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Olaniran AO, Hiralal L, Mokoena MP, Pillay B. Flavour-active volatile compounds in beer: production, regulation and control. JOURNAL OF THE INSTITUTE OF BREWING 2017. [DOI: 10.1002/jib.389] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ademola O. Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science; University of KwaZulu-Natal; Private Bag X54001 Durban 4000 Republic of South Africa
| | - Lettisha Hiralal
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science; University of KwaZulu-Natal; Private Bag X54001 Durban 4000 Republic of South Africa
| | - Mduduzi P. Mokoena
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science; University of KwaZulu-Natal; Private Bag X54001 Durban 4000 Republic of South Africa
| | - Balakrishna Pillay
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science; University of KwaZulu-Natal; Private Bag X54001 Durban 4000 Republic of South Africa
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Lu C, Yin J, Zhao F, Li F, Lu W. Metabolomics analysis of the effect of dissolved oxygen on spinosad production by Saccharopolyspora spinosa. Antonie van Leeuwenhoek 2017; 110:677-685. [DOI: 10.1007/s10482-017-0835-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/19/2017] [Indexed: 11/30/2022]
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3
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Liang M, Zhou X, Xu C. Systems biology in biofuel. PHYSICAL SCIENCES REVIEWS 2016. [DOI: 10.1515/psr-2016-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Genetic Enhancement of Saccharomyces cerevisiae for First and Second Generation Ethanol Production. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1201/b19347-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Raut MP, Couto N, Pham TK, Evans C, Noirel J, Wright PC. Quantitative proteomic analysis of the influence of lignin on biofuel production by Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:113. [PMID: 27247624 PMCID: PMC4886415 DOI: 10.1186/s13068-016-0523-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/09/2016] [Indexed: 05/30/2023]
Abstract
BACKGROUND Clostridium acetobutylicum has been a focus of research because of its ability to produce high-value compounds that can be used as biofuels. Lignocellulose is a promising feedstock, but the lignin-cellulose-hemicellulose biomass complex requires chemical pre-treatment to yield fermentable saccharides, including cellulose-derived cellobiose, prior to bioproduction of acetone-butanol-ethanol (ABE) and hydrogen. Fermentation capability is limited by lignin and thus process optimization requires knowledge of lignin inhibition. The effects of lignin on cellular metabolism were evaluated for C. acetobutylicum grown on medium containing either cellobiose only or cellobiose plus lignin. Microscopy, gas chromatography and 8-plex iTRAQ-based quantitative proteomic technologies were applied to interrogate the effect of lignin on cellular morphology, fermentation and the proteome. RESULTS Our results demonstrate that C. acetobutylicum has reduced performance for solvent production when lignin is present in the medium. Medium supplemented with 1 g L(-1) of lignin led to delay and decreased solvents production (ethanol; 0.47 g L(-1) for cellobiose and 0.27 g L(-1) for cellobiose plus lignin and butanol; 0.13 g L(-1) for cellobiose and 0.04 g L(-1) for cellobiose plus lignin) at 20 and 48 h, respectively, resulting in the accumulation of acetic acid and butyric acid. Of 583 identified proteins (FDR < 1 %), 328 proteins were quantified with at least two unique peptides. Up- or down-regulation of protein expression was determined by comparison of exponential and stationary phases of cellobiose in the presence and absence of lignin. Of relevance, glycolysis and fermentative pathways were mostly down-regulated, during exponential and stationary growth phases in presence of lignin. Moreover, proteins involved in DNA repair, transcription/translation and GTP/ATP-dependent activities were also significantly affected and these changes were associated with altered cell morphology. CONCLUSIONS This is the first comprehensive analysis of the cellular responses of C. acetobutylicum to lignin at metabolic and physiological levels. These data will enable targeted metabolic engineering strategies to optimize biofuel production from biomass by overcoming limitations imposed by the presence of lignin.
