1
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Lanz MC, Zhang S, Swaffer MP, Ziv I, Götz LH, Kim J, McCarthy F, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. Nat Struct Mol Biol 2024:10.1038/s41594-024-01353-z. [PMID: 39048803 DOI: 10.1038/s41594-024-01353-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. In the present study, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that the ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in a manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.
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Affiliation(s)
- Michael C Lanz
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA.
| | - Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | | | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Frank McCarthy
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Joshua E Elias
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub San Francisco, Stanford University, Stanford, CA, USA.
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2
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Ren H, Lan Q, Zhou S, Lyu Y, Yu Y, Zhou J, Mo W, Lu H. Coupling thermotolerance and high production of recombinant protein by CYR1 N1546K mutation via cAMP signaling cascades. Commun Biol 2024; 7:627. [PMID: 38789513 PMCID: PMC11126729 DOI: 10.1038/s42003-024-06341-z] [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: 11/23/2023] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
In recombinant protein-producing yeast strains, cells experience high production-related stresses similar to high temperatures. It is possible to increase recombinant protein production by enhancing thermotolerance, but few studies have focused on this topic. Here we aim to identify cellular regulators that can simultaneously activate thermotolerance and high yield of recombinant protein. Through screening at 46 °C, a heat-resistant Kluyveromyces marxianus (K. marxianus) strain FDHY23 is isolated. It also exhibits enhanced recombinant protein productivity at both 30 °C and high temperatures. The CYR1N1546K mutation is identified as responsible for FDHY23's improved phenotype, characterized by weakened adenylate cyclase activity and reduced cAMP production. Introducing this mutation into the wild-type strain greatly enhances both thermotolerance and recombinant protein yields. RNA-seq analysis reveals that under high temperature and recombinant protein production conditions, CYR1 mutation-induced reduction in cAMP levels can stimulate cells to improve its energy supply system and optimize material synthesis, meanwhile enhance stress resistance, based on the altered cAMP signaling cascades. Our study provides CYR1 mutation as a novel target to overcome the bottleneck in achieving high production of recombinant proteins under high temperature conditions, and also offers a convenient approach for high-throughput screening of recombinant proteins with high yields.
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Affiliation(s)
- Haiyan Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Qing Lan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Shihao Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Yilin Lyu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Wenjuan Mo
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
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3
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Fay JC, Alonso-del-Real J, Miller JH, Querol A. Divergence in the Saccharomyces Species' Heat Shock Response Is Indicative of Their Thermal Tolerance. Genome Biol Evol 2023; 15:evad207. [PMID: 37972247 PMCID: PMC10683043 DOI: 10.1093/gbe/evad207] [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: 07/12/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
The Saccharomyces species have diverged in their thermal growth profile. Both Saccharomyces cerevisiae and Saccharomyces paradoxus grow at temperatures well above the maximum growth temperature of Saccharomyces kudriavzevii and Saccharomyces uvarum but grow more poorly at lower temperatures. In response to thermal shifts, organisms activate a stress response that includes heat shock proteins involved in protein homeostasis and acquisition of thermal tolerance. To determine whether Saccharomyces species have diverged in their response to temperature, we measured changes in gene expression in response to a 12 °C increase or decrease in temperature for four Saccharomyces species and their six pairwise hybrids. To ensure coverage of subtelomeric gene families, we sequenced, assembled, and annotated a complete S. uvarum genome. In response to heat, the cryophilic species showed a stronger stress response than the thermophilic species, and the hybrids showed a mixture of parental responses that depended on the time point. After an initial strong response indicative of high thermal stress, hybrids with a thermophilic parent resolved their heat shock response to become similar to their thermophilic parent. Within the hybrids, only a small number of temperature-responsive genes showed consistent differences between alleles from the thermophilic and cryophilic species. Our results show that divergence in the heat shock response is mainly a consequence of a strain's thermal tolerance, suggesting that cellular factors that signal heat stress or resolve heat-induced changes are relevant to thermal divergence in the Saccharomyces species.
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Affiliation(s)
- Justin C Fay
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Javier Alonso-del-Real
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - James H Miller
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Amparo Querol
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
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4
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Harvey HJ, Hendry AC, Chirico M, Archer DB, Avery SV. Adaptation to sorbic acid in low sugar promotes resistance of yeast to the preservative. Heliyon 2023; 9:e22057. [PMID: 38034742 PMCID: PMC10682675 DOI: 10.1016/j.heliyon.2023.e22057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023] Open
Abstract
The weak acid sorbic acid is a common preservative used in soft drink beverages to control microbial spoilage. Consumers and industry are increasingly transitioning to low-sugar food formulations, but potential impacts of reduced sugar on sorbic acid efficacy are barely characterised. In this study, we report enhanced sorbic acid resistance of yeast in low-glucose conditions. We had anticipated that low glucose would induce respiratory metabolism, which was shown previously to be targeted by sorbic acid. However, a shift from respiratory to fermentative metabolism upon sorbic acid exposure of Saccharomyces cerevisiae was correlated with relative resistance to sorbic acid in low glucose. Fermentation-negative yeast species did not show the low-glucose resistance phenotype. Phenotypes observed for certain yeast deletion strains suggested roles for glucose signalling and repression pathways in the sorbic acid resistance at low glucose. This low-glucose induced sorbic acid resistance was reversed by supplementing yeast cultures with succinic acid, a metabolic intermediate of respiratory metabolism (and a food-safe additive) that promoted respiration. The results indicate that metabolic adaptation of yeast can promote sorbic acid resistance at low glucose, a consideration for the preservation of foodstuffs as both food producers and consumers move towards a reduced sugar landscape.
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Affiliation(s)
- Harry J. Harvey
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alex C. Hendry
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marcella Chirico
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - David B. Archer
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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5
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Lanz MC, Zhang S, Swaffer MP, Hernández Götz L, McCarty F, Ziv I, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562558. [PMID: 37905015 PMCID: PMC10614910 DOI: 10.1101/2023.10.16.562558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how size influences cell physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be biochemically different. Here, we corroborate these results in mouse hepatocytes and extend our analysis using yeast. We find that size-dependent proteome changes are highly conserved and mostly independent of metabolic state. As eukaryotic cells grow larger, the dilution of the genome elicits a starvation-like proteome phenotype, suggesting that growth in large cells is limited by the genome in a manner analogous to a limiting nutrient. We also demonstrate that the proteomes of replicatively-aged yeast are primarily determined by their large size. Overall, our data suggest that genome concentration is a universal determinant of proteome content in growing cells.
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6
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Wagner ER, Gasch AP. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 2023; 9:786. [PMID: 37623557 PMCID: PMC10455348 DOI: 10.3390/jof9080786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
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Affiliation(s)
- Ellen R. Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Fay JC, Alonso-Del-Real J, Miller JH, Querol A. Divergence in the Saccharomyces species' heat shock response is indicative of their thermal tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547718. [PMID: 37461527 PMCID: PMC10349932 DOI: 10.1101/2023.07.04.547718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The Saccharomyces species have diverged in their thermal growth profile. Both S. cerevisiae and S. paradoxus grow at temperatures well above the maximum growth temperature of S. kudriavzevii and S. uvarum, but grow more poorly at lower temperatures. In response to thermal shifts, organisms activate a stress response that includes heat shock proteins involved in protein homeostasis and acquisition of thermal tolerance. To determine whether Saccharomyces species have diverged in their response to temperature we measured changes in gene expression in response to a 12°C increase or decrease in temperature for four Saccharomyces species and their six pairwise hybrids. To ensure coverage of subtelomeric gene families we sequenced, assembled and annotated a complete S. uvarum genome. All the strains exhibited a stronger response to heat than cold treatment. In response to heat, the cryophilic species showed a stronger response than the thermophilic species. The hybrids showed a mixture of parental stress responses depending on the time point. After the initial response, hybrids with a thermophilic parent were more similar to S. cerevisiae and S. paradoxus, and the S. cerevisiae × S. paradoxus hybrid showed the weakest heat shock response. Within the hybrids a small subset of temperature responsive genes showed species specific responses but most were also hybrid specific. Our results show that divergence in the heat shock response is indicative of a strain's thermal tolerance, suggesting that cellular factors that signal heat stress or resolve heat induced changes are relevant to thermal divergence in the Saccharomyces species.
