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Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
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Abstract
Microorganisms cooperate with each other to protect themselves from environmental stressors. An extreme case of such cooperation is regulated cell death for the benefit of other cells. Dying cells can provide surviving cells with nutrients or induce their stress response by transmitting an alarm signal; however, the role of dead cells in microbial communities is unclear. Here, we searched for types of stressors the protection from which can be achieved by death of a subpopulation of cells. Thus, we compared the survival of Saccharomyces cerevisiae cells upon exposure to various stressors in the presence of additionally supplemented living versus dead cells. We found that dead cells contribute to yeast community resistance against macrolide antifungals (e.g., amphotericin B [AmB] and filipin) to a greater extent than living cells. Dead yeast cells absorbed more macrolide filipin than control cells because they exposed intracellular sterol-rich membranes. We also showed that, upon the addition of lethal concentrations of AmB, supplementation with AmB-sensitive cells but not with AmB-resistant cells enabled the survival of wild-type cells. Together, our data suggest that cell-to-cell heterogeneity in sensitivity to AmB can be an adaptive mechanism helping yeast communities to resist macrolides, which are naturally occurring antifungal agents. IMPORTANCE Eukaryotic microorganisms harbor elements of programmed cell death (PCD) mechanisms that are homologous to the PCD of multicellular metazoa. However, it is still debated whether microbial PCD has an adaptive role or whether the processes of cell death are an aimless operation in self-regulating molecular mechanisms. Here, we demonstrated that dying yeast cells provide an instant benefit for their community by absorbing macrolides, which are bacterium-derived antifungals. Our results illustrate the principle that the death of a microorganism can contribute to the survival of its kin and suggest that early plasma membrane permeabilization improves community-level protection. The latter makes a striking contrast to the manifestations of apoptosis in higher eukaryotes, the process by which plasma membranes maintain integrity.
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Johnstone P, Mast E, Hughes E, Peng H. Development of a small-scale rotary lobe-pump cell culture model for examining cell damage in large-scale N-1 seed perfusion process. Biotechnol Prog 2020; 36:e3044. [PMID: 32594624 DOI: 10.1002/btpr.3044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/12/2022]
Abstract
Perfusion technology has been identified as a process improvement capable of eliminating some of the constraints in cell culture and allows for high cell densities and viabilities. However, when implementing this N-1 seed perfusion platform in large-scale manufacturing, unexpected cell damage was observed as early as Day 1. Given that the shear rate within recirculation hollow fibers was normalized and aligned correctly across bench, pilot, and manufacture scale, the primary mitigation was placed on the rotary lobe pump. Lowering the pump rate in manufacture scale successfully alleviated the cell damage. To understand the source of cell damage within the pump, a small-scale rotary lobe-pump robustness model was developed. Testing different pump flow rates and back pressures, it was concluded that high back pressure can cause cell damage. The back pressure within the system can cause back flow and high shear within small clearances inside the pump, which lead to the primary cell damage observed at a large scale. This shear level can be significantly higher than the shear in the hollow fiber. This pump robustness model can be utilized to aid the perfusion skid design, including pump operation efficiency and cell shear sensitivity. Methods to reduce the back pressure and cell shearing were determined to better predict manufacturing performance in the future.
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Affiliation(s)
| | - Elena Mast
- Manufacturing Sciences, Biogen, Durham, North Carolina, USA
| | - Erik Hughes
- Manufacturing Sciences, Biogen, Durham, North Carolina, USA
| | - Haofan Peng
- Manufacturing Sciences, Biogen, Durham, North Carolina, USA
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Heins AL, Reyelt J, Schmidt M, Kranz H, Weuster-Botz D. Development and characterization of Escherichia coli triple reporter strains for investigation of population heterogeneity in bioprocesses. Microb Cell Fact 2020; 19:14. [PMID: 31992282 PMCID: PMC6988206 DOI: 10.1186/s12934-020-1283-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/12/2020] [Indexed: 12/17/2022] Open
Abstract
Background Today there is an increasing demand for high yielding robust and cost efficient biotechnological production processes. Although cells in these processes originate from isogenic cultures, heterogeneity induced by intrinsic and extrinsic influences is omnipresent. To increase understanding of this mechanistically poorly understood phenomenon, advanced tools that provide insights into single cell physiology are needed. Results Two Escherichia coli triple reporter strains have been designed based on the industrially relevant production host E. coli BL21(DE3) and a modified version thereof, E. coli T7E2. The strains carry three different fluorescence proteins chromosomally integrated. Single cell growth is followed with EmeraldGFP (EmGFP)-expression together with the ribosomal promoter rrnB. General stress response of single cells is monitored by expression of sigma factor rpoS with mStrawberry, whereas expression of the nar-operon together with TagRFP657 gives information about oxygen limitation of single cells. First, the strains were characterized in batch operated stirred-tank bioreactors in comparison to wildtype E. coli BL21(DE3). Afterwards, applicability of the triple reporter strains for investigation of population heterogeneity in bioprocesses was demonstrated in continuous processes in stirred-tank bioreactors at different growth rates and in response to glucose and oxygen perturbation simulating gradients on industrial scale. Population and single cell level physiology was monitored evaluating general physiology and flow cytometry analysis of fluorescence distributions of the triple reporter strains. Although both triple reporter strains reflected physiological changes that were expected based on the expression characteristics of the marker proteins, the triple reporter strain based on E. coli T7E2 showed higher sensitivity in response to environmental changes. For both strains, noise in gene expression was observed during transition from phases of non-growth to growth. Apparently, under some process conditions, e.g. the stationary phase in batch cultures, the fluorescence response of EmGFP and mStrawberry is preserved, whereas TagRFP657 showed a distinct response. Conclusions Single cell growth, general stress response and oxygen limitation of single cells could be followed using the two triple reporter strains developed in this study. They represent valuable tools to study population heterogeneity in bioprocesses significantly increasing the level of information compared to the use of single reporter strains.