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Affiliation(s)
- Mahendra P. Raut
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Narciso Couto
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Trong K. Pham
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Caroline Evans
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Josselin Noirel
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
- />Chaire de Bioinformatique, LGBA, Conservatoire National Des Arts Et Métiers, 75003 Paris, France
| | - Phillip C. Wright
- />The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
- />School of Chemical Engineering and Advanced Materials, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
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Elias E, Chandran C S, Chandran N, Souza FG, Thomas S. Segmental dynamics, morphology and thermomechanical properties of electrospun poly(ε-caprolactone) nanofibers in the presence of an interacting filler. RSC Adv 2016. [DOI: 10.1039/c5ra24251g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The effect of addition of an interacting nanofiller (Cloisite 10A) on the segmental dynamics, morphology and thermal stability of poly(ε-caprolactone) (PCL) is subjected to detailed investigation.
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Affiliation(s)
- Eldho Elias
- School of Chemical Science
- Mahatma Gandhi University
- Kottayam
- India
- International and Inter University Center for Nanoscience and Nanotechnology
| | - Sarath Chandran C
- School of Chemical Science
- Mahatma Gandhi University
- Kottayam
- India
- International and Inter University Center for Nanoscience and Nanotechnology
| | - Nithin Chandran
- School of Chemical Science
- Mahatma Gandhi University
- Kottayam
- India
- International and Inter University Center for Nanoscience and Nanotechnology
| | - Fernando G. Souza
- Programa de Engenharia Civil
- COPPE
- Universidade Federal de Rio de Janeiro
- Centro de Tecnologia – Cidade Universitária
- Brasil
| | - Sabu Thomas
- School of Chemical Science
- Mahatma Gandhi University
- Kottayam
- India
- International and Inter University Center for Nanoscience and Nanotechnology
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Stein K, Chiang HL. Exocytosis and Endocytosis of Small Vesicles across the Plasma Membrane in Saccharomyces cerevisiae. MEMBRANES 2014; 4:608-29. [PMID: 25192542 PMCID: PMC4194051 DOI: 10.3390/membranes4030608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/02/2014] [Accepted: 08/18/2014] [Indexed: 12/14/2022]
Abstract
When Saccharomyces cerevisiae is starved of glucose, the gluconeogenic enzymes fructose-1,6-bisphosphatase (FBPase), phosphoenolpyruvate carboxykinase, isocitrate lyase, and malate dehydrogenase, as well as the non-gluconeogenic enzymes glyceraldehyde-3-phosphate dehydrogenase and cyclophilin A, are secreted into the periplasm. In the extracellular fraction, these secreted proteins are associated with small vesicles that account for more than 90% of the total number of extracellular structures observed. When glucose is added to glucose-starved cells, FBPase is internalized and associated with clusters of small vesicles in the cytoplasm. Specifically, the internalization of FBPase results in the decline of FBPase and vesicles in the extracellular fraction and their appearance in the cytoplasm. The clearance of extracellular vesicles and vesicle-associated proteins from the extracellular fraction is dependent on the endocytosis gene END3. This internalization is regulated when cells are transferred from low to high glucose. It is rapidly occurring and is a high capacity process, as clusters of vesicles occupy 10%–20% of the total volume in the cytoplasm in glucose re-fed cells. FBPase internalization also requires the VPS34 gene encoding PI3K. Following internalization, FBPase is delivered to the vacuole for degradation, whereas proteins that are not degraded may be recycled.
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Affiliation(s)
- Kathryn Stein
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Hui-Ling Chiang
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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Hollinshead W, He L, Tang YJ. Biofuel production: an odyssey from metabolic engineering to fermentation scale-up. Front Microbiol 2014; 5:344. [PMID: 25071754 PMCID: PMC4088188 DOI: 10.3389/fmicb.2014.00344] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/20/2014] [Indexed: 12/21/2022] Open
Abstract
Metabolic engineering has developed microbial cell factories that can convert renewable carbon sources into biofuels. Current molecular biology tools can efficiently alter enzyme levels to redirect carbon fluxes toward biofuel production, but low product yield and titer in large bioreactors prevent the fulfillment of cheap biofuels. There are three major roadblocks preventing economical biofuel production. First, carbon fluxes from the substrate dissipate into a complex metabolic network. Besides the desired product, microbial hosts direct carbon flux to synthesize biomass, overflow metabolites, and heterologous enzymes. Second, microbial hosts need to oxidize a large portion of the substrate to generate both ATP and NAD(P)H to power biofuel synthesis. High cell maintenance, triggered by the metabolic burdens from genetic modifications, can significantly affect the ATP supply. Thereby, fermentation of advanced biofuels (such as biodiesel and hydrocarbons) often requires aerobic respiration to resolve the ATP shortage. Third, mass transfer limitations in large bioreactors create heterogeneous growth conditions and micro-environmental fluctuations (such as suboptimal O2 level and pH) that induce metabolic stresses and genetic instability. To overcome these limitations, fermentation engineering should merge with systems metabolic engineering. Modern fermentation engineers need to adopt new metabolic flux analysis tools that integrate kinetics, hydrodynamics, and 13C-proteomics, to reveal the dynamic physiologies of the microbial host under large bioreactor conditions. Based on metabolic analyses, fermentation engineers may employ rational pathway modifications, synthetic biology circuits, and bioreactor control algorithms to optimize large-scale biofuel production.