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Affiliation(s)
- Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Javier Alonso-Del-Real
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Valencia, Spain
- Present position: Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - James H Miller
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Amparo Querol
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Valencia, Spain
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8
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Lertsriwong S, Boonvitthya N, Glinwong C. Schwanniomyces etchellsii, acid-thermotolerant yeasts from urban city soil. World J Microbiol Biotechnol 2023; 39:159. [PMID: 37067620 DOI: 10.1007/s11274-023-03602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/02/2023] [Indexed: 04/18/2023]
Abstract
Acid-tolerant yeasts are one of the important keys to producing ethanol from acidic substrates, especially from molasses and agricultural waste. In this study, selected cultivars of yeasts isolated from a variety of locations such as botanical gardens in Thailand urban areas, which are often found highly polluted in the air such as carbon dioxide which is a cause of acid rain. There is limited information about how tolerant yeasts, are or their functional properties related to the environment. Yeast species were determined by using the 18S rDNA sequence guide. The level of acid tolerance was evaluated by adding to the culture medium lactic acid (300-900 mM), acetic acid (100-400 mM), and propionic acid (25-100 mM). 18S rDNA analysis has shown a %similarity of the nucleotide sequence higher than 98.65% compared to the database. Schwanniomyces etchellsii strains found in urban city soil were notable for their tolerance of lactic acid up to 100 mM. There are two main types of yeasts in overall acid tolerance: S. etchellsii, which is recognized as an osmotic pressure-resistant species that is highly resistant to fermentation inhibitors and produces ethanol; and Schizosaccharomyces pombe, which cell wall has been reported to be characterized by accumulation of α-(1,3)-glucan and malic acid can be used in metabolic pathways. The results show that S. pombe, isolated from rice paddy fields, can grow efficiently in acetic and propionic acid up to 400 mM and 100 mM, respectively. This species could be cultured in ethanol at a concentration of 12.5% (v/v). Moreover, it presented high ethanol and acetic acid production of 14.5-15.9 g/L and 7-10 g/L, respectively, with or without acidic conditions. In comparison, S. etchellsii, isolated from the botanical garden soil, which is grown in acetic, propionic, and lactic acid, was also indicated to be an organic acid-tolerant species.
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Affiliation(s)
- Supattra Lertsriwong
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Biofuels By Biocatalysts Research Unit, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Chompunuch Glinwong
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Biofuels By Biocatalysts Research Unit, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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9
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Terhorst A, Sandikci A, Whittaker CA, Szórádi T, Holt LJ, Neurohr GE, Amon A. The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae. Front Cell Dev Biol 2023; 11:1118766. [PMID: 37123399 PMCID: PMC10130656 DOI: 10.3389/fcell.2023.1118766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
Prolonged cell cycle arrests occur naturally in differentiated cells and in response to various stresses such as nutrient deprivation or treatment with chemotherapeutic agents. Whether and how cells survive prolonged cell cycle arrests is not clear. Here, we used S. cerevisiae to compare physiological cell cycle arrests and genetically induced arrests in G1-, meta- and anaphase. Prolonged cell cycle arrest led to growth attenuation in all studied conditions, coincided with activation of the Environmental Stress Response (ESR) and with a reduced ribosome content as determined by whole ribosome purification and TMT mass spectrometry. Suppression of the ESR through hyperactivation of the Ras/PKA pathway reduced cell viability during prolonged arrests, demonstrating a cytoprotective role of the ESR. Attenuation of cell growth and activation of stress induced signaling pathways also occur in arrested human cell lines, raising the possibility that the response to prolonged cell cycle arrest is conserved.
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Affiliation(s)
- Allegra Terhorst
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Arzu Sandikci
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Charles A. Whittaker
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tamás Szórádi
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Liam J. Holt
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Gabriel E. Neurohr
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- *Correspondence: Gabriel E. Neurohr,
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
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10
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Johnston N, Cline G, Strobel SA. Cells Adapt to Resist Fluoride through Metabolic Deactivation and Intracellular Acidification. Chem Res Toxicol 2022; 35:2085-2096. [PMID: 36282204 PMCID: PMC9683101 DOI: 10.1021/acs.chemrestox.2c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Indexed: 01/09/2023]
Abstract
Fluoride is highly abundant in the environment. Many organisms have adapted specific defense mechanisms against high concentrations of fluoride, including the expression of proteins capable of removing fluoride from cells. However, these fluoride transporters have not been identified in all organisms, and even organisms that express fluoride transporters vary in tolerance capabilities across species, individuals, and even tissue types. This suggests that alternative factors influence fluoride tolerance. We screened for adaptation against fluoride toxicity through an unbiased mutagenesis assay conducted on Saccharomyces cerevisiae lacking the fluoride exporter FEX, the primary mechanism of fluoride resistance. Over 80 independent fluoride-hardened strains were generated, with anywhere from 100- to 1200-fold increased fluoride tolerance compared to the original strain. The whole genome of each mutant strain was sequenced and compared to the wild type. The fluoride-hardened strains utilized a combination of phenotypes that individually conferred fluoride tolerance. These included intracellular acidification, cellular dormancy, nutrient storage, and a communal behavior reminiscent of flocculation. Of particular importance to fluoride resistance was intracellular acidification, which served to reverse the accumulation of fluoride and lead to its excretion from the cell as HF without the activity of a fluoride-specific protein transporter. This transport mechanism was also observed in wild-type yeast through a manual mutation to lower their cytoplasmic pH. The results demonstrate that the yeast developed a protein-free adaptation for removing an intracellular toxicant.
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Affiliation(s)
- Nichole
R. Johnston
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven 06477, Connecticut, United States
| | - Gary Cline
- Department
of Internal Medicine, Yale School of Medicine, New Haven 06510, Connecticut, United States
| | - Scott A. Strobel
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven 06477, Connecticut, United States
- Department
of Chemistry, Yale University, New Haven 06477, Connecticut, United States
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11
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Ercan O, den Besten HMW, Smid EJ, Kleerebezem M. The growth-survival trade-off is hard-wired in the Lactococcus lactis gene regulation network. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:632-636. [PMID: 35445553 PMCID: PMC9544163 DOI: 10.1111/1758-2229.13073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Most microbes reside in oligotrophic environments for extended periods of time, requiring survival strategies that maintain proliferative capacity. We demonstrate that the non-spore-forming Lactococcus lactis KF147 progressively activates the expression of stress-associated functions in response to the declining growth rate elicited by prolonged retentostat cultivation, which coincides with up to 104 -fold increased stress tolerance. Our findings provide a quantified view of the transcription and stress-tolerance adaptations underlying the growth-survival trade-off in L. lactis, and exemplify the hard-wiring of this trade-off in the lactococcal gene regulation network.
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Affiliation(s)
- Onur Ercan
- TiFN, Agro Business Park 82Wageningen6708 PWThe Netherlands
- NIZO Food Research, P.O. Box 20Ede6710 BAThe Netherlands
| | - Heidy M. W. den Besten
- Laboratory of Food MicrobiologyWageningen University, P.O. Box 17Wageningen6700 AAThe Netherlands
| | - Eddy J. Smid
- TiFN, Agro Business Park 82Wageningen6708 PWThe Netherlands
- Laboratory of Food MicrobiologyWageningen University, P.O. Box 17Wageningen6700 AAThe Netherlands
| | - Michiel Kleerebezem
- TiFN, Agro Business Park 82Wageningen6708 PWThe Netherlands
- NIZO Food Research, P.O. Box 20Ede6710 BAThe Netherlands
- Host Microbe InteractomicsWageningen University, P.O. Box 338Wageningen6700 AHThe Netherlands
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12
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Hemeg HA. Combatting persisted and biofilm antimicrobial resistant bacterial by using nanoparticles. Z NATURFORSCH C 2022; 77:365-378. [PMID: 35234019 DOI: 10.1515/znc-2021-0296] [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: 11/24/2021] [Accepted: 02/04/2022] [Indexed: 11/15/2022]
Abstract
Some bacteria can withstand the existence of an antibiotic without undergoing any genetic changes. They are neither cysts nor spores and are one of the causes of disease recurrence, accounting for about 1% of the biofilm. There are numerous approaches to eradication and combating biofilm-forming organisms. Nanotechnology is one of them, and it has shown promising results against persister cells. In the review, we go over the persister cell and biofilm in extensive detail. This includes the biofilm formation cycle, antibiotic resistance, and treatment with various nanoparticles. Furthermore, the gene-level mechanism of persister cell formation and its therapeutic interventions with nanoparticles were discussed.