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Affiliation(s)
- Anna-Lena Heins
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Jan Reyelt
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Marlen Schmidt
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Harald Kranz
- Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Dirk Weuster-Botz
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
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Heins AL, Johanson T, Han S, Lundin L, Carlquist M, Gernaey KV, Sørensen SJ, Eliasson Lantz A. Quantitative Flow Cytometry to Understand Population Heterogeneity in Response to Changes in Substrate Availability in Escherichia coli and Saccharomyces cerevisiae Chemostats. Front Bioeng Biotechnol 2019; 7:187. [PMID: 31448270 PMCID: PMC6691397 DOI: 10.3389/fbioe.2019.00187] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022] Open
Abstract
Microbial cells in bioprocesses are usually described with averaged parameters. But in fact, single cells within populations vary greatly in characteristics such as stress resistance, especially in response to carbon source gradients. Our aim was to introduce tools to quantify population heterogeneity in bioprocesses using a combination of reporter strains, flow cytometry, and easily comprehensible parameters. We calculated mean, mode, peak width, and coefficient of variance to describe distribution characteristics and temporal shifts in fluorescence intensity. The skewness and the slope of cumulative distribution function plots illustrated differences in distribution shape. These parameters are person-independent and precise. We demonstrated this by quantifying growth-related population heterogeneity of Saccharomyces cerevisiae and Escherichia coli reporter strains in steady-state of aerobic glucose-limited chemostat cultures at different dilution rates and in response to glucose pulses. Generally, slow-growing cells showed stronger responses to glucose excess than fast-growing cells. Cell robustness, measured as membrane integrity after exposure to freeze-thaw treatment, of fast-growing cells was strongly affected in subpopulations of low membrane robustness. Glucose pulses protected subpopulations of fast-growing but not slower-growing yeast cells against membrane damage. Our parameters could successfully describe population heterogeneity, thereby revealing physiological characteristics that might have been overlooked during traditional averaged analysis.
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Affiliation(s)
- Anna-Lena Heins
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | | | - Shanshan Han
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luisa Lundin
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anna Eliasson Lantz
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
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Heins AL, Weuster-Botz D. Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives. Bioprocess Biosyst Eng 2018. [PMID: 29541890 DOI: 10.1007/s00449-018-1922-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions. A step in between investigation of populations and single cells is studying subpopulations with distinct properties that differ from the rest of the population with sub-omics methods which are also presented here. Moreover, the current knowledge about population heterogeneity in bioprocesses is summarized for relevant industrial production hosts and mixed cultures, as they provide the unique opportunity to distribute metabolic burden and optimize production processes in a way that is impossible in traditional monocultures. In the end, approaches to explain the underlying mechanism of population heterogeneity and the evidences found to support each hypothesis are presented. For instance, population heterogeneity serving as a bet-hedging strategy that is used as coordinated action against bioprocess-related stresses while at the same time spreading the risk between individual cells as it ensures the survival of least a part of the population in any environment the cells encounter.
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Affiliation(s)
- Anna-Lena Heins
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
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Brink DP, Borgström C, Tueros FG, Gorwa-Grauslund MF. Real-time monitoring of the sugar sensing in Saccharomyces cerevisiae indicates endogenous mechanisms for xylose signaling. Microb Cell Fact 2016; 15:183. [PMID: 27776527 PMCID: PMC5078928 DOI: 10.1186/s12934-016-0580-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/14/2016] [Indexed: 12/03/2022] Open
Abstract
Background The sugar sensing and carbon catabolite repression in Baker’s yeast Saccharomyces cerevisiae is governed by three major signaling pathways that connect carbon source recognition with transcriptional regulation. Here we present a screening method based on a non-invasive in vivo reporter system for real-time, single-cell screening of the sugar signaling state in S. cerevisiae in response to changing carbon conditions, with a main focus on the response to glucose and xylose. Results The artificial reporter system was constructed by coupling a green fluorescent protein gene (yEGFP3) downstream of endogenous yeast promoters from the Snf3p/Rgt2p, SNF1/Mig1p and cAMP/PKA signaling pathways: HXT1p/2p/4p; SUC2p, CAT8p; TPS1p/2p and TEF4p respectively. A panel of eight biosensors strains was generated by single copy chromosomal integration of the different constructs in a W303-derived strain. The signaling biosensors were validated for their functionality with flow cytometry by comparing the fluorescence intensity (FI) response in the presence of high or nearly depleted glucose to the known induction/repression conditions of the eight different promoters. The FI signal correlated with the known patterns of the selected promoters while maintaining a non-invasive property on the cellular phenotype, as was demonstrated in terms of growth, metabolites and enzyme activity. Conclusions Once verified, the sensors were used to evaluate the signaling response to varying conditions of extracellular glucose, glycerol and xylose by screening in 96-well microtiter plates. We show that these yeast strains, which do not harbor any recombinant pathways for xylose utilization, are lacking a signaling response for extracellular xylose. However, for the HXT2p/4p sensors, a shift in the flow cytometry population dynamics indicated that internalized xylose does affect the signaling. These results suggest that the previously observed effects of this pentose on the S. cerevisiae physiology and gene regulation can be attributed to xylose and not only to a lack of glucose. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0580-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden.
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Felipe G Tueros
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
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Hewitt SK, Foster DS, Dyer PS, Avery SV. Phenotypic heterogeneity in fungi: Importance and methodology. FUNGAL BIOL REV 2016. [DOI: 10.1016/j.fbr.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Fischer S, Engstler C, Procopio S, Becker T. EGFP-based evaluation of temperature inducible native promoters of industrial ale yeast by using a high throughput system. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pénicaud C, Landaud S, Jamme F, Talbot P, Bouix M, Ghorbal S, Fonseca F. Physiological and biochemical responses of Yarrowia lipolytica to dehydration induced by air-drying and freezing. PLoS One 2014; 9:e111138. [PMID: 25350121 PMCID: PMC4211883 DOI: 10.1371/journal.pone.0111138] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/29/2014] [Indexed: 11/23/2022] Open
Abstract
Organisms that can withstand anhydrobiosis possess the unique ability to temporarily and reversibly suspend their metabolism for the periods when they live in a dehydrated state. However, the mechanisms underlying the cell's ability to tolerate dehydration are far from being fully understood. The objective of this study was to highlight, for the first time, the cellular damage to Yarrowia lipolytica as a result of dehydration induced by drying/rehydration and freezing/thawing. Cellular response was evaluated through cell cultivability determined by plate counts, esterase activity and membrane integrity assessed by flow cytometry, and the biochemical composition of cells as determined by FT-IR spectroscopy. The effects of the harvesting time (in the log or stationary phase) and of the addition of a protective molecule, trehalose, were investigated. All freshly harvested cells exhibited esterase activity and no alteration of membrane integrity. Cells freshly harvested in the stationary phase presented spectral contributions suggesting lower nucleic acid content and thicker cell walls, as well as longer lipid chains than cells harvested in the log phase. Moreover, it was found that drying/rehydration induced cell plasma membrane permeabilization, loss of esterase activity with concomitant protein denaturation, wall damage and oxidation of nucleic acids. Plasma membrane permeabilization and loss of esterase activity could be reduced by harvesting in the stationary phase and/or with trehalose addition. Protein denaturation and wall damage could be reduced by harvesting in the stationary phase. In addition, it was shown that measurements of loss of membrane integrity and preservation of esterase activity were suitable indicators of loss and preservation of cultivability, respectively. Conversely, no clear effect of freezing/thawing could be observed, probably because of the favorable operating conditions applied. These results give insights into Y. lipolytica mechanisms of cellular response to dehydration and provide a basis to better understand its ability to tolerate anhydrobiosis.