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Affiliation(s)
- Whitney Hollinshead
- Department of Energy, Environmental and Chemical Engineering, Washington University St. Louis, MO, USA
| | - Lian He
- Department of Energy, Environmental and Chemical Engineering, Washington University St. Louis, MO, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University St. Louis, MO, USA
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Giardina BJ, Stanley BA, Chiang HL. Glucose induces rapid changes in the secretome of Saccharomyces cerevisiae. Proteome Sci 2014; 12:9. [PMID: 24520859 PMCID: PMC3927832 DOI: 10.1186/1477-5956-12-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/31/2014] [Indexed: 12/14/2022] Open
Abstract
Background Protein secretion is a fundamental process in all living cells. Proteins can either be secreted via the classical or non-classical pathways. In Saccharomyces cerevisiae, gluconeogenic enzymes are in the extracellular fraction/periplasm when cells are grown in media containing low glucose. Following a transfer of cells to high glucose media, their levels in the extracellular fraction are reduced rapidly. We hypothesized that changes in the secretome were not restricted to gluconeogenic enzymes. The goal of the current study was to use a proteomic approach to identify extracellular proteins whose levels changed when cells were transferred from low to high glucose media. Results We performed two iTRAQ experiments and identified 347 proteins that were present in the extracellular fraction including metabolic enzymes, proteins involved in oxidative stress, protein folding, and proteins with unknown functions. Most of these proteins did not contain typical ER-Golgi signal sequences. Moreover, levels of many of these proteins decreased upon a transfer of cells from media containing low to high glucose media. Using an extraction procedure and Western blotting, we confirmed that the metabolic enzymes (glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, glucose-6-phosphate dehydrogenase, pyruvate decarboxylase), proteins involved in oxidative stress (superoxide dismutase and thioredoxin), and heat shock proteins (Ssa1p, Hsc82p, and Hsp104p) were in the extracellular fraction during growth in low glucose and that the levels of these extracellular proteins were reduced when cells were transferred to media containing high glucose. These proteins were associated with membranes in vesicle-enriched fraction. We also showed that small vesicles were present in the extracellular fraction in cells grown in low glucose. Following a transfer from low to high glucose media for 30 minutes, 98% of these vesicles disappeared from the extracellular fraction. Conclusions Our data indicate that transferring cells from low to high glucose media induces a rapid decline in levels of a large number of extracellular proteins and the disappearance of small vesicles from the extracellular fraction. Therefore, we conclude that the secretome undergoes dynamic changes during transition from glucose-deficient to glucose-rich media. Most of these extracellular proteins do not contain typical ER signal sequences, suggesting that they are secreted via the non-classical pathway.
