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Sirisena S, Chan S, Roberts N, Dal Maso S, Gras SL, J O Martin G. Influence of yeast growth conditions and proteolytic enzymes on the amino acid profiles of yeast hydrolysates: Implications for taste and nutrition. Food Chem 2024; 437:137906. [PMID: 37939420 DOI: 10.1016/j.foodchem.2023.137906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/10/2023]
Abstract
This study investigated the effects of aerobic and anaerobic growth and proteolytic enzymes on the amino acid content of yeast hydrolysates in relation to taste and nutrition. Saccharomyces cerevisiae ATCC5574 was grown under fed-batch aerobic or batch anaerobic conditions. Intracellular glutamic acid (Glu) concentrations were 18-fold higher in aerobic yeast. Hydrolysis with papain and alkaline protease released more amino acids (AA) than simple autolysis or hydrolysis with bromelain, most significantly when applied to aerobic yeast (∼2-fold increase). Autolysates and bromelain hydrolysates from aerobic yeast had low levels of bitter and essential AAs, with high levels of umami Glu. Papain and alkaline protease hydrolysates of aerobic yeast had high levels of umami, bitter and essential AAs. Autolysates/hydrolysates from anaerobic yeast had moderate, high, and low levels of bitter, essential and umami AAs. Selection of both yeast growth conditions and hydrolysis enzyme can manipulate the free AA profile and yield of hydrolysates.
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Affiliation(s)
- Sameera Sirisena
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sitha Chan
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nic Roberts
- Bega Foods, 1 Vegemite Way, Port Melbourne, Victoria 3207, Australia
| | - Sandra Dal Maso
- Bega Foods, 1 Vegemite Way, Port Melbourne, Victoria 3207, Australia
| | - Sally L Gras
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia; The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gregory J O Martin
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
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2
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Ridder MD, van den Brandeler W, Altiner M, Daran-Lapujade P, Pabst M. Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast. Mol Cell Proteomics 2023; 22:100552. [PMID: 37076048 DOI: 10.1016/j.mcpro.2023.100552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimising biosynthetic routes. Recent studies have demonstrated the potential of resource and proteomic allocation data in enhancing models for metabolic processes. However, comprehensive and accurate proteome dynamics data that can be used for such approaches are still very limited. Therefore, we performed a quantitative proteome dynamics study to comprehensively cover the transition from exponential to stationary phase for both aerobically and anaerobically grown yeast cells. The combination of highly controlled reactor experiments, biological replicates and standardised sample preparation procedures ensured reproducibility and accuracy. Additionally, we selected the CEN.PK lineage for our experiments because of its relevance for both fundamental and applied research. Together with the prototrophic, standard haploid strain CEN.PK113-7D, we also investigated an engineered strain with genetic minimisation of the glycolytic pathway, resulting in the quantitative assessment of 54 proteomes. The anaerobic cultures showed remarkably less proteome-level changes compared to the aerobic cultures, during transition from the exponential to the stationary phase as a consequence of the lack of the diauxic shift in the absence of oxygen. These results support the notion that anaerobically growing cells lack resources to adequately adapt to starvation. This proteome dynamics study constitutes an important step towards better understanding of the impact of glucose exhaustion and oxygen on the complex proteome allocation process in yeast. Finally, the established proteome dynamics data provide a valuable resource for the development of resource allocation models as well as for metabolic engineering efforts.
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Affiliation(s)
- Maxime den Ridder
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wiebeke van den Brandeler
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Meryem Altiner
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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3
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Morales-Amparano MB, Ramos-Clamont Montfort G, Baqueiro-Peña I, Robles-Burgueño MDR, Vázquez-Moreno L, Huerta-Ocampo JÁ. Proteomic response of Saccharomyces boulardii to simulated gastrointestinal conditions and encapsulation. Food Sci Biotechnol 2019; 28:831-840. [PMID: 31093441 PMCID: PMC6484100 DOI: 10.1007/s10068-018-0508-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 12/31/2022] Open
Abstract
Probiotics are live microorganisms conferring health benefits when administered in adequate amounts. However, the passage through the gastrointestinal tract represents a challenge due to pH variations, proteases, and bile salts. This study aimed to evaluate the proteomic response of Saccharomyces boulardii to simulated gastrointestinal digestion and the influence of encapsulation on yeast viability. Different pH values and time periods simulating the passage through different sections of the gastrointestinal tract were applied to unencapsulated and encapsulated yeasts. Encapsulation in 0.5% calcium alginate did not improve yeast survival or induce changes in protein patterns whereas protein extracts from control and digested yeasts showed remarkable differences when separated by SDS-PAGE. Protein bands were analyzed by tandem mass spectrometry. Protein identification revealed unique proteins that changed acutely in abundance after simulated digestion. Carbohydrate metabolism, protein processing, and oxide-reduction were the biological processes most affected by simulated gastrointestinal digestion in S. boulardii.