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Affiliation(s)
- Caroline Pénicaud
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | | | - Pauline Talbot
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Marielle Bouix
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Sarrah Ghorbal
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Fernanda Fonseca
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
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Hellweger FL, Fredrick ND, Berges JA. Age-correlated stress resistance improves fitness of yeast: support from agent-based simulations. BMC SYSTEMS BIOLOGY 2014; 8:18. [PMID: 24529069 PMCID: PMC3927587 DOI: 10.1186/1752-0509-8-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/12/2014] [Indexed: 01/02/2023]
Abstract
BACKGROUND Resistance to stress is often heterogeneous among individuals within a population, which helps protect against intermittent stress (bet hedging). This is also the case for heat shock resistance in the budding yeast Saccharomyces cerevisiae. Interestingly, the resistance appears to be continuously distributed (vs. binary, switch-like) and correlated with replicative age (vs. random). Older, slower-growing cells are more resistant than younger, faster-growing ones. Is there a fitness benefit to age-correlated stress resistance? RESULTS Here this hypothesis is explored using a simple agent-based model, which simulates a population of individual cells that grow and replicate. Cells age by accumulating damage, which lowers their growth rate. They synthesize trehalose at a metabolic cost, which helps protect against heat shock. Proteins Tsl1 and Tps3 (trehalose synthase complex regulatory subunit TSL1 and TPS3) represent the trehalose synthesis complex and they are expressed using constant, age-dependent and stochastic terms. The model was constrained by calibration and comparison to data from the literature, including individual-based observations obtained using high-throughput microscopy and flow cytometry. A heterogeneity network was developed, which highlights the predominant sources and pathways of resistance heterogeneity. To determine the best trehalose synthesis strategy, model strains with different Tsl1/Tps3 expression parameters were placed in competition in an environment with intermittent heat shocks. CONCLUSIONS For high severities and low frequencies of heat shock, the winning strain used an age-dependent bet hedging strategy, which shows that there can be a benefit to age-correlated stress resistance. The study also illustrates the utility of combining individual-based observations and modeling to understand mechanisms underlying population heterogeneity, and the effect on fitness.
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Affiliation(s)
- Ferdi L Hellweger
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA
| | - Neil D Fredrick
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA
| | - John A Berges
- Department of Biological Sciences and School of Freshwater Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
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Török Z, Crul T, Maresca B, Schütz GJ, Viana F, Dindia L, Piotto S, Brameshuber M, Balogh G, Péter M, Porta A, Trapani A, Gombos I, Glatz A, Gungor B, Peksel B, Vigh L, Csoboz B, Horváth I, Vijayan MM, Hooper PL, Harwood JL, Vigh L. Plasma membranes as heat stress sensors: from lipid-controlled molecular switches to therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1594-618. [PMID: 24374314 DOI: 10.1016/j.bbamem.2013.12.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/09/2013] [Accepted: 12/18/2013] [Indexed: 12/31/2022]
Abstract
The classic heat shock (stress) response (HSR) was originally attributed to protein denaturation. However, heat shock protein (Hsp) induction occurs in many circumstances where no protein denaturation is observed. Recently considerable evidence has been accumulated to the favor of the "Membrane Sensor Hypothesis" which predicts that the level of Hsps can be changed as a result of alterations to the plasma membrane. This is especially pertinent to mild heat shock, such as occurs in fever. In this condition the sensitivity of many transient receptor potential (TRP) channels is particularly notable. Small temperature stresses can modulate TRP gating significantly and this is influenced by lipids. In addition, stress hormones often modify plasma membrane structure and function and thus initiate a cascade of events, which may affect HSR. The major transactivator heat shock factor-1 integrates the signals originating from the plasma membrane and orchestrates the expression of individual heat shock genes. We describe how these observations can be tested at the molecular level, for example, with the use of membrane perturbers and through computational calculations. An important fact which now starts to be addressed is that membranes are not homogeneous nor do all cells react identically. Lipidomics and cell profiling are beginning to address the above two points. Finally, we observe that a deregulated HSR is found in a large number of important diseases where more detailed knowledge of the molecular mechanisms involved may offer timely opportunities for clinical interventions and new, innovative drug treatments. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.
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Affiliation(s)
- Zsolt Török
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary.
| | - Tim Crul
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Bruno Maresca
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Gerhard J Schütz
- Institute of Applied Physics, Vienna University of Technology, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Felix Viana
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, 03550 San Juan de Alicante, Spain
| | - Laura Dindia
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Mario Brameshuber
- Institute of Applied Physics, Vienna University of Technology, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Gábor Balogh
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Mária Péter
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Alfonso Trapani
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Imre Gombos
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Attila Glatz
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Burcin Gungor
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Begüm Peksel
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - László Vigh
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Bálint Csoboz
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Ibolya Horváth
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Mathilakath M Vijayan
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada; Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Phillip L Hooper
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Medical School, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| | - László Vigh
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary.