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Affiliation(s)
| | | | - Hui-Ling Chiang
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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Lv YJ, Wang X, Ma Q, Bai X, Li BZ, Zhang W, Yuan YJ. Proteomic analysis reveals complex metabolic regulation in Saccharomyces cerevisiae cells against multiple inhibitors stress. Appl Microbiol Biotechnol 2014; 98:2207-21. [PMID: 24442506 DOI: 10.1007/s00253-014-5519-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 12/20/2013] [Accepted: 12/28/2013] [Indexed: 11/24/2022]
Abstract
Toxic compounds including acids, furans, and phenols (AFP) were generated from the pretreatment of lignocellulose. We cultivated Saccharomyces cerevisiae cells in a batch mode, besides the cell culture of original yeast strain in AFP-free medium which was referred as C0, three independent subcultures were cultivated under multiple inhibitors AFP and were referred as C1, C2, and C3 in time sequence. Comparing to C0, the cell density was lowered while the ethanol yield was maintained stably in the three yeast cultures under AFP stress, and the lag phase of C1 was extended while the lag phases of C2 and C3 were not extended. In proteomic analysis, 194 and 215 unique proteins were identified as differently expressed proteins at lag phase and exponential phase, respectively. Specifically, the yeast cells co-regulated protein folding and protein synthesis process to prevent the generation of misfolded proteins and to save cellular energy, they increased the activity of glycolysis, redirected metabolic flux towards phosphate pentose pathway and the biosynthesis of ethanol instead of the biosynthesis of glycerol and acetic acid, and they upregulated several oxidoreductases especially at lag phase and induced programmed cell death at exponential phase. When the yeast cells were cultivated under AFP stress, the new metabolism homeostasis in favor of cellular energy and redox homeostasis was generated in C1, then it was inherited and optimized in C2 and C3, enabling the yeast cells in C2 and C3 to enter the exponential phase in a short period after inoculation, which thus significantly shortened the fermentation time.
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Affiliation(s)
- Ya-Jin Lv
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, People's Republic of China
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12
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Kroll K, Pähtz V, Kniemeyer O. Elucidating the fungal stress response by proteomics. J Proteomics 2013; 97:151-63. [PMID: 23756228 DOI: 10.1016/j.jprot.2013.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/09/2013] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
Abstract
Fungal species need to cope with stress, both in the natural environment and during interaction of human- or plant pathogenic fungi with their host. Many regulatory circuits governing the fungal stress response have already been discovered. However, there are still large gaps in the knowledge concerning the changes of the proteome during adaptation to environmental stress conditions. With the application of proteomic methods, particularly 2D-gel and gel-free, LC/MS-based methods, first insights into the composition and dynamic changes of the fungal stress proteome could be obtained. Here, we review the recent proteome data generated for filamentous fungi and yeasts. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Kristin Kroll
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany
| | - Vera Pähtz
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), 07747 Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), 07747 Jena, Germany.
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Mutations of the TATA-binding protein confer enhanced tolerance to hyperosmotic stress in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2013; 97:8227-38. [PMID: 23709042 DOI: 10.1007/s00253-013-4985-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/28/2013] [Accepted: 05/05/2013] [Indexed: 11/27/2022]
Abstract
Previously, it was shown that overexpression of either of two SPT15 mutant alleles, SPT15-M2 and SPT15-M3, which encode mutant TATA-binding proteins, confer enhanced ethanol tolerance in Saccharomyces cerevisiae. In this study, we demonstrated that strains overexpressing SPT15-M2 or SPT15-M3 were tolerant to hyperosmotic stress caused by high concentrations of glucose, salt, and sorbitol. The enhanced tolerance to high glucose concentrations in particular improved ethanol production from very high gravity (VHG) ethanol fermentations. The strains displayed constitutive and sustained activation of Hog1, a central kinase in the high osmolarity glycerol (HOG) signal transduction pathway of S. cerevisiae. However, the cell growth defect known to be caused by constitutive and sustained activation of Hog1 was not observed. We also found that reactive oxygen species (ROS) were accumulated to a less extent upon exposure to high glucose concentration in our osmotolerant strains. We identified six new genes (GPH1, HSP12, AIM17, SSA4, USV1, and IGD1), the individual deletion of which renders cells sensitive to 50 % glucose. In spite of the presence of multiple copies of stress response element in their promoters, it was apparent that those genes were not controlled at the transcriptional level by the HOG pathway under the high glucose conditions. Combined with previously published results, overexpression of SPT15-M2 or SPT15-M3 clearly provides a basis for improved tolerance to ethanol and osmotic stress, which enables construction of strains of any genetic background that need enhanced tolerance to high concentrations of ethanol and glucose, promoting the feasibility for VHG ethanol fermentation.