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Affiliation(s)
- Martha Beatriz Morales-Amparano
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - Gabriela Ramos-Clamont Montfort
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - Itzamná Baqueiro-Peña
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - María del Refugio Robles-Burgueño
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - Luz Vázquez-Moreno
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - José Ángel Huerta-Ocampo
- CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
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4
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Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism. PLoS One 2017; 12:e0172742. [PMID: 28241048 PMCID: PMC5328394 DOI: 10.1371/journal.pone.0172742] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/08/2017] [Indexed: 12/25/2022] Open
Abstract
Central carbon metabolism is controlled by modulating the protein abundance profiles of enzymes that maintain the essential systems in living organisms. In this study, metabolic adaptation mechanisms in the model organism Saccharomyces cerevisiae were investigated by direct determination of enzyme abundance levels in 30 wild type and mutant strains. We performed a targeted proteome analysis using S. cerevisiae strains that lack genes encoding the enzymes responsible for central carbon metabolism. Our analysis revealed that at least 30% of the observed variations in enzyme abundance levels could be explained by global regulatory mechanisms. A enzyme-enzyme co-abundance analysis revealed that the abundances of enzyme proteins involved in the trehalose metabolism and glycolysis changed in a coordinated manner under the control of the transcription factors for global regulation. The remaining variations were derived from local mechanisms such as a mutant-specific increase in the abundances of remote enzymes. The proteome data also suggested that, although the functional compensation of the deficient enzyme was attained by using more resources for protein biosynthesis, available resources for the biosynthesis of the enzymes responsible for central metabolism were not abundant in S. cerevisiae cells. These results showed that global and local regulation of enzyme abundance levels shape central carbon metabolism in S. cerevisiae by using a limited resource for protein biosynthesis.
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Li B, Tian X, Wang C, Zeng X, Xing Y, Ling H, Yin W, Tian L, Meng Z, Zhang J, Guo S. SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus. Sci Rep 2017; 7:41283. [PMID: 28134344 PMCID: PMC5278369 DOI: 10.1038/srep41283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/19/2016] [Indexed: 02/03/2023] Open
Abstract
Understanding the initiation and maturing mechanisms is important for rational manipulating sclerotia differentiation and growth from hypha of Polyporus umbellatus. Proteomes in P. umbellatus sclerotia and hyphae at initial, developmental and mature phases were studied. 1391 proteins were identified by nano-liquid chromatograph-mass spectrometry (LC-MS) in Data Dependant Acquisition mode, and 1234 proteins were quantified successfully by Sequential Window Acquisition of all THeoretical fragment ion spectra-MS (SWATH-MS) technology. There were 347 differentially expressed proteins (DEPs) in sclerotia at initial phase compared with those in hypha, and the DEP profiles were dynamically changing with sclerotia growth. Oxidative stress (OS) in sclerotia at initial phase was indicated by the repressed proteins of respiratory chain, tricarboxylic acid cycle and the activation of glycolysis/gluconeogenesis pathways were determined based on DEPs. The impact of glycolysis/gluconeogenesis on sclerotium induction was further verified by glycerol addition assays, in which 5% glycerol significantly increased sclerotial differentiation rate and biomass. It can be speculated that OS played essential roles in triggering sclerotia differentiation from hypha of P. umbellatus, whereas antioxidant activity associated with glycolysis is critical for sclerotia growth. These findings reveal a mechanism for sclerotial differentiation in P. umbellatus, which may also be applicable for other fungi.