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Dhar R, Sägesser R, Weikert C, Wagner A. Yeast Adapts to a Changing Stressful Environment by Evolving Cross-Protection and Anticipatory Gene Regulation. Mol Biol Evol 2012; 30:573-88. [DOI: 10.1093/molbev/mss253] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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15
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Çakar ZP, Turanlı-Yıldız B, Alkım C, Yılmaz Ü. Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties. FEMS Yeast Res 2011; 12:171-82. [DOI: 10.1111/j.1567-1364.2011.00775.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/21/2011] [Accepted: 11/21/2011] [Indexed: 12/25/2022] Open
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Experimental methods and modeling techniques for description of cell population heterogeneity. Biotechnol Adv 2011; 29:575-99. [DOI: 10.1016/j.biotechadv.2011.03.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/04/2011] [Accepted: 03/31/2011] [Indexed: 11/24/2022]
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Zakrzewska A, van Eikenhorst G, Burggraaff JEC, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ. Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Mol Biol Cell 2011; 22:4435-46. [PMID: 21965291 PMCID: PMC3216668 DOI: 10.1091/mbc.e10-08-0721] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A genome-wide analysis of the acquisition of stress cross-tolerance shows that reduction of growth rate is an important determinant of severe stress survival. Cellular functions important for the coupling of growth rate to stress resistance are identified, as are those required for cross-tolerance acquisition independent of growth rate reduction. All organisms have evolved to cope with changes in environmental conditions, ensuring the optimal combination of proliferation and survival. In yeast, exposure to a mild stress leads to an increased tolerance for other stresses. This suggests that yeast uses information from the environment to prepare for future threats. We used the yeast knockout collection to systematically investigate the genes and functions involved in severe stress survival and in the acquisition of stress (cross-) tolerance. Besides genes and functions relevant for survival of heat, acid, and oxidative stress, we found an inverse correlation between mutant growth rate and stress survival. Using chemostat cultures, we confirmed that growth rate governs stress tolerance, with higher growth efficiency at low growth rates liberating the energy for these investments. Cellular functions required for stress tolerance acquisition, independent of the reduction in growth rate, were involved in vesicular transport, the Rpd3 histone deacetylase complex, and the mitotic cell cycle. Stress resistance and acquired stress tolerance in Saccharomyces cerevisiae are governed by a combination of stress-specific and general processes. The reduction of growth rate, irrespective of the cause of this reduction, leads to redistribution of resources toward stress tolerance functions, thus preparing the cells for impending change.
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Affiliation(s)
- Anna Zakrzewska
- Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, Netherlands
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Single-cell analysis of S. cerevisiae growth recovery after a sublethal heat-stress applied during an alcoholic fermentation. J Ind Microbiol Biotechnol 2010; 38:687-96. [DOI: 10.1007/s10295-010-0814-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 08/10/2010] [Indexed: 10/19/2022]
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19
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Díaz M, Herrero M, García LA, Quirós C. Application of flow cytometry to industrial microbial bioprocesses. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2009.07.013] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Smigic N, Rajkovic A, Nielsen DS, Arneborg N, Siegumfeldt H, Devlieghere F. Survival of lactic acid and chlorine dioxide treated Campylobacter jejuni under suboptimal conditions of pH, temperature and modified atmosphere. Int J Food Microbiol 2010; 141 Suppl 1:S140-6. [PMID: 20149937 DOI: 10.1016/j.ijfoodmicro.2010.01.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 01/18/2010] [Accepted: 01/19/2010] [Indexed: 11/29/2022]
Abstract
As mild decontamination treatments are gaining more and more interest due to increased consumer demands for fresh foods, it is of great importance to establish the influence of decontamination treatments on the subsequent bacterial behaviour under suboptimal storage conditions. For this purpose Campylobacter jejuni cells treated with lactic acid (LA, 3% lactic acid, pH 4.0, 2 min) or chlorine dioxide (ClO(2), 20 ppm, 2 min) were inoculated in Bolton broth (pH 6.0) and incubated under 80% O(2)/20% N(2), 80% CO(2)/20% N(2), air or micro-aerophilic (10% CO(2)/85% N(2)/5% O(2)) atmosphere, at 4 degrees C during 7 days. Treatment with water served as a control. The most suppressive atmosphere for the survival of C. jejuni was O(2)-rich atmosphere, followed by air, micro-aerophilic and CO(2)-rich atmosphere. The survival of C. jejuni was dependent on the type of initial decontamination treatment, with water treated cells showing the greatest survival followed by LA and ClO(2) treated cells. Intracellular pH (pH(i)) of individual C. jejuni cells was determined using Fluorescence Ratio Imaging Microscopy (FRIM). At all tested conditions, different subpopulation of the cells could be distinguished based on their pH(i) values. The pH(i) response was independent on the surrounding atmosphere since similar distribution of the subpopulations was observed for all tested atmospheres. However, the pH(i) response was dependent on the initial decontamination treatment. The investigation of intracellular parameters gave an insight into pathogen behaviour under stressful conditions at intracellular level. The results obtained in this study highlighted the importance of combining decontamination technologies with subsequent preservation techniques to the control survival and growth of foodborne pathogens.
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Affiliation(s)
- Nada Smigic
- Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Food2Know, Ghent, Belgium
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Van Derlinden E, Bernaerts K, Van Impe J. UnravellingEscherichia colidynamics close to the maximum growth temperature through heterogeneous modelling. Lett Appl Microbiol 2009; 49:659-65. [DOI: 10.1111/j.1472-765x.2009.02688.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Minois N, Lagona F, Frajnt M, Vaupel JW. Plasticity of death rates in stationary phase in Saccharomyces cerevisiae. Aging Cell 2009; 8:36-44. [PMID: 19053971 DOI: 10.1111/j.1474-9726.2008.00446.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
For the species that have been most carefully studied, mortality rises with age and then plateaus or declines at advanced ages, except for yeast. Remarkably, mortality for yeast can rise, fall and rise again. In the present study we investigated (i) if this complicated shape could be modulated by environmental conditions by measuring mortality with different food media and temperature; (ii) if it is triggered by biological heterogeneity by measuring mortality in stationary phase in populations fractionated into subpopulations of young, virgin cells, and replicatively older, non-virgin cells. We also discussed the results of a staining method to measure viability instead of measuring the number of cells able to exit stationary phase and form a colony. We showed that different shapes of age-specific death rates were observed and that their appearance depended on the environmental conditions. Furthermore, biological heterogeneity explained the shapes of mortality with homogeneous populations of young, virgin cells exhibiting a simple shape of mortality in conditions under which more heterogeneous populations of older cells or unfractionated populations displayed complicated death rates. Finally, the staining method suggested that cells lost the capacity to exit stationary phase and to divide long before they died in stationary phase. These results explain a phenomenon that was puzzling because it appeared to reflect a radical departure from mortality patterns observed for other species.