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Affiliation(s)
- Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Monawra 41411, Saudi Arabia
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13
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Kokina A, Tanilas K, Ozolina Z, Pleiko K, Shvirksts K, Vamza I, Liepins J. Purine Auxotrophic Starvation Evokes Phenotype Similar to Stationary Phase Cells in Budding Yeast. J Fungi (Basel) 2021; 8:29. [PMID: 35049969 PMCID: PMC8780165 DOI: 10.3390/jof8010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 11/25/2022] Open
Abstract
Purine auxotrophy is an abundant trait among eukaryotic parasites and a typical marker for many budding yeast strains. Supplementation with an additional purine source (such as adenine) is necessary to cultivate these strains. If not supplied in adequate amounts, purine starvation sets in. We explored purine starvation effects in a model organism, a budding yeast Saccharomyces cerevisiae ade8 knockout, at the level of cellular morphology, central carbon metabolism, and global transcriptome. We observed that purine-starved cells stopped their cycle in G1/G0 state and accumulated trehalose, and the intracellular concentration of AXP decreased, but adenylate charge remained stable. Cells became tolerant to severe environmental stresses. Intracellular RNA concentration decreased, and massive downregulation of ribosomal biosynthesis genes occurred. We proved that the expression of new proteins during purine starvation is critical for cells to attain stress tolerance phenotype Msn2/4p targets are upregulated in purine-starved cells when compared to cells cultivated in purine-rich media. The overall transcriptomic response to purine starvation resembles that of stationary phase cells. Our results demonstrate that the induction of a strong stress resistance phenotype in budding yeast can be caused not only by natural starvation, but also starvation for metabolic intermediates, such as purines.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Kristel Tanilas
- Center of Food and Fermentation Technologies, Akadeemia Tee 15A, 12618 Tallinn, Estonia;
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Karlis Pleiko
- Faculty of Medicine, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia;
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Karlis Shvirksts
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Ilze Vamza
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
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14
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Bioinspired synthesize of CuO nanoparticles using Cylindrospermum stagnale for antibacterial, anticancer and larvicidal applications. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01940-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Leudjo Taka A, Fosso-Kankeu E, Naidoo EB, Yangkou Mbianda X. Recent development in antimicrobial activity of biopolymer-inorganic nanoparticle composites with water disinfection potential: a comprehensive review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:26252-26268. [PMID: 33788086 DOI: 10.1007/s11356-021-13373-z] [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: 07/07/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Nowadays, water-borne diseases including hepatitis remain the critical health challenge due to the inadequate supply of potable and safe water for human activities. The major cause is that the pathogenic microorganisms causing diseases have developed resistance against common techniques used by sewage water treatment plants for water disinfection. Therefore, there is a need to improve these conventional water treatment techniques by taking into consideration the application of nanotechnology for wastewater purification. The main aim of this paper is to provide a review on the synthesis of biopolymer-inorganic nanoparticle composites (BINCs), their used as antimicrobial compounds for water disinfection, as well as to elaborate on their antimicrobial mechanism of action. The microbial properties affecting the activity of antimicrobial compounds are also evaluated.
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Affiliation(s)
- Anny Leudjo Taka
- Institute of Chemical & Biotechnology, Vaal University of Technology, Southern Gauteng Science and Technology Park, Sebokeng Campus, Vanderbijlpark, 1983, South Africa
- Department of Chemistry, Vaal University of Technology, Vanderbijlpark Campus, Vanderbijlpark, South Africa
| | - Elvis Fosso-Kankeu
- School of Chemical and Minerals Engineering, Faculty of Engineering, North West University, Potchefstroom Campus, Potchefstroom, South Africa
| | - Eliazer Bobby Naidoo
- Institute of Chemical & Biotechnology, Vaal University of Technology, Southern Gauteng Science and Technology Park, Sebokeng Campus, Vanderbijlpark, 1983, South Africa.
- Department of Chemistry, Vaal University of Technology, Vanderbijlpark Campus, Vanderbijlpark, South Africa.
| | - Xavier Yangkou Mbianda
- Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg, 2028, South Africa.
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16
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Stress-induced growth rate reduction restricts metabolic resource utilization to modulate osmo-adaptation time. Cell Rep 2021; 34:108854. [PMID: 33730573 DOI: 10.1016/j.celrep.2021.108854] [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: 01/22/2021] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 01/15/2023] Open
Abstract
A near-constant feature of stress responses is a downregulation or arrest of the cell cycle, resulting in transient growth slowdown. To investigate the role of growth slowdown in the hyperosmotic shock response of S. cerevisiae, we perturbed the G1/S checkpoint protein Sic1 to enable osmo-stress response activation with diminished growth slowdown. We document that in this mutant, adaptation to stress is accelerated rather than delayed. This accelerated recovery of the mutant proceeds by liquidation of internal glycogen stores, which are then shunted into the osmo-shock response. Therefore, osmo-adaptation in wild-type cells is delayed because growth slowdown prevents full accessibility to cellular glycogen stores. However, faster adaptation comes at the cost of acute sensitivity to subsequent osmo-stresses. We suggest that stress-induced growth slowdown acts as an arbiter to regulate the resources devoted to osmo-shock, balancing short-term adaptation with long-term robustness.
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17
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Tra Bi CY, Kouakou-Kouamé CA, N'guessan FK, Djè MK, Montet D. Phenotypic characterization of indigenous Saccharomyces cerevisiae strains associated with sorghum beer and palm wines. World J Microbiol Biotechnol 2021; 37:24. [PMID: 33427964 DOI: 10.1007/s11274-020-02990-4] [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: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
In order to phenotypically characterized Saccharomyces cerevisiae strains isolated from sorghum beer and palm wines for a possible selection of a starter culture, 30 strains were tested for killer activity, temperature resistance, ethanol tolerance, carbohydrate fermentation, enzyme profile and sorghum wort fermentation. Of the tested strains, three showed a killer profile, while four showed a neutral profile and 23 were found to be sensitive to K2 toxin. Temperatures of 40 °C and 44 °C allowed to distinguish strains into four thermal groups with only three strains may grow at 44 °C. Almost tested strains were tolerant to 5% ethanol with viability rates up to 73%. But at 10% and 15% ethanol, respectively 18 and 7 strains were tolerant. Carbohydrate fermentation revealed 13 fermentation profiles, including one typical and 12 atypical profiles. The typical profile strains (16.13% of the strains) fermented glucose, galactose, fructose, sucrose, maltose, trehalose and raffinose. Most of the strains secreted lipases (mainly esterase and esterase-lipase), proteases (mainly valine and cysteine arylamidase, chrymotrypsin) and phosphatases (mainly acid phosphatase and naphthol phosphohydrolase). On contrary, only five strains isolated from sorghum beer exhibited glucosidase activity, mainly α-glucosidase. The analyse of fermented sorghum wort revealed that fermentative performance is strain dependent. Furthermore, the Hierarchical Cluster Analysis showed that the strains were separated in three distinct clusters with the strains from sorghum beer clustered separately.
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Affiliation(s)
- Charles Y Tra Bi
- Institut de Recherche sur les Energies Nouvelles (IREN), Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Côte d'Ivoire
| | - Clémentine A Kouakou-Kouamé
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Côte d'Ivoire
| | - Florent K N'guessan
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Côte d'Ivoire.
| | - Marcellin K Djè
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Côte d'Ivoire
| | - Didier Montet
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, CIRAD, UMR Qualisud, TA 95B/16, 34398, Montpellier Cedex 5, France
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18
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de Graff AMR, Mosedale DE, Sharp T, Dill KA, Grainger DJ. Proteostasis is adaptive: Balancing chaperone holdases against foldases. PLoS Comput Biol 2020; 16:e1008460. [PMID: 33315891 PMCID: PMC7769611 DOI: 10.1371/journal.pcbi.1008460] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/28/2020] [Accepted: 10/20/2020] [Indexed: 11/23/2022] Open
Abstract
Because a cell must adapt to different stresses and growth rates, its proteostasis system must too. How do cells detect and adjust proteome folding to different conditions? Here, we explore a biophysical cost-benefit principle, namely that the cell should keep its proteome as folded as possible at the minimum possible energy cost. This can be achieved by differential expression of chaperones–balancing foldases (which accelerate folding) against holdases (which act as parking spots). The model captures changes in the foldase-holdase ratio observed both within organisms during aging and across organisms of varying metabolic rates. This work describes a simple biophysical mechanism by which cellular proteostasis adapts to meet the needs of a changing growth environment. Cells must maintain low levels of protein unfolding to avoid deleterious outcomes such as protein aggregation, oxidative damage, or premature degradation. The proteins responsible for this, called chaperones, come in two main varieties: ATP-consuming “foldases” that help clients fold and ATP-independent “holdases” that hold unfolded proteins until a foldase arrives. While foldases are necessary for folding, they are expensive to have in high quantities. Given that chaperones are abundant and costly, cells are under strong selective pressure to find economical combinations of foldases and holdases for maintaining low levels of unfolded protein. Yet, it is presently unclear what the ideal combination is and how it varies with growth conditions. By examining a toy model of chaperone function and minimizing the total cost of folding at different rates of protein synthesis, we find that while foldases are necessary at fast growth, holdases become increasingly effective at slow growth. Unexpectedly, total chaperone requirements were predicted to increase as synthesis slows, consistent with observations across age in worms, as well as across species with varying metabolic rates. This work thus provides a general framework for understanding the chaperone requirements of a proteome in terms of an energy minimization principle.
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Affiliation(s)
| | | | - Tilly Sharp
- Methuselah Health UK Ltd, Cambridge, United Kingdom
| | - Ken A. Dill
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America
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19
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Yang J, Tavazoie S. Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress. PLoS One 2020; 15:e0239528. [PMID: 33170850 PMCID: PMC7654773 DOI: 10.1371/journal.pone.0239528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been the subject of many studies aimed at understanding mechanisms of adaptation to environmental stresses. Most of these studies have focused on adaptation to sub-lethal stresses, upon which a stereotypic transcriptional program called the environmental stress response (ESR) is activated. However, the genetic and regulatory factors that underlie the adaptation and survival of yeast cells to stresses that cross the lethality threshold have not been systematically studied. Here, we utilized a combination of gene expression profiling, deletion-library fitness profiling, and experimental evolution to systematically explore adaptation of S. cerevisiae to acute exposure to threshold lethal ethanol concentrations—a stress with important biotechnological implications. We found that yeast cells activate a rapid transcriptional reprogramming process that is likely adaptive in terms of post-stress survival. We also utilized repeated cycles of lethal ethanol exposure to evolve yeast strains with substantially higher ethanol tolerance and survival. Importantly, these strains displayed bulk growth-rates that were indistinguishable from the parental wild-type strain. Remarkably, these hyper-ethanol tolerant strains had reprogrammed their pre-stress gene expression states to match the likely adaptive post-stress response in the wild-type strain. Our studies reveal critical determinants of yeast survival to lethal ethanol stress and highlight potentially general principles that may underlie evolutionary adaptation to lethal stresses in general.