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Huang EL, Orsat V, Shah MB, Hettich RL, VerBerkmoes NC, Lefsrud MG. The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique. J Proteomics 2012; 75:5206-14. [DOI: 10.1016/j.jprot.2012.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 05/07/2012] [Accepted: 06/04/2012] [Indexed: 01/23/2023]
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Giardina BJ, Stanley BA, Chiang HL. Comparative proteomic analysis of transition of saccharomyces cerevisiae from glucose-deficient medium to glucose-rich medium. Proteome Sci 2012; 10:40. [PMID: 22691627 PMCID: PMC3607935 DOI: 10.1186/1477-5956-10-40] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 05/29/2012] [Indexed: 12/26/2022] Open
Abstract
Background When glucose is added to Saccharomyces cerevisiae grown in non-fermentable carbon sources, genes encoding ribosomal, cell-cycle, and glycolytic proteins are induced. By contrast, genes involved in mitochondrial functions, gluconeogenesis, and the utilization of other carbon sources are repressed. Glucose also causes the activation of the plasma membrane ATPase and the inactivation of gluconeogenic enzymes and mitochondrial enzymes. The goals of this study were to use the iTRAQ-labeling mass spectrometry technique to identify proteins whose relative levels change in response to glucose re-feeding and to correlate changes in protein abundance with changes in transcription and enzymatic activities. We used an experimental condition that causes the degradation of gluconeogenic enzymes when glucose starved cells are replenished with glucose. Identification of these enzymes as being down-regulated by glucose served as an internal control. Furthermore, we sought to identify new proteins that were either up-regulated or down-regulated by glucose. Results We have identified new and known proteins that change their relative levels in cells that were transferred from medium containing low glucose to medium containing high glucose. Up-regulated proteins included ribosomal subunits, proteins involved in protein translation, and the plasma membrane ATPase. Down-regulated proteins included small heat shock proteins, mitochondrial proteins, glycolytic enzymes, and gluconeogenic enzymes. Ach1p is involved in acetate metabolism and is also down-regulated by glucose. Conclusions We have identified known proteins that have previously been reported to be regulated by glucose as well as new glucose-regulated proteins. Up-regulation of ribosomal proteins and proteins involved in translation may lead to an increase in protein synthesis and in nutrient uptake. Down-regulation of glycolytic enzymes, gluconeogenic enzymes, and mitochondrial proteins may result in changes in glycolysis, gluconeogenesis, and mitochondrial functions. These changes may be beneficial for glucose-starved cells to adapt to the addition of glucose.
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Affiliation(s)
- Bennett J Giardina
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
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Dos Santos SC, Teixeira MC, Cabrito TR, Sá-Correia I. Yeast toxicogenomics: genome-wide responses to chemical stresses with impact in environmental health, pharmacology, and biotechnology. Front Genet 2012; 3:63. [PMID: 22529852 PMCID: PMC3329712 DOI: 10.3389/fgene.2012.00063] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/03/2012] [Indexed: 01/20/2023] Open
Abstract
The emerging transdisciplinary field of Toxicogenomics aims to study the cell response to a given toxicant at the genome, transcriptome, proteome, and metabolome levels. This approach is expected to provide earlier and more sensitive biomarkers of toxicological responses and help in the delineation of regulatory risk assessment. The use of model organisms to gather such genomic information, through the exploitation of Omics and Bioinformatics approaches and tools, together with more focused molecular and cellular biology studies are rapidly increasing our understanding and providing an integrative view on how cells interact with their environment. The use of the model eukaryote Saccharomyces cerevisiae in the field of Toxicogenomics is discussed in this review. Despite the limitations intrinsic to the use of such a simple single cell experimental model, S. cerevisiae appears to be very useful as a first screening tool, limiting the use of animal models. Moreover, it is also one of the most interesting systems to obtain a truly global understanding of the toxicological response and resistance mechanisms, being in the frontline of systems biology research and developments. The impact of the knowledge gathered in the yeast model, through the use of Toxicogenomics approaches, is highlighted here by its use in prediction of toxicological outcomes of exposure to pesticides and pharmaceutical drugs, but also by its impact in biotechnology, namely in the development of more robust crops and in the improvement of yeast strains as cell factories.