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Affiliation(s)
- Nadège Minois
- Max Planck Institute for Demographic Research, Rostock, Germany.
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Choi JK, Hwang S, Kim YJ. Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes. PLoS One 2008; 3:e3002. [PMID: 18714342 PMCID: PMC2500160 DOI: 10.1371/journal.pone.0003002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/29/2008] [Indexed: 01/23/2023] Open
Abstract
Phenotypic diversity and fidelity can be balanced by controlling stochastic molecular mechanisms. Epigenetic silencing is one that has a critical role in stress response. Here we show that in yeast, incomplete silencing increases stochastic noise in gene expression, probably owing to unstable chromatin structure. Telomere position effect is suggested as one mechanism. Expression diversity in a population achieved in this way may render a subset of cells to readily respond to various acute stresses. By contrast, strong silencing tends to suppress noisy expression of genes, in particular those involved in life cycle control. In this regime, chromatin may act as a noise filter for precisely regulated responses to environmental signals that induce huge phenotypic changes such as a cell fate transition. These results propose modulation of chromatin stability as an important determinant of environmental adaptation and cellular differentiation.
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Affiliation(s)
- Jung Kyoon Choi
- Department of Biochemistry, Yonsei University, Seoul, Republic of Korea
| | - Sohyun Hwang
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Young-Joon Kim
- Department of Biochemistry, Yonsei University, Seoul, Republic of Korea
- * E-mail:
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Pujol N, Cypowyj S, Ziegler K, Millet A, Astrain A, Goncharov A, Jin Y, Chisholm AD, Ewbank JJ. Distinct innate immune responses to infection and wounding in the C. elegans epidermis. Curr Biol 2008; 18:481-9. [PMID: 18394898 PMCID: PMC2394561 DOI: 10.1016/j.cub.2008.02.079] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 02/21/2008] [Accepted: 02/22/2008] [Indexed: 11/29/2022]
Abstract
BACKGROUND In many animals, the epidermis is in permanent contact with the environment and represents a first line of defense against pathogens and injury. Infection of the nematode Caenorhabditis elegans by the natural fungal pathogen Drechmeria coniospora induces the expression in the epidermis of antimicrobial peptide (AMP) genes such as nlp-29. Here, we tested the hypothesis that injury might also alter AMP gene expression and sought to characterize the mechanisms that regulate the innate immune response. RESULTS Injury induces a wound-healing response in C. elegans that includes induction of nlp-29 in the epidermis. We find that a conserved p38-MAP kinase cascade is required in the epidermis for the response to both infection and wounding. Through a forward genetic screen, we isolated mutants that failed to induce nlp-29 expression after D. coniospora infection. We identify a kinase, NIPI-3, related to human Tribbles homolog 1, that is likely to act upstream of the MAPKK SEK-1. We find NIPI-3 is required only for nlp-29 induction after infection and not after wounding. CONCLUSIONS Our results show that the C. elegans epidermis actively responds to wounding and infection via distinct pathways that converge on a conserved signaling cassette that controls the expression of the AMP gene nlp-29. A comparison between these results and MAP kinase signaling in yeast gives insights into the possible origin and evolution of innate immunity.
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Affiliation(s)
- Nathalie Pujol
- Centre d'Immunologie de Marseille-Luminy, Université de la Méditerranée, Case 906, 13288 Marseille cedex 9, France
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Ryley J, Pereira-Smith OM. Microfluidics device for single cell gene expression analysis in Saccharomyces cerevisiae. Yeast 2007; 23:1065-73. [PMID: 17083143 DOI: 10.1002/yea.1412] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We have measured single-cell gene expression over time using a microfluidics-based flow cell which physically traps individual yeast using microm-sized structures (yeast jails). Our goal was to determine variability of gene expression within a cell over time, as well as variability between individual cells. In our flow cell system, yeast jails are fabricated out of PDMS and gene expression is visualized using fluorescently-tagged proteins of interest. Previously, single-cell yeast work has been done using micromanipulation on agar, or FACS. In the present device agar is eliminated, resulting in a superior optical system. The flow of media through the flow cell washes daughter cells away, eliminating the need for micromanipulation. Unlike FACS, the described device can track individual yeast over a time course of many hours. The flow cells are compatible with the needs of quantitative fluorescence microscopy, and allow simultaneous measurements to be done on a large number of individual yeast. We used these flow cells to determine the expression of HSP104-GFPand RAS2-YFP, genes known to affect yeast life span. The results demonstrate inter-cell variation in expression of both genes that could not have been detected without this single-cell analysis.
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Affiliation(s)
- James Ryley
- University of Texas Health Science Center at San Antonio, Sam and Ann Barshop Institute for Longevity and Ageing Studies, Department of Cellular and Structural Biology, San Antonio, TX 78245-3207, USA.
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Herrero M, Quirós C, García LA, Díaz M. Use of flow cytometry to follow the physiological states of microorganisms in cider fermentation processes. Appl Environ Microbiol 2006; 72:6725-33. [PMID: 17021224 PMCID: PMC1610271 DOI: 10.1128/aem.01183-06] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The flow cytometry (FC) technique used with certain fluorescent dyes (ChemChrome V6 [CV6], DRAQ5, and PI) has proven useful to label and to detect different physiological states of yeast and malolactic bacterium starters conducting cider fermentation over time (by performing sequential inoculation of microorganisms). First, the technique was tested with pure cultures of both types of microorganisms grown in synthetic media under different induced stress conditions. Metabolically active cells detected by FC and by the standard plate-counting method for both types of microorganisms in fresh overnight pure cultures gave good correlations between the two techniques in samples taken at this stage. Otherwise, combining the results obtained by FC and plating during alcoholic and malolactic fermentation over time in the cider-making process, different subpopulations were detected, showing significant differences between the methods. A small number of studies have applied the FC technique to analyze fermentation processes and mixed cultures over time. The results were used to postulate equations explaining the different physiological states in cell populations taken from fresh, pure overnight cultures under nonstress conditions or cells subjected to stress conditions over time, either under a pure-culture fermentation process (in this work, corresponding to alcoholic fermentation) or under mixed-fermentation conditions (for the malolactic-fermentation phase), that could be useful to improve the control of the processes.