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Affiliation(s)
- Jamie Yang
- Department of Systems Biology, Columbia University, New York City, New York, United States of America
- Department of Biochemistry and Molecular Biology, Columbia University, New York City, New York, United States of America
| | - Saeed Tavazoie
- Department of Systems Biology, Columbia University, New York City, New York, United States of America
- Department of Biochemistry and Molecular Biology, Columbia University, New York City, New York, United States of America
- Department of Biological Sciences, Columbia University, New York City, New York, United States of America
- * E-mail:
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20
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Wohlgemuth F, Gomes RL, Singleton I, Rawson FJ, Avery SV. Top-Down Characterization of an Antimicrobial Sanitizer, Leading From Quenchers of Efficacy to Mode of Action. Front Microbiol 2020; 11:575157. [PMID: 33101251 PMCID: PMC7546784 DOI: 10.3389/fmicb.2020.575157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/07/2020] [Indexed: 01/29/2023] Open
Abstract
We developed a top-down strategy to characterize an antimicrobial, oxidizing sanitizer, which has diverse proposed applications including surface-sanitization of fresh foods, and with benefits for water resilience. The strategy involved finding quenchers of antimicrobial activity then antimicrobial mode of action, by identifying key chemical reaction partners starting from complex matrices, narrowing down reactivity to specific organic molecules within cells. The sanitizer electrolyzed-water (EW) retained partial fungicidal activity against the food-spoilage fungus Aspergillus niger at high levels of added soils (30–750 mg mL–1), commonly associated with harvested produce. Soil with high organic load (98 mg g–1) gave stronger EW inactivation. Marked inactivation by a complex organics mix (YEPD medium) was linked to its protein-rich components. Addition of pure proteins or amino acids (≤1 mg mL–1) fully suppressed EW activity. Mechanism was interrogated further with the yeast model, corroborating marked suppression of EW action by the amino acid methionine. Pre-culture with methionine increased resistance to EW, sodium hypochlorite, or chlorine-free ozonated water. Overexpression of methionine sulfoxide reductases (which reduce oxidized methionine) protected against EW. Fluoroprobe-based analyses indicated that methionine and cysteine inactivate free chlorine species in EW. Intracellular methionine oxidation can disturb cellular FeS-clusters and we showed that EW treatment impairs FeS-enzyme activity. The study establishes the value of a top-down approach for multi-level characterization of sanitizer efficacy and action. The results reveal proteins and amino acids as key quenchers of EW activity and, among the amino acids, the importance of methionine oxidation and FeS-cluster damage for antimicrobial mode-of-action.
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Affiliation(s)
| | - Rachel L Gomes
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Ian Singleton
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Frankie J Rawson
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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21
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Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. J Proteome Res 2020; 19:1183-1195. [PMID: 32027144 DOI: 10.1021/acs.jproteome.9b00704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells respond to environmental perturbations and insults through modulating protein abundance and function. However, the majority of studies have focused on changes in RNA abundance because quantitative transcriptomics has historically been more facile than quantitative proteomics. Modern Orbitrap mass spectrometers now provide sensitive and deep proteome coverage, allowing direct, global quantification of not only protein abundance but also post-translational modifications (PTMs) that regulate protein activity. We implemented and validated using the well-characterized heat shock response of budding yeast, a tandem mass tagging (TMT), triple-stage mass spectrometry (MS3) strategy to measure global changes in the proteome during the yeast heat shock response over nine time points. We report that basic-pH, ultra-high performance liquid chromatography (UPLC) fractionation of tryptic peptides yields superfractions of minimal redundancy, a crucial requirement for deep coverage and quantification by subsequent LC-MS3. We quantified 2275 proteins across three biological replicates and found that differential expression peaked near 90 min following heat shock (with 868 differentially expressed proteins at 5% false discovery rate). The sensitivity of the approach also allowed us to detect changes in the relative abundance of ubiquitination and phosphorylation PTMs over time. Remarkably, relative quantification of post-translationally modified peptides revealed striking evidence of regulation of the heat shock response by protein PTMs. These data demonstrate that the high precision of TMT-MS3 enables peptide-level quantification of samples, which can reveal important regulation of protein abundance and regulatory PTMs under various experimental conditions.
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Affiliation(s)
- Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rebecca E Hardman
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas 72701, United States.,Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rick D Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Jeffrey A Lewis
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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22
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Hakkaart X, Liu Y, Hulst M, El Masoudi A, Peuscher E, Pronk J, van Gulik W, Daran-Lapujade P. Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO 2 levels. Biotechnol Bioeng 2020; 117:721-735. [PMID: 31654410 PMCID: PMC7028085 DOI: 10.1002/bit.27210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/12/2019] [Accepted: 10/22/2019] [Indexed: 12/21/2022]
Abstract
Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic‐acid yield and recovery include slow growth, low pH, and high CO2. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO2 (50%) on slow‐growing chemostat and retentostat cultures of the reference strain S. cerevisiae CEN.PK113‐7D. Combined exposure to low pH and high CO2 led to increased maintenance‐energy requirements and death rates in aerobic, glucose‐limited cultures. Further experiments showed that these effects were predominantly caused by low pH. Growth under ammonium‐limited, energy‐excess conditions did not aggravate or ameliorate these adverse impacts. Despite the absence of a synergistic effect of low pH and high CO2 on physiology, high CO2 strongly affected genome‐wide transcriptional responses to low pH. Interference of high CO2 with low‐pH signaling is consistent with low‐pH and high‐CO2 signals being relayed via common (MAPK) signaling pathways, notably the cell wall integrity, high‐osmolarity glycerol, and calcineurin pathways. This study highlights the need to further increase robustness of cell factories to low pH for carboxylic‐acid production, even in organisms that are already applied at industrial scale.
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Affiliation(s)
- Xavier Hakkaart
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Yaya Liu
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Mandy Hulst
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Anissa El Masoudi
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Eveline Peuscher
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Jack Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg, Delft, The Netherlands
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23
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Hackley RK, Schmid AK. Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. J Mol Biol 2019; 431:4147-4166. [PMID: 31437442 PMCID: PMC7419163 DOI: 10.1016/j.jmb.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Abstract
The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.
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Affiliation(s)
- Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA.
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24
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Repressive Gene Regulation Synchronizes Development with Cellular Metabolism. Cell 2019; 178:980-992.e17. [PMID: 31353220 DOI: 10.1016/j.cell.2019.06.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/06/2019] [Accepted: 06/12/2019] [Indexed: 01/06/2023]
Abstract
Metabolic conditions affect the developmental tempo of animals. Developmental gene regulatory networks (GRNs) must therefore synchronize their dynamics with a variable timescale. We find that layered repression of genes couples GRN output with variable metabolism. When repressors of transcription or mRNA and protein stability are lost, fewer errors in Drosophila development occur when metabolism is lowered. We demonstrate the universality of this phenomenon by eliminating the entire microRNA family of repressors and find that development to maturity can be largely rescued when metabolism is reduced. Using a mathematical model that replicates GRN dynamics, we find that lowering metabolism suppresses the emergence of developmental errors by curtailing the influence of auxiliary repressors on GRN output. We experimentally show that gene expression dynamics are less affected by loss of repressors when metabolism is reduced. Thus, layered repression provides robustness through error suppression and may provide an evolutionary route to a shorter reproductive cycle.
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25
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Jamróz E, Kulawik P, Kopel P. The Effect of Nanofillers on the Functional Properties of Biopolymer-based Films: A Review. Polymers (Basel) 2019; 11:E675. [PMID: 31013855 PMCID: PMC6523406 DOI: 10.3390/polym11040675] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022] Open
Abstract
Waste from non-degradable plastics is becoming an increasingly serious problem. Therefore, more and more research focuses on the development of materials with biodegradable properties. Bio-polymers are excellent raw materials for the production of such materials. Bio-based biopolymer films reinforced with nanostructures have become an interesting area of research. Nanocomposite films are a group of materials that mainly consist of bio-based natural (e.g., chitosan, starch) and synthetic (e.g., poly(lactic acid)) polymers and nanofillers (clay, organic, inorganic, or carbon nanostructures), with different properties. The interaction between environmentally friendly biopolymers and nanofillers leads to the improved functionality of nanocomposite materials. Depending on the properties of nanofillers, new or improved properties of nanocomposites can be obtained such as: barrier properties, improved mechanical strength, antimicrobial, and antioxidant properties or thermal stability. This review compiles information about biopolymers used as the matrix for the films with nanofillers as the active agents. Particular emphasis has been placed on the influence of nanofillers on functional properties of biopolymer films and their possible use within the food industry and food packaging systems. The possible applications of those nanocomposite films within other industries (medicine, drug and chemical industry, tissue engineering) is also briefly summarized.
