organize individual organisms into communities, such that the fitness of the group is greater than the fitness of isolated individuals. Within the fungal kingdom, the ability of many yeast species to organize into communities is crucial for their growth and survival, and this property has important impacts both on the economy and on human health. Over the last few years, studies of Saccharomyces cerevisiae have revealed several fundamental properties of yeast communities. First, strain-to-strain variation in the structures of these groups is attributable in part to variability in the expression and functions of adhesin proteins. Second, the extracellular matrix surrounding these communities can protect them from environmental stress and may also be important in cell signaling. Finally, diffusible signals between cells contribute to community organization so that different regions of a community express different genes and adopt different cell fates. These findings provide an arena in which to view fundamental mechanisms by which contacts and signals between individual organisms allow them to assemble into functional communities.
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37
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General and molecular microbiology and microbial genetics in the IM CAS. J Ind Microbiol Biotechnol 2010; 37:1227-39. [DOI: 10.1007/s10295-010-0859-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 08/20/2010] [Indexed: 11/28/2022]
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38
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Abdelwahid E, Rolland S, Teng X, Conradt B, Hardwick JM, White K. Mitochondrial involvement in cell death of non-mammalian eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:597-607. [PMID: 20950655 DOI: 10.1016/j.bbamcr.2010.10.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/29/2010] [Accepted: 10/04/2010] [Indexed: 12/28/2022]
Abstract
Although mitochondria are essential organelles for long-term survival of eukaryotic cells, recent discoveries in biochemistry and genetics have advanced our understanding of the requirements for mitochondria in cell death. Much of what we understand about cell death is based on the identification of conserved cell death genes in Drosophila melanogaster and Caenorhabditis elegans. However, the role of mitochondria in cell death in these models has been much less clear. Considering the active role that mitochondria play in apoptosis in mammalian cells, the mitochondrial contribution to cell death in non-mammalian systems has been an area of active investigation. In this article, we review the current research on this topic in three non-mammalian models, C. elegans, Drosophila, and Saccharomyces cerevisiae. In addition, we discuss how non-mammalian models have provided important insight into the mechanisms of human disease as they relate to the mitochondrial pathway of cell death. The unique perspective derived from each of these model systems provides a more complete understanding of mitochondria in programmed cell death. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.
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Affiliation(s)
- Eltyeb Abdelwahid
- Cutaneous Biology Research Center, Massachusetts General Hospital/Harvard Medical School, Building 149, 13th Street, Charlestown, MA 02129, USA
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39
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St'ovíček V, Váchová L, Kuthan M, Palková Z. General factors important for the formation of structured biofilm-like yeast colonies. Fungal Genet Biol 2010; 47:1012-22. [PMID: 20728557 DOI: 10.1016/j.fgb.2010.08.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 08/06/2010] [Accepted: 08/11/2010] [Indexed: 12/30/2022]
Abstract
The lifestyle of wild and laboratory yeast strains significantly differs. In contrast to the smooth colonies of laboratory strains, wild Saccharomyces cerevisiae strains form biofilm-like, strikingly structured colonies possessing distinctive traits enabling them to better survive in hostile environments in the wild. Here, comparing three sets of strains forming differently structured colonies (fluffy, semi-fluffy and smooth), each derived from ancestors with distinct genetic backgrounds isolated from natural settings (BR-88, BR-99 and BR-103), we specified the factors essential for the formation of structured colonies, i.e. for the lifestyle most likely to be preferred in the wild. The ability to form an abundant extracellular matrix (ECM) is one of the features typical for structured colonies. ECM influences colony architecture and many other physiological properties, such as the capability to retain water in a 2-fold surplus to wet cell biomass. ECM composition, however, differs among distinct strains, depending on their particular genetic background. We further show that the expression of certain genes (AQY1, FLO11) is also strictly related to the particular colony morphology, being highest in the most structured colonies. Flo11p adhesin, important for cell-cell and cell-surface adhesion, is essential for the formation of fluffy colonies and thus significantly contributes to the phenotype variability of wild yeast strains. On the other hand, surprisingly, neither the cell shape nor budding pattern nor the ability to form pseudohyphae directly influences the formation of three-dimensional fluffy colony architecture.
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Affiliation(s)
- Vratislav St'ovíček
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, Prague 2, Czech Republic
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40
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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