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Affiliation(s)
- Mónica Herrero
- Department of Chemical Engineering and Environmental Technology, University of Oviedo, Oviedo, Spain
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Abstract
Single cells in genetically homogeneous microbial cultures exhibit marked phenotypic individuality, a biological phenomenon that is considered to bolster the fitness of populations. Major phenotypes that are characterized by heterogeneity span the breadth of microbiology, in fields ranging from pathogenicity to ecology. The cell cycle, cell ageing and epigenetic regulation are proven drivers of heterogeneity in several of the best-known phenotypic examples. However, the full contribution of factors such as stochastic gene expression is yet to be realized.
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Affiliation(s)
- Simon V Avery
- School of Biology, Institute of Genetics, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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Hornbaek T, Brockhoff PB, Siegumfeldt H, Budde BB. Two subpopulations of Listeria monocytogenes occur at subinhibitory concentrations of leucocin 4010 and nisin. Appl Environ Microbiol 2006; 72:1631-8. [PMID: 16461719 PMCID: PMC1392907 DOI: 10.1128/aem.72.2.1631-1638.2006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 11/29/2005] [Indexed: 11/20/2022] Open
Abstract
In situ analyses of single Listeria monocytogenes cells at subinhibitory concentrations of leucocin 4010 and nisin revealed two subpopulations when measured by fluorescence ratio imaging microscopy (FRIM) after staining with 5(6)-carboxyfluorescein diacetate succinimidyl ester. One subpopulation consisted of cells with a dissipated pH gradient (DeltapH), and the other consisted of cells that maintained DeltapH. The proportion of cells belonging to each subpopulation was estimated, and the concentrations of bacteriocins required to dissipate DeltapH for 90% of the cell population (ED90) was predicted. ED90 increased after the addition of sodium chloride (1 to 3% [wt/vol]) to the bacteriocin solutions, while ED90 decreased by the addition of sodium nitrite (60 and 100 ppm). Other meat additives, including sodium phosphate, sodium lactate, sodium citrate, and sodium acetate slightly increased ED90. The inhibitory effect of sodium chloride on the antilisterial activity of leucocin 4010 and nisin was confirmed on the surfaces of meat sausages. This study highlights the important practical implications of applying subinhibitory concentrations of bacteriocins, which results in unaffected target cells. In situ analyses by FRIM in combination with modeling of single-cell data can be applied to ensure that sufficient concentrations of bacteriocins are used in food preservation.
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Affiliation(s)
- Tina Hornbaek
- Department of Food Science, The Royal Veterinary and Agricultural University, Frederiksberg, Denmark
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29
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Avery SV. Cell individuality: the bistability of competence development. Trends Microbiol 2005; 13:459-62. [PMID: 16112577 DOI: 10.1016/j.tim.2005.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 07/18/2005] [Accepted: 08/10/2005] [Indexed: 11/29/2022]
Abstract
Heterogeneous development of competence among cells of the bacterium Bacillus subtilis provides an appealing model of cell individuality, an area that is currently attracting considerable research interest. Under appropriate conditions, only a fraction of cells in an isogenic culture become competent for transformation. Two experimental studies have now pinpointed the same auto-stimulatory feedback loop of gene expression as the principal requirement for the establishment of this 'bistable' response.
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Affiliation(s)
- Simon V Avery
- School of Biology, Institute of Genetics, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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Drakulic T, Temple MD, Guido R, Jarolim S, Breitenbach M, Attfield PV, Dawes IW. Involvement of oxidative stress response genes in redox homeostasis, the level of reactive oxygen species, and ageing in Saccharomyces cerevisiae. FEMS Yeast Res 2005; 5:1215-28. [PMID: 16087409 DOI: 10.1016/j.femsyr.2005.06.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 06/02/2005] [Accepted: 06/03/2005] [Indexed: 10/25/2022] Open
Abstract
Saccharomyces cerevisiae mutants lacking oxidative stress response genes were used to investigate which genes are required under normal aerobic conditions to maintain cellular redox homeostasis, using intracellular glutathione redox potential (glutathione E(h)) to indicate the redox environment of the cells. Levels of reactive oxygen species (ROS) and mitochondrial membrane potentials (MMP) were also assessed by FACS using dihydroethidium and rhodamine 123 as fluorescent probes. Cells became more oxidised as strains shifted from exponential growth to stationary phase. During both phases the presence of reduced thioredoxin and the activity of glutathione reductase were important for redox homeostasis. Thioredoxin reductase contributed less during exponential phase when there was a strong requirement for active Yap1p transcription factor, but was critical during stationary phase. The absence of ROS detoxification systems, such as catalases or superoxide dismutases, had a lesser effect on glutathione E(h), but a more pronounced effect on ROS levels and MMP. These results reflect the major shift in ROS generation as cells switch from fermentative to respiratory metabolism and also showed that there was not a strong correlation between ROS production, MMP and cellular redox environment. Heterogeneity was detected in populations of strains with compromised anti-oxidant defences, and as cells aged they shifted from one cell type with low ROS content to another with much higher intracellular ROS.
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Affiliation(s)
- Tamara Drakulic
- Ramaciotti Centre for Gene Function Analysis and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, Australia
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Abstract
The fungal spoilage of ingredients of food manufacture is an economic problem, often causes product loss and may constitute a health hazard. To effectively combat fungal food spoilage, a mechanistic understanding of tolerance for, and adaptation to, the preservation method used is crucial. Both are dependent on the genetic make-up and growth history of the organism. In the post-genomic era we are arriving at a situation in which, in the model organism Saccharomyces cerevisiae, physiological data, classical molecular biology and whole-genome responses can be combined to obtain explanatory and predictive models for growth. For food spoilage fungi we have not yet reached such a level of understanding, but we may use the knowledge gained for S. cerevisiae for the prevention of spoilage.