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Affiliation(s)
- Ewelina Jamróz
- Institute of Chemistry, University of Agriculture in Cracow, Balicka Street 122, PL-30-149 Kraków, Poland.
| | - Piotr Kulawik
- Department of Animal Products Processing, University of Agriculture, Balicka Street 122, PL-30-149 Kraków, Poland.
| | - Pavel Kopel
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00 Brno, Czech Republic.
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26
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Sanchez de Groot N, Torrent Burgas M, Ravarani CN, Trusina A, Ventura S, Babu MM. The fitness cost and benefit of phase-separated protein deposits. Mol Syst Biol 2019; 15:e8075. [PMID: 30962358 PMCID: PMC6452874 DOI: 10.15252/msb.20178075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase-separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can influence cell-to-cell variation in free protein abundance between individuals of a cell population (i.e., gene expression noise). This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase-separated assemblies and may influence cell fitness.
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Affiliation(s)
- Natalia Sanchez de Groot
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK .,Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc Torrent Burgas
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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Ali K, Ahmed B, Ansari SM, Saquib Q, Al-Khedhairy AA, Dwivedi S, Alshaeri M, Khan MS, Musarrat J. Comparative in situ ROS mediated killing of bacteria with bulk analogue, Eucalyptus leaf extract (ELE)-capped and bare surface copper oxide nanoparticles. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 100:747-758. [PMID: 30948112 DOI: 10.1016/j.msec.2019.03.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Abstract
This study demonstrates a simple one-pot green method for biosynthesis of terpenoids encapsulated copper oxide nanoparticles (CuONPs) using aqueous leaf extract of Eucalyptus globulus (ELE), as reducing, dispersing, and stabilizing agent. Indeed, the greater attachment and internalization of ELE-CuONPs in Gram-positive and -negative biofilm producing clinical bacterial isolates validated the hypothesis that terpenoids encapsulated CuONPs are more stable and effective antibacterial and antibiofilm agent vis-à-vis commercially available nano and micro sized analogues. Gas chromatography-mass spectroscopy (GC-MS) analysis of pristine ELE identified 17 types of terpenoids based on their mass-to-charge (m/z) ratios. Amongst them four bioactive terpenoids viz. terpineols, 2,6-octadienal-3,7-dimethyl, benzamidophenyl-4-benzoate and β-eudesmol were found associated with the CuONPs as ELE-cap, and most likely involved in the nucleation and stabilization of ELE-CuONPs. Further, the Fourier transformed infrared (FTIR) analysis of ELE-CuONPs also implicated other functional biomolecules like proteins, sugars, alkenes, etc. with ELE terpenoids corona. Flow cytometric (FCM) data exhibited significantly enhanced intracellular uptake propensity of terpenoids encapsulated ELE-CuONPs and accumulation of intracellular reactive oxygen species (ROS), which ensued killing of planktonic cells of extended spectrum β-lactamases (ESβL) producing Escherichia coli-336 (E. coli-336), Pseudomonas aeruginosa-621 (P. aeruginosa-621) and methicillin-resistant Staphylococcus aureus-1 (MRSA-1) clinical isolates compared to the bare surface commercial nano-CuO and bulk sized CuO. The study for the first-time demonstrated the (i) differential bio-nano interface activities due to ELE surface and varied cell wall composition of test bacterial isolates, (ii) antibacterial effect and biofilm inhibition due to disruption of proteins involved in adhesion and biofilm formation triggered by CuONPs induced intracellular oxidative stress, and (iii) indigenous terpenoids-capped bio-inspired CuONPs are more stable and effective antibacterial and antibiofilm agent as compared with commercially available nano-CuO and bulk-CuO.
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Affiliation(s)
- Khursheed Ali
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Bilal Ahmed
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Sabiha M Ansari
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sourabh Dwivedi
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Majed Alshaeri
- Faculty of Science, Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Saghir Khan
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Javed Musarrat
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India; School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu & Kashmir, India.
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Pandey AK, Kumar M, Kumari S, Kumari P, Yusuf F, Jakeer S, Naz S, Chandna P, Bhatnagar I, Gaur NA. Evaluation of divergent yeast genera for fermentation-associated stresses and identification of a robust sugarcane distillery waste isolate Saccharomyces cerevisiae NGY10 for lignocellulosic ethanol production in SHF and SSF. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:40. [PMID: 30858877 PMCID: PMC6391804 DOI: 10.1186/s13068-019-1379-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Lignocellulosic hydrolysates contain a mixture of hexose (C6)/pentose (C5) sugars and pretreatment-generated inhibitors (furans, weak acids and phenolics). Therefore, robust yeast isolates with characteristics of C6/C5 fermentation and tolerance to pretreatment-derived inhibitors are pre-requisite for efficient lignocellulosic material based biorefineries. Moreover, use of thermotolerant yeast isolates will further reduce cooling cost, contamination during fermentation, and required for developing simultaneous saccharification and fermentation (SSF), simultaneous saccharification and co-fermentation (SScF), and consolidated bio-processing (CBP) strategies. RESULTS In this study, we evaluated thirty-five yeast isolates (belonging to six genera including Saccharomyces, Kluyveromyces, Candida, Scheffersomyces, Ogatea and Wickerhamomyces) for pretreatment-generated inhibitors {furfural, 5-hydroxymethyl furfural (5-HMF) and acetic acid} and thermotolerant phenotypes along with the fermentation performances at 40 °C. Among them, a sugarcane distillery waste isolate, Saccharomyces cerevisiae NGY10 produced maximum 49.77 ± 0.34 g/l and 46.81 ± 21.98 g/l ethanol with the efficiency of 97.39% and 93.54% at 30 °C and 40 °C, respectively, in 24 h using glucose as a carbon source. Furthermore, isolate NGY10 produced 12.25 ± 0.09 g/l and 7.18 ± 0.14 g/l of ethanol with 92.81% and 91.58% efficiency via SHF, and 30.22 g/l and 25.77 g/l ethanol with 86.43% and 73.29% efficiency via SSF using acid- and alkali-pretreated rice straw as carbon sources, respectively, at 40 °C. In addition, isolate NGY10 also produced 92.31 ± 3.39 g/l (11.7% v/v) and 33.66 ± 1.04 g/l (4.26% v/v) ethanol at 40 °C with the yields of 81.49% and 73.87% in the presence of 30% w/v glucose or 4× concentrated acid-pretreated rice straw hydrolysate, respectively. Moreover, isolate NGY10 displayed furfural- (1.5 g/l), 5-HMF (3.0 g/l), acetic acid- (0.2% v/v) and ethanol-(10.0% v/v) tolerant phenotypes. CONCLUSION A sugarcane distillery waste isolate NGY10 demonstrated high potential for ethanol production, C5 metabolic engineering and developing strategies for SSF, SScF and CBP.
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Affiliation(s)
- Ajay Kumar Pandey
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Mohit Kumar
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Sonam Kumari
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Priya Kumari
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Farnaz Yusuf
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Shaik Jakeer
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Sumera Naz
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Piyush Chandna
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Ishita Bhatnagar
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
| | - Naseem A. Gaur
- Yeast Biofuel Group, DBT-ICGEB Center for Advanced Bioenergy Research, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
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29
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Dhar R, Missarova AM, Lehner B, Carey LB. Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation. eLife 2019; 8:38904. [PMID: 30638445 PMCID: PMC6366901 DOI: 10.7554/elife.38904] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/13/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially in their proliferation rates, stress tolerance, and drug resistance, with important implications for the treatment of infections and cancer. To investigate the causes of cell-to-cell variation in proliferation, we used a high-throughput automated microscopy assay to quantify the impact of deleting >1500 genes in yeast. Mutations affecting mitochondria were particularly variable in their outcome. In both mutant and wild-type cells mitochondrial membrane potential - but not amount - varied substantially across individual cells and predicted cell-to-cell variation in proliferation, mutation outcome, stress tolerance, and resistance to a clinically used anti-fungal drug. These results suggest an important role for cell-to-cell variation in the state of an organelle in single cell phenotypic variation.
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Affiliation(s)
- Riddhiman Dhar
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Alsu M Missarova
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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30
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Abstract
Growth rate is one of the most important and most complex phenotypic characteristics of unicellular microorganisms, which determines the genetic mutations that dominate at the population level, and ultimately whether the population will survive. Translating changes at the genetic level to their growth-rate consequences remains a subject of intense interest, since such a mapping could rationally direct experiments to optimize antibiotic efficacy or bioreactor productivity. In this work, we directly map transcriptional profiles to growth rates by gathering published gene-expression data from Escherichia coli and Saccharomyces cerevisiae with corresponding growth-rate measurements. Using a machine-learning technique called k-nearest-neighbors regression, we build a model which predicts growth rate from gene expression. By exploiting the correlated nature of gene expression and sparsifying the model, we capture 81% of the variance in growth rate of the E. coli dataset, while reducing the number of features from >4,000 to 9. In S. cerevisiae, we account for 89% of the variance in growth rate, while reducing from >5,500 dimensions to 18. Such a model provides a basis for selecting successful strategies from among the combinatorial number of experimental possibilities when attempting to optimize complex phenotypic traits like growth rate.