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Affiliation(s)
- Sandra C Dos Santos
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Technical University of Lisbon Lisbon, Portugal
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Abstract
Whilst the study of yeast genomes and transcriptomes is in an advanced state, there is still much to learn about the resulting proteins in terms of cataloging, characterization of post-translational modifications, turnover, and the dynamics of sub-cellular localization and interactions. Analysis of the transcripts gives little insight into function or diversity as changes in RNA levels do not always correlate with the resulting protein abundance. A number of global and targeted attempts have been made to catalog and characterize the yeast proteome and we describe here the methods used to gain a greater understanding of the yeast proteome. This comprehensive review also describes future approaches that will aid completion in identifying and characterizing the remaining 20% of the undetermined yeast proteome as well as giving new insight into protein dynamics.
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Affiliation(s)
- Johanna Rees
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
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Puligundla P, Smogrovicova D, Obulam VSR, Ko S. Very high gravity (VHG) ethanolic brewing and fermentation: a research update. J Ind Microbiol Biotechnol 2011; 38:1133-44. [DOI: 10.1007/s10295-011-0999-3] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 06/07/2011] [Indexed: 11/30/2022]
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Szopinska A, Morsomme P. Quantitative Proteomic Approaches and Their Application in the Study of Yeast Stress Responses. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:639-49. [DOI: 10.1089/omi.2010.0045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Aleksandra Szopinska
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud Louvain-la-Neuve, Belgium
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Teixeira MC, Raposo LR, Palma M, Sá-Correia I. Identification of genes required for maximal tolerance to high-glucose concentrations, as those present in industrial alcoholic fermentation media, through a chemogenomics approach. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:201-10. [PMID: 20210661 DOI: 10.1089/omi.2009.0149] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chemogenomics, the study of genomic responses to chemical compounds, has the potential to elucidate the basis of cellular resistance to those chemicals. This knowledge can be applied to improve the performance of strains of industrial interest. In this study, a collection of approximately 5,000 haploid single deletion mutants of Saccharomyces cerevisiae in which each nonessential yeast gene was individually deleted, was screened for strains with increased susceptibility toward stress induced by high-glucose concentration (30% w/v), one of the main stresses occurring during industrial alcoholic fermentation processes aiming the production of alcoholic beverages or bio-ethanol. Forty-four determinants of resistance to high-glucose stress were identified. The most significant Gene Ontology (GO) terms enriched in this dataset are vacuolar organization, late endosome to vacuole transport, and regulation of transcription. Clustering the identified resistance determinants by their known physical and genetic interactions further highlighted the importance of nutrient metabolism control in this context. A concentration of 30% (w/v) of glucose was found to perturb vacuolar function, by reducing cell ability to maintain the physiological acidification of the vacuolar lumen. This stress also affects the active rate of proton efflux through the plasma membrane. Based on results of published studies, the present work revealed shared determinants of yeast resistance to high-glucose and ethanol stresses, including genes involved in vacuolar function, cell wall biogenesis (ANP1), and in the transcriptional control of nutrient metabolism (GCN4 and GCR1), with possible impact on the design of more robust strains to be used in industrial alcoholic fermentation processes.
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Affiliation(s)
- Miguel C Teixeira
- IBB-Institute for Biotechnology and BioEngineering, Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Lisboa, Portugal
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Guidi F, Francesca G, Magherini F, Francesca M, Gamberi T, Tania G, Borro M, Marina B, Simmaco M, Maurizio S, Modesti A, Alessandra M. Effect of different glucose concentrations on proteome of Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1516-25. [PMID: 20362699 DOI: 10.1016/j.bbapap.2010.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 03/16/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
Abstract
We performed a proteomic study to understand how Saccharomyces cerevisiae adapts its metabolism during the exponential growth on three different concentrations of glucose; this information will be necessary to understand yeast carbon metabolism in different environments. We induced a natural diauxic shift by growing yeast cells in glucose restriction thus having a fast and complete glucose exhaustion. We noticed differential expressions of groups of proteins. Cells in high glucose have a decreased growth rate during the initial phase of fermentation; in glucose restriction and in high glucose we found an over-expression of a protein (Peroxiredoxin) involved in protection against oxidative stress insult. The information obtained in our study validates the application of a proteomic approach for the identification of the molecular bases of environmental variations such as fermentation in high glucose and during a naturally induced diauxic shift.