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Affiliation(s)
- Bing Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Xiaofang Tian
- Pharmaceutical department of China-Japan Friendship Hospital, Beijing 100029 P. R. China
| | - Chunlan Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Xu Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Yongmei Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Hong Ling
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Wanqiang Yin
- Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Lixia Tian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Zhixia Meng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193 P. R. China
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Hung CW, Klein T, Cassidy L, Linke D, Lange S, Anders U, Bureik M, Heinzle E, Schneider K, Tholey A. Comparative Proteome Analysis in Schizosaccharomyces pombe Identifies Metabolic Targets to Improve Protein Production and Secretion. Mol Cell Proteomics 2016; 15:3090-3106. [PMID: 27477394 DOI: 10.1074/mcp.m115.051474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 01/09/2023] Open
Abstract
Protein secretion in yeast is a complex process and its efficiency depends on a variety of parameters. We performed a comparative proteome analysis of a set of Schizosaccharomyces pombe strains producing the α-glucosidase maltase in increasing amounts to investigate the overall proteomic response of the cell to the burden of protein production along the various steps of protein production and secretion. Proteome analysis of these strains, utilizing an isobaric labeling/two dimensional LC-MALDI MS approach, revealed complex changes, from chaperones and secretory transport machinery to proteins controlling transcription and translation. We also found an unexpectedly high amount of changes in enzyme levels of the central carbon metabolism and a significant up-regulation of several amino acid biosyntheses. These amino acids were partially underrepresented in the cellular protein compared with the composition of the model protein. Additional feeding of these amino acids resulted in a 1.5-fold increase in protein secretion. Membrane fluidity was identified as a second bottleneck for high-level protein secretion and addition of fluconazole to the culture caused a significant decrease in ergosterol levels, whereas protein secretion could be further increased by a factor of 2.1. In summary, we show that high level protein secretion causes global changes of protein expression levels in the cell and that precursor availability and membrane composition limit protein secretion in this yeast. In this respect, comparative proteome analysis is a powerful tool to identify targets for an efficient increase of protein production and secretion in S. pombe Data are available via ProteomeXchange with identifiers PXD002693 and PXD003016.
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Affiliation(s)
- Chien-Wen Hung
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tobias Klein
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Liam Cassidy
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Dennis Linke
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Sabrina Lange
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Uwe Anders
- ¶Roche Diagnostics GmbH, 68305 Mannheim, Germany
| | - Matthias Bureik
- ‖PomBioTech GmbH, 66123 Saarbrücken, Germany; **School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Elmar Heinzle
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Konstantin Schneider
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Andreas Tholey
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany;
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7
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Çakır T. Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach. Sci Rep 2015; 5:14563. [PMID: 26411587 PMCID: PMC4585941 DOI: 10.1038/srep14563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 08/28/2015] [Indexed: 12/16/2022] Open
Abstract
A systems-based investigation of the effect of perturbations on metabolic machinery is crucial to elucidate the mechanism behind perturbations. One way to investigate the perturbation-induced changes within the cell metabolism is to focus on pathway-level effects. In this study, three different perturbation types (genetic, environmental and disease-based) are analyzed to compute a list of reporter pathways, metabolic pathways which are significantly affected from a perturbation. The most common omics data type, transcriptome, is used as an input to the bioinformatic analysis. The pathways are scored by two alternative approaches: by averaging the changes in the expression levels of the genes controlling the associated reactions (reaction-centric), and by averaging the changes in the associated metabolites which were scored based on the associated genes (metabolite-centric). The analysis reveals the superiority of the novel metabolite-centric approach over the commonly used reaction-centric approach since it is based on metabolites which better represent the cross-talk among different pathways, enabling a more global and realistic cataloguing of network-wide perturbation effects.
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Affiliation(s)
- Tunahan Çakır
- Gebze Technical University, Department of Bioengineering, 41400, Gebze, Kocaeli, Turkey
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8
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Wolf AS, Grayhack EJ. Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats. RNA (NEW YORK, N.Y.) 2015; 21:935-45. [PMID: 25792604 PMCID: PMC4408800 DOI: 10.1261/rna.049080.114] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/14/2015] [Indexed: 05/09/2023]
Abstract
Quality control systems monitor and stop translation at some ribosomal stalls, but it is unknown if halting translation at such stalls actually prevents synthesis of abnormal polypeptides. In yeast, ribosome stalling occurs at Arg CGA codon repeats, with even two consecutive CGA codons able to reduce translation by up to 50%. The conserved eukaryotic Asc1 protein limits translation through internal Arg CGA codon repeats. We show that, in the absence of Asc1 protein, ribosomes continue translating at CGA codons, but undergo substantial frameshifting with dramatically higher levels of frameshifting occurring with additional repeats of CGA codons. Frameshifting depends upon the slow or inefficient decoding of these codons, since frameshifting is suppressed by increased expression of the native tRNA(Arg(ICG)) that decodes CGA codons by wobble decoding. Moreover, the extent of frameshifting is modulated by the position of the CGA codon repeat relative to the translation start site. Thus, translation fidelity depends upon Asc1-mediated quality control.