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31
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Jing W, Camellato B, Roney IJ, Kaern M, Godin M. Measuring Single-Cell Phenotypic Growth Heterogeneity Using a Microfluidic Cell Volume Sensor. Sci Rep 2018; 8:17809. [PMID: 30546021 PMCID: PMC6293012 DOI: 10.1038/s41598-018-36000-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/13/2018] [Indexed: 12/24/2022] Open
Abstract
An imaging-integrated microfluidic cell volume sensor was used to evaluate the volumetric growth rate of single cells from a Saccharomyces cerevisiae population exhibiting two phenotypic expression states of the PDR5 gene. This gene grants multidrug resistance by transcribing a membrane transporter capable of pumping out cytotoxic compounds from the cell. Utilizing fluorescent markers, single cells were isolated and trapped, then their growth rates were measured in two on-chip environments: rich media and media dosed with the antibiotic cycloheximide. Approximating growth rates to first-order, we assessed the fitness of individual cells and found that those with low PDR5 expression had higher fitness in rich media whereas cells with high PDR5 expression had higher fitness in the presence of the drug. Moreover, the drug dramatically reduced the fitness of cells with low PDR5 expression but had comparatively minimal impact on the fitness of cells with high PDR5 expression. Our experiments show the utility of this imaging-integrated microfluidic cell volume sensor for high-resolution, single-cell analysis, as well as its potential application for studies that characterize and compare the fitness and morphology of individual cells from heterogeneous populations under different growth conditions.
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Affiliation(s)
- Wenyang Jing
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Brendan Camellato
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Ian J Roney
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Mads Kaern
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michel Godin
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada. .,Ottawa-Carleton Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario, Canada. .,Department of Mechanical Engineering, University of Ottawa, Ottawa, Ontario, Canada.
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32
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Zacchetti B, Wösten HA, Claessen D. Multiscale heterogeneity in filamentous microbes. Biotechnol Adv 2018; 36:2138-2149. [DOI: 10.1016/j.biotechadv.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/15/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
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33
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Li S, Giardina DM, Siegal ML. Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors. PLoS Genet 2018; 14:e1007744. [PMID: 30388117 PMCID: PMC6241136 DOI: 10.1371/journal.pgen.1007744] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 11/14/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023] Open
Abstract
Genetically identical cells exhibit extensive phenotypic variation even under constant and benign conditions. This so-called nongenetic heterogeneity has important clinical implications: within tumors and microbial infections, cells show nongenetic heterogeneity in growth rate and in susceptibility to drugs or stress. The budding yeast, Saccharomyces cerevisiae, shows a similar form of nongenetic heterogeneity in which growth rate correlates positively with susceptibility to acute heat stress at the single-cell level. Using genetic and chemical perturbations, combined with high-throughput single-cell assays of yeast growth and gene expression, we show here that heterogeneity in intracellular cyclic AMP (cAMP) levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies this nongenetic heterogeneity. Lower levels of cAMP correspond to slower growth, as shown by direct comparison of cAMP concentration in subpopulations enriched for slower vs. faster growing cells. Concordantly, an endogenous reporter of this pathway’s activity correlates with growth in individual cells. The paralogs Msn2 and Msn4 differ in their roles in nongenetic heterogeneity in a way that demonstrates slow growth and stress tolerance are not inevitably linked. Heterogeneity in growth rate requires each, whereas only Msn2 is required for heterogeneity in expression of Tsl1, a subunit of trehalose synthase that contributes to acute-stress tolerance. Perturbing nongenetic heterogeneity by mutating genes in this pathway, or by culturing wild-type cells with the cell-permeable cAMP analog 8-bromo-cAMP or the PKA inhibitor H89, significantly impacts survival of acute heat stress. Perturbations that increase intracellular cAMP levels reduce the slower-growing subpopulation and increase susceptibility to acute heat stress, whereas PKA inhibition slows growth and decreases susceptibility to acute heat stress. Loss of Msn2 reduces, but does not completely eliminate, the correlation in individual cells between growth rate and acute-stress survival, suggesting a major role for the Msn2 pathway in nongenetic heterogeneity but also a residual benefit of slow growth. Our results shed light on the genetic control of nongenetic heterogeneity and suggest a possible means of defeating bet-hedging pathogens or tumor cells by making them more uniformly susceptible to treatment. Nongenetic heterogeneity exists when a trait differs among individuals that have identical genotypes and environments. A clonal population can maximize its long-term success in an uncertain environment by diversifying its phenotypes via nongenetic heterogeneity: the currently unfavored ones may become the favored ones when conditions change. Nongenetic heterogeneity has clinical relevance. For example, populations of tumor cells or infectious microbes show cell-to-cell differences in growth and in drug or stress tolerance. This heterogeneity hampers efficient treatment and can potentiate harmful evolution of a tumor or pathogen. We show that in budding yeast, heterogeneity in intracellular cyclic AMP levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies the nongenetic heterogeneity of both single-cell growth rate and acute heat-stress tolerance. Perturbations of this pathway significantly affect population survival upon acute heat stress. These results illuminate a mechanism of nongenetic heterogeneity and suggest the potential value of antitumor or antifungal treatment strategies that target nongenetic heterogeneity to render the tumor or pathogen population more uniformly susceptible to a second drug that aims to kill.
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Affiliation(s)
- Shuang Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Daniella M. Giardina
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Mark L. Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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34
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Negut I, Grumezescu V, Grumezescu AM. Treatment Strategies for Infected Wounds. Molecules 2018; 23:E2392. [PMID: 30231567 PMCID: PMC6225154 DOI: 10.3390/molecules23092392] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 12/22/2022] Open
Abstract
The treatment of skin wounds is a key research domain owing to the important functional and aesthetic role of this tissue. When the skin is impaired, bacteria can soon infiltrate into underlying tissues which can lead to life-threatening infections. Consequently, effective treatments are necessary to deal with such pathological conditions. Recently, wound dressings loaded with antimicrobial agents have emerged as viable options to reduce wound bacterial colonization and infection, in order to improve the healing process. In this paper, we present an overview of the most prominent antibiotic-embedded wound dressings, as well as the limitations of their use. A promising, but still an underrated group of potential antibacterial agents that can be integrated into wound dressings are natural products, especially essential oils. Some of the most commonly used essential oils against multidrug-resistant microorganisms, such as tea tree, St. John's Wort, lavender and oregano, together with their incorporation into wound dressings are presented. In addition, another natural product that exhibits encouraging antibacterial activity is honey. We highlight recent results of several studies carried out by researchers from different regions of the world on wound dressings impregnated with honey, with a special emphasis on Manuka honey. Finally, we highlight recent advances in using nanoparticles as platforms to increase the effect of pharmaceutical formulations aimed at wound healing. Silver, gold, and zinc nanoparticles alone or functionalized with diverse antimicrobial compounds have been integrated into wound dressings and demonstrated therapeutic effects on wounds.
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Affiliation(s)
- Irina Negut
- National Institute for Lasers, Plasma and Radiation Physics, Magurele RO-77125, Romania.
- Faculty of Physics, University of Bucharest, Magurele 077125, Romania.
| | - Valentina Grumezescu
- National Institute for Lasers, Plasma and Radiation Physics, Magurele RO-77125, Romania.
- Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, Bucharest 011061, Romania.
| | - Alexandru Mihai Grumezescu
- Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, Bucharest 011061, Romania.
- Research Institute of University of Bucharest, ICUB, Bucharest 050107, Romania.
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35
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Ho YH, Shishkova E, Hose J, Coon JJ, Gasch AP. Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress. Curr Biol 2018; 28:2673-2680.e4. [PMID: 30078561 DOI: 10.1016/j.cub.2018.06.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/24/2018] [Accepted: 06/19/2018] [Indexed: 12/29/2022]
Abstract
Stress tolerance and rapid growth are often competing interests in cells. Upon severe environmental stress, many organisms activate defense systems concurrent with growth arrest. There has been debate as to whether aspects of the stress-activated transcriptome are regulated by stress or an indirect byproduct of reduced proliferation. For example, stressed Saccharomyces cerevisiae cells mount a common gene expression program called the environmental stress response (ESR) [1] comprised of ∼300 induced (iESR) transcripts involved in stress defense and ∼600 reduced (rESR) mRNAs encoding ribosomal proteins (RPs) and ribosome biogenesis factors (RiBi) important for division. Because ESR activation also correlates with reduced growth rate in nutrient-restricted chemostats and prolonged G1 in slow-growing mutants, an alternate proposal is that the ESR is simply a consequence of reduced division [2-5]. A major challenge is that past studies did not separate effects of division arrest and stress defense; thus, the true responsiveness of the ESR-and the purpose of stress-dependent rESR repression in particular-remains unclear. Here, we decoupled cell division from the stress response by following transcriptome, proteome, and polysome changes in arrested cells responding to acute stress. We show that the ESR cannot be explained by changes in growth rate or cell-cycle phase during stress acclimation. Instead, failure to repress rESR transcripts reduces polysome association of induced transcripts, delaying production of their proteins. Our results suggest that stressed cells alleviate competition for translation factors by removing mRNAs and ribosomes from the translating pool, directing translational capacity toward induced transcripts to accelerate protein production.