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Affiliation(s)
- Francesca Guidi
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni, 50, 50134 Firenze, Italy
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22
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Lin FM, Tan Y, Yuan YJ. Temporal quantitative proteomics of Saccharomyces cerevisiae in response to a nonlethal concentration of furfural. Proteomics 2009; 9:5471-83. [DOI: 10.1002/pmic.200900100] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Blankley RT, Gaskell SJ, Whetton AD, Dive C, Baker PN, Myers JE. A proof-of-principle gel-free proteomics strategy for the identification of predictive biomarkers for the onset of pre-eclampsia. BJOG 2009; 116:1473-80. [DOI: 10.1111/j.1471-0528.2009.02283.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Nam H, Lee J, Lee D. Computational identification of altered metabolism using gene expression and metabolic pathways. Biotechnol Bioeng 2009; 103:835-43. [PMID: 19378263 DOI: 10.1002/bit.22320] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Understanding altered metabolism is an important issue because altered metabolism is often revealed as a cause or an effect in pathogenesis. It has also been shown to be an important factor in the manipulation of an organism's metabolism in metabolic engineering. Unfortunately, it is not yet possible to measure the concentration levels of all metabolites in the genome-wide scale of a metabolic network; consequently, a method that infers the alteration of metabolism is beneficial. The present study proposes a computational method that identifies genome-wide altered metabolism by analyzing functional units of KEGG pathways. As control of a metabolic pathway is accomplished by altering the activity of at least one rate-determining step enzyme, not all gene expressions of enzymes in the pathway demonstrate significant changes even if the pathway is altered. Therefore, we measure the alteration levels of a metabolic pathway by selectively observing expression levels of significantly changed genes in a pathway. The proposed method was applied to two strains of Saccharomyces cerevisiae gene expression profiles measured in very high-gravity (VHG) fermentation. The method identified altered metabolic pathways whose properties are related to ethanol and osmotic stress responses which had been known to be observed in VHG fermentation because of the high sugar concentration in growth media and high ethanol concentration in fermentation products. With the identified altered pathways, the proposed method achieved best accuracy and sensitivity rates for the Red Star (RS) strain compared to other three related studies (gene-set enrichment analysis (GSEA), significance analysis of microarray to gene set (SAM-GS), reporter metabolite), and for the CEN.PK 113-7D (CEN) strain, the proposed method and the GSEA method showed comparably similar performances.
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Affiliation(s)
- Hojung Nam
- Department of Bio and Brain Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu, Daejeon, Republic of Korea
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25
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McDonagh B, Ogueta S, Lasarte G, Padilla CA, Bárcena JA. Shotgun redox proteomics identifies specifically modified cysteines in key metabolic enzymes under oxidative stress in Saccharomyces cerevisiae. J Proteomics 2009; 72:677-89. [PMID: 19367685 DOI: 10.1016/j.jprot.2009.01.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Post-translational redox modification of thiol groups can form the molecular basis of antioxidative protection and redox control. We have implemented a shotgun redox proteomic technique to identify the precise cysteines reversibly oxidised in key proteins. The method was applied to Saccharomyces cerevisiae subjected to peroxide treatment. Enrichment by covalent redox affinity chromatography allowed the isolation of a "redox subpeptidome" that was analysed by LC-MS/MS. Unique peptides containing specific reversibly oxidised cysteines were used to identify over 70 proteins in control and treated samples of which 27 were consistently present in all replicates. In most cases, the redox modification negatively affects their function and slows down their metabolic pathways. Integration of the data provides a snapshot consistent with a metabolic defensive strategy, regulating key enzymes by redox modification, redirecting energy toward ribulose-5-phosphate recycling for NADPH production and antioxidative defence.This generally applicable method has allowed us to discover new redox regulated proteins (DAHP and carbamoylphosphate synthases, Doa1p) and to precisely identify target cysteines in a number of known ones.