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Affiliation(s)
- Andrew S Wolf
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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9
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Anhydrobiosis in yeast: is it possible to reach anhydrobiosis for yeast grown in conditions with severe oxygen limitation? Antonie van Leeuwenhoek 2014; 106:211-7. [PMID: 24791685 DOI: 10.1007/s10482-014-0182-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/18/2014] [Indexed: 01/26/2023]
Abstract
The yeast Saccharomyces cerevisiae was shown to be extremely sensitive to dehydration-rehydration treatments when stationary phase cells were subjected to conditions of severe oxygen limitation, unlike the same cells grown in aerobic conditions. The viability of dehydrated anaerobically grown yeast cells never exceeded 2 %. It was not possible to increase this viability using gradual rehydration of dry cells in water vapour, which usually strongly reduces damage to intracellular membranes. Specific pre-dehydration treatments significantly increased the resistance of anaerobic yeast to drying. Thus, incubation of cells with trehalose (100 mM), increased the viability of dehydrated cells after slow rehydration in water vapour to 30 %. Similarly, pre-incubation of cells in 1 M xylitol or glycerol enabled up to 50-60 % of cells to successfully enter a viable state of anhydrobiosis after subsequent rehydration. We presume that trehalose and sugar alcohols function mainly according to a water replacement hypothesis, as well as initiating various protective intracellular reactions.
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10
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Song J, Tamura Y, Yoshihisa T, Endo T. A novel import route for an N-anchor mitochondrial outer membrane protein aided by the TIM23 complex. EMBO Rep 2014; 15:670-7. [PMID: 24781694 DOI: 10.1002/embr.201338142] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The membrane topology of Om45 in the yeast mitochondrial outer membrane (OM) is under debate. Here, we confirm that Om45 is anchored to the OM from the intermembrane space (IMS) by its N-terminal hydrophobic segment. We show that import of Om45 requires the presequence receptors, Tom20 and Tom22, and the import channel of Tom40. Unlike any of the known OM proteins, Om45 import requires the TIM23 complex in the inner membrane, a translocator for presequence-containing proteins, and the membrane potential (ΔΨ). Therefore, Om45 is anchored to the OM via the IMS by a novel import pathway involving the TIM23 complex.
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Affiliation(s)
- Jiyao Song
- Department of Chemistry, Graduate School of Science Nagoya University, Chikusa-ku Nagoya, Japan
| | - Yasushi Tamura
- Research Center for Materials Science Nagoya University, Chikusa-ku Nagoya, Japan
| | - Tohru Yoshihisa
- Graduate School of Life Science University of Hyogo, Hyogo, Japan
| | - Toshiya Endo
- Department of Chemistry, Graduate School of Science Nagoya University, Chikusa-ku Nagoya, Japan Structural Biology Research Center Nagoya University, Chikusa-ku Nagoya, Japan JST CREST Nagoya University, Chikusa-ku Nagoya, Japan
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11
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He X, Zhu X, Wang X, Wang W, Dai Y, Yan Q. Nuclear modifier MTO2 modulates the aminoglycoside-sensitivity of mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae. PLoS One 2013; 8:e81490. [PMID: 24339937 PMCID: PMC3858254 DOI: 10.1371/journal.pone.0081490] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 10/14/2013] [Indexed: 12/23/2022] Open
Abstract
The phenotypic manifestations of mitochondrial DNA (mtDNA) mutations are modulated by mitochondrial DNA haplotypes, nuclear modifier genes and environmental factors. The yeast mitochondrial 15S rRNA C1477G (PR or PR454) mutation corresponds to the human 12S rRNA C1494T and A1555G mutations, which are well known as primary factors for aminoglycoside-induced nonsyndromic deafness. Here we report that the deletion of the nuclear modifier gene MTO2 suppressed the aminoglycoside-sensitivity of mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae. First, the strain with a single mtDNA C1477G mutation exhibited hypersensitivity to neomycin. Functional assays indicated that the steady-state transcription level of mitochondrial DNA, the mitochondrial respiratory rate, and the membrane potential decreased significantly after neomycin treatment. The impaired mitochondria could not produce sufficient energy to maintain cell viability. Second, when the mto2 null and the mitochondrial C1477G mutations co-existed (mto2(PR)), the oxygen consumption rate in the double mutant decreased markedly compared to that of the control strains (MTO2(PS), mto2(PS) and MTO2(PR)). The expression levels of the key glycolytic genes HXK2, PFK1 and PYK1 in the mto2(PR) strain were stimulated by neomycin and up-regulated by 89%, 112% and 55%, respectively. The enhanced glycolysis compensated for the respiratory energy deficits, and could be inhibited by the glycolytic enzyme inhibitor. Our findings in yeast will provide a new insight into the pathogenesis of human deafness.