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Affiliation(s)
- Gertien J Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands
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Chapter 10 Non-affinity sensing technology: the exploitation of biocatalytic events for environmental analysis. BIOSENSORS AND MODERN BIOSPECIFIC ANALYTICAL TECHNIQUES 2005. [DOI: 10.1016/s0166-526x(05)44010-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kuang Y, Biran I, Walt DR. Simultaneously Monitoring Gene Expression Kinetics and Genetic Noise in Single Cells by Optical Well Arrays. Anal Chem 2004; 76:6282-6. [PMID: 15516119 DOI: 10.1021/ac049053f] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An optical fiber based well array platform was used for simultaneous, dynamic gene expression monitoring from hundreds of individual live Escherichia coli cells carrying promoter-fluorescent reporter gene fusions. High information content about gene expression kinetics and cell-to-cell gene expression variability can be collected from a single experiment. These data are invaluable for investigating gene regulation and gene networks as well as for systems biology applications.
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Affiliation(s)
- Yina Kuang
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, USA
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Brehm-Stecher BF, Johnson EA. Single-cell microbiology: tools, technologies, and applications. Microbiol Mol Biol Rev 2004; 68:538-59, table of contents. [PMID: 15353569 PMCID: PMC515252 DOI: 10.1128/mmbr.68.3.538-559.2004] [Citation(s) in RCA: 297] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The field of microbiology has traditionally been concerned with and focused on studies at the population level. Information on how cells respond to their environment, interact with each other, or undergo complex processes such as cellular differentiation or gene expression has been obtained mostly by inference from population-level data. Individual microorganisms, even those in supposedly "clonal" populations, may differ widely from each other in terms of their genetic composition, physiology, biochemistry, or behavior. This genetic and phenotypic heterogeneity has important practical consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. New appreciation of the importance of cellular heterogeneity, coupled with recent advances in technology, has driven the development of new tools and techniques for the study of individual microbial cells. Because observations made at the single-cell level are not subject to the "averaging" effects characteristic of bulk-phase, population-level methods, they offer the unique capacity to observe discrete microbiological phenomena unavailable using traditional approaches. As a result, scientists have been able to characterize microorganisms, their activities, and their interactions at unprecedented levels of detail.
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Affiliation(s)
- Byron F Brehm-Stecher
- Department of Food Microbiology and Toxicology, University of Wisconsin-Madison Food Research Institute, 1925 Willow Drive, Madison, WI 53706, USA
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Abstract
A biosensor composed of a high-density living bacterial cell array was fabricated by inserting bacteria into a microwell array formed on one end of an imaging fiber bundle. The size of each microwell allows only one cell to occupy each well. In this biosensor, E. coli cells carrying a recA::gfp fusion were used as sensing components for genotoxin detection. Each fiber in the array has its own light pathway, enabling thousands of individual cell responses to be monitored simultaneously with both spatial and temporal resolution. The biosensor was capable of performing cell-based functional sensing of a genotoxin with high sensitivity and short incubation times (1 ng/mL mitomycin C after 90 min). Dose-response curves for several genotoxins were obtained. The biosensors demonstrated an active sensing lifetime of more than 6 h and a shelf lifetime of two weeks.
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Affiliation(s)
- Yina Kuang
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, USA
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Desmyter L, Dewaele S, Reekmans R, Nystrom T, Contreras R, Chen C. Expression of the human ferritin light chain in a frataxin mutant yeast affects ageing and cell death. Exp Gerontol 2004; 39:707-15. [PMID: 15130665 DOI: 10.1016/j.exger.2004.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Revised: 10/31/2003] [Accepted: 01/22/2004] [Indexed: 10/26/2022]
Abstract
Ferritin is one of the major eukaryotic proteins involved in regulating iron metabolism and maintaining iron homeostasis. However, Saccaromyces cerevisiae is an exception, possessing no ferritin and using other means to store excess iron. The only potential iron storage protein identified in yeast so far is the homologue of human frataxin (YFH1p). In this study, we found that dysfunction of yeast frataxin shortens mean lifespan by 49% compared to the WT control. Interestingly, the human ferritin L gene can, at least partially, complement the function of yeast frataxin, extending lifespan and protecting cells from death induced by oxidative stress or excess iron. Our findings indicate that ferritin L can perform functions in yeast that are similar to its functions in mammals, and suggest that common mechanisms may exist for preventing iron and oxidative damage in single- and multi-cellular eukaryotic organisms. Clearly, elucidation of the function of human ferritin in yeast would help in gaining a better understanding the molecular basis of iron storage diseases.
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Affiliation(s)
- Liesbeth Desmyter
- Fundamental and Applied Molecular Biology, Ghent University and Flanders Interuniversity Institute for Biotechnology, VIB Technologiepark 927 B-9052, Ghent Zwijnaarde, Belgium
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Chen C, Dewaele S, Braeckman B, Desmyter L, Verstraelen J, Borgonie G, Vanfleteren J, Contreras R. A high-throughput screening system for genes extending life-span. Exp Gerontol 2004; 38:1051-63. [PMID: 14580858 DOI: 10.1016/s0531-5565(03)00186-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We developed a high-throughput functional genomic screening system that allows identification of genes prolonging life-span in the baker's yeast Saccharomyces cerevisiae. The method is based on isolating yeast mother cells with extended number of cell divisions as indicated by the increased number of bud scars on their surface. Fluorescently labelled Wheat Germ Agglutinin was used for specific staining of chitin, a major component of bud scars. Screening of a human HepG2 cDNA expression library in yeast resulted in the isolation of 12 yeast transformants with a potentially prolonged life-span. The transgene in one of the lines was identified as ferritin light chain (FTL) and studied in more detail. Yeast cells containing FTL showed an enhanced iron and H(2)O(2) resistance, a reduced cell death rate and an increased number of cell divisions. Overexpression of FTL in the nematode Caenorhabditis elegans resulted in a life-span increase of 8% confirming our yeast observations in a multicellular organism. Our data demonstrate that this method permits a fast screening of libraries for hunting genes involved in ageing processes.