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Affiliation(s)
- Yi-Hsuan Ho
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Evgenia Shishkova
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA.
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36
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Di Gianvito P, Perpetuini G, Tittarelli F, Schirone M, Arfelli G, Piva A, Patrignani F, Lanciotti R, Olivastri L, Suzzi G, Tofalo R. Impact of Saccharomyces cerevisiae strains on traditional sparkling wines production. Food Res Int 2018; 109:552-560. [DOI: 10.1016/j.foodres.2018.04.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/16/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
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37
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Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell 2018; 29:897-910. [PMID: 29444955 PMCID: PMC5896929 DOI: 10.1091/mbc.e17-11-0666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Metabolic dysregulation leading to sugar-phosphate accumulation is toxic in organisms ranging from bacteria to humans. By comparing two models of sugar-phosphate toxicity in Saccharomyces cerevisiae, we demonstrate that toxicity occurs, at least in part, through multiple, isomer-specific mechanisms, rather than a single general mechanism.
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Affiliation(s)
- Patrick A Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Ariel Schieler
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Jonathan C Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Maxim Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Matthew Volpe
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Sanford J Silverman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yifan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
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38
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Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 2017; 15:e2004050. [PMID: 29240790 PMCID: PMC5746276 DOI: 10.1371/journal.pbio.2004050] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells. Genetically identical cells growing in the same environment can vary in their cellular state and behavior. Such heterogeneity may explain why some cells in an isogenic population can survive sudden severe environmental stress whereas other cells succumb. Cell-to-cell variation in gene expression has been linked to variable stress survival, but how and why transcript levels vary across the transcriptome in single cells is only beginning to emerge. Here, we used single-cell RNA sequencing (scRNA-seq) to measure cell-to-cell heterogeneity in the transcriptome of budding yeast (Saccharomyces cerevisiae). We find surprising patterns of variation across known sets of transcription factor targets, indicating that cells vary in their transcriptome profile both before and after stress exposure. scRNA-seq analysis combined with live-cell imaging of transcription factor activation dynamics revealed some cells in which the stress response was coordinately activated and other cells in which the traditional response was decoupled, suggesting unrecognized regulatory nuances that expand our understanding of stress response and survival.
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Affiliation(s)
- Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Feiqiao Brian Yu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Leah E. Escalante
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mike Place
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Rhonda Bacher
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jad Kanbar
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Doina Ciobanu
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis. mSystems 2017; 2:mSystems00032-17. [PMID: 28951888 PMCID: PMC5605881 DOI: 10.1128/msystems.00032-17] [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: 05/03/2017] [Accepted: 08/03/2017] [Indexed: 11/26/2022] Open
Abstract
To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, salinity, and pH and under other conditions. In order to understand the cause-effect relationships between the dynamic function of the stress network and ultimate physiological consequences, this study characterized the physiological role of nearly one-third of all regulatory proteins known as transcription factors (TFs) in an archaeal organism. Using a unique quantitative phenotyping approach, we discovered functions for many novel TFs and revealed important secondary functions for known TFs. Surprisingly, many TFs are required for resisting multiple stressors, suggesting cross-regulation of stress responses. Through extensive validation experiments, we map the physiological roles of these novel TFs in stress response back to their position in the regulatory network wiring. This study advances understanding of the mechanisms underlying how microorganisms resist extreme stress. Given the generality of the methods employed, we expect that this study will enable future studies on how regulatory networks adjust cellular physiology in a diversity of organisms. Gene regulatory networks (GRNs) are critical for dynamic transcriptional responses to environmental stress. However, the mechanisms by which GRN regulation adjusts physiology to enable stress survival remain unclear. Here we investigate the functions of transcription factors (TFs) within the global GRN of the stress-tolerant archaeal microorganism Halobacterium salinarum. We measured growth phenotypes of a panel of TF deletion mutants in high temporal resolution under heat shock, oxidative stress, and low-salinity conditions. To quantitate the noncanonical functional forms of the growth trajectories observed for these mutants, we developed a novel modeling framework based on Gaussian process regression and functional analysis of variance (FANOVA). We employ unique statistical tests to determine the significance of differential growth relative to the growth of the control strain. This analysis recapitulated known TF functions, revealed novel functions, and identified surprising secondary functions for characterized TFs. Strikingly, we observed that the majority of the TFs studied were required for growth under multiple stress conditions, pinpointing regulatory connections between the conditions tested. Correlations between quantitative phenotype trajectories of mutants are predictive of TF-TF connections within the GRN. These phenotypes are strongly concordant with predictions from statistical GRN models inferred from gene expression data alone. With genome-wide and targeted data sets, we provide detailed functional validation of novel TFs required for extreme oxidative stress and heat shock survival. Together, results presented in this study suggest that many TFs function under multiple conditions, thereby revealing high interconnectivity within the GRN and identifying the specific TFs required for communication between networks responding to disparate stressors. IMPORTANCE To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, salinity, and pH and under other conditions. In order to understand the cause-effect relationships between the dynamic function of the stress network and ultimate physiological consequences, this study characterized the physiological role of nearly one-third of all regulatory proteins known as transcription factors (TFs) in an archaeal organism. Using a unique quantitative phenotyping approach, we discovered functions for many novel TFs and revealed important secondary functions for known TFs. Surprisingly, many TFs are required for resisting multiple stressors, suggesting cross-regulation of stress responses. Through extensive validation experiments, we map the physiological roles of these novel TFs in stress response back to their position in the regulatory network wiring. This study advances understanding of the mechanisms underlying how microorganisms resist extreme stress. Given the generality of the methods employed, we expect that this study will enable future studies on how regulatory networks adjust cellular physiology in a diversity of organisms.
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Aldea M, Jenkins K, Csikász-Nagy A. Growth Rate as a Direct Regulator of the Start Network to Set Cell Size. Front Cell Dev Biol 2017; 5:57. [PMID: 28603712 PMCID: PMC5445111 DOI: 10.3389/fcell.2017.00057] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
Cells are able to adjust their growth and size to external inputs to comply with specific fates and developmental programs. Molecular pathways controlling growth also have an enormous impact in cell size, and bacteria, yeast, or epithelial cells modify their size as a function of growth rate. This universal feature suggests that growth (mass) and proliferation (cell number) rates are subject to general coordinating mechanisms. However, the underlying molecular connections are still a matter of debate. Here we review the current ideas on growth and cell size control, and focus on the possible mechanisms that could link the biosynthetic machinery to the Start network in budding yeast. In particular, we discuss the role of molecular chaperones in a competition framework to explain cell size control by growth at the individual cell level.
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Affiliation(s)
- Martí Aldea
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones CientíficasBarcelona, Spain.,Departament de Ciències Bàsiques, Universitat Internacional de CatalunyaBarcelona, Spain
| | - Kirsten Jenkins
- Randall Division of Cell and Molecular Biophysics and Institute of Mathematical and Molecular Biomedicine, King's College LondonLondon, United Kingdom
| | - Attila Csikász-Nagy
- Randall Division of Cell and Molecular Biophysics and Institute of Mathematical and Molecular Biomedicine, King's College LondonLondon, United Kingdom.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic UniversityBudapest, Hungary
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Growth inhibition and antibiofilm potential of Ag nanoparticles coated with lectin, an arthropod immune molecule. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 170:208-216. [DOI: 10.1016/j.jphotobiol.2017.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/05/2017] [Accepted: 04/11/2017] [Indexed: 01/15/2023]
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42
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Barium Hexaferrite Magnetic Fluid: Preparation, Characterization and the In Vitro Identification of Cytotoxicity and Antibacterial Activity. J Inorg Organomet Polym Mater 2017. [DOI: 10.1007/s10904-017-0527-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Bacterial proteostasis balances energy and chaperone utilization efficiently. Proc Natl Acad Sci U S A 2017; 114:E2654-E2661. [PMID: 28292901 DOI: 10.1073/pnas.1620646114] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chaperones are protein complexes that help to fold and disaggregate a cell's proteins. It is not understood how four major chaperone systems of Escherichia coli work together in proteostasis: the recognition, sorting, folding, and disaggregating of the cell's many different proteins. Here, we model this machine. We combine extensive data on chaperoning, folding, and aggregation rates with expression levels of proteins and chaperones measured at different growth rates. We find that the proteostasis machine recognizes and sorts a client protein based on two biophysical properties of the client's misfolded state (M state): its stability and its kinetic accessibility from its unfolded state (U state). The machine is energy-efficient (the sickest proteins use the most ATP-expensive chaperones), comprehensive (it can handle any type of protein), and economical (the chaperone concentrations are just high enough to keep the whole proteome folded and disaggregated but no higher). The cell needs higher chaperone levels in two situations: fast growth (when protein production rates are high) and very slow growth (to mitigate the effects of protein degradation). This type of model complements experimental knowledge by showing how the various chaperones work together to achieve the broad folding and disaggregation needs of the cell.