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Affiliation(s)
- Xiangyu He
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoyu Zhu
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xuexiang Wang
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Wang
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Dai
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qingfeng Yan
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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12
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Usbeck JC, Kern CC, Vogel RF, Behr J. Optimization of experimental and modelling parameters for the differentiation of beverage spoiling yeasts by Matrix-Assisted-Laser-Desorption/Ionization–Time-of-Flight Mass Spectrometry (MALDI–TOF MS) in response to varying growth conditions. Food Microbiol 2013; 36:379-87. [DOI: 10.1016/j.fm.2013.07.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/30/2013] [Accepted: 07/12/2013] [Indexed: 01/24/2023]
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13
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Rachfall N, Schmitt K, Bandau S, Smolinski N, Ehrenreich A, Valerius O, Braus GH. RACK1/Asc1p, a ribosomal node in cellular signaling. Mol Cell Proteomics 2012; 12:87-105. [PMID: 23071099 DOI: 10.1074/mcp.m112.017277] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
RACK1/Asc1p and its essential orthologues in higher eukaryotes, such as RACK1 in metazoa, are involved in several distinct cellular signaling processes. The implications of a total deletion have never been assessed in a comprehensive manner. This study reveals the major cellular processes affected in a Saccharomyces cerevisiae Δasc1 deletion background via de novo proteome and transcriptome analysis, as well as subsequent phenotypical characterizations. The deletion of ASC1 reduces iron uptake and causes nitrosative stress, both known indicators for hypoxia, which manifests in a shift of energy metabolism from respiration to fermentation in the Δasc1 strain. Asc1p further impacts cellular metabolism through its regulative role in the MAP kinase signal transduction pathways of invasive/filamentous growth and cell wall integrity. In the Δasc1 mutant strain, aberrations from the expected cellular response, mediated by these pathways, can be observed and are linked to changes in protein abundances of pathway-targeted transcription factors. Evidence of the translational regulation of such transcription factors suggests that ribosomal Asc1p is involved in signal transduction pathways and controls the biosynthesis of the respective final transcriptional regulators.
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Affiliation(s)
- Nicole Rachfall
- Institute of Microbiology and Genetics, Georg-August Universität, D-37077 Göttingen, Germany
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14
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Gelis S, Curto M, Valledor L, González A, Ariño J, Jorrín J, Ramos J. Adaptation to potassium starvation of wild-type and K(+)-transport mutant (trk1,2) of Saccharomyces cerevisiae: 2-dimensional gel electrophoresis-based proteomic approach. Microbiologyopen 2012; 1:182-93. [PMID: 22950024 PMCID: PMC3426419 DOI: 10.1002/mbo3.23] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 03/29/2012] [Accepted: 05/03/2012] [Indexed: 01/20/2023] Open
Abstract
Saccharomyces cerevisiae wild-type (BY4741) and the corresponding mutant lacking the plasma membrane main potassium uptake systems (trk1,trk2) were used to analyze the consequences of K(+) starvation following a proteomic approach. In order to trigger high-affinity mode of potassium transport, cells were transferred to potassium-free medium. Protein profile was followed by two-dimensional (2-D) gels in samples taken at 0, 30, 60, 120, 180, and 300 min during starvation. We observed a general decrease of protein content during starvation that was especially drastic in the mutant strain as it was the case of an important number of proteins involved in glycolysis. On the contrary, we identified proteins related to stress response and alternative energetic metabolism that remained clearly present. Neural network-based analysis indicated that wild type was able to adapt much faster than the mutant to the stress process. We conclude that complete potassium starvation is a stressful process for yeast cells, especially for potassium transport mutants, and we propose that less stressing conditions should be used in order to study potassium homeostasis in yeast.