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Affiliation(s)
- Cuiying Chen
- Fundamental and Applied Molecular Biology, Ghent University and Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9000, Ghent, Belgium
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38
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Sumner ER, Avery AM, Houghton JE, Robins RA, Avery SV. Cell cycle- and age-dependent activation of Sod1p drives the formation of stress resistant cell subpopulations within clonal yeast cultures. Mol Microbiol 2004; 50:857-70. [PMID: 14617147 DOI: 10.1046/j.1365-2958.2003.03715.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phenotypic heterogeneity describes non-genetic variation that exists between individual cells within isogenic populations. The basis for such heterogeneity is not well understood, but it is evident in a wide range of cellular functions and phenotypes and may be fundamental to the fitness of microorganisms. Here we use a suite of novel assays applied to yeast, to provide an explanation for the classic example of heterogeneous resistance to stress (copper). Cell cycle stage and replicative cell age, but not mitochondrial content, were found to be principal parameters underpinning differential Cu resistance: cell cycle-synchronized cells had relatively uniform Cu resistances, and replicative cell-age profiles differed markedly in sorted Cu-resistant and Cu-sensitive subpopulations. From a range of potential Cu-sensitive mutants, cup1Delta cells lacking Cu-metallothionein, and particularly sod1Delta cells lacking Cu, Zn-superoxide dismutase, exhibited diminished heterogeneity. Furthermore, age-dependent Cu resistance was largely abolished in cup1Delta and sod1Delta cells, whereas cell cycle-dependent Cu resistance was suppressed in sod1Delta cells. Sod1p activity oscillated approximately fivefold during the cell cycle, with peak activity coinciding with peak Cu-resistance. Thus, phenotypic heterogeneity in copper resistance is not stochastic but is driven by the progression of individual cells through the cell cycle and ageing, and is primarily dependent on only Sod1p, out of several gene products that can influence the averaged phenotype. We propose that such heterogeneity provides an important insurance mechanism for organisms; creating subpopulations that are pre-equipped for varied activities as needs may arise (e.g. when faced with stress), but without the permanent metabolic costs of constitutive expression.
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Affiliation(s)
- Edward R Sumner
- School of Biology, University of Nottingham, University Park, Nottingham, UK
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Jacquet M, Renault G, Lallet S, De Mey J, Goldbeter A. Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae. J Cell Biol 2003; 161:497-505. [PMID: 12732613 PMCID: PMC2172953 DOI: 10.1083/jcb.200303030] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Msn2 and Msn4 are two related transcriptional activators that mediate a general response to stress in yeast Saccharomyces cerevisiae by eliciting the expression of specific sets of genes. In response to stress or nutritional limitation, Msn2 and Msn4 migrate from the cytoplasm to the nucleus. Using GFP-tagged constructs and high-resolution time-lapse video microscopy on single cells, we show that light emitted by the microscope also triggers this migration. Unexpectedly, the population of Msn2 or Msn4 molecules shuttles repetitively into and out of the nucleus with a periodicity of a few minutes. A large heterogeneity in the oscillatory response to stress is observed between individual cells. This periodic behavior, which can be induced by various types of stress, at intermediate stress levels, is not dependent upon protein synthesis and persists when the DNA-binding domain of Msn2 is removed. The cAMP-PKA pathway controls the sensitivity of the oscillatory nucleocytoplasmic shuttling. In the absence of PKA, Msn4 continues to oscillate while Msn2 is maintained in the nucleus. We show that a computational model based on the possibility that Msn2 and Msn4 participate in autoregulatory loops controlling their subcellular localization can account for the oscillatory behavior of the two transcription factors.
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Affiliation(s)
- Michel Jacquet
- Laboratoire Information Génétique et Développement, Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique (CNRS)/UPS UMR 8621, Université Paris-Sud, Orsay, France.
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40
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Abstract
A live cell array biosensor was fabricated by immobilizing bacterial cells on the face of an optical imaging fiber containing a high-density array of microwells. Each microwell accommodates a single bacterium that was genetically engineered to respond to a specific analyte. A genetically modified Escherichia coli strain, containing the lacZ reporter gene fused to the heavy metal-responsive gene promoter zntA, was used to fabricate a mercury biosensor. A plasmid carrying the gene coding for the enhanced cyan fluorescent protein (ECFP) was also introduced into this sensing strain to identify the cell locations in the array. Single cell lacZ expression was measured when the array was exposed to mercury and a response to 100nM Hg(2+) could be detected after a 1-h incubation time. The optical imaging fiber-based single bacterial cell array is a flexible and sensitive biosensor platform that can be used to monitor the expression of different reporter genes and accommodate a variety of sensing strains.
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Affiliation(s)
- Israel Biran
- The Max Tishler Laboratory for Organic Chemistry, Department of Chemistry, Tufts University, Medford, MA 02155, USA
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41
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Brul S, Coote P, Oomes S, Mensonides F, Hellingwerf K, Klis F. Physiological actions of preservative agents: prospective of use of modern microbiological techniques in assessing microbial behaviour in food preservation. Int J Food Microbiol 2002; 79:55-64. [PMID: 12382685 DOI: 10.1016/s0168-1605(02)00179-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this mini-review, various aspects of homeostasis of microbial cells and its perturbation by antimicrobial agents will be discussed. First, outlining the position that the physiological studies on microbial behaviour using the modern molecular tools should have in food science sets the scene for the studies. Subsequently, the advent of functional genomics is discussed that allows full coverage of cellular reactions at unprecedented levels. Examples of weak organic acid resistance, the stress response against natural antimicrobial agents and responses against physicochemical factors show how we can now "open the black box" that microbes are, look inside and begin to understand how different cellular signalling cables are wired together. Using the analogy with machines, it will be indicated how the use of various signalling systems depends on the availability of substrates "fuel" to let the systems act in the context of the minimum energetic requirement cells have to let their housekeeping systems run. The outlook illustrates how new insights might be used to device knowledge-based rather than empirical combinations of preservation systems and how risk assessment models might be deviced that link the mechanistic insight to risk distributions of events in food manufacturing.
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Affiliation(s)
- Stanley Brul
- Department of Microbiology, University of Amsterdam, Netherlands.
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Brul S, Klis F, Oomes S, Montijn R, Schuren F, Coote P, Hellingwerf K. Detailed process design based on genomics of survivors of food preservation processes. Trends Food Sci Technol 2002. [DOI: 10.1016/s0924-2244(02)00161-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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43
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Sumner ER, Avery SV. Phenotypic heterogeneity: differential stress resistance among individual cells of the yeast Saccharomyces cerevisiae. MICROBIOLOGY (READING, ENGLAND) 2002; 148:345-351. [PMID: 11832498 DOI: 10.1099/00221287-148-2-345] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Edward R Sumner
- School of Life and Environmental Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK1
| | - Simon V Avery
- School of Life and Environmental Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK1
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44
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Current awareness on yeast. Yeast 2001; 18:1357-64. [PMID: 11571760 DOI: 10.1002/yea.690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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