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Bioprospecting thermotolerant ethanologenic yeasts for simultaneous saccharification and fermentation from diverse environments. J Biosci Bioeng 2017; 123:342-346. [DOI: 10.1016/j.jbiosc.2016.10.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 11/21/2022]
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45
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Tonner PD, Darnell CL, Engelhardt BE, Schmid AK. Detecting differential growth of microbial populations with Gaussian process regression. Genome Res 2017; 27:320-333. [PMID: 27864351 PMCID: PMC5287237 DOI: 10.1101/gr.210286.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/15/2016] [Indexed: 02/06/2023]
Abstract
Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist to capture microbial population growth measurements. However, current models are designed to quantify growth under conditions for which growth has a specific functional form. Extensions to these models are required to quantify the effects of perturbations, which often exhibit nonstandard growth curves. Rather than assume specific functional forms for experimental perturbations, we developed a general and robust model of microbial population growth curves using Gaussian process (GP) regression. GP regression modeling of high-resolution time-series growth data enables accurate quantification of population growth and allows explicit control of effects from other covariates such as genetic background. This framework substantially outperforms commonly used microbial population growth models, particularly when modeling growth data from environmentally stressed populations. We apply the GP growth model and develop statistical tests to quantify the differential effects of environmental perturbations on microbial growth across a large compendium of genotypes in archaea and yeast. This method accurately identifies known transcriptional regulators and implicates novel regulators of growth under standard and stress conditions in the model archaeal organism Halobacterium salinarum For yeast, our method correctly identifies known phenotypes for a diversity of genetic backgrounds under cyclohexamide stress and also detects previously unidentified oxidative stress sensitivity across a subset of strains. Together, these results demonstrate that the GP models are interpretable, recapitulating biological knowledge of growth response while providing new insights into the relevant parameters affecting microbial population growth.
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Affiliation(s)
- Peter D Tonner
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
- Biology Department, Duke University, Durham, North Carolina 27708, USA
| | - Cynthia L Darnell
- Biology Department, Duke University, Durham, North Carolina 27708, USA
| | - Barbara E Engelhardt
- Computer Science Department, Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey 08540, USA
| | - Amy K Schmid
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
- Biology Department, Duke University, Durham, North Carolina 27708, USA
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Vos T, Hakkaart XDV, de Hulster EAF, van Maris AJA, Pronk JT, Daran-Lapujade P. Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates. Microb Cell Fact 2016; 15:111. [PMID: 27317316 PMCID: PMC4912818 DOI: 10.1186/s12934-016-0501-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/31/2016] [Indexed: 11/24/2022] Open
Abstract
Background Saccharomyces cerevisiae is an established microbial platform for production of native and non-native compounds. When product pathways compete with growth for precursors and energy, uncoupling of growth and product formation could increase product yields and decrease formation of biomass as a by-product. Studying non-growing, metabolically active yeast cultures is a first step towards developing S. cerevisiae as a robust, non-growing cell factory. Microbial physiology at near-zero growth rates can be studied in retentostats, which are continuous-cultivation systems with full biomass retention. Hitherto, retentostat studies on S. cerevisiae have focused on anaerobic conditions, which bear limited relevance for aerobic industrial processes. The present study uses aerobic, glucose-limited retentostats to explore the physiology of non-dividing, respiring S. cerevisiae cultures, with a focus on industrially relevant features. Results Retentostat feeding regimes for smooth transition from exponential growth in glucose-limited chemostat cultures to near-zero growth rates were obtained by model-aided experimental design. During 20 days of retentostats cultivation, the specific growth rate gradually decreased from 0.025 h−1 to below 0.001 h−1, while culture viability remained above 80 %. The maintenance requirement for ATP (mATP) was estimated at 0.63 ± 0.04 mmol ATP (g biomass)−1 h−1, which is ca. 35 % lower than previously estimated for anaerobic retentostats. Concomitant with decreasing growth rate in aerobic retentostats, transcriptional down-regulation of genes involved in biosynthesis and up-regulation of stress-responsive genes resembled transcriptional regulation patterns observed for anaerobic retentostats. The heat-shock tolerance in aerobic retentostats far exceeded previously reported levels in stationary-phase batch cultures. While in situ metabolic fluxes in retentostats were intentionally low due to extreme caloric restriction, off-line measurements revealed that cultures retained a high metabolic capacity. Conclusions This study provides the most accurate estimation yet of the maintenance-energy coefficient in aerobic cultures of S. cerevisiae, which is a key parameter for modelling of industrial aerobic, glucose-limited fed-batch processes. The observed extreme heat-shock tolerance and high metabolic capacity at near-zero growth rates demonstrate the intrinsic potential of S. cerevisiae as a robust, non-dividing microbial cell factory for energy-intensive products. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0501-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tim Vos
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Xavier D V Hakkaart
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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Splicing-Mediated Autoregulation Modulates Rpl22p Expression in Saccharomyces cerevisiae. PLoS Genet 2016; 12:e1005999. [PMID: 27097027 PMCID: PMC4838235 DOI: 10.1371/journal.pgen.1005999] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/30/2016] [Indexed: 01/07/2023] Open
Abstract
In Saccharomyces cerevisiae, splicing is critical for expression of ribosomal protein genes (RPGs), which are among the most highly expressed genes and are tightly regulated according to growth and environmental conditions. However, knowledge of the precise mechanisms by which RPG pre-mRNA splicing is regulated on a gene-by-gene basis is lacking. Here we show that Rpl22p has an extraribosomal role in the inhibition of splicing of the RPL22B pre-mRNA transcript. A stem loop secondary structure within the intron is necessary for pre-mRNA binding by Rpl22p in vivo and splicing inhibition in vivo and in vitro and can rescue splicing inhibition in vitro when added in trans to splicing reactions. Splicing inhibition by Rpl22p may be partly attributed to the reduction of co-transcriptional U1 snRNP recruitment to the pre-mRNA at the RPL22B locus. We further demonstrate that the inhibition of RPL22B pre-mRNA splicing contributes to the down-regulation of mature transcript during specific stress conditions, and provide evidence hinting at a regulatory role for this mechanism in conditions of suppressed ribosome biogenesis. These results demonstrate an autoregulatory mechanism that fine-tunes the expression of the Rpl22 protein and by extension Rpl22p paralog composition according to the cellular demands for ribosome biogenesis. Ribosomes are responsible for protein production in all living cells, serving as the grounds for the translation of genetic information from RNA to protein. Given the vital role of the ribosome in protein assembly, ribosome components are highly expressed and are subject to tight regulation. Some ribosomal proteins are also known to engage in extra-ribosomal activities. In our study, we demonstrate that the ribosomal protein Rpl22p is able to regulate its own expression by inhibiting the processing of its own RNA transcript, leading to degradation of the RNA. We also show that this self-imposed regulation plays a role in limiting RPL22 transcript levels in specific stress conditions. We suggest that this mechanism may impact the composition of ribosomes by influencing the availability of the Rpl22p paralogs.
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49
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Martí-Raga M, Marullo P, Beltran G, Mas A. Nitrogen modulation of yeast fitness and viability during sparkling wine production. Food Microbiol 2016. [DOI: 10.1016/j.fm.2015.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Chávez S, García-Martínez J, Delgado-Ramos L, Pérez-Ortín JE. The importance of controlling mRNA turnover during cell proliferation. Curr Genet 2016; 62:701-710. [PMID: 27007479 DOI: 10.1007/s00294-016-0594-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/13/2022]
Abstract
Microbial gene expression depends not only on specific regulatory mechanisms, but also on cellular growth because important global parameters, such as abundance of mRNAs and ribosomes, could be growth rate dependent. Understanding these global effects is necessary to quantitatively judge gene regulation. In the last few years, transcriptomic works in budding yeast have shown that a large fraction of its genes is coordinately regulated with growth rate. As mRNA levels depend simultaneously on synthesis and degradation rates, those studies were unable to discriminate the respective roles of both arms of the equilibrium process. We recently analyzed 80 different genomic experiments and found a positive and parallel correlation between both RNA polymerase II transcription and mRNA degradation with growth rates. Thus, the total mRNA concentration remains roughly constant. Some gene groups, however, regulate their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulate their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lower mRNA levels by reducing mRNA stability or the transcription rate, respectively. We critically review here these results and analyze them in relation to their possible extrapolation to other organisms and in relation to the new questions they open.
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Affiliation(s)
- Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - José García-Martínez
- Departamento de Genética, Universitat de València, Burjassot, Spain.,ERI Biotecmed, Universitat de València, Burjassot, Spain
| | - Lidia Delgado-Ramos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain. .,ERI Biotecmed, Universitat de València, Burjassot, Spain.
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