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Affiliation(s)
- Samuel Gelis
- Department of Microbiology, University of CórdobaCórdoba, Spain
| | - Miguel Curto
- Department of Biochemistry and Molecular Biology, Agricultural and Plant Biochemistry and Proteomics Research Group, University of CórdobaCórdoba, Spain
| | - Luis Valledor
- Molecular Systems Biology, University of ViennaVienna, Austria
| | - Asier González
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaBellaterra 08193, Barcelona, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaBellaterra 08193, Barcelona, Spain
| | - Jesús Jorrín
- Department of Biochemistry and Molecular Biology, Agricultural and Plant Biochemistry and Proteomics Research Group, University of CórdobaCórdoba, Spain
| | - José Ramos
- Department of Microbiology, University of CórdobaCórdoba, Spain
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15
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Hodurova Z, Ferreira L, Sánchez-Juanes F, Dominguez A, Gbelska Y. Cytosolic proteome of Kluyveromyces lactis affected by the multidrug resistance regulating transcription factor KlPdr1p. J Proteomics 2012; 75:5316-26. [DOI: 10.1016/j.jprot.2012.06.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/25/2012] [Accepted: 06/13/2012] [Indexed: 01/25/2023]
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16
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Henke RM, Dastidar RG, Shah A, Cadinu D, Yao X, Hooda J, Zhang L. Hypoxia elicits broad and systematic changes in protein subcellular localization. Am J Physiol Cell Physiol 2011; 301:C913-28. [PMID: 21753182 DOI: 10.1152/ajpcell.00481.2010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oxygen provides a crucial energy source in eukaryotic cells. Hence, eukaryotes ranging from yeast to humans have developed sophisticated mechanisms to respond to changes in oxygen levels. Regulation of protein localization, like protein modifications, can be an effective mechanism to control protein function and activity. However, the contribution of protein localization in oxygen signaling has not been examined on a genomewide scale. Here, we examine how hypoxia affects protein distribution on a genomewide scale in the model eukaryote, the yeast Saccharomyces cerevisiae. We demonstrate, by live cell imaging, that hypoxia alters the cellular distribution of 203 proteins in yeast. These hypoxia-redistributed proteins include an array of proteins with important functions in various organelles. Many of them are nuclear and are components of key regulatory complexes, such as transcriptional regulatory and chromatin remodeling complexes. Under hypoxia, these proteins are synthesized and retained in the cytosol. Upon reoxygenation, they relocalize effectively to their normal cellular compartments, such as the nucleus, mitochondria, endoplasmic reticulum, and cell periphery. The resumption of the normal cellular locations of many proteins can occur even when protein synthesis is inhibited. Furthermore, we show that the changes in protein distribution induced by hypoxia follow a slower trajectory than those induced by reoxygenation. These results show that the regulation of protein localization is a common and potentially dominant mechanism underlying oxygen signaling and regulation. These results may have broad implications in understanding oxygen signaling and hypoxia responses in higher eukaryotes such as humans.
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Affiliation(s)
- Robert Michael Henke
- Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, 75080, USA
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17
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Rintala E, Jouhten P, Toivari M, Wiebe MG, Maaheimo H, Penttilä M, Ruohonen L. Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:461-76. [PMID: 21348598 DOI: 10.1089/omi.2010.0082] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In industrial fermentations of Saccharomyces cerevisiae, transient changes in oxygen concentration commonly occur and it is important to understand the behavior of cells during these changes. Glucose-limited chemostat cultivations were used to study the time-dependent effect of sudden oxygen depletion on the transcriptome of S. cerevisiae cells initially in fully aerobic or oxygen-limited conditions. The overall responses to anaerobic conditions of cells initially in different conditions were very similar. Independent of initial culture conditions, transient downregulation of genes related to growth and cell proliferation, mitochondrial translation and protein import, and sulphate assimilation was seen. In addition, transient or permanent upregulation of genes related to protein degradation, and phosphate and amino acid uptake was observed in all cultures. However, only in the initially oxygen-limited cultures was a transient upregulation of genes related to fatty acid oxidation, peroxisomal biogenesis, oxidative phosphorylation, TCA cycle, response to oxidative stress, and pentose phosphate pathway observed. Furthermore, from the initially oxygen-limited conditions, a rapid response around the metabolites of upper glycolysis and the pentose phosphate pathway was seen, while from the initially fully aerobic conditions, a slower response around the pathways for utilization of respiratory carbon sources was observed.
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Affiliation(s)
- Eija Rintala
- VTT Technical Research Centre of Finland, Finland.
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18
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Van Mulders SE, Stassen C, Daenen L, Devreese B, Siewers V, van Eijsden RGE, Nielsen J, Delvaux FR, Willaert R. The influence of microgravity on invasive growth in Saccharomyces cerevisiae. ASTROBIOLOGY 2011; 11:45-55. [PMID: 21345087 DOI: 10.1089/ast.2010.0518] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This study investigates the effects of microgravity on colony growth and the morphological transition from single cells to short invasive filaments in the model eukaryotic organism Saccharomyces cerevisiae. Two-dimensional spreading of the yeast colonies grown on semi-solid agar medium was reduced under microgravity in the Σ1278b laboratory strain but not in the CMBSESA1 industrial strain. This was supported by the Σ1278b proteome map under microgravity conditions, which revealed upregulation of proteins linked to anaerobic conditions. The Σ1278b strain showed a reduced invasive growth in the center of the yeast colony. Bud scar distribution was slightly affected, with a switch toward more random budding. Together, microgravity conditions disturb spatially programmed budding patterns and generate strain-dependent growth differences in yeast colonies on semi-solid medium.