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Affiliation(s)
- Brian McDonagh
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Universidad de Córdoba, Cordoba, Spain
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Cheng JS, Zhou X, Ding MZ, Yuan YJ. Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation. Appl Microbiol Biotechnol 2009; 83:909-23. [PMID: 19488749 DOI: 10.1007/s00253-009-2037-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 05/03/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022]
Abstract
The responses and adaptation mechanisms of the industrial Saccharomyces cerevisiae to vacuum fermentation were explored using proteomic approach. After qualitative and quantitative analyses, a total of 106 spots corresponding to 68 different proteins were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The differentially expressed proteins were involved in amino acid and carbohydrate metabolisms, various signal pathways (Ras/MAPK, Ras-cyclic adenosine monophosphate, and HOG pathway), and heat shock and oxidative responses. Among them, alternations in levels of 17 proteins associated with carbohydrate metabolisms, in particular, the upregulations of proteins involved in glycolysis, trehalose biosynthesis, and the pentose phosphate pathway, suggested vacuum-induced redistribution of the metabolic fluxes. The upregulation of 17 heat stress and oxidative response proteins indicated that multifactors contributed to oxidative stresses by affecting cell redox homeostasis. Taken together with upregulation in 14-3-3 proteins levels, 22 proteins were detected in multispots, respectively, indicating that vacuum might have promoted posttranslational modifications of some proteins in S. cerevisiae. Further investigation revealed that the elevations of the differentially expressed proteins were mainly derived from vacuum stress rather than the absence of oxygen. These findings provide new molecular mechanisms for understanding of adaptation and tolerance of yeast to vacuum fermentation.
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Zhao XQ, Bai FW. Mechanisms of yeast stress tolerance and its manipulation for efficient fuel ethanol production. J Biotechnol 2009; 144:23-30. [PMID: 19446584 DOI: 10.1016/j.jbiotec.2009.05.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 04/28/2009] [Accepted: 05/06/2009] [Indexed: 11/17/2022]
Abstract
Yeast strains of Saccharomyces cerevisiae have been extensively studied in recent years for fuel ethanol production, in which yeast cells are exposed to various stresses such as high temperature, ethanol inhibition, and osmotic pressure from product and substrate sugars as well as the inhibitory substances released from the pretreatment of lignocellulosic biomass. An in-depth understanding of the mechanism of yeast stress tolerance contributes to breeding more robust strains for ethanol production, especially under very high gravity conditions. Taking advantage of the "omics" technology, the stress response and defense mechanism of yeast cells during ethanol fermentation were further explored, and the newly emerged tools such as genome shuffling and global transcription machinery engineering have been applied to breed stress resistant yeast strains for ethanol production. In this review, the latest development of stress tolerance mechanisms was focused, and improvement of yeast stress tolerance by both random and rational tools was presented.
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Affiliation(s)
- X Q Zhao
- Department of Bioscience and Bioengineering, Dalian University of Technology, China
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28
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Lacerda CMR, Reardon KF. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:75-87. [PMID: 19279070 DOI: 10.1093/bfgp/elp005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.
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Affiliation(s)
- Carla M R Lacerda
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA
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29
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Cheng JS, Qiao B, Yuan YJ. Comparative proteome analysis of robust Saccharomyces cerevisiae insights into industrial continuous and batch fermentation. Appl Microbiol Biotechnol 2008; 81:327-38. [DOI: 10.1007/s00253-008-1733-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 09/22/2008] [Accepted: 09/25/2008] [Indexed: 10/21/2022]
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30
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Pham TK, Wright PC. The Proteomic Response of Saccharomyces cerevisiae in Very High Glucose Conditions with Amino Acid Supplementation. J Proteome Res 2008; 7:4766-74. [DOI: 10.1021/pr800331s] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Trong Khoa Pham
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
| | - Phillip C. Wright
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
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31
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Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol 2008; 19:228-34. [PMID: 18515068 DOI: 10.1016/j.copbio.2008.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 05/05/2008] [Accepted: 05/07/2008] [Indexed: 01/23/2023]
Abstract
Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.
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Pham TK, Wright PC. Proteomic Analysis of Calcium Alginate-Immobilized Saccharomyces cerevisiae under High-Gravity Fermentation Conditions. J Proteome Res 2008; 7:515-25. [DOI: 10.1021/pr070391h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Trong Khoa Pham
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Phillip C. Wright
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
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33
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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