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19
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Baumann K, Carnicer M, Dragosits M, Graf AB, Stadlmann J, Jouhten P, Maaheimo H, Gasser B, Albiol J, Mattanovich D, Ferrer P. A multi-level study of recombinant Pichia pastoris in different oxygen conditions. BMC SYSTEMS BIOLOGY 2010; 4:141. [PMID: 20969759 PMCID: PMC2987880 DOI: 10.1186/1752-0509-4-141] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 10/22/2010] [Indexed: 12/24/2022]
Abstract
Background Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive responses to such stresses are extensively studied in Saccharomyces cerevisiae, little is known about their impact on the physiology of Pichia pastoris. We have recently reported a beneficial effect of hypoxia on recombinant Fab secretion in P. pastoris chemostat cultivations. As a consequence, a systems biology approach was used to comprehensively identify cellular adaptations to low oxygen availability and the additional burden of protein production. Gene expression profiling was combined with proteomic analyses and the 13C isotope labelling based experimental determination of metabolic fluxes in the central carbon metabolism. Results The physiological adaptation of P. pastoris to hypoxia showed distinct traits in relation to the model yeast S. cerevisiae. There was a positive correlation between the transcriptomic, proteomic and metabolic fluxes adaptation of P. pastoris core metabolism to hypoxia, yielding clear evidence of a strong transcriptional regulation component of key pathways such as glycolysis, pentose phosphate pathway and TCA cycle. In addition, the adaptation to reduced oxygen revealed important changes in lipid metabolism, stress responses, as well as protein folding and trafficking. Conclusions This systems level study helped to understand the physiological adaptations of cellular mechanisms to low oxygen availability in a recombinant P. pastoris strain. Remarkably, the integration of data from three different levels allowed for the identification of differences in the regulation of the core metabolism between P. pastoris and S. cerevisiae. Detailed comparative analysis of the transcriptomic data also led to new insights into the gene expression profiles of several cellular processes that are not only susceptible to low oxygen concentrations, but might also contribute to enhanced protein secretion.
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Affiliation(s)
- Kristin Baumann
- Department of Chemical Engineering, Autonomous University of Barcelona, Spain
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20
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Curto M, Valledor L, Navarrete C, Gutiérrez D, Sychrova H, Ramos J, Jorrin J. 2-DE based proteomic analysis of Saccharomyces cerevisiae wild and K+ transport-affected mutant (trk1,2) strains at the growth exponential and stationary phases. J Proteomics 2010; 73:2316-35. [PMID: 20638488 DOI: 10.1016/j.jprot.2010.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 06/22/2010] [Accepted: 07/06/2010] [Indexed: 12/27/2022]
Abstract
By using a 2-DE based workflow, the proteome of wild and potassium transport mutant trk1,2 under optimal growth potassium concentration (50mM) has been analyzed. At the exponential and stationary phases, both strains showed similar growth, morphology potassium content, and Vmax of rubidium transport, the only difference found being the Km values for this potassium analogue transport, higher for the mutant (20mM) than for the wild (3-6mM) cells. Proteins were buffer-extracted, precipitated, solubilized, quantified, and subjected to 2-DE analysis in the 5-8 pH range. More differences in protein content (37-64mgg(-1) cell dry weight) and number of resolved spots (178-307) were found between growth phases than between strains. In all, 164 spots showed no differences between samples and a total of 105 were considered to be differential after ANOVA test. 171 proteins, corresponding to 71 unique gene products have been identified, this set being dominated by cytosolic species and glycolitic enzymes. The ranking of the more abundant spots revealed no differences between samples and indicated fermentative metabolism, and active cell wall biosynthesis, redox homeostasis, biosynthesis of amino acids, coenzymes, nucleotides, and RNA, and protein turnover, apart from cell division and growth. PCA analysis allowed the separation of growth phases (PC1 and 2) and strains at the stationary phase (PC3 and 4), but not at the exponential one. These results are also supported by clustering analysis. As a general tendency, a number of spots newly appeared at the stationary phase in wild type, and to a lesser extent, in the mutant. These up-accumulated spots corresponded to glycolitic enzymes, indicating a more active glucose catabolism, accompanied by an accumulation of methylglyoxal detoxification, and redox-homeostasis enzymes. Also, more extensive proteolysis was observed at the stationary phase with this resulting in an accumulation of low Mr protein species.
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Affiliation(s)
- Miguel Curto
- Agricultural and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
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21
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Jami MS, Barreiro C, García-Estrada C, Martín JF. Proteome analysis of the penicillin producer Penicillium chrysogenum: characterization of protein changes during the industrial strain improvement. Mol Cell Proteomics 2010; 9:1182-98. [PMID: 20154335 PMCID: PMC2877979 DOI: 10.1074/mcp.m900327-mcp200] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 01/15/2010] [Indexed: 11/06/2022] Open
Abstract
Proteomics is a powerful tool to understand the molecular mechanisms causing the production of high penicillin titers by industrial strains of the filamentous fungus Penicillium chrysogenum as the result of strain improvement programs. Penicillin biosynthesis is an excellent model system for many other bioactive microbial metabolites. The recent publication of the P. chrysogenum genome has established the basis to understand the molecular processes underlying penicillin overproduction. We report here the proteome reference map of P. chrysogenum Wisconsin 54-1255 (the genome project reference strain) together with an in-depth study of the changes produced in three different strains of this filamentous fungus during industrial strain improvement. Two-dimensional gel electrophoresis, peptide mass fingerprinting, and tandem mass spectrometry were used for protein identification. Around 1000 spots were visualized by "blue silver" colloidal Coomassie staining in a non-linear pI range from 3 to 10 with high resolution, which allowed the identification of 950 proteins (549 different proteins and isoforms). Comparison among the cytosolic proteomes of the wild-type NRRL 1951, Wisconsin 54-1255 (an improved, moderate penicillin producer), and AS-P-78 (a penicillin high producer) strains indicated that global metabolic reorganizations occurred during the strain improvement program. The main changes observed in the high producer strains were increases of cysteine biosynthesis (a penicillin precursor), enzymes of the pentose phosphate pathway, and stress response proteins together with a reduction in virulence and in the biosynthesis of other secondary metabolites different from penicillin (pigments and isoflavonoids). In the wild-type strain, we identified enzymes to utilize cellulose, sorbitol, and other carbon sources that have been lost in the high penicillin producer strains. Changes in the levels of a few specific proteins correlated well with the improved penicillin biosynthesis in the high producer strains. These results provide useful information to improve the production of many other bioactive secondary metabolites.
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Affiliation(s)
- Mohammad-Saeid Jami
- From the ‡Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain and
| | - Carlos Barreiro
- ¶INBIOTEC, Instituto de Biotecnología de León, Avenida Real No. 1, Parque Científico de León, 24006 León, Spain
| | - Carlos García-Estrada
- ¶INBIOTEC, Instituto de Biotecnología de León, Avenida Real No. 1, Parque Científico de León, 24006 León, Spain
| | - Juan-Francisco Martín
- From the ‡Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain and
- ¶INBIOTEC, Instituto de Biotecnología de León, Avenida Real No. 1, Parque Científico de León, 24006 León, Spain
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Mechanism of de novo branched-chain amino acid synthesis as an alternative electron sink in hypoxic Aspergillus nidulans cells. Appl Environ Microbiol 2010; 76:1507-15. [PMID: 20081005 DOI: 10.1128/aem.02135-09] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although branched-chain amino acids are synthesized as building blocks of proteins, we found that the fungus Aspergillus nidulans excretes them into the culture medium under hypoxia. The transcription of predicted genes for synthesizing branched-chain amino acids was upregulated by hypoxia. A knockout strain of the gene encoding the large subunit of acetohydroxy acid synthase (AHAS), which catalyzes the initial reaction of the synthesis, required branched-chain amino acids for growth and excreted very little of them. Pyruvate, a substrate for AHAS, increased the amount of hypoxic excretion in the wild-type strain. These results indicated that the fungus responds to hypoxia by synthesizing branched-chain amino acids via a de novo mechanism. We also found that the small subunit of AHAS regulated hypoxic branched-chain amino acid production as well as cellular AHAS activity. The AHAS knockout resulted in higher ratios of NADH/NAD(+) and NADPH/NADP(+) under hypoxia, indicating that the branched-chain amino acid synthesis contributed to NAD(+) and NADP(+) regeneration. The production of branched-chain amino acids and the hypoxic induction of involved genes were partly repressed in the presence of glucose, where cells produced ethanol and lactate and increased levels of lactate dehydrogenase activity. These indicated that hypoxic branched-chain amino acid synthesis is a unique alternative mechanism that functions in the absence of glucose-to-ethanol/lactate fermentation and oxygen respiration.
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1623] [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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